From 51f2fe6542009e744486aac6b0691042691ac37a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:27:39 +0200 Subject: gnu: Add r-consrank. * gnu/packages/cran.scm (r-consrank): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 688621343e9..1f6b18f7d4e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31900,6 +31900,33 @@ a Huber regression warm start. Confidence intervals for regression coefficients are constructed using multiplier bootstrap.") (license license:gpl3))) +(define-public r-consrank + (package + (name "r-consrank") + (version "2.1.3") + (source (origin + (method url-fetch) + (uri (cran-uri "ConsRank" version)) + (sha256 + (base32 + "0v1dr7zj2fpgncymakv5qszdrlqzvc5zxfyc3yrsj09gbm0gvyby")))) + (properties `((upstream-name . "ConsRank"))) + (build-system r-build-system) + (propagated-inputs (list r-gtools r-proxy r-rgl r-rlist r-tidyr)) + (home-page "https://www.r-project.org/") + (synopsis + "Compute median rankings according to Kemeny's axiomatic approach") + (description + "This package lets you compute the median ranking according to Kemeny's +axiomatic approach. Rankings can or cannot contain ties, rankings can be both +complete or incomplete. The package contains both branch-and-bound algorithms +and heuristic solutions recently proposed. The searching space of the +solution can either be restricted to the universe of the permutations or +unrestricted to all possible ties. The package also provides some useful +utilities for deal with preference rankings, including both element-weight +Kemeny distance and correlation coefficient.") + (license license:gpl3))) + (define-public r-fastshap (package (name "r-fastshap") -- cgit v1.2.3 From f69e0f79272f788f8c78837f7c6cdfe04e0aea07 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:30:37 +0200 Subject: gnu: r-rgdal: Update to 1.6-7. * gnu/packages/cran.scm (r-rgdal): Update to 1.6-7. [properties]: Add hints to the updater. --- gnu/packages/cran.scm | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1f6b18f7d4e..7840563a6b0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25192,14 +25192,18 @@ effect size.") (define-public r-rgdal (package (name "r-rgdal") - (version "1.6-6") + (version "1.6-7") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 - (base32 "16irhw858771bc8ikshxk3ddpd7ymwgqmhnac4g7f160vymdfhnp")))) - (properties `((upstream-name . "rgdal"))) + (base32 "0cxfmm7niixw3dnbqm7a00603dyqjrphajqx0q5vjpdhmpyysp2m")))) + (properties + `((upstream-name . "rgdal") + (updater-extra-inputs . ("gdal" "proj")) + ;; These are only needed for Windows + (updater-ignored-inputs . ("curl" "openssl" "openssh" "pcre2")))) (build-system r-build-system) (inputs (list gdal proj zlib)) -- cgit v1.2.3 From 01d9a691be55d1565cb78f528bd8d059e442f315 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:31:20 +0200 Subject: gnu: r-rmarkdown: Update to 2.22. * gnu/packages/statistics.scm (r-rmarkdown): Update to 2.22. [properties]: Add hints to the updater. --- gnu/packages/statistics.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 450bf933dbb..2db8afac7fd 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2866,14 +2866,16 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "2.21") + (version "2.22") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "0a5czn18clfnw0a9nd5v98ah4h47i32423s6jdf126ni4aj20ny2")))) - (properties `((upstream-name . "rmarkdown"))) + (base32 "1f47ccph09ilqlr0bnyrxkadja4ddp4klvb933aws3rya0cmaqy6")))) + (properties + `((upstream-name . "rmarkdown") + (updater-extra-propagated-inputs . ("pandoc")))) (build-system r-build-system) (propagated-inputs (list r-bslib -- cgit v1.2.3 From a8ac423090025753662c99f93afbd7c50bb99066 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:01 +0200 Subject: gnu: r-ggpicrust2: Update to 1.7.0. * gnu/packages/bioconductor.scm (r-ggpicrust2): Update to 1.7.0. [propagated-inputs]: Add r-circlize. [native-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec52cd6e2db..00701c4463c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10313,17 +10313,18 @@ fitting of some classes of graphical Markov models.") (define-public r-ggpicrust2 (package (name "r-ggpicrust2") - (version "1.6.5") + (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "ggpicrust2" version)) (sha256 (base32 - "02ais1y3z85vykxd9975gz33s80d1nhivly6a07y98dbmlzjyr6a")))) + "0rw2nrmnniff5hb56r21rk0mphba74fppxsa5ps2xamg1a63qfyw")))) (properties `((upstream-name . "ggpicrust2"))) (build-system r-build-system) (propagated-inputs (list r-aldex2 r-aplot + r-circlize r-deseq2 r-dplyr r-edger @@ -10341,6 +10342,7 @@ fitting of some classes of graphical Markov models.") r-summarizedexperiment r-tibble r-tidyr)) + (native-inputs (list r-knitr)) (home-page "https://github.com/cafferychen777/ggpicrust2") (synopsis "Make PICRUSt2 output analysis and visualization easier") (description -- cgit v1.2.3 From 6b07e527522ccbec1200e64b142ea38413cb118d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:01 +0200 Subject: gnu: r-ggrastr: Update to 1.0.2. * gnu/packages/cran.scm (r-ggrastr): Update to 1.0.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7840563a6b0..b3c2a923f9d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1927,13 +1927,13 @@ Prism-look is achieved with @code{theme_prism()} and (define-public r-ggrastr (package (name "r-ggrastr") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "ggrastr" version)) (sha256 (base32 - "07sx5wlawfyb0zy5am2q1ajhkdym5r9ih47p57l8bv4dlc7ykml2")))) + "1l90mlb6bqq98ifmlbs5481vch9inmzdnvnz192adklrr9nl09yb")))) (properties `((upstream-name . "ggrastr"))) (build-system r-build-system) (propagated-inputs (list r-cairo r-ggbeeswarm r-ggplot2 r-png r-ragg)) -- cgit v1.2.3 From 4c14c0a574e1b3b3ba4ae9f03f2cbf48c49e46ff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:01 +0200 Subject: gnu: r-sp: Update to 1.6-1. * gnu/packages/cran.scm (r-sp): Update to 1.6-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b3c2a923f9d..3f6236ad7f9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6203,13 +6203,13 @@ most popular ones.") (define-public r-sp (package (name "r-sp") - (version "1.6-0") + (version "1.6-1") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 - (base32 "1npwz49qmlqz46jrwlmv4929hb3wv3whxzj1bplyipp7h2z7z5zm")))) + (base32 "09d3jhk7iwjfhzyq0cwws1p5gspj9nxww5x7xvngh8hr9gan5wkn")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) -- cgit v1.2.3 From c34e0df73eba929b31fc0357534dcde469506b78 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:01 +0200 Subject: gnu: r-ucminf: Update to 1.2.0. * gnu/packages/cran.scm (r-ucminf): Update to 1.2.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3f6236ad7f9..a5230f0ac73 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7784,14 +7784,14 @@ or between integer vectors representing generic sequences.") (define-public r-ucminf (package (name "r-ucminf") - (version "1.1-4.3") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "ucminf" version)) (sha256 (base32 - "1vjrbavj909wlsyb82dq3rybk0nqay6vl81f2qiqrm12ks9pw3js")))) + "1x3d3l500kyqamzfjpz4qc38d6d3sha9av3rpxz0m4dhms28zpas")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ucminf/") -- cgit v1.2.3 From 2ebd2d1050a00f7f40cdfdedfea5ac921fdba984 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:01 +0200 Subject: gnu: r-catdap: Update to 1.3.7. * gnu/packages/cran.scm (r-catdap): Update to 1.3.7. [propagated-inputs]: Add r-rcolorbrewer. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a5230f0ac73..543ca1dbf78 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10804,15 +10804,17 @@ methods.") (define-public r-catdap (package (name "r-catdap") - (version "1.3.5") + (version "1.3.7") (source (origin (method url-fetch) (uri (cran-uri "catdap" version)) (sha256 (base32 - "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5")))) + "0z84bx808hy70bkzdda9l42ljh9i9pz07isxq756axi7nr0ky6p9")))) (build-system r-build-system) + (propagated-inputs + (list r-rcolorbrewer)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/catdap/") -- cgit v1.2.3 From e0e8974176fa3580a91d657512768d62a86c5a3a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:02 +0200 Subject: gnu: r-maptools: Update to 1.1-7. * gnu/packages/cran.scm (r-maptools): Update to 1.1-7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 543ca1dbf78..6ac0032339a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11025,14 +11025,14 @@ simple method for converting between file types.") (define-public r-maptools (package (name "r-maptools") - (version "1.1-6") + (version "1.1-7") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 - "024kyq81gwpl7shil63nng1z6pgqcwy6j6wj44gj7ch3vd9dz9fn")))) + "0m576fzaaqbz1pqjv585841k93xnmx844kpsjzivmpfyvhbmw81v")))) (build-system r-build-system) (propagated-inputs (list r-foreign r-lattice r-sp)) -- cgit v1.2.3 From 1a9d42ad1e98ae933dba2a59615f43f91fbb0ec3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:02 +0200 Subject: gnu: r-biasedurn: Update to 2.0.10. * gnu/packages/cran.scm (r-biasedurn): Update to 2.0.10. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6ac0032339a..9c021f13f8f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12771,14 +12771,14 @@ contains or can be specified by the user.") (define-public r-biasedurn (package (name "r-biasedurn") - (version "2.0.9") + (version "2.0.10") (source (origin (method url-fetch) (uri (cran-uri "BiasedUrn" version)) (sha256 (base32 - "02bb81x1hfvhm6qlcvp88bdpm1fhqak9cjbqz1r7fhg2qfxjpims")))) + "0jv0zvz1zs34h12zdgn3lqmn7hfkk2z6fkwbd9mlyddf34rkvfqv")))) (properties `((upstream-name . "BiasedUrn"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/BiasedUrn/") -- cgit v1.2.3 From 399657122b373d880ff44522987ae13fb046a291 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:02 +0200 Subject: gnu: r-performance: Update to 0.10.4. * gnu/packages/cran.scm (r-performance): Update to 0.10.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9c021f13f8f..7320c69dc4c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15320,14 +15320,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.10.3") + (version "0.10.4") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "1l4sr6cgg8rkgs5w98a36n79b1lbg241p60grsnz12hskppa1a6q")))) + "0ddwfkrzwbj1bykvifzrb11hs5kh2a6ykr3ac1hi7cqpqikymfna")))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight)) -- cgit v1.2.3 From 385b7f6ce6a352e8432f95abce2e8bd7ff81c20a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:02 +0200 Subject: gnu: r-ontologyindex: Update to 2.11. * gnu/packages/cran.scm (r-ontologyindex): Update to 2.11. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7320c69dc4c..4853d894b67 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18190,14 +18190,14 @@ library.") (define-public r-ontologyindex (package (name "r-ontologyindex") - (version "2.10") + (version "2.11") (source (origin (method url-fetch) (uri (cran-uri "ontologyIndex" version)) (sha256 (base32 - "0hisb9scxyyqkxhxhvgsgwix54pkq0zma3xq3ywczyazvzcxd5f9")))) + "17ndvqvb74b980gpb3hpg9bd68bb5f52k9s1i2kd1f9cdrdjvw97")))) (properties `((upstream-name . "ontologyIndex"))) (build-system r-build-system) (native-inputs -- cgit v1.2.3 From 0ca364577ab7719beb1ba2e1068f0c0c4faf86aa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:02 +0200 Subject: gnu: r-assertive-code: Update to 0.0-4. * gnu/packages/cran.scm (r-assertive-code): Update to 0.0-4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4853d894b67..2873210c033 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18578,14 +18578,14 @@ packages.") (define-public r-assertive-code (package (name "r-assertive-code") - (version "0.0-3") + (version "0.0-4") (source (origin (method url-fetch) (uri (cran-uri "assertive.code" version)) (sha256 (base32 - "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g")))) + "11qkhbjyxw0njzhcszyc2452518yrn3jr5l4n9jnzq10xms090ig")))) (properties `((upstream-name . "assertive.code"))) (build-system r-build-system) -- cgit v1.2.3 From d3bf7c1852a15d511f036a04fa9bdbd62fa6fc85 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:02 +0200 Subject: gnu: r-adabag: Update to 5.0. * gnu/packages/cran.scm (r-adabag): Update to 5.0. [propagated-inputs]: Add r-consrank, r-dplyr, and r-tidyr. --- gnu/packages/cran.scm | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2873210c033..6327a52fdde 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27924,18 +27924,24 @@ classification and regression models.") (define-public r-adabag (package (name "r-adabag") - (version "4.3") + (version "5.0") (source (origin (method url-fetch) (uri (cran-uri "adabag" version)) (sha256 (base32 - "1v4cl50wbv834cpbwkkhaq5wf8s746fp8xkjrwvyw912x6b2zmik")))) + "03nnqgia61pavic9l6av0hh81wilxlkrx3g244ypar1fv9ppan7c")))) (properties `((upstream-name . "adabag"))) (build-system r-build-system) (propagated-inputs - (list r-caret r-doparallel r-foreach r-rpart)) + (list r-caret + r-consrank + r-doparallel + r-dplyr + r-foreach + r-rpart + r-tidyr)) (home-page "https://cran.r-project.org/web/packages/adabag/") (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging") (description -- cgit v1.2.3 From 885811d599ce7cc308238e55e5f14a56e8df0196 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:02 +0200 Subject: gnu: r-regsem: Update to 1.9.5. * gnu/packages/cran.scm (r-regsem): Update to 1.9.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6327a52fdde..049630c6331 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29539,14 +29539,14 @@ least squares.") (define-public r-regsem (package (name "r-regsem") - (version "1.9.3") + (version "1.9.5") (source (origin (method url-fetch) (uri (cran-uri "regsem" version)) (sha256 (base32 - "0vpizmdml55naxmhy9nfcm9ylhy15p9na7l0c6z3rvk29ck3g3sw")))) + "0lvsy7byrhiizyhwnwr22v8g36735nb0liyzl1nzk0py9rjbv4kk")))) (properties `((upstream-name . "regsem"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 944bcae0d41476f2fae4f531ad58d3327679239b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:02 +0200 Subject: gnu: r-stanheaders: Update to 2.26.26. * gnu/packages/cran.scm (r-stanheaders): Update to 2.26.26. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 049630c6331..43091007def 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29566,14 +29566,14 @@ perform @dfn{exploratory mediation} (XMed).") (define-public r-stanheaders (package (name "r-stanheaders") - (version "2.26.25") + (version "2.26.26") (source (origin (method url-fetch) (uri (cran-uri "StanHeaders" version)) (sha256 (base32 - "1xds719xga7144mxirjnqxmcv1ncj5fb5z247blm4dkbn9q2vg4k")))) + "1jr5sflqhg70jkgz3x0q9nrk2xjzm1l4zmyc7j89m755b209sq4k")))) (properties `((upstream-name . "StanHeaders"))) (build-system r-build-system) (inputs (list pandoc)) -- cgit v1.2.3 From e786bef04825a5b8bd109471259d9c81ea530884 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:03 +0200 Subject: gnu: r-projpred: Update to 2.6.0. * gnu/packages/cran.scm (r-projpred): Update to 2.6.0. [propagated-inputs]: Remove r-ucminf; add r-scales. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 43091007def..0839e42d299 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31277,14 +31277,14 @@ here.") (define-public r-projpred (package (name "r-projpred") - (version "2.5.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (cran-uri "projpred" version)) (sha256 (base32 - "0faf0hq5kvibqyzgqqz2sdqms8g3vvxy6calpm6d2wzmbczi5v5n")))) + "1nkil537n43sz0ajkcyr0i38hb852qgcdxlgnirqkl0w98ax2hac")))) (properties `((upstream-name . "projpred"))) (build-system r-build-system) (propagated-inputs @@ -31302,7 +31302,7 @@ here.") r-rcpp r-rcpparmadillo r-rstantools - r-ucminf)) + r-scales)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://mc-stan.org/projpred/") (synopsis "Projection predictive feature selection") -- cgit v1.2.3 From a0660408562dfb37419bf3a483bccdc650c4b9c1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:03 +0200 Subject: gnu: r-shapforxgboost: Update to 0.1.3. * gnu/packages/cran.scm (r-shapforxgboost): Update to 0.1.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0839e42d299..e69c2f14cc1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31714,14 +31714,14 @@ designed to be distributed and efficient with the following goals: (define-public r-shapforxgboost (package (name "r-shapforxgboost") - (version "0.1.1") + (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "SHAPforxgboost" version)) (sha256 (base32 - "106nsf02b1w3yshb55lwnyw1rl1a60162v2wk8znjz3b4ln3mqj5")))) + "0b3h6py80a0dmb8f8j4h7a7d0k6ld8l0qr24r8pxxy7dbqbyxh5x")))) (properties `((upstream-name . "SHAPforxgboost"))) (build-system r-build-system) -- cgit v1.2.3 From 6c321bbded3246e308a3bb0a44074db35d1c7b13 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:03 +0200 Subject: gnu: r-scico: Update to 1.4.0. * gnu/packages/cran.scm (r-scico): Update to 1.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e69c2f14cc1..ea424d4f62c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33434,13 +33434,13 @@ observations.") (define-public r-scico (package (name "r-scico") - (version "1.3.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "scico" version)) (sha256 - (base32 "1f2czfhzdpi5dqjbxvbrrcnxjpylc5zzghj70ihlh2agq3n9hw5g")))) + (base32 "1zcsqmsr9vjs4krz8vmq4z59wh6x25g9ca6yxb0wlq58nmws77k6")))) (properties `((upstream-name . "scico"))) (build-system r-build-system) (propagated-inputs (list r-scales)) -- cgit v1.2.3 From fccc10b655694a900a40ba75feb9cd3726712eaf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:03 +0200 Subject: gnu: r-stringfish: Update to 0.15.8. * gnu/packages/cran.scm (r-stringfish): Update to 0.15.8. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ea424d4f62c..d8221fd0fcd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -36992,14 +36992,14 @@ the @code{raster} package that is suitable for extracting raster values using (define-public r-stringfish (package (name "r-stringfish") - (version "0.15.7") + (version "0.15.8") (source (origin (method url-fetch) (uri (cran-uri "stringfish" version)) (sha256 (base32 - "0ddpsi7z0kzqgbq9y646pk9afclq0r7ak22zsdh0i93ni0x71c9l")))) + "16w3i3d7jw2s1hzxr3mngrh7yjxvhswqdlpjw5g4z25i84lixcnz")))) (properties `((upstream-name . "stringfish"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3f8a983caebadb39473759e99968eb0d7c4e6d92 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:03 +0200 Subject: gnu: r-mvtnorm: Update to 1.2-0. * gnu/packages/statistics.scm (r-mvtnorm): Update to 1.2-0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 2db8afac7fd..ae9b020ee9f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4174,13 +4174,13 @@ vignettes.") (define-public r-mvtnorm (package (name "r-mvtnorm") - (version "1.1-3") + (version "1.2-0") (source (origin (method url-fetch) (uri (cran-uri "mvtnorm" version)) (sha256 (base32 - "0j14q2bkc14v35s5k03sw44zsssrd2qjljlwzj014qxs74hk0kpz")))) + "1q1bmsvd10iz003xlsd40dj5bhmy2069p88ydf9f4gj56mysnlpm")))) (build-system r-build-system) (native-inputs (list gfortran)) -- cgit v1.2.3 From 79b52c60e931714672f00204800c97b5f7e1c627 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:03 +0200 Subject: gnu: r-matrixstats: Update to 1.0.0. * gnu/packages/statistics.scm (r-matrixstats): Update to 1.0.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index ae9b020ee9f..fc98c456cd4 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4193,13 +4193,13 @@ t-probabilities, quantiles, random deviates and densities.") (define-public r-matrixstats (package (name "r-matrixstats") - (version "0.63.0") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "matrixStats" version)) (sha256 (base32 - "0pqz6mn5l7inh464yj45i6rf8ycab0zdvvjczwsv0bkl442bc060")))) + "0vxd7g1fm4x0f72bs1xfik1d4yklvpjdyg1hpx86pl8fwr86i1wl")))) (properties `((upstream-name . "matrixStats"))) (build-system r-build-system) (arguments -- cgit v1.2.3 From da71721db152a338f5d2c35ca3a703fe5df12b27 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Jun 2023 08:32:03 +0200 Subject: gnu: r-biased-urn: Update to 2.0.10. * gnu/packages/statistics.scm (r-biased-urn): Update to 2.0.10. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index fc98c456cd4..e025653338b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4507,14 +4507,14 @@ data behind them) can be viewed and modified in a web browser.") (define-public r-biased-urn (package (name "r-biased-urn") - (version "2.0.9") + (version "2.0.10") (source (origin (method url-fetch) (uri (cran-uri "BiasedUrn" version)) (sha256 (base32 - "02bb81x1hfvhm6qlcvp88bdpm1fhqak9cjbqz1r7fhg2qfxjpims")))) + "0jv0zvz1zs34h12zdgn3lqmn7hfkk2z6fkwbd9mlyddf34rkvfqv")))) (properties `((upstream-name . "BiasedUrn"))) (build-system r-build-system) (home-page "https://www.agner.org/random/") -- cgit v1.2.3 From f2f8e2fa2fdc3e144c89212a28b1a97db34cf28a Mon Sep 17 00:00:00 2001 From: Antero Mejr Date: Tue, 25 Apr 2023 02:06:51 +0000 Subject: gnu: notcurses: Update to 3.0.9. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/notcurses.scm (notcurses): Update to 3.0.9. Signed-off-by: 宋文武 --- gnu/packages/notcurses.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/notcurses.scm b/gnu/packages/notcurses.scm index bb0086d4b35..591bed23ef7 100644 --- a/gnu/packages/notcurses.scm +++ b/gnu/packages/notcurses.scm @@ -35,7 +35,7 @@ (define-public notcurses (package (name "notcurses") - (version "3.0.8") + (version "3.0.9") (source (origin (method url-fetch) @@ -48,7 +48,7 @@ "+dfsg.1.orig.tar.xz")) (file-name (string-append name "-" version ".tar.xz")) (sha256 - (base32 "1nz32nqh7fn4i06hvl8ndkm0z4g08a6wzhilvv8ggx2hc5axsz89")))) + (base32 "1sj2m7sil2i3yw73z15947kypsp0rnapwpwanwzam15lbicc8c3y")))) (build-system cmake-build-system) (arguments `(#:make-flags -- cgit v1.2.3 From 1569f7d77e4e302e7eb9058291b74a494a934683 Mon Sep 17 00:00:00 2001 From: Antero Mejr Date: Tue, 25 Apr 2023 02:06:52 +0000 Subject: gnu: Add s7-bootstrap. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lisp.scm (s7-bootstrap): New variable. Signed-off-by: 宋文武 --- gnu/packages/lisp.scm | 102 +++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 101 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index 000c8e8e666..5ac378d06d9 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -57,6 +57,7 @@ #:use-module (guix build-system haskell) #:use-module (guix build-system trivial) #:use-module (gnu packages admin) + #:use-module (gnu packages algebra) #:use-module (gnu packages base) #:use-module (gnu packages bash) #:use-module (gnu packages bdw-gc) @@ -83,6 +84,7 @@ #:use-module (gnu packages maths) #:use-module (gnu packages multiprecision) #:use-module (gnu packages ncurses) + #:use-module (gnu packages notcurses) #:use-module (gnu packages onc-rpc) #:use-module (gnu packages perl) #:use-module (gnu packages readline) @@ -93,7 +95,8 @@ #:use-module (gnu packages tls) #:use-module (gnu packages version-control) #:use-module (gnu packages xorg) - #:use-module (ice-9 match)) + #:use-module (ice-9 match) + #:use-module (srfi srfi-1)) (define-public cl-asdf (package @@ -1478,3 +1481,100 @@ includes a compiler as well as an interpreter.") license:expat ;; cii/LICENSE license:gpl2+ ;; nana/gdb/test.c and others under nana/ license:bsd-3)))) ;; bench/* + +(define-public s7-bootstrap + ;; Need s7-bootstrap to build libc_s7.so (for the REPL) and run tests + (let ((commit "a5b4bb49f8bcd7c33ae2366065fc8c254b734460") ;no releases + (revision "0")) + (hidden-package + (package + (name "s7-bootstrap") + (version (git-version "23.3" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://cm-gitlab.stanford.edu/bil/s7.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03n1axdlypzmbgzrhlwfqwa1xiw36hi25j2hwc7vw77mz90cd9f8")))) + (build-system gnu-build-system) + (arguments + (list #:tests? #f ;no tests in bootstrap + #:phases #~(modify-phases %standard-phases + (delete 'configure) ;no configure + (replace 'build + (lambda _ + ;; using build commands from s7 home page + (display "[BUILD] repl\n") + (invoke #$(cc-for-target) "s7.c" "-o" "repl" + "-I." "-O2" "-g" + "-DWITH_MAIN" + (string-append + "-DS7_LOAD_PATH=\"" + #$output "/share/s7/scm\"") + "-ldl" "-lm" + "-Wl,-export-dynamic") + (display "[BUILD] nrepl\n") + (invoke #$(cc-for-target) "s7.c" "-o" "nrepl" + "-I." "-O2" "-g" + "-DWITH_MAIN" "-DWITH_NOTCURSES" + (string-append + "-DS7_LOAD_PATH=\"" + #$output "/share/s7/scm\"") + "-ldl" "-lm" "-lnotcurses-core" + "-Wl,-export-dynamic") + (display "[BUILD] libarb_s7.so\n") + (invoke #$(cc-for-target) "libarb_s7.c" + "-I." "-O2" "-g" + "-shared" "-o" "libarb_s7.so" + "-larb" "-lflint" "-lmpc" "-fPIC") + (display "[BUILD] libnotcurses_s7.so\n") + (invoke #$(cc-for-target) "notcurses_s7.c" + "-I." "-O2" "-g" + "-shared" "-o" "libnotcurses_s7.so" + "-lnotcurses-core" "-fPIC") + ;; Need s7.o and ffitest for tests + (display "[BUILD] s7.o\n") + (invoke #$(cc-for-target) "-c" "s7.c" "-o" + "s7.o" "-I." "-O2" "-ldl" "-lm") + (display "[BUILD] ffitest\n") + (invoke #$(cc-for-target) "-o" "ffitest" + "ffitest.c" "-g2" "s7.o" "-lm" "-I." + "-ldl" "-Wl,-export-dynamic"))) + (add-before 'check 'install-scm + ;; scm files need to be installed before testing + (lambda _ + (for-each (lambda (x) + (install-file + x (string-append + #$output "/share/s7/scm/"))) + (find-files "." "\\.scm")))) + (replace 'install + (lambda _ + (let ((bin (string-append #$output "/bin")) + (share (string-append #$output + "/share/s7/")) + (doc (string-append #$output + "/share/doc/s7/")) + (lib (string-append #$output "/lib")) + (inc (string-append #$output "/include/"))) + (install-file "repl" bin) + (install-file "nrepl" bin) + (install-file "ffitest" bin) + (install-file "libarb_s7.so" lib) + (install-file "libnotcurses_s7.so" lib) + (install-file "s7.c" share) + (install-file "s7.h" inc) + (install-file "s7.html" doc))))))) + (inputs (list arb flint mpc notcurses)) + (home-page "https://ccrma.stanford.edu/software/snd/snd/s7.html") + (synopsis "Scheme interpreter intended as an extension language") + (description + "s7 is a Scheme interpreter intended as an extension language for +other applications. It exists as just two files, @code{s7.c} and @code{s7.h}, +that may be copied into the source tree of another application. There are no +libraries, no run-time init files, and no configuration scripts. It can also +be built as a stand-alone REPL interpreter.") + (license license:bsd-0))))) -- cgit v1.2.3 From 76b7c50645cfba9554af9c80768765c5b714b893 Mon Sep 17 00:00:00 2001 From: Antero Mejr Date: Tue, 25 Apr 2023 02:06:53 +0000 Subject: gnu: Add s7. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lisp.scm (s7): New variable. Signed-off-by: 宋文武 --- gnu/packages/lisp.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index 5ac378d06d9..c053da9cd5d 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -1578,3 +1578,32 @@ that may be copied into the source tree of another application. There are no libraries, no run-time init files, and no configuration scripts. It can also be built as a stand-alone REPL interpreter.") (license license:bsd-0))))) + +(define-public s7 + (package + (inherit s7-bootstrap) + (name "s7") + (arguments + (substitute-keyword-arguments (package-arguments s7-bootstrap) + ((#:tests? _) #t) + ((#:phases phases) + #~(modify-phases #$phases + (add-after 'unpack 'patch + (lambda _ + (substitute* "s7.c" + (("libc_s7.so") + (string-append #$output "/lib/libc_s7.so"))))) + (add-after 'build 'build-full + (lambda _ + (invoke "repl" "./libc.scm"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "repl" "./s7test.scm")))) + (add-after 'install 'install-full + (lambda _ + (install-file "libc_s7.so" + (string-append #$output "/lib/")) + (delete-file (string-append #$output "/bin/ffitest")))))))) + (native-inputs (list s7-bootstrap)) + (properties (alist-delete 'hidden? (package-properties s7-bootstrap))))) -- cgit v1.2.3 From 9cf6833033a4c4dd821dcc7a886fcffb83a34185 Mon Sep 17 00:00:00 2001 From: Andy Tai Date: Sat, 25 Mar 2023 03:19:12 -0700 Subject: gnu: Remove obs-spectralizer. As project no longer developed and not building with current obs. * gnu/packages/video.scm (obs-spectralizer): Remove variable. Signed-off-by: Christopher Baines --- gnu/packages/video.scm | 31 ------------------------------- 1 file changed, 31 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index ab19c2dd8c0..3b6af31b76b 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -3475,37 +3475,6 @@ and JACK.") (home-page "https://obsproject.com") (license license:gpl2+))) -(define-public obs-spectralizer - (package - (name "obs-spectralizer") - (version "1.3.3") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/univrsal/spectralizer") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - - ;; Remove bundled Windows DLLs. - (snippet '(delete-file-recursively "fftw3")) - (modules '((guix build utils))) - - (sha256 - (base32 - "0q75cnyqydpvfda51zm9gxqj3wqr99ad0lxzjhw0ld67qvj1ag6i")))) - (build-system cmake-build-system) - (arguments - `(#:tests? #f - #:configure-flags - (list "-DGLOBAL_INSTALLATION=ON" "-DUSE_CMAKE_LIBDIR=ON"))) - (inputs (list obs fftw)) - (home-page "https://github.com/univrsal/spectralizer") - (synopsis "OBS plugin for audio visualization") - (description "This OBS plugins allows you to vizualize MPD and internal -OBS audio sources.") - (license license:gpl2))) - (define-public obs-websocket (package (name "obs-websocket") -- cgit v1.2.3 From c5aeb15267706d241dfecf8115f8f5f984efb4d4 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sat, 3 Jun 2023 12:21:31 +0100 Subject: gnu: guix-build-coordinator: Update to 0-85.c44d485. * gnu/packages/package-management.scm (guix-build-coordinator): Update to 0-85.c44d485. --- gnu/packages/package-management.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 3006631b661..a856ff2726e 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1384,8 +1384,8 @@ environments.") "0k9zkdyyzir3fvlbcfcqy17k28b51i20rpbjwlx2i1mwd2pw9cxc"))))))) (define-public guix-build-coordinator - (let ((commit "99981dc3270d79ae0b83f94386e26cc75a7162b3") - (revision "84")) + (let ((commit "c44d485bba42034804beb47afc23005c4e73ea96") + (revision "85")) (package (name "guix-build-coordinator") (version (git-version "0" revision commit)) @@ -1396,7 +1396,7 @@ environments.") (commit commit))) (sha256 (base32 - "047qqqhpcg5rrzgpp2qlijn6rhlm2ipqhqr1yj1lrnx12dld2kqk")) + "1y69yrmmifdp55l5c5b8iiq0llwpggxmq6a4233cdll3bhfxaicl")) (file-name (string-append name "-" version "-checkout")))) (build-system gnu-build-system) (arguments -- cgit v1.2.3 From f30f8ecc6961f181f670c960fa57ffa2442c0217 Mon Sep 17 00:00:00 2001 From: gemmaro Date: Sun, 28 May 2023 23:54:04 +0900 Subject: gnu: python-zulip: Fix test failure. * gnu/packages/messaging.scm (python-zulip): Fix test failure. Signed-off-by: Christopher Baines --- gnu/packages/messaging.scm | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 46170ff31ec..00897ea4519 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -39,6 +39,7 @@ ;;; Copyright © 2022 Giovanni Biscuolo ;;; Copyright © 2023 Giacomo Leidi ;;; Copyright © 2023 Yovan Naumovski +;;; Copyright © 2023 gemmaro ;;; ;;; This file is part of GNU Guix. ;;; @@ -3085,7 +3086,13 @@ designed for experienced users.") (file-name (git-file-name name version)) (sha256 (base32 - "0da1ki1v252avy27j6d7snnc0gyq0xa9fypm3qdmxhw2w79d6q36")))) + "0da1ki1v252avy27j6d7snnc0gyq0xa9fypm3qdmxhw2w79d6q36")) + (modules '((guix build utils))) + (snippet + '(begin + ;; TODO: This is fixed upstream in later versions + (substitute* "zulip/tests/test_default_arguments.py" + (("optional arguments:") "options:")))))) (build-system python-build-system) (arguments `(#:phases -- cgit v1.2.3 From e8eb389594eea005d355b0ae9fe6fd2b089513df Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Mon, 29 May 2023 00:50:33 +0300 Subject: gnu: guile-png: Update to 0.5.0. * gnu/packages/guile-xyz.scm (guile-png): Update to 0.5.0. Signed-off-by: Christopher Baines --- gnu/packages/guile-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 474022003fe..d8684bb8184 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -3843,7 +3843,7 @@ debugging code.") (define-public guile-png (package (name "guile-png") - (version "0.4.1") + (version "0.5.0") (source (origin (method git-fetch) (uri (git-reference @@ -3852,7 +3852,7 @@ debugging code.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1vkhv0dip0na6d9g478i587n5y6046vn5rsjmfnbibi9yx4rkrf8")))) + "0dnahq05mwxzbsqb0qjkyysylc54qr8l5839zyc4sanl2syzhvwk")))) (build-system gnu-build-system) (arguments `(#:make-flags '("GUILE_AUTO_COMPILE=0"))) ;to prevent guild warnings -- cgit v1.2.3 From 66c9b82fed3c59ee07187898592c688c82fed273 Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Mon, 29 May 2023 10:31:52 +0800 Subject: gnu: emacs-straight-el: Update to 0-2.039e5c9. * gnu/packages/emacs-xyz.scm (emacs-straight-el): Update to 0-2.039e5c9. Signed-off-by: Christopher Baines --- gnu/packages/emacs-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 7575049ea36..b77bd0aa830 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -36463,8 +36463,8 @@ headlines, keywords, tables and source blocks.") (license license:gpl3+)))) ; License is in pyimport.el (define-public emacs-straight-el - (let ((commit "f21103d97d180fba0b6e2e86ebb0b6269219ef2c") - (revision "1")) + (let ((commit "039e5c9a9b5c00749602afb41341e9e77ba09429") + (revision "2")) (package (name "emacs-straight-el") (version (git-version "0" revision commit)) @@ -36477,7 +36477,7 @@ headlines, keywords, tables and source blocks.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "1dqhb7kx4hr3cm4gj6qdk9aav05vc016y4nks2dj1sy88wia6wsv")))) + (base32 "05avzakgkwzrj1pxa1pkcv96knqq4mnkv2cszn4cs4kmvr2mchxm")))) (build-system emacs-build-system) (arguments (list -- cgit v1.2.3 From bb3454a83f902d4750e3618e9e23e4ce8f0ca3c6 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sat, 3 Jun 2023 22:10:51 +0300 Subject: gnu: notcurses: Enable building without pandoc. * gnu/packages/notcurses.scm (notcurses)[arguments]: Adjust configure-flags to not use pandoc on systems where pandoc isn't supported. [native-inputs]: Don't include pandoc on systems where it isn't supported. --- gnu/packages/notcurses.scm | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/notcurses.scm b/gnu/packages/notcurses.scm index 591bed23ef7..20b2cbb2250 100644 --- a/gnu/packages/notcurses.scm +++ b/gnu/packages/notcurses.scm @@ -1,5 +1,6 @@ ;;; Copyright © 2021 Blake Shaw ;;; Copyright © 2022 Marius Bakke +;;; Copyright © 2023 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -59,6 +60,10 @@ "-DUSE_COVERAGE=off" ;; Do not build HTML documentation "-DUSE_DOXYGEN=off" + ;; Unfortunately this disables the manpages. + ,@(if (supported-package? pandoc) + '() + '("-DUSE_PANDOC=off")) ;; Don't include mouse support "-DUSE_GPM=off" ;; Use FFmpeg for multimedia support @@ -66,9 +71,12 @@ ;; Follow the Debian Free Software Guidelines, omitting nonfree content. "-DDFSG_BUILD=ON"))) (native-inputs - (list pkg-config - pandoc - doctest)) + (append + (list pkg-config) + (if (supported-package? pandoc) + (list pandoc) + '()) + (list doctest))) (inputs (list ffmpeg libdeflate -- cgit v1.2.3 From b3492964c2573993b65c20f6e7d16c29cfd6f4f5 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Sat, 3 Jun 2023 22:10:28 +0100 Subject: gnu: font-charter: Remove woff2 output. The font-build-system now installs web fonts too. So, a separate woff2 output is not necessary. * gnu/packages/fonts.scm (font-charter)[outputs, arguments]: Delete. --- gnu/packages/fonts.scm | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index 0a897fcf0b8..91e7ccc49f1 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -19,7 +19,7 @@ ;;; Copyright © 2017 Alex Griffin ;;; Copyright © 2017 Clément Lassieur ;;; Copyright © 2017 Brendan Tildesley -;;; Copyright © 2017, 2018, 2019, 2020, 2022 Arun Isaac +;;; Copyright © 2017–2023 Arun Isaac ;;; Copyright © 2017 Mohammed Sadiq ;;; Copyright © 2018 Charlie Ritter ;;; Copyright © 2018 Gabriel Hondet @@ -2845,18 +2845,7 @@ optimized for using musical symbols inline with regular text.") (file-name (string-append name "-" version ".zip")) (sha256 (base32 "1j8iv2dl695zrabs2knb7jsky8mjis29a2ddpna4by8mlvqrf0ml")))) - (outputs '("out" "woff2")) (build-system font-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'install 'install-woff2 - (lambda* (#:key outputs #:allow-other-keys) - (let ((dest (string-append (assoc-ref outputs "woff2") - "/share/fonts/woff2"))) - (for-each (lambda (file) - (install-file file dest)) - (find-files "." "\\.woff2$")))))))) (home-page "https://practicaltypography.com/charter.html") (synopsis "Charter fonts in OpenType and TrueType formats") (description "Charter was designed by Matthew Carter in 1987 and was -- cgit v1.2.3 From 07ac0cb722b2a40f1d8c4362d2c1d80298a9a60a Mon Sep 17 00:00:00 2001 From: Zhu Zihao Date: Fri, 19 May 2023 19:51:41 +0800 Subject: gnu: d-feet: Fix build errors when using Meson 1.1.0. Fix the build error: data/meson.build:15:0: ERROR: Function does not take positional arguments. data/meson.build:27:0: ERROR: Function does not take positional arguments. * gnu/packages/patches/d-feet-drop-unused-meson-argument.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it here. * gnu/packages/gnome.scm (d-feet)[source]: Use it here. Signed-off-by: Liliana Marie Prikler --- gnu/local.mk | 1 + gnu/packages/gnome.scm | 5 ++- .../d-feet-drop-unused-meson-argument.patch | 36 ++++++++++++++++++++++ 3 files changed, 41 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/d-feet-drop-unused-meson-argument.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 09a4617dafd..7aa4f72d32c 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1033,6 +1033,7 @@ dist_patch_DATA = \ %D%/packages/patches/curl-use-ssl-cert-env.patch \ %D%/packages/patches/cursynth-wave-rand.patch \ %D%/packages/patches/cvs-CVE-2017-12836.patch \ + %D%/packages/patches/d-feet-drop-unused-meson-argument.patch \ %D%/packages/patches/date-output-pkg-config-files.patch \ %D%/packages/patches/datefudge-gettimeofday.patch \ %D%/packages/patches/dbacl-include-locale.h.patch \ diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 324feedcf72..90b72731f6c 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -76,6 +76,7 @@ ;;; Copyright © 2023 Kaelyn Takata ;;; Copyright © 2023 Juliana Sims ;;; Copyright © 2023 Dominik Delgado Steuter +;;; Copyright © 2023 Zhu Zihao ;;; ;;; This file is part of GNU Guix. ;;; @@ -7199,7 +7200,9 @@ principles are simplicity and standards compliance.") name "-" version ".tar.xz")) (sha256 (base32 - "1jqw5ndpgyb0zxh0g21ai1911lfrm56vz18xbccfqm4sk95wwcw7")))) + "1jqw5ndpgyb0zxh0g21ai1911lfrm56vz18xbccfqm4sk95wwcw7")) + (patches + (search-patches "d-feet-drop-unused-meson-argument.patch")))) (build-system meson-build-system) (arguments (list diff --git a/gnu/packages/patches/d-feet-drop-unused-meson-argument.patch b/gnu/packages/patches/d-feet-drop-unused-meson-argument.patch new file mode 100644 index 00000000000..5d728d7d60a --- /dev/null +++ b/gnu/packages/patches/d-feet-drop-unused-meson-argument.patch @@ -0,0 +1,36 @@ +From 05465d486afdba116dbc22fc22c1e6573aea4f22 Mon Sep 17 00:00:00 2001 +From: Jan Beich +Date: Mon, 24 Jan 2022 12:11:57 +0000 +Subject: [PATCH] meson: drop unused argument for i18n.merge_file() + +Ignored in Meson < 0.60.0, deprecated since 0.60.1 and fatal since 0.61.0. + +data/meson.build:15:0: ERROR: Function does not take positional arguments. +data/meson.build:27:0: ERROR: Function does not take positional arguments. +--- + data/meson.build | 2 -- + 1 file changed, 2 deletions(-) + +diff --git a/data/meson.build b/data/meson.build +index 026bd80..3b03b94 100644 +--- a/data/meson.build ++++ b/data/meson.build +@@ -13,7 +13,6 @@ desktop_in = configure_file( + ) + + i18n.merge_file( +- desktop, + type: 'desktop', + input: desktop_in, + output: '@BASENAME@', +@@ -25,7 +24,6 @@ i18n.merge_file( + appdata = df_namespace + '.appdata.xml' + + i18n.merge_file( +- appdata, + input: appdata + '.in', + output: '@BASENAME@', + po_dir: po_dir, +-- +GitLab + -- cgit v1.2.3 From 0d6749be37890dd24d2b46ace5752ac96160dc12 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 30 May 2023 23:18:38 -0400 Subject: gnu: mpd: Update to 0.23.13. * gnu/packages/mpd.scm (mpd): Update to 0.23.13. Signed-off-by: Liliana Marie Prikler --- gnu/packages/mpd.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 5005da4e878..1b0acc81dbe 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -118,7 +118,7 @@ interfacing MPD in the C, C++ & Objective C languages.") (define-public mpd (package (name "mpd") - (version "0.23.12") + (version "0.23.13") (source (origin (method url-fetch) (uri @@ -127,7 +127,7 @@ interfacing MPD in the C, C++ & Objective C languages.") "/mpd-" version ".tar.xz")) (sha256 (base32 - "1rq2hyfvwwri3sivab747csza2i096y7m8563rl5mhpchhiadz5p")))) + "06fmy68lfrsi5y03l53dnwcynqhwh5f5vhdpbsr8lzmvzgk02sx9")))) (build-system meson-build-system) (arguments (list -- cgit v1.2.3 From 709fd0e5e0a318c7272776efc6472487e8a28ddd Mon Sep 17 00:00:00 2001 From: Bruno Victal Date: Fri, 26 May 2023 08:06:20 +0100 Subject: gnu: mpd: Enable tests. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit With this, ninja will no longer report “no work to do” when inside the `check' phase. * gnu/packages/mpd.scm [arguments]<#:configure-flags>: Add “-Dtest=true”. [native-inputs]: Add googletest and zip. Remove cmake. Signed-off-by: Liliana Marie Prikler --- gnu/packages/mpd.scm | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 1b0acc81dbe..3259217989b 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -132,7 +132,8 @@ interfacing MPD in the C, C++ & Objective C languages.") (arguments (list #:configure-flags #~(list "-Ddocumentation=enabled" - "-Dsystemd=enabled") + "-Dsystemd=enabled" + "-Dtest=true") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'enable-elogind @@ -182,7 +183,12 @@ interfacing MPD in the C, C++ & Objective C languages.") yajl zlib zziplib))) - (native-inputs (list cmake pkg-config python-sphinx)) + (native-inputs (list pkg-config python-sphinx googletest + ;; See test/meson.build for information about these + ;; additional dependencies. + ;; + ;; Used when zziplib feature is enabled. + zip)) ;; Missing optional inputs: ;; libcdio_paranoia ;; libmms -- cgit v1.2.3 From 65bce4d9f9302bc798717d73548bbe5ceb802151 Mon Sep 17 00:00:00 2001 From: Bruno Victal Date: Fri, 26 May 2023 08:06:21 +0100 Subject: gnu: mpd: Split outputs. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The HTML manual accounts for more than 40% of the package size. * gnu/packages/mpd.scm (mpd)[outputs]: Add 'doc' output. [arguments]<#:phases>: Add ‘split-package’. Signed-off-by: Liliana Marie Prikler --- gnu/packages/mpd.scm | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 3259217989b..9884bc04878 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -146,7 +146,15 @@ interfacing MPD in the C, C++ & Objective C languages.") (("systemd_dep = declare_dependency" all) (string-append "_" all))) (substitute* "meson.build" - (("systemd_dep,") "systemd_dep, _systemd_dep,"))))))) + (("systemd_dep,") "systemd_dep, _systemd_dep,")))) + (add-after 'install 'split-package + (lambda _ + ;; The HTML manual accounts for over 40% of the disk + ;; space used by the package. + (let* ((old (string-append #$output "/share/doc")) + (new (string-append #$output:doc "/share/doc"))) + (mkdir-p (dirname new)) + (rename-file old new))))))) (inputs (append (if (target-linux?) (list liburing) '()) (list ao @@ -189,6 +197,7 @@ interfacing MPD in the C, C++ & Objective C languages.") ;; ;; Used when zziplib feature is enabled. zip)) + (outputs (list "out" "doc")) ;; Missing optional inputs: ;; libcdio_paranoia ;; libmms -- cgit v1.2.3 From f4f5ee6ad6e2432f52e37c549211df8f1cdbb571 Mon Sep 17 00:00:00 2001 From: muradm Date: Mon, 22 May 2023 22:06:51 +0300 Subject: services: screen-locker-service-type: Configurable PAM and setuid. screen-locker-service-type by default does both define PAM entry and make program setuid binary. Normally both methods are mutually exclusive, if binary has setuid set it does not really needs PAM, otherway around also similar, if PAM is enabled binary should not relay on setuid. Recent swaylock package now compiled with PAM support. When PAM support is compiled in, swaylock rejects executing if binary is also setuid program. This change turns screen-locker-configuration from strict PAM AND setuid to more flexible PAM AND/OR setuid. Allowing swaylock to be configured properly while supporting other screen locker preferences. * gnu/services/xorg.scm (screen-locker-configuration): Switch from define-record-type to define-configuration. [using-pam?]: New field to control PAM entry existence. [using-setuid?]: New field to control setuid binary existence. (screen-locker-pam-services): Should not make unix-pam-service if using-pam? is set to #f. (screen-locker-setuid-programs): Should not make program setuid program if using-setuid? is set to #f. (screen-locker-generate-doc): Internal function to generate configuration documentation. (screen-locker-service): Adapt to new screen-locker-configuration. * gnu/services/desktop.scm (desktop-services-for-system): Adapt to new screen-locker-configuration. * doc/guix.texi: Reflect new changes to screen-locker-configuration. Signed-off-by: Josselin Poiret --- doc/guix-cookbook.texi | 5 +++- doc/guix.texi | 40 +++++++++++++++++++++++------ gnu/services/desktop.scm | 6 +++-- gnu/services/xorg.scm | 65 +++++++++++++++++++++++++++++------------------- 4 files changed, 81 insertions(+), 35 deletions(-) (limited to 'gnu') diff --git a/doc/guix-cookbook.texi b/doc/guix-cookbook.texi index b1ffa72c0e6..b9f5f6b6a9b 100644 --- a/doc/guix-cookbook.texi +++ b/doc/guix-cookbook.texi @@ -2147,7 +2147,10 @@ be made setuid-root so it can authenticate users, and it needs a PAM service. Th can be achieved by adding the following service to your @file{config.scm}: @lisp -(screen-locker-service slock) +(service screen-locker-services-type + (screen-locker-configuration + (name "slock") + (program (file-append slock "/bin/slock")))) @end lisp If you manually lock your screen, e.g. by directly calling slock when you want to lock diff --git a/doc/guix.texi b/doc/guix.texi index 7f8d8d66e92..db37676e128 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -97,7 +97,7 @@ Copyright @copyright{} 2021 Hui Lu@* Copyright @copyright{} 2021 pukkamustard@* Copyright @copyright{} 2021 Alice Brenon@* Copyright @copyright{} 2021, 2022 Josselin Poiret@* -Copyright @copyright{} 2021 muradm@* +Copyright @copyright{} 2021, 2023 muradm@* Copyright @copyright{} 2021, 2022 Andrew Tropin@* Copyright @copyright{} 2021 Sarah Morgensen@* Copyright @copyright{} 2022 Remco van 't Veer@* @@ -22530,37 +22530,63 @@ Usually the X server is started by a login manager. @defvar screen-locker-service-type Type for a service that adds a package for a screen locker or screen -saver to the set of setuid programs and add a PAM entry for it. The +saver to the set of setuid programs and/or add a PAM entry for it. The value for this service is a @code{} object. +While the default behavior is to setup both a setuid program and PAM +entry, these two methods are redundant. Screen locker programs may not +execute when PAM is configured and @code{setuid} is set on their +executable. In this case, @code{using-setuid?} can be set to @code{#f}. + For example, to make XlockMore usable: @lisp (service screen-locker-service-type (screen-locker-configuration - "xlock" (file-append xlockmore "/bin/xlock") #f)) + (name "xlock") + (program (file-append xlockmore "/bin/xlock")))) @end lisp makes the good ol' XlockMore usable. + +For example, swaylock fails to execute when compiled with PAM support +and setuid enabled. One can thus disable setuid: + +@lisp +(service screen-locker-service-type + (screen-locker-configuration + (name "swaylock") + (program (file-append xlockmore "/bin/xlock")) + (using-pam? #t) + (using-setuid? #f))) +@end lisp + @end defvar @deftp {Data Type} screen-locker-configuration -Data type representing the configuration of -@code{screen-locker-service-type}. +Available @code{screen-locker-configuration} fields are: @table @asis @item @code{name} (type: string) Name of the screen locker. -@item @code{program} (type: gexp) +@item @code{program} (type: file-like) Path to the executable for the screen locker as a G-Expression. -@item @code{allow-empty-password?} (type: boolean) +@item @code{allow-empty-password?} (default: @code{#f}) (type: boolean) Whether to allow empty passwords. +@item @code{using-pam?} (default: @code{#t}) (type: boolean) +Whether to setup PAM entry. + +@item @code{using-setuid?} (default: @code{#t}) (type: boolean) +Whether to setup program as setuid binary. + @end table + @end deftp + @node Printing Services @subsection Printing Services diff --git a/gnu/services/desktop.scm b/gnu/services/desktop.scm index 64eac1117d7..a63748b652f 100644 --- a/gnu/services/desktop.scm +++ b/gnu/services/desktop.scm @@ -1839,10 +1839,12 @@ applications needing access to be root.") ;; Screen lockers are a pretty useful thing and these are small. (service screen-locker-service-type (screen-locker-configuration - "slock" (file-append slock "/bin/slock") #f)) + (name "slock") + (program (file-append slock "/bin/slock")))) (service screen-locker-service-type (screen-locker-configuration - "xlock" (file-append xlockmore "/bin/xlock") #f)) + (name "xlock") + (program (file-append xlockmore "/bin/xlock")))) ;; Add udev rules for MTP devices so that non-root users can access ;; them. diff --git a/gnu/services/xorg.scm b/gnu/services/xorg.scm index 8b6080fd264..f8cf9f25b67 100644 --- a/gnu/services/xorg.scm +++ b/gnu/services/xorg.scm @@ -13,6 +13,7 @@ ;;; Copyright © 2021 Josselin Poiret ;;; Copyright © 2022 Chris Marusich ;;; Copyright © 2022 Maxim Cournoyer +;;; Copyright © 2023 muradm ;;; ;;; This file is part of GNU Guix. ;;; @@ -112,6 +113,8 @@ screen-locker-configuration-name screen-locker-configuration-program screen-locker-configuration-allow-empty-password? + screen-locker-configuration-using-pam? + screen-locker-configuration-using-setuid? screen-locker-service-type screen-locker-service ; deprecated @@ -703,30 +706,38 @@ reboot_cmd " shepherd "/sbin/reboot\n" ;;; Screen lockers & co. ;;; -(define-record-type - (screen-locker-configuration name program allow-empty-password?) - screen-locker-configuration? - (name screen-locker-configuration-name) ;string - (program screen-locker-configuration-program) ;gexp +(define-configuration/no-serialization screen-locker-configuration + (name + string + "Name of the screen locker.") + (program + file-like + "Path to the executable for the screen locker as a G-Expression.") (allow-empty-password? - screen-locker-configuration-allow-empty-password?)) ;Boolean - -(define-deprecated/public-alias - screen-locker - screen-locker-configuration) - -(define-deprecated/public-alias - screen-locker? - screen-locker-configuration?) - -(define screen-locker-pam-services - (match-lambda - (($ name _ empty?) - (list (unix-pam-service name - #:allow-empty-passwords? empty?))))) + (boolean #f) + "Whether to allow empty passwords.") + (using-pam? + (boolean #t) + "Whether to setup PAM entry.") + (using-setuid? + (boolean #t) + "Whether to setup program as setuid binary.")) + +(define (screen-locker-pam-services config) + (match-record config + (name allow-empty-password? using-pam?) + (if using-pam? + (list (unix-pam-service name + #:allow-empty-passwords? + allow-empty-password?)) + '()))) -(define screen-locker-setuid-programs - (compose list file-like->setuid-program screen-locker-configuration-program)) +(define (screen-locker-setuid-programs config) + (match-record config + (name program using-setuid?) + (if using-setuid? + (list (file-like->setuid-program program)) + '()))) (define screen-locker-service-type (service-type (name 'screen-locker) @@ -740,6 +751,9 @@ reboot_cmd " shepherd "/sbin/reboot\n" the graphical server by making it setuid-root, so it can authenticate users, and by creating a PAM service for it."))) +(define (screen-locker-generate-doc) + (configuration->documentation 'screen-locker-configuration)) + (define-deprecated (screen-locker-service package #:optional (program (package-name package)) @@ -755,9 +769,10 @@ for it. For example: makes the good ol' XlockMore usable." (service screen-locker-service-type - (screen-locker-configuration program - (file-append package "/bin/" program) - allow-empty-passwords?))) + (screen-locker-configuration + (name program) + (program (file-append package "/bin/" program)) + (allow-empty-password? allow-empty-passwords?)))) ;;; -- cgit v1.2.3 From 94879ff743530a1b8aef7283578bba2a80fa9f80 Mon Sep 17 00:00:00 2001 From: Felix Lechner Date: Sun, 28 May 2023 17:19:17 -0700 Subject: gnu: heimdal: Run autoreconf. * gnu/packages/kerberos.scm (heimdal): Run autoreconf. Signed-off-by: Josselin Poiret --- gnu/packages/kerberos.scm | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/kerberos.scm b/gnu/packages/kerberos.scm index c553f8180ac..f06410b8f82 100644 --- a/gnu/packages/kerberos.scm +++ b/gnu/packages/kerberos.scm @@ -183,14 +183,7 @@ After installation, the system administrator should generate keys using (base32 "0f4dblav859p5hn7b2jdj1akw6d8p32as6bj6zym19kghh3s51zx")) (patches - (search-patches "heimdal-CVE-2022-45142.patch")) - (modules '((guix build utils))) - (snippet - '(begin - (substitute* "configure" - (("User=.*$") "User=Guix\n") - (("Host=.*$") "Host=GNU") - (("Date=.*$") "Date=2022\n")))))) + (search-patches "heimdal-CVE-2022-45142.patch")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -223,7 +216,12 @@ After installation, the system administrator should generate keys using #:phases (modify-phases %standard-phases (add-before 'configure 'pre-configure (lambda* (#:key inputs #:allow-other-keys) + (invoke (search-input-file inputs "bin/autoreconf") "--install" "--force") (substitute* "configure" + ;; Reproducible build date, etc. + (("User=.*$") "User=Guix\n") + (("Host=.*$") "Host=GNU\n") + (("Date=.*$") "Date=2022\n") ;; The e2fsprogs input is included for libcom_err, ;; let's use it even if cross-compiling. (("test \"\\$\\{krb_cv_com_err\\}\" = \"yes\"") @@ -255,12 +253,17 @@ After installation, the system administrator should generate keys using (format #t "#!~a~%exit 1~%" (which "sh"))))))) ;; Tests fail when run in parallel. #:parallel-tests? #f)) - (native-inputs (list bison + (native-inputs (list autoconf + automake + bison e2fsprogs ;for 'compile_et' flex + libtool texinfo unzip ;for tests pkg-config + perl + perl-json python)) (inputs (list readline bash-minimal -- cgit v1.2.3 From d89247150fe6e97c2fceed8d578fd119a782624d Mon Sep 17 00:00:00 2001 From: Felix Lechner Date: Sun, 28 May 2023 17:19:18 -0700 Subject: gnu: heimdal: Drop obsolete and insecure user tools. According to messages from the Heimdal maintainers Brian May and Nico Williams, no one should be using their version of 'su' anymore. It was deleted from the development branch five years ago [1] and is only being shipped because the 7.8.0 is based on an older, stable branch. [1] https://github.com/heimdal/heimdal/commit/8a77f45aff366b1cd8c70c43ce63eb16a0c9839c Following the directions from the maintainers, this commit drops all executables built from the ./appl folder via deletion of that SUBDIR from the top-level Makefile.am. Unfortunately, the heimdal-discuss mailing list does not appear to have a public archive. The relevant SMTP Message-Id was: * gnu/packages/kerberos.scm (heimdal): Drop obsolete and insecure user tools. Signed-off-by: Josselin Poiret --- gnu/packages/kerberos.scm | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/kerberos.scm b/gnu/packages/kerberos.scm index f06410b8f82..241881ea477 100644 --- a/gnu/packages/kerberos.scm +++ b/gnu/packages/kerberos.scm @@ -214,6 +214,12 @@ After installation, the system administrator should generate keys using "/libexec/heimdal"))) #~())) #:phases (modify-phases %standard-phases + ;; Skip the appl folder as obsolete per message from Brian May + ;; + (add-after 'unpack 'drop-obsolete-executables + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("Makefile.am") + (("appl") "")))) (add-before 'configure 'pre-configure (lambda* (#:key inputs #:allow-other-keys) (invoke (search-input-file inputs "bin/autoreconf") "--install" "--force") @@ -230,15 +236,6 @@ After installation, the system administrator should generate keys using ;; which confuses heimdal. (("ac_cv_prog_COMPILE_ET=\\$\\{with_cross_tools\\}compile_et") "ac_cv_PROG_COMPILE_ET=compile_et")) - (substitute* '("appl/afsutil/pagsh.c" "appl/su/su.c") - (("/bin/sh") - (search-input-file inputs "bin/sh")) - ;; Use the cross-compiled bash instead of the - ;; native bash (XXX shouldn't _PATH_BSHELL point - ;; to a cross-compiled bash?). - (("_PATH_BSHELL") - (string-append - "\"" (search-input-file inputs "bin/sh") "\""))) (substitute* '("tools/Makefile.in") (("/bin/sh") (which "sh"))))) (add-before 'check 'pre-check -- cgit v1.2.3 From b741218e919bfd386772322c1dcb286446bc4c90 Mon Sep 17 00:00:00 2001 From: Josselin Poiret Date: Fri, 2 Jun 2023 21:59:48 +0200 Subject: gnu: proot: Update to 5.4.0 and fix clone3 behavior. * gnu/packages/patches/proot-add-clone3.patch: New patch. * gnu/packages/linux.scm (proot): Update to 5.4.0, and add pending upstream patch to fix buggy pthread support. * gnu/local.mk (dist_patch_DATA): Register it. --- gnu/local.mk | 1 + gnu/packages/linux.scm | 7 +- gnu/packages/patches/proot-add-clone3.patch | 114 ++++++++++++++++++++++++++++ 3 files changed, 120 insertions(+), 2 deletions(-) create mode 100644 gnu/packages/patches/proot-add-clone3.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 7aa4f72d32c..7be3cc54640 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1750,6 +1750,7 @@ dist_patch_DATA = \ %D%/packages/patches/procmail-ambiguous-getline-debian.patch \ %D%/packages/patches/procmail-CVE-2014-3618.patch \ %D%/packages/patches/procmail-CVE-2017-16844.patch \ + %D%/packages/patches/proot-add-clone3.patch \ %D%/packages/patches/protobuf-fix-build-on-32bit.patch \ %D%/packages/patches/psm-arch.patch \ %D%/packages/patches/psm-disable-memory-stats.patch \ diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index fc6f3cbda55..501ac9d19c1 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -8159,7 +8159,7 @@ Text-based output formats: CSV, XML, Netfilter's LOG, Netfilter's conntrack (define-public proot (package (name "proot") - (version "5.3.0") + (version "5.4.0") (source (origin (method git-fetch) @@ -8168,7 +8168,10 @@ Text-based output formats: CSV, XML, Netfilter's LOG, Netfilter's conntrack (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1r1ga3xbwq5kx4i8ihj1p6nmgaa14lfkwxzpsbdcmfh1jimpbmzk")))) + (base32 "186qsg4yvisqjgf8w5jxhnlig7x341vpqwcgp8as3r59qmqkpmk7")) + ;; Waiting for upstream inclusion at + ;; https://github.com/proot-me/proot/pull/355 + (patches (search-patches "proot-add-clone3.patch")))) (build-system gnu-build-system) ;; Many architectures are not supported (see: ;; https://github.com/proot-me/proot/blob/master/src/arch.h#L51). diff --git a/gnu/packages/patches/proot-add-clone3.patch b/gnu/packages/patches/proot-add-clone3.patch new file mode 100644 index 00000000000..c09d99a743f --- /dev/null +++ b/gnu/packages/patches/proot-add-clone3.patch @@ -0,0 +1,114 @@ +From 4699a580ca1aeecd35742494eb0259ee962e89a8 Mon Sep 17 00:00:00 2001 +Message-Id: <4699a580ca1aeecd35742494eb0259ee962e89a8.1685735399.git.dev@jpoiret.xyz> +From: Josselin Poiret +Date: Fri, 2 Jun 2023 21:42:31 +0200 +Subject: [PATCH] Add clone3. + +From: Josselin Poiret + +--- + src/syscall/sysnums-arm.h | 1 + + src/syscall/sysnums-arm64.h | 1 + + src/syscall/sysnums-i386.h | 1 + + src/syscall/sysnums-sh4.h | 1 + + src/syscall/sysnums-x32.h | 1 + + src/syscall/sysnums-x86_64.h | 1 + + src/syscall/sysnums.list | 1 + + src/tracee/tracee.c | 4 ++++ + 8 files changed, 11 insertions(+) + +diff --git a/src/syscall/sysnums-arm.h b/src/syscall/sysnums-arm.h +index dfd512f..306e2b1 100644 +--- a/src/syscall/sysnums-arm.h ++++ b/src/syscall/sysnums-arm.h +@@ -341,4 +341,5 @@ static const Sysnum sysnums_arm[] = { + [ 382 ] = PR_renameat2, + [ 397 ] = PR_statx, + [ 412 ] = PR_utimensat_time64, ++ [ 435 ] = PR_clone3, + }; +diff --git a/src/syscall/sysnums-arm64.h b/src/syscall/sysnums-arm64.h +index dfb9889..65ccc4e 100644 +--- a/src/syscall/sysnums-arm64.h ++++ b/src/syscall/sysnums-arm64.h +@@ -264,4 +264,5 @@ static const Sysnum sysnums_arm64[] = { + [ 275 ] = PR_sched_getattr, + [ 276 ] = PR_renameat2, + [ 291 ] = PR_statx, ++ [ 435 ] = PR_clone3, + }; +diff --git a/src/syscall/sysnums-i386.h b/src/syscall/sysnums-i386.h +index 3bbb70e..0f3daf2 100644 +--- a/src/syscall/sysnums-i386.h ++++ b/src/syscall/sysnums-i386.h +@@ -353,4 +353,5 @@ static const Sysnum sysnums_i386[] = { + [ 353 ] = PR_renameat2, + [ 383 ] = PR_statx, + [ 412 ] = PR_utimensat_time64, ++ [ 435 ] = PR_clone3, + }; +diff --git a/src/syscall/sysnums-sh4.h b/src/syscall/sysnums-sh4.h +index 1d3758c..09acca6 100644 +--- a/src/syscall/sysnums-sh4.h ++++ b/src/syscall/sysnums-sh4.h +@@ -344,4 +344,5 @@ static const Sysnum sysnums_sh4[] = { + [ 369 ] = PR_sched_setattr, + [ 370 ] = PR_sched_getattr, + [ 371 ] = PR_renameat2, ++ [ 435 ] = PR_clone3, + }; +diff --git a/src/syscall/sysnums-x32.h b/src/syscall/sysnums-x32.h +index 448c699..a9fdb48 100644 +--- a/src/syscall/sysnums-x32.h ++++ b/src/syscall/sysnums-x32.h +@@ -277,6 +277,7 @@ static const Sysnum sysnums_x32[] = { + [ 315 ] = PR_sched_getattr, + [ 316 ] = PR_renameat2, + [ 332 ] = PR_statx, ++ [ 435 ] = PR_clone3, + [ 439 ] = PR_faccessat2, + [ 512 ] = PR_rt_sigaction, + [ 513 ] = PR_rt_sigreturn, +diff --git a/src/syscall/sysnums-x86_64.h b/src/syscall/sysnums-x86_64.h +index 92229f8..9840b4a 100644 +--- a/src/syscall/sysnums-x86_64.h ++++ b/src/syscall/sysnums-x86_64.h +@@ -319,5 +319,6 @@ static const Sysnum sysnums_x86_64[] = { + [ 315 ] = PR_sched_getattr, + [ 316 ] = PR_renameat2, + [ 332 ] = PR_statx, ++ [ 435 ] = PR_clone3, + [ 439 ] = PR_faccessat2, + }; +diff --git a/src/syscall/sysnums.list b/src/syscall/sysnums.list +index 1d6e666..2b6c9b2 100644 +--- a/src/syscall/sysnums.list ++++ b/src/syscall/sysnums.list +@@ -38,6 +38,7 @@ SYSNUM(clock_gettime) + SYSNUM(clock_nanosleep) + SYSNUM(clock_settime) + SYSNUM(clone) ++SYSNUM(clone3) + SYSNUM(close) + SYSNUM(connect) + SYSNUM(creat) +diff --git a/src/tracee/tracee.c b/src/tracee/tracee.c +index 58ab7df..9b16f6a 100644 +--- a/src/tracee/tracee.c ++++ b/src/tracee/tracee.c +@@ -403,6 +403,10 @@ int new_child(Tracee *parent, word_t clone_flags) + status = fetch_regs(parent); + if (status >= 0 && get_sysnum(parent, CURRENT) == PR_clone) + clone_flags = peek_reg(parent, CURRENT, SYSARG_1); ++ else if (status >= 0 && get_sysnum(parent, CURRENT) == PR_clone3) ++ // Look at the first word of the clone_args structure, which ++ // contains the usual clone flags. ++ clone_flags = peek_word(parent, peek_reg(parent, CURRENT, SYSARG_1)); + + /* Get the pid of the parent's new child. */ + status = ptrace(PTRACE_GETEVENTMSG, parent->pid, NULL, &pid); + +base-commit: bd5a5f63d72f8210d8cee76195eb9f0749e5bd70 +-- +2.40.1 + -- cgit v1.2.3 From f72f3a909a41dce5dc4512c30d4cd0673bc6560f Mon Sep 17 00:00:00 2001 From: kiasoc5 Date: Mon, 29 May 2023 17:53:41 -0400 Subject: gnu: sbsigntools: Update to 0.9.5. This fixes a build failure with openssl-3. * gnu/packages/efi.scm (sbsigntools): Update to 0.9.5. [arguments]: Remove trailing #t's. Use Gexps. Use "this-package-input". Simplify lambdas. [inputs]: Remove labels. Signed-off-by: Josselin Poiret --- gnu/packages/efi.scm | 59 ++++++++++++++++++++++++++-------------------------- 1 file changed, 29 insertions(+), 30 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/efi.scm b/gnu/packages/efi.scm index 75eb24bf860..499745eba1a 100644 --- a/gnu/packages/efi.scm +++ b/gnu/packages/efi.scm @@ -30,6 +30,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix build-system gnu) #:use-module (guix download) + #:use-module (guix gexp) #:use-module (guix git-download) #:use-module (guix packages) #:use-module (guix utils) @@ -99,7 +100,7 @@ information.") (define-public sbsigntools (package (name "sbsigntools") - (version "0.9.4") + (version "0.9.5") (source (origin (method git-fetch) @@ -110,34 +111,32 @@ information.") (recursive? #t))) (file-name (git-file-name name version)) (sha256 - (base32 "1y76wy65y6k10mjl2dm5hb5ms475alr4s080xzj8y833x01xvf3m")))) + (base32 "060n6w0dx1mrilhdv482ncckanqz6pdv53piimiki0bm15d2fcp4")))) (build-system gnu-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-more-shebangs - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "lib/ccan.git/tools/create-ccan-tree" - (("#!/bin/bash") - (string-append "#!" - (assoc-ref inputs "bash") - "/bin/bash"))) - #t)) - (add-after 'unpack 'patch - (lambda* (#:key inputs outputs #:allow-other-keys) - (substitute* '("configure.ac" - "tests/Makefile.am") - (("/usr/include/efi") - (string-append (assoc-ref inputs "gnu-efi") - "/include/efi")) - (("/usr/lib/gnuefi") - (string-append (assoc-ref inputs "gnu-efi") - "/lib"))) - #t)) - (add-after 'unpack 'setenv - (lambda _ - (setenv "CC" "gcc") - #t))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-more-shebangs + (lambda* (#:key inputs native-inputs #:allow-other-keys) + (substitute* "lib/ccan.git/tools/create-ccan-tree" + (("#!/bin/bash") + (string-append "#!" + (search-input-file (or native-inputs inputs) + "/bin/bash")))))) + (add-after 'unpack 'patch + (lambda _ + (substitute* '("configure.ac" + "tests/Makefile.am") + (("/usr/include/efi") + (string-append #$(this-package-input "gnu-efi") + "/include/efi")) + (("/usr/lib/gnuefi") + (string-append #$(this-package-input "gnu-efi") + "/lib"))))) + (add-after 'unpack 'setenv + (lambda _ + (setenv "CC" #$(cc-for-target))))))) (native-inputs (list autoconf automake @@ -146,9 +145,9 @@ information.") pkg-config util-linux)) ; getopt (inputs - `(("gnu-efi" ,gnu-efi) - ("libuuid" ,util-linux "lib") - ("openssl" ,openssl))) + (list gnu-efi + `(,util-linux "lib") ; libuuid + openssl)) (synopsis "EFI signing tools") (description "This package provides tools for signing EFI binaries.") (home-page "https://git.kernel.org/pub/scm/linux/kernel/git/jejb/sbsigntools.git/") -- cgit v1.2.3 From 89f8fc9c95791acc402444d09dfb503f494b1db8 Mon Sep 17 00:00:00 2001 From: Josselin Poiret Date: Wed, 1 Mar 2023 16:31:38 +0100 Subject: gnu: Add ghc-peano. * gnu/packages/haskell-xyz.scm (ghc-peano): New variable. --- gnu/packages/haskell-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm index 929ee08387a..9852fdcc8bb 100644 --- a/gnu/packages/haskell-xyz.scm +++ b/gnu/packages/haskell-xyz.scm @@ -31,6 +31,7 @@ ;;; Copyright © 2021–2023 Alice BRENON ;;; Copyright © 2021 John Kehayias ;;; Copyright © 2022 jgart +;;; Copyright © 2023 Josselin Poiret ;;; ;;; This file is part of GNU Guix. ;;; @@ -8602,6 +8603,26 @@ of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.") (license license:bsd-3))) +(define-public ghc-peano + (package + (name "ghc-peano") + (version "0.1.0.1") + (source (origin + (method url-fetch) + (uri (hackage-uri "peano" version)) + (sha256 + (base32 + "0yzcxrl41dacvx2wkyxjj7hgvz56l4qb59r4h9rmaqd7jcwx5z9i")))) + (build-system haskell-build-system) + (arguments + `(#:cabal-revision ("3" + "0wl22dnz6ld300cg6id3lw991bp8kdfi8h0nbv37vn79i1zdcj5n"))) + (home-page "http://hackage.haskell.org/package/peano") + (synopsis "Peano numbers") + (description "Provides an efficient Haskell implementation of Peano +numbers") + (license license:bsd-3))) + (define-public ghc-persistent (package (name "ghc-persistent") -- cgit v1.2.3 From cc67085077c06b560840d24b3d00624313904206 Mon Sep 17 00:00:00 2001 From: Josselin Poiret Date: Wed, 1 Mar 2023 16:32:31 +0100 Subject: gnu: Add ghc-vector-hashtables. * gnu/packages/haskell-xyz.scm (ghc-vector-hashtables): New variable. --- gnu/packages/haskell-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm index 9852fdcc8bb..a819698710b 100644 --- a/gnu/packages/haskell-xyz.scm +++ b/gnu/packages/haskell-xyz.scm @@ -13329,6 +13329,27 @@ the vector; then you can execute the builder to actually produce the vector.") (license license:expat))) +(define-public ghc-vector-hashtables + (package + (name "ghc-vector-hashtables") + (version "0.1.1.2") + (source (origin + (method url-fetch) + (uri (hackage-uri "vector-hashtables" version)) + (sha256 + (base32 + "0hrjvy9qg1m5g3w91zxy4syqmp8jk7ajjbxbzkhy282dwfigkyd2")))) + (build-system haskell-build-system) + (inputs (list ghc-primitive ghc-vector ghc-hashable)) + (native-inputs (list ghc-hspec ghc-quickcheck ghc-quickcheck-instances + hspec-discover)) + (home-page "https://github.com/klapaucius/vector-hashtables#readme") + (synopsis "Efficient vector-based mutable hashtables implementation") + (description + "This package provides efficient vector-based hashtable implementation +similar to .NET Generic Dictionary implementation (at the time of 2015).") + (license license:bsd-3))) + (define-public ghc-vector-th-unbox (package (name "ghc-vector-th-unbox") -- cgit v1.2.3 From af5d228b1303989812e48093769715fd19df5042 Mon Sep 17 00:00:00 2001 From: Josselin Poiret Date: Wed, 1 Mar 2023 16:33:52 +0100 Subject: gnu: agda: Update to 2.6.3 and switch to git-fetch. * gnu/packages/agda.scm (agda): Update to 2.6.3, switch to fetching using git so that doc files are included, and add new dependency ghc-vector-hashtables. --- gnu/packages/agda.scm | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm index 7128a3f1084..fc1085ec094 100644 --- a/gnu/packages/agda.scm +++ b/gnu/packages/agda.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2018, 2022 Tobias Geerinckx-Rice ;;; Copyright © 2018 John Soo ;;; Copyright © 2019 Ludovic Courtès +;;; Copyright © 2023 Josselin Poiret ;;; ;;; This file is part of GNU Guix. ;;; @@ -37,15 +38,17 @@ (define-public agda (package (name "agda") - (version "2.6.2.2") + (version "2.6.3") (source (origin - (method url-fetch) - (uri (hackage-uri "Agda" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/agda/agda.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "0yjjbhc593ylrm4mq4j01nkdvh7xqsg5in30wxj4y53vf5hkggp5")))) + (base32 "1s7zd01i8pmvi90ywx497kc07z50nah7h0fc2dn6jzb132k5sh1q")))) (build-system haskell-build-system) - (properties '((upstream-name . "Agda"))) (inputs (list ghc-aeson ghc-alex @@ -68,6 +71,7 @@ ghc-strict ghc-unordered-containers ghc-uri-encode + ghc-vector-hashtables ghc-zlib)) (arguments (list #:modules `((guix build haskell-build-system) -- cgit v1.2.3 From 789db27c51501e77ac7be0411e1f979234cf02f5 Mon Sep 17 00:00:00 2001 From: Josselin Poiret Date: Wed, 1 Mar 2023 16:34:59 +0100 Subject: gnu: agda: Build info manual. * gnu/packages/agda.scm (agda): Build the user manual as an info manual. --- gnu/packages/agda.scm | 21 ++++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm index fc1085ec094..7a28f69a0d5 100644 --- a/gnu/packages/agda.scm +++ b/gnu/packages/agda.scm @@ -26,6 +26,10 @@ #:use-module (gnu packages haskell-check) #:use-module (gnu packages haskell-web) #:use-module (gnu packages haskell-xyz) + #:use-module (gnu packages imagemagick) + #:use-module (gnu packages python) + #:use-module (gnu packages sphinx) + #:use-module (gnu packages texinfo) #:use-module (guix build-system emacs) #:use-module (guix build-system gnu) #:use-module (guix build-system haskell) @@ -73,6 +77,12 @@ ghc-uri-encode ghc-vector-hashtables ghc-zlib)) + (native-inputs + (list python + python-sphinx + python-sphinx-rtd-theme + texinfo + imagemagick)) (arguments (list #:modules `((guix build haskell-build-system) (guix build utils) @@ -89,7 +99,16 @@ (let ((agda-compiler (string-append #$output "/bin/agda"))) (for-each (cut invoke agda-compiler <>) (find-files (string-append #$output "/share") - "\\.agda$")))))))) + "\\.agda$"))))) + (add-after 'agda-compile 'install-info + (lambda _ + (with-directory-excursion "doc/user-manual" + (invoke "sphinx-build" "-b" "texinfo" + "." "_build_texinfo") + (with-directory-excursion "_build_texinfo" + (setenv "infodir" (string-append #$output + "/share/info")) + (invoke "make" "install-info")))))))) (home-page "https://wiki.portal.chalmers.se/agda/") (synopsis "Dependently typed functional programming language and proof assistant") -- cgit v1.2.3 From fe6c31e3338f73f94fcbe6fc6ff8b7543762060e Mon Sep 17 00:00:00 2001 From: Josselin Poiret Date: Wed, 8 Mar 2023 16:53:22 +0100 Subject: gnu: emacs-agda2-mode: No longer inherit from agda. * gnu/packages/agda.scm (emacs-agda2-mode): Remove it. Made no sense, as we only need the source, which we can refer to without inheriting the whole thing. --- gnu/packages/agda.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm index 7a28f69a0d5..9dfcc907ec0 100644 --- a/gnu/packages/agda.scm +++ b/gnu/packages/agda.scm @@ -129,10 +129,10 @@ such as Coq, Epigram and NuPRL.") (define-public emacs-agda2-mode (package - (inherit agda) (name "emacs-agda2-mode") + (version (package-version agda)) + (source (package-source agda)) (build-system emacs-build-system) - (inputs '()) (arguments `(#:phases (modify-phases %standard-phases @@ -141,7 +141,8 @@ such as Coq, Epigram and NuPRL.") (home-page "https://agda.readthedocs.io/en/latest/tools/emacs-mode.html") (synopsis "Emacs mode for Agda") (description "This Emacs mode enables interactive development with -Agda. It also aids the input of Unicode characters."))) +Agda. It also aids the input of Unicode characters.") + (license (package-license agda)))) (define-public agda-ial (package -- cgit v1.2.3 From ae29c9d26ef1bf90e45783c3ccad2b693a010b99 Mon Sep 17 00:00:00 2001 From: Josselin Poiret Date: Wed, 8 Mar 2023 16:56:16 +0100 Subject: gnu: emacs-agda2-mode: Switch to G-Exps. * gnu/packages/agda.scm (emacs-agda2-mode): Switch it up. --- gnu/packages/agda.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm index 9dfcc907ec0..d6c2e1e231e 100644 --- a/gnu/packages/agda.scm +++ b/gnu/packages/agda.scm @@ -134,10 +134,11 @@ such as Coq, Epigram and NuPRL.") (source (package-source agda)) (build-system emacs-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'enter-elisp-dir - (lambda _ (chdir "src/data/emacs-mode") #t))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'enter-elisp-dir + (lambda _ (chdir "src/data/emacs-mode")))))) (home-page "https://agda.readthedocs.io/en/latest/tools/emacs-mode.html") (synopsis "Emacs mode for Agda") (description "This Emacs mode enables interactive development with -- cgit v1.2.3 From 7a00ab05320997aeb3796689faf3167662bff287 Mon Sep 17 00:00:00 2001 From: Josselin Poiret Date: Sun, 30 Apr 2023 11:58:09 +0200 Subject: gnu: agda: Add AGDA_LIBDIRS search-path. * gnu/packages/patches/agda-libdirs-env-variable.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/agda.scm (agda): Patch agda, and add search path. --- gnu/local.mk | 1 + gnu/packages/agda.scm | 10 ++++- .../patches/agda-libdirs-env-variable.patch | 49 ++++++++++++++++++++++ 3 files changed, 59 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/agda-libdirs-env-variable.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 7be3cc54640..d38329ea950 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -885,6 +885,7 @@ dist_patch_DATA = \ %D%/packages/patches/aegisub-icu59-include-unistr.patch \ %D%/packages/patches/aegisub-boost68.patch \ %D%/packages/patches/aegisub-make43.patch \ + %D%/packages/patches/agda-libdirs-env-variable.patch \ %D%/packages/patches/agg-am_c_prototype.patch \ %D%/packages/patches/agg-2.5-gcc8.patch \ %D%/packages/patches/akonadi-paths.patch \ diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm index d6c2e1e231e..c73c238a35c 100644 --- a/gnu/packages/agda.scm +++ b/gnu/packages/agda.scm @@ -23,6 +23,7 @@ ;;; along with GNU Guix. If not, see . (define-module (gnu packages agda) + #:use-module (gnu packages) #:use-module (gnu packages haskell-check) #:use-module (gnu packages haskell-web) #:use-module (gnu packages haskell-xyz) @@ -51,7 +52,8 @@ (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1s7zd01i8pmvi90ywx497kc07z50nah7h0fc2dn6jzb132k5sh1q")))) + (base32 "1s7zd01i8pmvi90ywx497kc07z50nah7h0fc2dn6jzb132k5sh1q")) + (patches (search-patches "agda-libdirs-env-variable.patch")))) (build-system haskell-build-system) (inputs (list ghc-aeson @@ -109,6 +111,12 @@ (setenv "infodir" (string-append #$output "/share/info")) (invoke "make" "install-info")))))))) + (search-paths + (list (search-path-specification + (variable "AGDA_LIBDIRS") + (files (list "lib/agda"))))) + (native-search-paths + search-paths) (home-page "https://wiki.portal.chalmers.se/agda/") (synopsis "Dependently typed functional programming language and proof assistant") diff --git a/gnu/packages/patches/agda-libdirs-env-variable.patch b/gnu/packages/patches/agda-libdirs-env-variable.patch new file mode 100644 index 00000000000..3b291358a6a --- /dev/null +++ b/gnu/packages/patches/agda-libdirs-env-variable.patch @@ -0,0 +1,49 @@ +From 457bc7438a4f0801dbf332fa2369248bddf5da0c Mon Sep 17 00:00:00 2001 +Message-Id: <457bc7438a4f0801dbf332fa2369248bddf5da0c.1678309546.git.dev@jpoiret.xyz> +From: Josselin Poiret +Date: Wed, 8 Mar 2023 18:31:52 +0100 +Subject: [PATCH] Add environment variable for library directories + +AGDA_LIBDIRS is a new environment colon-separated variable for site libraries. +Agda will look for .agda-lib files directly inside direct descendants of these. +--- + src/full/Agda/Interaction/Library.hs | 16 ++++++++++++++-- + 1 file changed, 14 insertions(+), 2 deletions(-) + +diff --git a/src/full/Agda/Interaction/Library.hs b/src/full/Agda/Interaction/Library.hs +index 09c1f2a82..774cc3e74 100644 +--- a/src/full/Agda/Interaction/Library.hs ++++ b/src/full/Agda/Interaction/Library.hs +@@ -323,13 +323,25 @@ getInstalledLibraries overrideLibFile = mkLibM [] $ do + raiseErrors' [ LibrariesFileNotFound theOverrideLibFile ] + return [] + Right file -> do +- if not (lfExists file) then return [] else do ++ siteLibDirs <- liftIO $ fromMaybe [] . fmap splitAtColon . lookup "AGDA_LIBDIRS" <$> getEnvironment ++ siteLibs <- liftIO $ concat <$> mapM findSiteLibs siteLibDirs ++ if not (lfExists file) then parseLibFiles Nothing $ nubOn snd ((0,) <$> siteLibs) else do + ls <- liftIO $ stripCommentLines <$> UTF8.readFile (lfPath file) + files <- liftIO $ sequence [ (i, ) <$> expandEnvironmentVariables s | (i, s) <- ls ] +- parseLibFiles (Just file) $ nubOn snd files ++ parseLibFiles (Just file) $ nubOn snd (files ++ fmap (0,) siteLibs) + `catchIO` \ e -> do + raiseErrors' [ ReadError e "Failed to read installed libraries." ] + return [] ++ where splitAtColon :: String -> [String] ++ splitAtColon "" = [] ++ splitAtColon str = case break (==':') str of ++ (a, _:b) -> a : splitAtColon b ++ (a, "") -> [a] ++ findSiteLibs :: String -> IO [String] ++ findSiteLibs dir = do ++ subDirs <- filterM doesDirectoryExist =<< map (dir ) <$> listDirectory dir ++ subFiles <- mapM (\dir -> map (dir ) <$> listDirectory dir) subDirs ++ return $ concatMap (filter (List.isSuffixOf ".agda-lib")) subFiles + + -- | Parse the given library files. + -- + +base-commit: 183534bc41af5a53daf685122997dc98883f2be2 +-- +2.39.1 + -- cgit v1.2.3 From c1f8bcbbda4d90dc98d5e808049f008dffe6b979 Mon Sep 17 00:00:00 2001 From: Josselin Poiret Date: Sat, 29 Apr 2023 17:01:14 +0200 Subject: gnu: Add agda-stdlib. * gnu/packages/patches/agda-stdlib-use-runhaskell.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/agda.scm: New variable agda-stdlib. --- gnu/local.mk | 1 + gnu/packages/agda.scm | 38 ++++++++++++++++++++++ .../patches/agda-stdlib-use-runhaskell.patch | 28 ++++++++++++++++ 3 files changed, 67 insertions(+) create mode 100644 gnu/packages/patches/agda-stdlib-use-runhaskell.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index d38329ea950..2da6c5d59fe 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -886,6 +886,7 @@ dist_patch_DATA = \ %D%/packages/patches/aegisub-boost68.patch \ %D%/packages/patches/aegisub-make43.patch \ %D%/packages/patches/agda-libdirs-env-variable.patch \ + %D%/packages/patches/agda-stdlib-use-runhaskell.patch \ %D%/packages/patches/agg-am_c_prototype.patch \ %D%/packages/patches/agg-2.5-gcc8.patch \ %D%/packages/patches/akonadi-paths.patch \ diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm index c73c238a35c..dd427bff028 100644 --- a/gnu/packages/agda.scm +++ b/gnu/packages/agda.scm @@ -31,6 +31,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages sphinx) #:use-module (gnu packages texinfo) + #:use-module (guix build-system agda) #:use-module (guix build-system emacs) #:use-module (guix build-system gnu) #:use-module (guix build-system haskell) @@ -194,3 +195,40 @@ of theorems for booleans, natural numbers, and lists. It also has trees, tries, vectors, and rudimentary IO. A number of good ideas come from Agda's standard library.") (license license:expat))) + +(define-public agda-stdlib + (package + (name "agda-stdlib") + (version "1.7.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/agda/agda-stdlib") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "065hf24xjpciwdrvk4isslgcgi01q0k93ql0y1sjqqvy5ryg5xmy")))) + (build-system agda-build-system) + (arguments + (list + #:plan '(("^\\./README.agda$" "-i.")) + #:gnu-and-haskell? #t + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'generate-everything + (lambda* (#:key inputs native-inputs #:allow-other-keys) + (invoke + (search-input-file (or native-inputs inputs) "/bin/runhaskell") + "GenerateEverything.hs")))))) + (native-inputs (list ghc-filemanip)) + (synopsis "The Agda Standard Library") + (description + "The standard library aims to contain all the tools needed to write +both programs and proofs easily. While we always try and write efficient +code, we prioritize ease of proof over type-checking and normalization +performance. If computational performance is important to you, then perhaps +try agda-prelude instead.") + (home-page "https://wiki.portal.chalmers.se/agda/pmwiki.php") + (license license:expat))) + diff --git a/gnu/packages/patches/agda-stdlib-use-runhaskell.patch b/gnu/packages/patches/agda-stdlib-use-runhaskell.patch new file mode 100644 index 00000000000..21ce16689fa --- /dev/null +++ b/gnu/packages/patches/agda-stdlib-use-runhaskell.patch @@ -0,0 +1,28 @@ +From 3dc3c0856906d25bb697a4480a8457a69637cd51 Mon Sep 17 00:00:00 2001 +Message-Id: <3dc3c0856906d25bb697a4480a8457a69637cd51.1682798848.git.dev@jpoiret.xyz> +From: Josselin Poiret +Date: Sat, 29 Apr 2023 22:06:55 +0200 +Subject: [PATCH] Makefile: use runhaskell instead of cabal + +From: Josselin Poiret + +--- + GNUmakefile | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/GNUmakefile b/GNUmakefile +index c5d886e03..f3cb2a1e7 100644 +--- a/GNUmakefile ++++ b/GNUmakefile +@@ -21,7 +21,7 @@ Everything.agda: + # command `cabal install` is needed by cabal-install <= 2.4.*. I did + # not found any problem running both commands with different versions + # of cabal-install. See Issue #1001. +- cabal run GenerateEverything ++ runhaskell GenerateEverything + + .PHONY: listings + listings: Everything.agda +-- +2.39.2 + -- cgit v1.2.3 From 8203e8f3c9cf0462abb9f03e42e578fe28599c36 Mon Sep 17 00:00:00 2001 From: Josselin Poiret Date: Sun, 30 Apr 2023 12:10:06 +0200 Subject: gnu: Add agda-categories. * gnu/packages/patches/agda-categories-use-find.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/agda.scm: New variable agda-categories. --- gnu/local.mk | 2 ++ gnu/packages/agda.scm | 30 +++++++++++++++++++++ ...agda-categories-remove-incompatible-flags.patch | 31 ++++++++++++++++++++++ .../patches/agda-categories-use-find.patch | 31 ++++++++++++++++++++++ 4 files changed, 94 insertions(+) create mode 100644 gnu/packages/patches/agda-categories-remove-incompatible-flags.patch create mode 100644 gnu/packages/patches/agda-categories-use-find.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 2da6c5d59fe..9adf5933186 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -885,6 +885,8 @@ dist_patch_DATA = \ %D%/packages/patches/aegisub-icu59-include-unistr.patch \ %D%/packages/patches/aegisub-boost68.patch \ %D%/packages/patches/aegisub-make43.patch \ + %D%/packages/patches/agda-categories-remove-incompatible-flags.patch \ + %D%/packages/patches/agda-categories-use-find.patch \ %D%/packages/patches/agda-libdirs-env-variable.patch \ %D%/packages/patches/agda-stdlib-use-runhaskell.patch \ %D%/packages/patches/agg-am_c_prototype.patch \ diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm index dd427bff028..16573e6d57f 100644 --- a/gnu/packages/agda.scm +++ b/gnu/packages/agda.scm @@ -232,3 +232,33 @@ try agda-prelude instead.") (home-page "https://wiki.portal.chalmers.se/agda/pmwiki.php") (license license:expat))) +(define-public agda-categories + (package + (name "agda-categories") + (version "0.1.7.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/agda/agda-categories.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0xwgm2mfl2pxipsv31bin8p14y1yhd9n27lv3clvsxd4z9yc034m")) + (patches (search-patches "agda-categories-remove-incompatible-flags.patch" + "agda-categories-use-find.patch")))) + (build-system agda-build-system) + (arguments + (list + #:gnu-and-haskell? #t + #:phases + #~(modify-phases %standard-phases + (replace 'build + (lambda _ + (invoke "make")))))) + (propagated-inputs + (list agda-stdlib)) + (synopsis "New Categories library for Agda") + (description "A new Categories library for Agda") + (home-page "https://github.com/agda/agda-categories") + (license license:expat))) diff --git a/gnu/packages/patches/agda-categories-remove-incompatible-flags.patch b/gnu/packages/patches/agda-categories-remove-incompatible-flags.patch new file mode 100644 index 00000000000..dc33af7cf95 --- /dev/null +++ b/gnu/packages/patches/agda-categories-remove-incompatible-flags.patch @@ -0,0 +1,31 @@ +From 3d73d59617281c6ae9c19032eae381ff77fd2e65 Mon Sep 17 00:00:00 2001 +Message-Id: <3d73d59617281c6ae9c19032eae381ff77fd2e65.1682841188.git.dev@jpoiret.xyz> +From: Josselin Poiret +Date: Sun, 30 Apr 2023 09:51:12 +0200 +Subject: [PATCH] Remove stdlib-incompatible flags + +From: Josselin Poiret + +--- + Makefile | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Makefile b/Makefile +index 68846579..ba5923a2 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,6 +1,6 @@ + .PHONY: test Everything.agda clean + +-OTHEROPTS = --auto-inline -Werror ++OTHEROPTS = + + RTSARGS = +RTS -M6G -A128M -RTS ${OTHEROPTS} + + +base-commit: 20397e93a60ed1439ed57ee76ae377c66a5eb8d9 +prerequisite-patch-id: da10df58fa86d08b31174a01db7b9a02377aba55 +prerequisite-patch-id: 508dabd923ba9ac1ee4d8dab6697432b4bd8ba18 +-- +2.39.2 + diff --git a/gnu/packages/patches/agda-categories-use-find.patch b/gnu/packages/patches/agda-categories-use-find.patch new file mode 100644 index 00000000000..772352a0cba --- /dev/null +++ b/gnu/packages/patches/agda-categories-use-find.patch @@ -0,0 +1,31 @@ +From 53922aedd81d5111d9007b41235aa12eaa2a863d Mon Sep 17 00:00:00 2001 +Message-Id: <53922aedd81d5111d9007b41235aa12eaa2a863d.1682840933.git.dev@jpoiret.xyz> +From: Josselin Poiret +Date: Sun, 30 Apr 2023 09:48:21 +0200 +Subject: [PATCH] Use find instead of git ls-tree in Makefile + +From: Josselin Poiret + +--- + Makefile | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Makefile b/Makefile +index 158802d1..68846579 100644 +--- a/Makefile ++++ b/Makefile +@@ -11,7 +11,7 @@ html: Everything.agda + agda ${RTSARGS} --html -i. Everything.agda + + Everything.agda: +- git ls-tree --full-tree -r --name-only HEAD | grep '^src/[^\.]*.agda' | sed -e 's|^src/[/]*|import |' -e 's|/|.|g' -e 's/.agda//' -e '/import Everything/d' | LC_COLLATE='C' sort > Everything.agda ++ find src -iname '*.agda' | sed -e 's|^src/[/]*|import |' -e 's|/|.|g' -e 's/.agda//' -e '/import Everything/d' | LC_COLLATE='C' sort > Everything.agda + + clean: + find . -name '*.agdai' -exec rm \{\} \; + +base-commit: 20397e93a60ed1439ed57ee76ae377c66a5eb8d9 +prerequisite-patch-id: da10df58fa86d08b31174a01db7b9a02377aba55 +-- +2.39.2 + -- cgit v1.2.3 From cf2c3f797003a67c9a8d3c1400a480c617f89eda Mon Sep 17 00:00:00 2001 From: Josselin Poiret Date: Sun, 30 Apr 2023 12:12:00 +0200 Subject: gnu: Add agda-cubical. * gnu/packages/agda.scm: New variable agda-cubical. --- gnu/packages/agda.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm index 16573e6d57f..240a51de1ae 100644 --- a/gnu/packages/agda.scm +++ b/gnu/packages/agda.scm @@ -262,3 +262,36 @@ try agda-prelude instead.") (description "A new Categories library for Agda") (home-page "https://github.com/agda/agda-categories") (license license:expat))) + +(define-public agda-cubical + ;; Upstream's HEAD follows the latest Agda release, but they don't release + ;; until a newer Agda release comes up, so their releases are always one + ;; version late. + (let* ((revision "1") + (commit "814d54b08b360b8e80828065f54b80e3a98a0092")) + (package + (name "agda-cubical") + (version (git-version "0.4" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/agda/cubical.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0d25gb1qzpx539k62qjsjq4xmzp34qk7n3hmd9y6v8slhrrxw312")))) + (build-system agda-build-system) + (arguments + (list + #:gnu-and-haskell? #t + #:phases + #~(modify-phases %standard-phases + (replace 'build + (lambda _ + (invoke "make")))))) + (synopsis "Standard library for Cubical Agda") + (description "A standard library for Cubical Agda, comparable to +agda-stdlib but using cubical methods.") + (home-page "https://github.com/agda/cubical") + (license license:expat)))) -- cgit v1.2.3 From 067e75e17a7f2c278eb6273824e33454d8e00566 Mon Sep 17 00:00:00 2001 From: Josselin Poiret Date: Sun, 30 Apr 2023 12:12:33 +0200 Subject: gnu: Add agda-1lab. * gnu/packages/agda.scm: New variable agda-1lab. --- gnu/packages/agda.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm index 240a51de1ae..bd7fe29f1ea 100644 --- a/gnu/packages/agda.scm +++ b/gnu/packages/agda.scm @@ -295,3 +295,32 @@ try agda-prelude instead.") agda-stdlib but using cubical methods.") (home-page "https://github.com/agda/cubical") (license license:expat)))) + +(define-public agda-1lab + ;; Upstream doesn't do releases (yet). Use a commit that builds with 2.6.3, + ;; since they use Agda HEAD. + (let* ((revision "1") + (commit "47ca1d23640a6f49a3abe3c2fe27738bcc10c9c6")) + (package + (name "agda-1lab") + (version (git-version "0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/plt-amy/1lab.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0j7mp6c0xd0849skdxzncklkxynxnyfrbpcjv4qp5p1xfn0dnfqx")))) + (build-system agda-build-system) + (arguments + (list #:plan '(("src/index\\.lagda\\.md$")))) + (synopsis "Reference resource for mathematics done in Homotopy Type Theory") + (description "A formalised, cross-linked reference resource for +mathematics done in Homotopy Type Theory. Unlike the HoTT book, the 1lab is +not a “linear” resource: Concepts are presented as a directed graph, with +links indicating dependencies.") + (home-page "https://1lab.dev") + (license license:agpl3)))) -- cgit v1.2.3 From e198fe4e942c58136dd4cb8ebf49cade58a8f5e3 Mon Sep 17 00:00:00 2001 From: Josselin Poiret Date: Sun, 4 Jun 2023 10:46:26 +0200 Subject: gnu: agda-ial: Update to ded30c410d5d40142249686572aa1acd1b2f8cc7. * gnu/packages/agda.scm (agda-ial): Update to ded30c410d5d40142249686572aa1acd1b2f8cc7, use agda-build-system, switch to G-Exps, reorder fields. --- gnu/packages/agda.scm | 65 ++++++++++++++++++++++++--------------------------- 1 file changed, 30 insertions(+), 35 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm index bd7fe29f1ea..88626b823c8 100644 --- a/gnu/packages/agda.scm +++ b/gnu/packages/agda.scm @@ -155,46 +155,41 @@ Agda. It also aids the input of Unicode characters.") (license (package-license agda)))) (define-public agda-ial - (package - (name "agda-ial") - (version "1.5.0") - (home-page "https://github.com/cedille/ial") - (source (origin - (method git-fetch) - (uri (git-reference (url home-page) - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0dlis6v6nzbscf713cmwlx8h9n2gxghci8y21qak3hp18gkxdp0g")))) - (build-system gnu-build-system) - (inputs - (list agda)) - (arguments - `(#:parallel-build? #f + (let ((revision "1") + ;; There hasn't been a release in a long time, and the last one + ;; doesn't build with Agda 2.6. + (commit "ded30c410d5d40142249686572aa1acd1b2f8cc7")) + (package + (name "agda-ial") + (version (git-version "1.5.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference (url "https://github.com/cedille/ial") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0xn6zvp1wnm0i84pz1rfbzfmayd15ch4i5s11ycd88d22pxd55dc")))) + (build-system agda-build-system) + (arguments + (list + #:gnu-and-haskell? #t #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-before 'build 'patch-dependencies - (lambda _ (patch-shebang "find-deps.sh") #t)) - (delete 'check) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (include (string-append out "/include/agda/ial"))) - (for-each (lambda (file) - (make-file-writable file) - (install-file file include)) - (find-files "." "\\.agdai?(-lib)?$")) - #t)))))) - (synopsis "The Iowa Agda Library") - (description - "The goal is to provide a concrete library focused on verification + #~(modify-phases %standard-phases + (add-before 'build 'patch-dependencies + (lambda _ (patch-shebang "find-deps.sh"))) + (replace 'build + (lambda _ + (invoke "make")))))) + (home-page "https://github.com/cedille/ial") + (synopsis "The Iowa Agda Library") + (description + "The goal is to provide a concrete library focused on verification examples, as opposed to mathematics. The library has a good number of theorems for booleans, natural numbers, and lists. It also has trees, tries, vectors, and rudimentary IO. A number of good ideas come from Agda's standard library.") - (license license:expat))) + (license license:expat)))) (define-public agda-stdlib (package -- cgit v1.2.3 From d84517805080ec51bab1921ac34c28adf3d88596 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Jun 2023 12:34:40 +0300 Subject: gnu: libdeflate: Use default tests. * gnu/packages/compression.scm (libdeflate)[arguments]: Adjust configure-flags to build the test suite. Remove custom 'check phase. --- gnu/packages/compression.scm | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 8a8b94c07b2..bedc6ecca92 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2015, 2016, 2017, 2018, 2020, 2021, 2022 Ricardo Wurmus ;;; Copyright © 2015, 2017, 2018 Leo Famulari ;;; Copyright © 2015 Jeff Mickey -;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Efraim Flashner +;;; Copyright © 2015-2023 Efraim Flashner ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2016 Danny Milosavljevic ;;; Copyright © 2016–2022 Tobias Geerinckx-Rice @@ -2687,12 +2687,8 @@ to their original, binary CD format.") (build-system cmake-build-system) (arguments (list #:configure-flags - #~(list "-DLIBDEFLATE_BUILD_STATIC_LIB=NO") - #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda _ - (invoke "../source/scripts/run_tests.sh")))))) + #~(list "-DLIBDEFLATE_BUILD_STATIC_LIB=NO" + "-DLIBDEFLATE_BUILD_TESTS=YES"))) (inputs (list zlib)) (home-page "https://github.com/ebiggers/libdeflate") -- cgit v1.2.3 From 81515a4029bd95f5c1d0964f65789fe8e5892142 Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Thu, 30 Mar 2023 22:46:03 +0800 Subject: gnu: libxtst: Fix cross-compiling to riscv64. * gnu/packages/xorg.scm (libxtst)[arguments]: When cross-compiling to riscv64, add phase to update config.{guess,sub}. [native-inputs]: When cross-compiling to riscv64, add config. Signed-off-by: Efraim Flashner --- gnu/packages/xorg.scm | 24 +++++++++++++++++++++--- 1 file changed, 21 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index d6c388739fe..7632dac1c4f 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -34,6 +34,7 @@ ;;; Copyright © 2021 Maxime Devos ;;; Copyright © 2021 qblade ;;; Copyright © 2021 Lu Hui +;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -4493,13 +4494,30 @@ cannot be adequately worked around on the client side of the wire.") "012jpyj7xfm653a9jcfqbzxyywdmwb2b5wr1dwylx14f3f54jma6")))) (build-system gnu-build-system) (arguments - '(#:configure-flags '("--disable-static"))) + `(#:configure-flags '("--disable-static") + ,@(if (and (target-riscv64?) + (%current-target-system)) + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'update-config + (lambda* (#:key native-inputs inputs #:allow-other-keys) + (for-each (lambda (file) + (install-file + (search-input-file + (or native-inputs inputs) + (string-append "/bin/" file)) ".")) + '("config.guess" "config.sub")))))) + '()))) (propagated-inputs (list libxi xorgproto)) (inputs - (list libx11)) + (list libx11)) (native-inputs - (list pkg-config)) + (append (if (and (target-riscv64?) + (%current-target-system)) + (list config) + '()) + (list pkg-config))) (home-page "https://www.x.org/wiki/") (synopsis "Xorg library for Xtest and Record extensions") (description -- cgit v1.2.3 From 0ee6c9ea01d1f69b3b7b2c2d79d62b68ffd268ed Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Tue, 28 Feb 2023 16:33:33 +0800 Subject: gnu: xcb-util-wm: Fix cross-compiling to riscv64. * gnu/packages/xorg.scm (xcb-util-wm)[arguments]: Add update-config-scripts phase when cross-compiling to riscv64. [native-inputs]: Add config when cross-compiling to riscv64. Signed-off-by: Efraim Flashner --- gnu/packages/xorg.scm | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 7632dac1c4f..e1a7cf96f95 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -5638,11 +5638,29 @@ The XCB util-renderutil module provides the following library: "0gra7hfyxajic4mjd63cpqvd20si53j1q3rbdlkqkahfciwq3gr8")))) (build-system gnu-build-system) (arguments - '(#:configure-flags '("--disable-static"))) + `(#:configure-flags '("--disable-static") + ,@(if (and (target-riscv64?) + (%current-target-system)) + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'update-config-scripts + (lambda* (#:key inputs native-inputs #:allow-other-keys) + ;; Replace outdated config.guess and config.sub. + (for-each (lambda (file) + (install-file + (search-input-file + (or native-inputs inputs) + (string-append "/bin/" file)) ".")) + '("config.guess" "config.sub")))))) + '()))) (propagated-inputs (list libxcb)) (native-inputs - (list m4 pkg-config)) + (append (if (and (target-riscv64?) + (%current-target-system)) + (list config) + '()) + (list m4 pkg-config))) (home-page "https://cgit.freedesktop.org/xcb/util-wm/") (synopsis "Client and window-manager helpers for ICCCM and EWMH") (description -- cgit v1.2.3 From 188da31fe5305a960bea88e1452ceeccfb53e1de Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Sun, 4 Jun 2023 14:55:11 +0300 Subject: gnu: mtdev: Fix cross-compiling to riscv64. * gnu/packages/xdisorg.scm (mtdev)[arguments]: When cross-compiling to riscv64 add a phase to update config.{guess,sub}. [native-inputs]: When cross-compiling to riscv64 add config. --- gnu/packages/xdisorg.scm | 25 +++++++++++++++++++++++-- 1 file changed, 23 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 462ac082f51..b8671d1cf68 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -41,7 +41,7 @@ ;;; Copyright © 2020 Gabriel Arazas ;;; Copyright © 2020 James Smith ;;; Copyright © 2020 B. Wilson -;;; Copyright © 2020, 2021 Zheng Junjie <873216071@qq.com> +;;; Copyright © 2020, 2021, 2023 Zheng Junjie <873216071@qq.com> ;;; Copyright © 2021, 2022, 2023 Maxim Cournoyer ;;; Copyright © 2021, 2022 Nicolas Goaziou ;;; Copyright © 2021 Xinglu Chen @@ -768,7 +768,28 @@ and Matrox.") (base32 "1q700h9dqcm3zl6c3gj0qxxjcx6ibw2c51wjijydhwdcm26v5mqm")))) (build-system gnu-build-system) - (arguments '(#:configure-flags '("--disable-static"))) + (arguments + `(#:configure-flags + '("--disable-static") + ,@(if (and (target-riscv64?) + (%current-target-system)) + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'update-config-scripts + (lambda* (#:key inputs native-inputs #:allow-other-keys) + ;; Replace outdated config.guess and config.sub. + (for-each (lambda (file) + (install-file + (search-input-file + (or native-inputs inputs) + (string-append "/bin/" file)) "./config-aux")) + '("config.guess" "config.sub")))))) + '()))) + (native-inputs + (if (and (target-riscv64?) + (%current-target-system)) + (list config) + '())) (home-page "https://bitmath.org/code/mtdev/") (synopsis "Multitouch protocol translation library") (description "Mtdev is a stand-alone library which transforms all -- cgit v1.2.3 From 3f45c3b12b5a4b319634a93db8a025591c3054ea Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Tue, 28 Feb 2023 16:33:37 +0800 Subject: gnu: gobject-introspection: Fix cross-compiling. * gnu/packages/glib.scm(gobject-introspection)[native-inputs]: When cross-compiling add python. Signed-off-by: Efraim Flashner --- gnu/packages/glib.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index dcc45e3310c..e988e8dc87f 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -556,7 +556,10 @@ be used when cross-compiling." "/_giscanner")))) #~())))) (native-inputs - `(("glib" ,glib "bin") + `(,@(if (%current-target-system) + `(("python" ,python)) + '()) + ("glib" ,glib "bin") ("pkg-config" ,pkg-config) ("bison" ,bison) ("flex" ,flex))) -- cgit v1.2.3 From 713da38002511f87b9bfc28a669df02d9c9b46fe Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Tue, 28 Feb 2023 16:33:38 +0800 Subject: gnu: gsettings-desktop-schemas: Fix cross-compiling. * gnu/packages/gnome.scm(gsettings-desktop-schemas)[inputs]: Add gobject-introspection. Signed-off-by: Efraim Flashner --- gnu/packages/gnome.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 90b72731f6c..22588ffe283 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -2702,7 +2702,7 @@ on the GNOME Desktop with a single simple application.") "/share/backgrounds/gnome")) ;; Do not reference fonts, that may not exist. (("'Source Code Pro 10'") "'Monospace 11'"))))))) - (inputs (list glib gnome-backgrounds)) + (inputs (list glib gnome-backgrounds gobject-introspection)) (native-inputs (list gettext-minimal `(,glib "bin") ;glib-compile-schemas, etc. gobject-introspection -- cgit v1.2.3 From 4f3e5548fcc2c0bbd9a5ecaf76a4fc63d2439aa3 Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Sat, 25 Mar 2023 12:50:59 +0800 Subject: gnu: libicns: Fix cross-compiling to riscv64. * gnu/packages/image.scm (libicns)[arguments]: When cross-compiling to riscv64, add phase to update-config-scripts. [native-inputs]: When cross-compiling to riscv64, add config. Signed-off-by: Efraim Flashner --- gnu/packages/image.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index d1330d17f7e..830989da788 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -595,6 +595,25 @@ maximum quality factor.") (base32 "1hjm8lwap7bjyyxsyi94fh5817xzqhk4kb5y0b7mb6675xw10prk")))) (build-system gnu-build-system) + (arguments + (if (and (target-riscv64?) + (%current-target-system)) + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'update-config-scripts + (lambda* (#:key native-inputs inputs #:allow-other-keys) + (for-each (lambda (file) + (install-file + (search-input-file + (or native-inputs inputs) + (string-append "/bin/" file)) ".")) + '("config.guess" "config.sub"))))) ) + '())) + (native-inputs + (if (and (target-riscv64?) + (%current-target-system)) + (list config) + '())) (inputs (list libpng jasper)) (home-page "https://icns.sourceforge.io/") -- cgit v1.2.3 From ae04b3996be99c89142866afdbba5151099b2064 Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Sat, 25 Mar 2023 12:51:34 +0800 Subject: gnu: jpegoptim: Fix cross-compiling to riscv64. * gnu/packages/image.scm (jpegoptim)[arguments]: When cross-compiling t riscv64, add phase to update-config-scripts. [native-inputs]: When cross-compiling to riscv64, add config. Signed-off-by: Efraim Flashner --- gnu/packages/image.scm | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 830989da788..06ace236363 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -571,9 +571,27 @@ official designation is ISO/IEC 29199-2). This library is an implementation of t (sha256 (base32 "06f6d08xvmsiki4mc1qs985gsjqmsxx793a93b72y25q84wbg9x9")))) (build-system gnu-build-system) - (inputs (list libjpeg-turbo)) (arguments - '(#:tests? #f)) ; no tests + `(#:tests? #f ; no tests + ,@(if (and (target-riscv64?) + (%current-target-system)) + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'update-config-scripts + (lambda* (#:key native-inputs inputs #:allow-other-keys) + (for-each (lambda (file) + (install-file + (search-input-file + (or native-inputs inputs) + (string-append "/bin/" file)) "./tools")) + '("config.guess" "config.sub")))))) + '()))) + (inputs (list libjpeg-turbo)) + (native-inputs + (if (and (target-riscv64?) + (%current-target-system)) + (list config) + '())) (synopsis "Optimize JPEG images") (description "jpegoptim provides lossless optimization (based on optimizing -- cgit v1.2.3 From 9d9e793da5ef179b82202ea9a9b44d149f47d94e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Jun 2023 19:01:52 +0300 Subject: gnu: tree: Update to 2.1.1. * gnu/packages/admin.scm (tree): Update to 2.1.1. [arguments]: Remove unneeded 'fix-manpage-version phase. --- gnu/packages/admin.scm | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index f0eed185dd4..3193aa1456c 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -9,7 +9,7 @@ ;;; Copyright © 2016, 2017, 2020 Leo Famulari ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016, 2017 Ricardo Wurmus -;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021, 2022 Efraim Flashner +;;; Copyright © 2016-2023 Efraim Flashner ;;; Copyright © 2016 Peter Feigl ;;; Copyright © 2016 John J. Foerch ;;; Copyright © 2016, 2017 Nikita @@ -2603,24 +2603,20 @@ characters can be replaced as well, as can UTF-8 characters.") (define-public tree (package (name "tree") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (string-append "https://mama.indstate.edu/users/ice/tree/src/tree-" version ".tgz")) (sha256 - (base32 "1xmbxgx72w7ddjlqsx1yys076hp3h7ll968bhdmdrc7jpwswaq01")))) + (base32 "1mchmdkq77d4c2mx7xmarccbk46a3sm2aqslarjwgxrs81gxbhyk")))) (build-system gnu-build-system) (arguments (list #:phases #~(modify-phases %standard-phases - (delete 'configure) ; No configure script. - (add-after 'unpack 'fix-manpage-version - (lambda _ - (substitute* "doc/tree.1" - (("Tree 2\\.0\\.0") (string-append "Tree " #$version)))))) + (delete 'configure)) ; No configure script. #:tests? #f ; No check target. #:make-flags #~(list (string-append "PREFIX=" #$output) -- cgit v1.2.3 From f8b82976d6160aaa6bc73727300b1ca6a7002258 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Jun 2023 21:06:47 +0300 Subject: gnu: urlscan: Update to 1.0.0. * gnu/packages/mail.scm (urlscan): Update to 1.0.0. [arguments]: Skip the test phase. [build-system]: Switch to the pyproject-build-system. [native-inputs]: Add python-hatch-vcs, python-hatchling. --- gnu/packages/mail.scm | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 02e0da2ec8e..ee6e19fcfe9 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -188,6 +188,7 @@ #:use-module (guix build-system meson) #:use-module (guix build-system perl) #:use-module (guix build-system python) + #:use-module (guix build-system pyproject) #:use-module (guix build-system trivial) #:use-module (srfi srfi-1) #:use-module (ice-9 match)) @@ -4039,16 +4040,20 @@ servers. The 4rev1 and 4 versions of IMAP are supported.") (define-public urlscan (package (name "urlscan") - (version "0.9.10") + (version "1.0.0") (source (origin (method url-fetch) (uri (pypi-uri "urlscan" version)) (sha256 - (base32 "1ir6dxifkd8hv048p65jyz4wyg6ll002fzvbmajpdnvs6mvkj1md")))) - (build-system python-build-system) + (base32 "0rxqdrss34rgnfmbn8ab976dchjbz72wp4ywqrdib119a5xnhqzh")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f)) ; No tests. (propagated-inputs (list python-urwid)) + (native-inputs + (list python-hatch-vcs python-hatchling)) (home-page "https://github.com/firecat53/urlscan") (synopsis "View/select the URLs in an email message or file") (description -- cgit v1.2.3 From c15470671ae4cf16def99fc5e3365ef5bf04f91c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Jun 2023 21:07:35 +0300 Subject: gnu: keepassxc: Update to 2.7.5. * gnu/packages/password-utils.scm (keepassxc): Update to 2.7.5. --- gnu/packages/password-utils.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index f5f301308a3..74e465d21ee 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Steve Sprang -;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Efraim Flashner +;;; Copyright © 2015-2023 Efraim Flashner ;;; Copyright © 2015 Aljosha Papsch ;;; Copyright © 2016 Christine Lemmer-Webber ;;; Copyright © 2016 Jessica Tallon @@ -142,7 +142,7 @@ human.") (define-public keepassxc (package (name "keepassxc") - (version "2.7.4") + (version "2.7.5") (source (origin (method url-fetch) @@ -150,7 +150,7 @@ human.") "/releases/download/" version "/keepassxc-" version "-src.tar.xz")) (sha256 - (base32 "1knywp38byq0jq9vdyp1ykha9prh09k1y5srwwkr6f503nb5402n")))) + (base32 "03002fncllr658mgl5s6an5wnh0a333qnkxad6aw85hqj004iqpd")))) (build-system cmake-build-system) (arguments (list -- cgit v1.2.3 From eed55a6544d5bda2245ec853e5fa4b28e1865bea Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Jun 2023 21:07:35 +0300 Subject: gnu: lagrange: Update to 1.16.3. * gnu/packages/web-browsers.scm (lagrange): Update to 1.16.3. --- gnu/packages/web-browsers.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index 1fe5ef5c82f..7d1f61be534 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -724,7 +724,7 @@ is fully configurable and extensible in Common Lisp.") (define-public lagrange (package (name "lagrange") - (version "1.15.9") + (version "1.16.3") (source (origin (method url-fetch) @@ -732,7 +732,7 @@ is fully configurable and extensible in Common Lisp.") (string-append "https://git.skyjake.fi/skyjake/lagrange/releases/" "download/v" version "/lagrange-" version ".tar.gz")) (sha256 - (base32 "19pn5nnlskyj7w61s9vg5c0vb0hpdyalj3m8znvs4lgw3463ijs3")) + (base32 "1kmhxacka0rixxv1r5vqjhxmdxll73b5w5ja18m1qpbk2sk00bg8")) (modules '((guix build utils))) (snippet '(begin -- cgit v1.2.3 From a95edc3d7bed8612e81fceaac35c86fb6533cfbb Mon Sep 17 00:00:00 2001 From: Timotej Lazar Date: Sun, 4 Jun 2023 19:49:58 +0200 Subject: gnu: mupdf: Update to 1.22.1. * gnu/packages/pdf.scm (mupdf): Update to 1.22.1. Signed-off-by: Efraim Flashner --- gnu/packages/pdf.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index ec4e4620f88..1f3cc4ba463 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -824,14 +824,14 @@ and based on PDF specification 1.7.") (define-public mupdf (package (name "mupdf") - (version "1.22.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (string-append "https://mupdf.com/downloads/archive/" "mupdf-" version "-source.tar.lz")) (sha256 - (base32 "0ghwam1c1izks1n2zq2pr8z67nvrx4njk5rla86b75l4pw58mmxy")) + (base32 "1px73qnazjvmbwf1fab8ad8j1dmiddg1mjb7zg7h9i1vp4bh7c1k")) (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1))) -- cgit v1.2.3 From 940665301de4effd065d24c167f619286f2adf4c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 5 Jun 2023 11:34:49 +0300 Subject: gnu: gcompris-qt: Update to 3.2. * gnu/packages/education.scm (gcompris-qt): Update to 3.2. [inputs]: Add qtcharts, qtquickcontrols2-5. Remove qtquickcontrols-5, qtxml-5. --- gnu/packages/education.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index 406c1c1a354..4118c84bbfd 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2016 Danny Milosavljevic ;;; Copyright © 2016, 2017 Ricardo Wurmus ;;; Copyright © 2016 Hartmut Goebel -;;; Copyright © 2017, 2018, 2019, 2020, 2021, 2022 Efraim Flashner +;;; Copyright © 2017-2023 Efraim Flashner ;;; Copyright © 2018–2021 Tobias Geerinckx-Rice ;;; Copyright © 2018-2023 Nicolas Goaziou ;;; Copyright © 2020 Robert Smith @@ -150,7 +150,7 @@ of categories with some of the activities available in that category. (define-public gcompris-qt (package (name "gcompris-qt") - (version "2.3") + (version "3.2") (source (origin (method url-fetch) @@ -158,7 +158,7 @@ of categories with some of the activities available in that category. "mirror://kde/stable/gcompris/qt/src/gcompris-qt-" version ".tar.xz")) (sha256 - (base32 "0qncknaaf168anh4cjp7dqz6qzgx948kvgr32j2vga8mjakqn1aj")))) + (base32 "06yisr5qd2ri8qgpmlri0yic45fdfcdjn12anp17f6kvv83lk2js")))) (build-system qt-build-system) (arguments `(#:phases @@ -183,13 +183,13 @@ of categories with some of the activities available in that category. (list openssl python-wrapper qtbase-5 + qtcharts qtdeclarative-5 qtgraphicaleffects qtmultimedia-5 - qtquickcontrols-5 + qtquickcontrols2-5 qtsensors - qtsvg-5 - qtxmlpatterns)) + qtsvg-5)) (home-page "https://gcompris.net/index-en.html") (synopsis "Educational games for small children") (description -- cgit v1.2.3 From 91e75bb35fd545dc3dc5275428ca4cc17123c76c Mon Sep 17 00:00:00 2001 From: Navid Afkhami Date: Mon, 5 Jun 2023 17:05:22 +0200 Subject: gnu: Add python-readpaf. * gnu/packages/bioinformatics.scm (python-readpaf): New variable. --- gnu/packages/bioinformatics.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0b67d8fbe65..251e46061fa 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1998,6 +1998,25 @@ alignments and perform the following operations: ") (license license:expat))) +(define-public python-readpaf + (package + (name "python-readpaf") + (version "0.0.10") + (source (origin + (method url-fetch) + (uri (pypi-uri "readpaf" version)) + (sha256 + (base32 + "15m6ffks4zwpp1ycwk6n02py6mw2yh7qr0vhpc178b91gldr97ia")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-pandas)) + (home-page "https://github.com/alexomics/read-paf") + (synopsis "Minimap2 PAF file reader") + (description + "This is a fast parser for minimap2 PAF (Pairwise mApping Format) +files.") + (license license:expat))) + (define-public bioperl-minimal (package (name "bioperl-minimal") -- cgit v1.2.3 From 6559adea29ae116f5fa882f88678e510001e2c88 Mon Sep 17 00:00:00 2001 From: Navid Afkhami Date: Mon, 5 Jun 2023 17:05:35 +0200 Subject: gnu: Add python-bulkvis. * gnu/packages/bioinformatics.scm (python-bulkvis): New variable. Co-authored-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 68 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 68 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 251e46061fa..5667fba6891 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1337,6 +1337,74 @@ pretty, publication-quality figures for next-generation sequencing experiments.") (license license:expat))) +(define-public python-bulkvis + (let ((commit "00a82a90c7e748a34af896e779d27e78a2c82b5e") + (revision "2")) + (package + (name "python-bulkvis") + (version (git-version "2.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/LooseLab/bulkVis") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02blai158xyyqcg0ljzkmfa6ci05m4awrl4njvp9nwfp717xq8n0")) + (modules '((guix build utils))) + (snippet + '(substitute* '("requirements.txt" + "setup.py") + (("tqdm~=4.46.1") "tqdm") + (("tornado~=6.0.4") "tornado") + (("pandas~=1.0.5") "pandas") + (("h5py~=2.10.0") "h5py") + ;; See below for com + (("bokeh~=2.1.0") "bokeh"))))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f ;There are no tests + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'bokeh-compatibility + (lambda _ + (substitute* "bulkvis/bulkvis.py" + (("import importlib" m) + (string-append m " +from bokeh.command.subcommand import Argument +from bokeh.util.dataclasses import entries\n")) + (("( *)_parser.add_argument" m indent) + (string-append + (string-join (list "if isinstance(opts, Argument):\n" + " opts = dict(entries(opts))\n") + indent 'prefix) + m)))))))) + (propagated-inputs (list python-bokeh + python-dill + python-h5py + python-joblib + python-matplotlib + python-numpy + python-pandas + python-plotly + python-readpaf + python-scikit-learn + python-scikit-image + python-scipy + python-seaborn + python-tornado-6 + python-tqdm + python-umap-learn)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/LooseLab/bulkVis") + (synopsis "Interactive visualization of bulk RNA-seq data") + (description + "This is a Python package for the interactive visualization of bulk +RNA-seq data. It provides a range of plotting functions and interactive tools +to explore and analyze bulk RNA-seq data.") + (license license:expat)))) + (define-public python-cell2cell (package (name "python-cell2cell") -- cgit v1.2.3 From 1671aa25d4b610b7d417218a44e2d1e102aea4ff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 5 Jun 2023 17:07:09 +0200 Subject: gnu: python-bokeh: Use Tornado 6. * gnu/packages/python-xyz.scm (python-bokeh)[propagated-inputs]: Replace python-tornado with python-tornado-6. --- gnu/packages/python-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 50a586d773e..e28e1ebeefe 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16408,7 +16408,7 @@ enhancements to optimization and data fitting problems.") python-packaging python-pillow python-pyyaml - python-tornado + python-tornado-6 python-typing-extensions)) (native-inputs (list python-beautifulsoup4 -- cgit v1.2.3 From 46fc4c01a0afadf4023131ed43f2d10416480061 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 5 Jun 2023 17:10:02 +0200 Subject: gnu: python-tenacity: Use Tornado 6. * gnu/packages/python-xyz.scm (python-tenacity)[native-inputs]: Replace python-tornado with python-tornado-6. --- gnu/packages/python-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e28e1ebeefe..8529fd2caac 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1344,7 +1344,7 @@ threads.") "0bwkvjpjfyi9dgszzad9aww2vc00w3bczjnbifi92cp7wch2l923")))) (build-system python-build-system) (native-inputs - (list python-setuptools-scm python-tornado python-typeguard + (list python-setuptools-scm python-tornado-6 python-typeguard python-pytest)) (arguments (list #:phases -- cgit v1.2.3 From 77d6d5783b0f698aa832ead809c65eb411cda341 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 5 Jun 2023 17:10:37 +0200 Subject: gnu: python-tenacity: Use pyproject-build-system. * gnu/packages/python-xyz.scm (python-tenacity)[build-system]: Use pyproject-build-system. [arguments]: Remove. --- gnu/packages/python-xyz.scm | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8529fd2caac..e6a73675575 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1342,15 +1342,10 @@ threads.") (sha256 (base32 "0bwkvjpjfyi9dgszzad9aww2vc00w3bczjnbifi92cp7wch2l923")))) - (build-system python-build-system) + (build-system pyproject-build-system) (native-inputs (list python-setuptools-scm python-tornado-6 python-typeguard python-pytest)) - (arguments - (list #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda _ (invoke "pytest" "-vv")))))) (home-page "https://github.com/jd/tenacity") (synopsis "Retrying library for python") (description "Tenacity is a general-purpose python library to simplify the -- cgit v1.2.3 From 4f2ec0f2d1f1cb136b109f9703f88cebb1356f12 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 5 Jun 2023 17:20:52 +0200 Subject: gnu: python-bulkvis: Reference upstream issue. * gnu/packages/bioinformatics.scm (python-bulkvis)[arguments]: Add comment with link to upstream issue for bokeh compatibility patch. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5667fba6891..509dc3358b4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1367,6 +1367,7 @@ experiments.") (list #:tests? #f ;There are no tests #:phases '(modify-phases %standard-phases + ;; See https://github.com/LooseLab/bulkvis/issues/58 (add-after 'unpack 'bokeh-compatibility (lambda _ (substitute* "bulkvis/bulkvis.py" -- cgit v1.2.3 From 52e0a77a1b66e2ba5fa0dbac2f1dad35856d0586 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 5 Jun 2023 17:55:38 +0200 Subject: gnu: proj-7: Add upstream patch. * gnu/packages/patches/proj-7-initialize-memory.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/geo.scm (proj-7)[source]: Add it. --- gnu/local.mk | 1 + gnu/packages/geo.scm | 4 +- .../patches/proj-7-initialize-memory.patch | 98 ++++++++++++++++++++++ 3 files changed, 102 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/proj-7-initialize-memory.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 9adf5933186..f9afb433e6b 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1754,6 +1754,7 @@ dist_patch_DATA = \ %D%/packages/patches/procmail-ambiguous-getline-debian.patch \ %D%/packages/patches/procmail-CVE-2014-3618.patch \ %D%/packages/patches/procmail-CVE-2017-16844.patch \ + %D%/packages/patches/proj-7-initialize-memory.patch \ %D%/packages/patches/proot-add-clone3.patch \ %D%/packages/patches/protobuf-fix-build-on-32bit.patch \ %D%/packages/patches/psm-arch.patch \ diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 25805fe2e5f..6ad3c87ff10 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -738,7 +738,9 @@ lets developers use the functionality of Proj in their own software.") version ".tar.gz")) (sha256 (base32 - "050apzdn0isxpsblys1shrl9ccli5vd32kgswlgx1imrbwpg915k")))) + "050apzdn0isxpsblys1shrl9ccli5vd32kgswlgx1imrbwpg915k")) + (patches + (search-patches "proj-7-initialize-memory.patch")))) (arguments `(#:configure-flags '("-DUSE_EXTERNAL_GTEST=ON") #:phases diff --git a/gnu/packages/patches/proj-7-initialize-memory.patch b/gnu/packages/patches/proj-7-initialize-memory.patch new file mode 100644 index 00000000000..81481f9a468 --- /dev/null +++ b/gnu/packages/patches/proj-7-initialize-memory.patch @@ -0,0 +1,98 @@ +From 6f1a3c4648bf06862dca0b3725cbb3b7ee0284e3 Mon Sep 17 00:00:00 2001 +From: Even Rouault +Date: Sat, 6 Mar 2021 22:12:27 +0100 +Subject: [PATCH] =?UTF-8?q?gie=5Fself=5Ftests:=20fix=20use=20of=20uninitia?= + =?UTF-8?q?lized=20memory=20(fixes=C2=A0#2557)?= +MIME-Version: 1.0 +Content-Type: text/plain; charset=UTF-8 +Content-Transfer-Encoding: 8bit + +--- + test/unit/gie_self_tests.cpp | 39 ++++++++++++++++++++++-------------- + 1 file changed, 24 insertions(+), 15 deletions(-) + +diff --git a/test/unit/gie_self_tests.cpp b/test/unit/gie_self_tests.cpp +index 4244766ebf..92f1c758dc 100644 +--- a/test/unit/gie_self_tests.cpp ++++ b/test/unit/gie_self_tests.cpp +@@ -268,8 +268,10 @@ TEST_F(gieTest, proj_create_crs_to_crs) { + ASSERT_TRUE(P != nullptr); + PJ_COORD a, b; + +- a.xy.x = 700000.0; +- a.xy.y = 6000000.0; ++ a.xyzt.x = 700000.0; ++ a.xyzt.y = 6000000.0; ++ a.xyzt.z = 0; ++ a.xyzt.t = HUGE_VAL; + b.xy.x = 307788.8761171057; + b.xy.y = 5999669.3036037628; + +@@ -306,8 +308,10 @@ TEST_F(gieTest, proj_create_crs_to_crs_EPSG_4326) { + PJ_COORD a, b; + + // Lat, long degrees +- a.xy.x = 0.0; +- a.xy.y = 3.0; ++ a.xyzt.x = 0.0; ++ a.xyzt.y = 3.0; ++ a.xyzt.z = 0; ++ a.xyzt.t = HUGE_VAL; + + b.xy.x = 500000.0; + b.xy.y = 0.0; +@@ -328,8 +332,10 @@ TEST_F(gieTest, proj_create_crs_to_crs_proj_longlat) { + PJ_COORD a, b; + + // Long, lat degrees +- a.xy.x = 3.0; +- a.xy.y = 0; ++ a.xyzt.x = 3.0; ++ a.xyzt.y = 0; ++ a.xyzt.z = 0; ++ a.xyzt.t = HUGE_VAL; + + b.xy.x = 500000.0; + b.xy.y = 0.0; +@@ -718,9 +724,10 @@ TEST(gie, proj_create_crs_to_crs_PULKOVO42_ETRS89) { + proj_destroy(target_crs); + + // Romania +- c.xyz.x = 45; // Lat +- c.xyz.y = 25; // Long +- c.xyz.z = 0; ++ c.xyzt.x = 45; // Lat ++ c.xyzt.y = 25; // Long ++ c.xyzt.z = 0; ++ c.xyzt.t = HUGE_VAL; + c = proj_trans(P, PJ_FWD, c); + EXPECT_NEAR(c.xy.x, 44.999701238, 1e-9); + EXPECT_NEAR(c.xy.y, 24.998474948, 1e-9); +@@ -740,9 +747,10 @@ TEST(gie, proj_create_crs_to_crs_PULKOVO42_ETRS89) { + EXPECT_NEAR(c.xy.x, 45, 1e-8); + EXPECT_NEAR(c.xy.y, 25, 1e-8); + +- c.xyz.x = 45; // Lat +- c.xyz.y = 25; // Long +- c.xyz.z = 0; ++ c.xyzt.x = 45; // Lat ++ c.xyzt.y = 25; // Long ++ c.xyzt.z = 0; ++ c.xyzt.t = HUGE_VAL; + proj_trans_generic(P, PJ_FWD, &(c.xyz.x), sizeof(double), 1, &(c.xyz.y), + sizeof(double), 1, &(c.xyz.z), sizeof(double), 1, + nullptr, 0, 0); +@@ -783,9 +791,10 @@ TEST(gie, proj_create_crs_to_crs_outside_area_of_use) { + EXPECT_EQ(P->fwd, nullptr); + + // Test point outside area of use of both candidate coordinate operations +- c.xyz.x = 58; // Lat in deg +- c.xyz.y = 5; // Long in deg +- c.xyz.z = 0; ++ c.xyzt.x = 58; // Lat in deg ++ c.xyzt.y = 5; // Long in deg ++ c.xyzt.z = 0; ++ c.xyzt.t = HUGE_VAL; + c = proj_trans(P, PJ_FWD, c); + EXPECT_NEAR(c.xy.x, 64.44444444444444, 1e-9); // Lat in grad + EXPECT_NEAR(c.xy.y, 2.958634259259258, 1e-9); // Long in grad -- cgit v1.2.3 From cad86f8dcdbb538bc5d00bae7333a0d07fd37365 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 5 Jun 2023 20:22:01 +0300 Subject: gnu: python-codespell: Update to 2.2.4. * gnu/packages/python-xyz.scm (python-codespell): Update to 2.2.4. [build-system]: Switch to pyproject-build-system. [native-inputs]: Remove python-check-manifest; add python-pygments and python-tomli. --- gnu/packages/python-xyz.scm | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e6a73675575..64139065308 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17230,19 +17230,23 @@ checking library.") (define-public python-codespell (package (name "python-codespell") - (version "2.1.0") + (version "2.2.4") (source (origin (method url-fetch) (uri (pypi-uri "codespell" version)) (sha256 - (base32 "1r9y714cz8m894rxp7pyvicr1lw2iid24vz6fxbl5wzy8ibgxlqr")))) - (build-system python-build-system) + (base32 "0fp8ihlj8q23qdfryj5pq8srl85vn8k8p6gq3zg9qz957i3j0ihb")))) + (build-system pyproject-build-system) (inputs (list python-chardet)) (native-inputs - (list python-check-manifest python-flake8 python-pytest - python-pytest-cov python-pytest-dependency)) + (list python-flake8 + python-pygments + python-pytest + python-pytest-cov + python-pytest-dependency + python-tomli)) (arguments `(#:phases (modify-phases %standard-phases -- cgit v1.2.3 From ff6bb37299c71d535eae472791357be3d66c0c12 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 5 Jun 2023 21:59:44 +0300 Subject: gnu: cpp-httplib: Update to 0.12.5. * gnu/packages/cpp.scm (cpp-httplib): Update to 0.12.5. [arguments]: Adjust configure-flags to build the tests. Add a make-flag to set CXX. Adjust custom 'disable-network-tests phase to skip more network tests. Remove custom 'check phase. [native-inputs]: Add googletest. --- gnu/packages/cpp.scm | 27 ++++++++++++++------------- 1 file changed, 14 insertions(+), 13 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm index 9983213f7fa..365b15a3b9c 100644 --- a/gnu/packages/cpp.scm +++ b/gnu/packages/cpp.scm @@ -25,7 +25,7 @@ ;;; Copyright © 2021 jgart ;;; Copyright © 2021 Julien Lepiller ;;; Copyright © 2021 Disseminate Dissent -;;; Copyright © 2022 Efraim Flashner +;;; Copyright © 2022, 2023 Efraim Flashner ;;; Copyright © 2022 muradm ;;; Copyright © 2022 Attila Lendvai ;;; Copyright © 2022 Arun Isaac @@ -821,7 +821,7 @@ tools: ;; header (package (name "cpp-httplib") - (version "0.8.8") + (version "0.12.5") (source (origin (method git-fetch) @@ -829,16 +829,19 @@ tools: (url "https://github.com/yhirose/cpp-httplib") (commit (string-append "v" version)))) (sha256 - (base32 "0c0gyfbvm34bgrqy9fhfxw1f8nb9zhf063j7xq91k892flb7qm1c")) + (base32 "1m1p6h1dsxg4kg5zziffb6xl8zgjbkw7gmgmmlnrhpl3bswam87n")) (file-name (git-file-name name version)))) (build-system cmake-build-system) (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON" + "-DHTTPLIB_TEST=ON" "-DHTTPLIB_COMPILE=ON" "-DHTTPLIB_REQUIRE_BROTLI=ON" "-DHTTPLIB_REQUIRE_OPENSSL=ON" "-DHTTPLIB_REQUIRE_ZLIB=ON") + #:make-flags + '(,(string-append "CXX=" (cxx-for-target))) #:phases (modify-phases %standard-phases (add-after 'unpack 'disable-network-tests @@ -850,21 +853,19 @@ tools: (string-append "(DISABLED_" test)))) ;; There are tests requiring network access, disable them '("AbsoluteRedirectTest" "BaseAuthTest" "CancelTest" + "ConnectionErrorTest" "ChunkedEncodingTest" "ChunkedEncodingTest" + "ClientDefaultHeadersTest" "DecodeWithChunkedEncoding" "DefaultHeadersTest" "DigestAuthTest" "HttpsToHttpRedirectTest" + "HostnameToIPConversionTest" "RangeTest" "RedirectTest" "RelativeRedirectTest" - "SSLClientTest" "SendAPI" "TooManyRedirectTest" "UrlWithSpace" - "YahooRedirectTest" "YahooRedirectTest")))) - (replace 'check - (lambda* (#:key source tests? #:allow-other-keys) - ;; openssl genrsa wants to write a file in the git checkout - (when tests? - (with-directory-excursion "../source/test" - (invoke "make")))))))) + "SSLClientTest" "SendAPI" + "SpecifyServerIPAddressTest" + "TooManyRedirectTest" "UrlWithSpace" + "YahooRedirectTest" "YahooRedirectTest"))))))) (native-inputs - ;; required to build shared lib - (list python)) + (list googletest python)) (inputs (list brotli openssl zlib)) (home-page "https://github.com/yhirose/cpp-httplib") -- cgit v1.2.3 From f598f5b870462afbb5a5770c1b16071bca63fc52 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 5 Jun 2023 22:05:13 +0300 Subject: gnu: blurhash: Update to 0.2.0. * gnu/packages/image.scm (blurhash): Update to 0.2.0. [native-inputs]: Remove cmake. Add pkg-config. --- gnu/packages/image.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 06ace236363..069a214b8ce 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -2142,7 +2142,7 @@ losslessly translates between SNG and PNG.") (define-public blurhash (package (name "blurhash") - (version "0.0.1") + (version "0.2.0") (source (origin (method git-fetch) @@ -2151,10 +2151,10 @@ losslessly translates between SNG and PNG.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0jy2iigarskwfhskyladbb6l92x1fb3i3vz4bvcks0za4w5hfxk5")))) + (base32 "0hx15fspava43z47kv17ivxv56g03fb2zf45dl07v3shickqxw0x")))) (build-system meson-build-system) (native-inputs - (list cmake doctest)) + (list doctest pkg-config)) (home-page "https://github.com/Nheko-Reborn/blurhash") (synopsis "C++ blurhash encoder/decoder") (description "Simple encoder and decoder for blurhashes. Contains a -- cgit v1.2.3 From b3dfa5b671a5a2b6d13eb514d2fc9400b7866561 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 5 Jun 2023 19:17:29 -0400 Subject: gnu: linux-libre: Update to 6.3.6. * gnu/packages/linux.scm (linux-libre-6.3-version): Update to 6.3.6. (linux-libre-6.3-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 501ac9d19c1..734f20f7206 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -485,7 +485,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-6.3-version "6.3.5") +(define-public linux-libre-6.3-version "6.3.6") (define-public linux-libre-6.3-gnu-revision "gnu") (define deblob-scripts-6.3 (linux-libre-deblob-scripts @@ -495,7 +495,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0la20slh52jm4cg4v2liphhqqx4808gm6pfqcxiawj13a4ps9ygk"))) (define-public linux-libre-6.3-pristine-source (let ((version linux-libre-6.3-version) - (hash (base32 "0pl2zypsmrnna69850jadccffxwg9xdfkldg0sv8m44b7n64gkgm"))) + (hash (base32 "1vr418rf0zd16fq4vaxda1w2ccng2n9l0ysakmgz9xqbz86iysks"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-6.3))) -- cgit v1.2.3 From 455e88bc848cb39514d8d8669cbb7b9b6db9fa60 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 5 Jun 2023 19:17:43 -0400 Subject: gnu: linux-libre 6.1: Update to 6.1.32. * gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.32. (linux-libre-6.1-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 734f20f7206..bc03a02e900 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -503,7 +503,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; -(define-public linux-libre-6.1-version "6.1.31") +(define-public linux-libre-6.1-version "6.1.32") (define-public linux-libre-6.1-gnu-revision "gnu") (define deblob-scripts-6.1 (linux-libre-deblob-scripts @@ -513,7 +513,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1yv15mb278wlrn8gb2yjm0mczirzixy668h221vcpbz416ibxx1m"))) (define-public linux-libre-6.1-pristine-source (let ((version linux-libre-6.1-version) - (hash (base32 "1hbkw290kmf1dj8a255ik1gk5fk458c88m348dwrc3lrl6xifsg8"))) + (hash (base32 "0v0saai735jzaj3dbpgp6sbdi95n3lmv78pbg1xy9fd2kfhbg23w"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-6.1))) -- cgit v1.2.3 From f9755ff2ac545bf90f50e64b6e70787b9b508427 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 5 Jun 2023 19:17:55 -0400 Subject: gnu: linux-libre 5.15: Update to 5.15.115. * gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.115. (linux-libre-5.15-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index bc03a02e900..16064cadae0 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -518,7 +518,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-6.1))) -(define-public linux-libre-5.15-version "5.15.114") +(define-public linux-libre-5.15-version "5.15.115") (define-public linux-libre-5.15-gnu-revision "gnu") (define deblob-scripts-5.15 (linux-libre-deblob-scripts @@ -528,7 +528,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "00n8c7ghfs36bvz0yjw6w9daf5zcgj94kxxn27bfyfm274rkddmz"))) (define-public linux-libre-5.15-pristine-source (let ((version linux-libre-5.15-version) - (hash (base32 "1lkpa9wv1qj90qdzzi71qf5dyy7mi95fixx3ymdp6xwz45fym0g9"))) + (hash (base32 "050j9z0wg5glgxwbmzfq4l8lv8y7g3nc2rz8342yjdcjfxh6h1qv"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.15))) -- cgit v1.2.3 From 00e2d8d8ae0db5c65e4c67313c374a4765894b07 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 5 Jun 2023 19:18:08 -0400 Subject: gnu: linux-libre 5.10: Update to 5.10.182. * gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.182. (linux-libre-5.10-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 16064cadae0..e6a61807dde 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -533,7 +533,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.15))) -(define-public linux-libre-5.10-version "5.10.181") +(define-public linux-libre-5.10-version "5.10.182") (define-public linux-libre-5.10-gnu-revision "gnu1") (define deblob-scripts-5.10 (linux-libre-deblob-scripts @@ -543,7 +543,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "12jhak2bw1jy2jk70vrm66kjvh0cd6c8f2qiy2bk40rq7bf62mr6"))) (define-public linux-libre-5.10-pristine-source (let ((version linux-libre-5.10-version) - (hash (base32 "1rx43dkxspris9529vl11blzhvsxnpaqr6yb3fy089az7yvwxrmc"))) + (hash (base32 "1xp9bxk2vyw29bq3z854ly4cj94z8i52yl5hq4a3l3j6564wb3ny"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.10))) -- cgit v1.2.3 From 8937898af9433c0b7a8d95a78c95e21576ae22e8 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 5 Jun 2023 19:18:21 -0400 Subject: gnu: linux-libre 5.4: Update to 5.4.245. * gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.245. (linux-libre-5.4-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index e6a61807dde..3bcc34374cf 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -548,7 +548,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.10))) -(define-public linux-libre-5.4-version "5.4.244") +(define-public linux-libre-5.4-version "5.4.245") (define-public linux-libre-5.4-gnu-revision "gnu1") (define deblob-scripts-5.4 (linux-libre-deblob-scripts @@ -558,7 +558,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "070j069sj6spy2wkzfzm1d5jd7pffm0s1m917wblc8d3x8pbgvf8"))) (define-public linux-libre-5.4-pristine-source (let ((version linux-libre-5.4-version) - (hash (base32 "06x20aq7bv86ghv2sdsz3q2rmqh8h389x5zksr53fyzdjl72ixch"))) + (hash (base32 "195ixy9l18mhwvzj7v63fkyifb9mysq950afxh6ixlpvg0c8h1wn"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.4))) -- cgit v1.2.3 From d6ae80c74200216fe7615739896fc1c6eacf7e7d Mon Sep 17 00:00:00 2001 From: Z572 <873216071@qq.com> Date: Tue, 6 Jun 2023 09:20:50 +0300 Subject: gnu: thc-ipv6: Do not build with "-march=native". * gnu/packages/networking.scm (thc-ipv6)[origin]: Add 'snippet'. [properties]: New field. Signed-off-by: Efraim Flashner --- gnu/packages/networking.scm | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 9dfc785f04e..2055ed93c75 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -59,6 +59,7 @@ ;;; Copyright © 2023 Sharlatan Hellseher ;;; Copyright © 2023 Bruno Victal ;;; Copyright © 2023 Yovan Naumovski +;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -3097,7 +3098,10 @@ The filters can be aggregated and exported in the most common formats.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "07kwika1zdq62s5p5z94xznm77dxjxdg8k0hrg7wygz50151nzmx")))) + (base32 "07kwika1zdq62s5p5z94xznm77dxjxdg8k0hrg7wygz50151nzmx")) + (modules '((guix build utils))) + (snippet '(begin (substitute* '("Makefile") + (("-march=native") "")))))) (build-system gnu-build-system) (arguments (list @@ -3126,6 +3130,7 @@ The filters can be aggregated and exported in the most common formats.") libpcap openssl perl)) + (properties '((tunable? . #t))) (home-page "https://github.com/vanhauser-thc/thc-ipv6") (synopsis "IPv6 security research toolkit") (description "The THC IPv6 Toolkit provides command-line tools and a library -- cgit v1.2.3 From cdbd87b6f3110082a51a5e221adc0c86a3913787 Mon Sep 17 00:00:00 2001 From: Jean-Pierre De Jesus DIAZ Date: Thu, 1 Jun 2023 15:32:34 +0200 Subject: gnu: libjaylink: Update to 0.3.1. * gnu/packages/embedded (libjaylink): Update to 0.3.1. Signed-off-by: Efraim Flashner --- gnu/packages/embedded.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm index 50a3abd1fda..2a90ca22d00 100644 --- a/gnu/packages/embedded.scm +++ b/gnu/packages/embedded.scm @@ -511,7 +511,7 @@ languages are C and C++.") (define-public libjaylink (package (name "libjaylink") - (version "0.2.0") + (version "0.3.1") (source (origin (method git-fetch) (uri (git-reference @@ -520,7 +520,7 @@ languages are C and C++.") (file-name (git-file-name name version)) (sha256 (base32 - "0ndyfh51hiqyv2yscpj6qd091w7myxxjid3a6rx8f6k233vy826q")))) + "1wps72ir2kwdr7dphx4vp6cy0d46dm3nkwbk0mpryn9la09l7lm1")))) (build-system gnu-build-system) (native-inputs (list autoconf automake libtool pkg-config)) -- cgit v1.2.3 From f351f2aaf2d02439eefd9baac8f5f3a1518584d8 Mon Sep 17 00:00:00 2001 From: Jean-Pierre De Jesus DIAZ Date: Thu, 1 Jun 2023 15:32:35 +0200 Subject: gnu: jimtcl: Update to 0.82. * gnu/packages/embedded (jimtcl): Update to 0.82. [arguments]: Use G-Expressions and update failing test, TTY test doesn't fail anymore. [inputs]: Add openssl as an input as now by default jimtcl enables the SSL configuration option. * gnu/packages/embedded (openocd): Support jimtcl 0.82. [arguments]: Link against libssl and libcrypto. [inputs]: Add openssl. Signed-off-by: Efraim Flashner --- gnu/packages/embedded.scm | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm index 2a90ca22d00..6efecf97007 100644 --- a/gnu/packages/embedded.scm +++ b/gnu/packages/embedded.scm @@ -69,6 +69,7 @@ #:use-module (gnu packages readline) #:use-module (gnu packages swig) #:use-module (gnu packages texinfo) + #:use-module (gnu packages tls) #:use-module (gnu packages version-control) #:use-module (gnu packages xorg) #:use-module (srfi srfi-1)) @@ -535,7 +536,7 @@ SEGGER J-Link and compatible devices.") (define-public jimtcl (package (name "jimtcl") - (version "0.80") + (version "0.82") (source (origin (method git-fetch) (uri (git-reference @@ -544,23 +545,22 @@ SEGGER J-Link and compatible devices.") (file-name (git-file-name name version)) (sha256 (base32 - "06rn60cx9sapc175vxvan87b8j5rkhh5gvvz7343xznzwlr0wcgk")))) + "01nxqzn41797ypph1vpwjfh3zqgks0l8ihh6932b4kb83apy6f08")))) (build-system gnu-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'configure - ;; This package doesn't use autoconf. - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (invoke "./configure" - (string-append "--prefix=" out))))) - (add-before 'check 'delete-failing-tests - (lambda _ - ;; XXX All but 1 TTY tests fail (Inappropriate ioctl for device). - (delete-file "tests/tty.test") - #t)) - ))) + (list #:phases + #~(modify-phases %standard-phases + (replace 'configure + ;; This package doesn't use autoconf. + (lambda _ + (invoke "./configure" + (string-append "--prefix=" #$output)))) + (add-before 'check 'delete-failing-tests + (lambda _ + ;; XXX All but 1 SSL tests fail (tries connecting to Google + ;; servers). + (delete-file "tests/ssl.test")))))) + (inputs (list openssl)) (native-inputs ;; For tests. (list inetutils)) ; for hostname @@ -592,10 +592,10 @@ language.") pkg-config texinfo)) (inputs - (list hidapi jimtcl libftdi libjaylink libusb-compat)) + (list hidapi jimtcl libftdi libjaylink libusb-compat openssl)) (arguments '(#:configure-flags - (append (list "LIBS=-lutil" + (append (list "LIBS=-lutil -lcrypto -lssl" "--disable-werror" "--enable-sysfsgpio" "--disable-internal-jimtcl" -- cgit v1.2.3 From e3cd3f03202c48cd8d777f4769b4e31fea8dcd60 Mon Sep 17 00:00:00 2001 From: Jean-Pierre De Jesus DIAZ Date: Thu, 1 Jun 2023 15:32:36 +0200 Subject: gnu: openocd: Update to 0.12.0. * gnu/packages/embedded.scm (openocd): Update to 0.12.0. [inputs]: Remove libusb-compat as openocd dropped support for libusb0. Signed-off-by: Efraim Flashner --- gnu/packages/embedded.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm index 6efecf97007..215007dd312 100644 --- a/gnu/packages/embedded.scm +++ b/gnu/packages/embedded.scm @@ -573,7 +573,7 @@ language.") (define-public openocd (package (name "openocd") - (version "0.11.0") + (version "0.12.0") (source (origin (method git-fetch) (uri (git-reference @@ -582,7 +582,7 @@ language.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0qi4sixwvw1i7c64sy221fsjs82qf3asmdk86g74ds2jjm3f8pzp")))) + "09wb11zlmrw6rx1bql3kafgi3ilzp9mhvb6j6rql216by06csing")))) (build-system gnu-build-system) (native-inputs (list autoconf @@ -592,7 +592,7 @@ language.") pkg-config texinfo)) (inputs - (list hidapi jimtcl libftdi libjaylink libusb-compat openssl)) + (list hidapi jimtcl libftdi libjaylink openssl)) (arguments '(#:configure-flags (append (list "LIBS=-lutil -lcrypto -lssl" -- cgit v1.2.3 From b019b49c74e51e42230da471f39bff9f642fbc24 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Fri, 2 Jun 2023 13:32:55 +0200 Subject: gnu: sbcl: Update to 2.3.5. * gnu/packages/lisp.scm (sbcl): Update to 2.3.5. --- gnu/packages/lisp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index c053da9cd5d..ed2399b9550 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -431,14 +431,14 @@ an interpreter, a compiler, a debugger, and much more.") (define-public sbcl (package (name "sbcl") - (version "2.3.2") + (version "2.3.5") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/sbcl/sbcl/" version "/sbcl-" version "-source.tar.bz2")) (sha256 - (base32 "1ahyrc3p9cf7y5zbgzvb9yxa8a480ccis4ksijlajck3z8n1dk24")) + (base32 "11ji5n65l31249r0v7hm0wc0yk2ila0y746nj36xn1cxrwh0gjc9")) (modules '((guix build utils))) (snippet '(begin -- cgit v1.2.3 From b30c60316c9c82f97bd38985980613f2a755d870 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Tue, 6 Jun 2023 10:00:52 +0200 Subject: gnu: txr: Update to 287. * gnu/packages/lisp.scm (txr): Update to 287. --- gnu/packages/lisp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index ed2399b9550..9e896cc8a5b 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -990,7 +990,7 @@ the HTML documentation of TXR.") (define-public txr (package (name "txr") - (version "286") + (version "287") (source (origin (method git-fetch) @@ -999,7 +999,7 @@ the HTML documentation of TXR.") (commit (string-append "txr-" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0c5prq9ans4qv8dgfn85555by9rb22p276g21w4mns0rqhjd0ij8")))) + (base32 "0bwa40l5c0dnpcpfbysqbv8ch58sycbb31dnskmhr387jlv938dl")))) (build-system gnu-build-system) (arguments (list #:configure-flags -- cgit v1.2.3 From 9ad8b0c2ef10d8de01bad25f54337c5df35aa842 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Mon, 5 Jun 2023 14:03:23 +0200 Subject: gnu: sbcl-stmx: Update to 2.0.5-2.f71e742. * gnu/packages/lisp-xyz.scm (sbcl-stmx): Update to 2.0.5-2.f71e742. [arguments]: Add 'fix-build' phase. --- gnu/packages/lisp-xyz.scm | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index fd09b4f52cd..8031ef53657 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -21176,9 +21176,10 @@ window it creates as just another output for your graphics, analogous to how (sbcl-package->cl-source-package sbcl-cepl)) (define-public sbcl-stmx - ;; No release for years and recent commits contain fixes for revent SBCL versions. - (let ((commit "a7bb44082cd53ee968965adff03d4351750711a1") - (revision "1")) + ;; No release for years and recent commits contain fixes for recent SBCL + ;; versions. + (let ((commit "f71e742a50b85e3abc0af9bb5f02802f218a1705") + (revision "2")) (package (name "sbcl-stmx") (version (git-version "2.0.5" revision commit)) @@ -21190,11 +21191,22 @@ window it creates as just another output for your graphics, analogous to how (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "1hfmh4vj271jdilir97qs6nqbi5nmn5alyls0w3d3xxqwi6ffqjs")))) + (base32 "0q739mlw3s3z5kclzccz4r64ag38ks11fmd38109qwjv5knn69jv")))) (build-system asdf-build-system/sbcl) (inputs (list sbcl-alexandria sbcl-bordeaux-threads sbcl-log4cl sbcl-closer-mop sbcl-trivial-garbage)) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-build + (lambda _ + (substitute* "asm/transaction.lisp" + (("\\(ftype \\(function \\(\\) fixnum\\) transaction-begin\\)") + "(ftype (function () (unsigned-byte 32)) transaction-begin)") + (("\\(values fixnum &optional\\)") + "(unsigned-byte 32)"))))))) (home-page "https://stmx.org/") (synopsis "High performance Transactional Memory for Common Lisp") (description -- cgit v1.2.3 From 181951207339508789b28ba7cb914f983319920f Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 6 Jun 2023 11:41:39 +0200 Subject: services: 'modify-services' preserves service ordering. Fixes . The regression was introduced in dbbc7e946131ba257728f1d05b96c4339b7ee88b, which changed the order of services. As a result, someone using 'modify-services' could find themselves with incorrect ordering of expressions in the "boot" script, whereby the cleanup expressions would come after (execl ".../shepherd"). This, in turn, would lead shepherd to error out at boot with EADDRINUSE on /var/run/shepherd/socket. * gnu/services.scm (%delete-service, %apply-clauses): Remove. (clause-alist): New macro. (apply-clauses): New procedure. (modify-services): Use it. Adjust docstring. * tests/services.scm ("modify-services: do nothing"): Remove 'sort' call. ("modify-services: delete service"): Likewise, and add 't4' service. ("modify-services: change value"): Remove 'sort' call and fix expected value. --- gnu/services.scm | 93 +++++++++++++++++++++++++++++++++++------------------- tests/services.scm | 37 +++++++++++----------- 2 files changed, 80 insertions(+), 50 deletions(-) (limited to 'gnu') diff --git a/gnu/services.scm b/gnu/services.scm index a990d297c9c..5410d319715 100644 --- a/gnu/services.scm +++ b/gnu/services.scm @@ -51,6 +51,7 @@ #:use-module (srfi srfi-26) #:use-module (srfi srfi-34) #:use-module (srfi srfi-35) + #:use-module (srfi srfi-71) #:use-module (ice-9 vlist) #:use-module (ice-9 match) #:autoload (ice-9 pretty-print) (pretty-print) @@ -297,35 +298,65 @@ singleton service type NAME, of which the returned service is an instance." (description "This is a simple service.")))) (service type value))) -(define (%delete-service kind services) - (let loop ((found #f) - (return '()) - (services services)) +(define-syntax clause-alist + (syntax-rules (=> delete) + "Build an alist of clauses. Each element has the form (KIND PROC LOC) +where PROC is the service transformation procedure to apply for KIND, and LOC +is the source location information." + ((_ (delete kind) rest ...) + (cons (list kind + (lambda (service) + #f) + (current-source-location)) + (clause-alist rest ...))) + ((_ (kind param => exp ...) rest ...) + (cons (list kind + (lambda (svc) + (let ((param (service-value svc))) + (service (service-kind svc) + (begin exp ...)))) + (current-source-location)) + (clause-alist rest ...))) + ((_) + '()))) + +(define (apply-clauses clauses services) + "Apply CLAUSES, an alist as returned by 'clause-alist', to SERVICES, a list +of services. Use each clause at most once; raise an error if a clause was not +used." + (let loop ((services services) + (clauses clauses) + (result '())) (match services - ('() - (if found - (values return found) - (raise (formatted-message + (() + (match clauses + (() ;all clauses fired, good + (reverse result)) + (((kind _ properties) _ ...) ;one or more clauses didn't match + (raise (make-compound-condition + (condition + (&error-location + (location (source-properties->location properties)))) + (formatted-message (G_ "modify-services: service '~a' not found in service list") - (service-type-name kind))))) - ((service . rest) - (if (eq? (service-kind service) kind) - (loop service return rest) - (loop found (cons service return) rest)))))) - -(define-syntax %apply-clauses - (syntax-rules (=> delete) - ((_ ((delete kind) . rest) services) - (%apply-clauses rest (%delete-service kind services))) - ((_ ((kind param => exp ...) . rest) services) - (call-with-values (lambda () (%delete-service kind services)) - (lambda (svcs found) - (let ((param (service-value found))) - (cons (service (service-kind found) - (begin exp ...)) - (%apply-clauses rest svcs)))))) - ((_ () services) - services))) + (service-type-name kind))))))) + ((head . tail) + (let ((service clauses + (fold2 (lambda (clause service remainder) + (match clause + ((kind proc properties) + (if (eq? kind (service-kind service)) + (values (proc service) remainder) + (values service + (cons clause remainder)))))) + head + '() + clauses))) + (loop tail + (reverse clauses) + (if service + (cons service result) + result))))))) (define-syntax modify-services (syntax-rules () @@ -358,11 +389,9 @@ Consider this example: It changes the configuration of the GUIX-SERVICE-TYPE instance, and that of all the MINGETTY-SERVICE-TYPE instances, and it deletes instances of the -UDEV-SERVICE-TYPE. - -This is a shorthand for (filter-map (lambda (svc) ...) %base-services)." - ((_ services . clauses) - (%apply-clauses clauses services)))) +UDEV-SERVICE-TYPE." + ((_ services clauses ...) + (apply-clauses (clause-alist clauses ...) services)))) ;;; diff --git a/tests/services.scm b/tests/services.scm index 8cdb1b2a314..20ff4d317e8 100644 --- a/tests/services.scm +++ b/tests/services.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015-2019, 2022 Ludovic Courtès +;;; Copyright © 2015-2019, 2022, 2023 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -287,7 +287,7 @@ (x x)))) (test-equal "modify-services: do nothing" - '(1 2 3) + '(1 2 3) ;note: service order must be preserved (let* ((t1 (service-type (name 't1) (extensions '()) (description ""))) @@ -298,12 +298,11 @@ (extensions '()) (description ""))) (services (list (service t1 1) (service t2 2) (service t3 3)))) - (sort (map service-value - (modify-services services)) - <))) + (map service-value + (modify-services services)))) (test-equal "modify-services: delete service" - '(1) + '(1 4) ;note: service order must be preserved (let* ((t1 (service-type (name 't1) (extensions '()) (description ""))) @@ -313,12 +312,15 @@ (t3 (service-type (name 't3) (extensions '()) (description ""))) - (services (list (service t1 1) (service t2 2) (service t3 3)))) - (sort (map service-value - (modify-services services - (delete t3) - (delete t2))) - <))) + (t4 (service-type (name 't4) + (extensions '()) + (description ""))) + (services (list (service t1 1) (service t2 2) + (service t3 3) (service t4 4)))) + (map service-value + (modify-services services + (delete t3) + (delete t2))))) (test-error "modify-services: delete non-existing service" #t @@ -336,7 +338,7 @@ (delete t3)))) (test-equal "modify-services: change value" - '(2 11 33) + '(11 2 33) ;note: service order must be preserved (let* ((t1 (service-type (name 't1) (extensions '()) (description ""))) @@ -347,11 +349,10 @@ (extensions '()) (description ""))) (services (list (service t1 1) (service t2 2) (service t3 3)))) - (sort (map service-value - (modify-services services - (t1 value => 11) - (t3 value => 33))) - <))) + (map service-value + (modify-services services + (t1 value => 11) + (t3 value => 33))))) (test-error "modify-services: change value for non-existing service" #t -- cgit v1.2.3 From f800e7e88b67f53aefc956e238eea5d65ca1bfa6 Mon Sep 17 00:00:00 2001 From: Navid Afkhami Date: Tue, 6 Jun 2023 11:33:27 +0200 Subject: gnu: Add r-caretensemble. * gnu/packages/cran.scm (r-caretensemble): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d8221fd0fcd..53c49e3ac7e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27921,6 +27921,37 @@ it may be seen by an animal with less acute vision.") classification and regression models.") (license license:gpl2+))) +(define-public r-caretensemble + (package + (name "r-caretensemble") + (version "2.0.2") + (source (origin + (method url-fetch) + (uri (cran-uri "caretEnsemble" version)) + (sha256 + (base32 + "0kagw1ilfz1yy1q0ysmkp3f13k08hiq84xk7d0xp5p7d5dsg7z6q")))) + (properties `((upstream-name . "caretEnsemble"))) + (build-system r-build-system) + (propagated-inputs (list r-caret + r-data-table + r-digest + r-ggplot2 + r-gridextra + r-lattice + r-pbapply + r-plyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/zachmayer/caretEnsemble") + (synopsis "Ensembles of caret models") + (description + "This is a framework for fitting multiple caret models. It uses the same +re-sampling strategy as well as creating ensembles of such models. Use +@code{caretList} to fit multiple models and then use @code{caretEnsemble} to +combine them greedily or @code{caretStack} to combine them using a caret +model.") + (license license:expat))) + (define-public r-adabag (package (name "r-adabag") -- cgit v1.2.3 From 0ae29db11d0c4a92d12b6cc604c868882336aced Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Jun 2023 13:04:14 +0200 Subject: gnu: python-anaconda-client: Fix build with Python 3.10. * gnu/packages/package-management.scm (python-anaconda-client)[build-system]: Use pyproject-bulid-system. [arguments]: Move contents of 'remove-network-tests phase to #:test-flags; drop trailing #T from 'set-HOME phase; add phase 'python3.10-compatibility; disable test_conda_root and test_conda_root_outside_root_environment. --- gnu/packages/package-management.scm | 53 ++++++++++++++++++++++--------------- 1 file changed, 31 insertions(+), 22 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index a856ff2726e..9532fd7187e 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013-2023 Ludovic Courtès -;;; Copyright © 2015, 2017, 2020, 2021, 2022 Ricardo Wurmus +;;; Copyright © 2015, 2017, 2020, 2021, 2022, 2023 Ricardo Wurmus ;;; Copyright © 2017 Muriithi Frederick Muriuki ;;; Copyright © 2017, 2018 Oleg Pykhalov ;;; Copyright © 2017 Roel Janssen @@ -120,6 +120,7 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system guile) #:use-module (guix build-system meson) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (guix build-system ruby) #:use-module (guix build-system trivial) @@ -917,7 +918,34 @@ transactions from C or Python.") (sha256 (base32 "1vyk0g0gci4z9psisb8h50zi3j1nwfdg1jw3j76cxv0brln0v3fw")))) - (build-system python-build-system) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; These tests require a network connection + '(append (map (lambda (file) + (string-append "--ignore=binstar_client/" file)) + (list "tests/test_upload.py" + "tests/test_authorizations.py" + "tests/test_login.py" + "tests/test_whoami.py" + "utils/notebook/tests/test_data_uri.py" + "utils/notebook/tests/test_base.py" + "utils/notebook/tests/test_downloader.py" + "inspect_package/tests/test_conda.py")) + ;; get_conda_root returns None + (list "-k" + "not test_conda_root \ +and not test_conda_root_outside_root_environment")) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'python3.10-compatibility + (lambda _ + (substitute* "binstar_client/utils/config.py" + (("collections.Mapping") "collections.abc.Mapping")))) + ;; This is needed for some tests. + (add-before 'check 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list python-clyent python-nbformat python-pyyaml python-requests)) (native-inputs @@ -926,27 +954,8 @@ transactions from C or Python.") python-freezegun python-mock python-pillow + python-pytest python-pytz)) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; This is needed for some tests. - (add-before 'check 'set-up-home - (lambda* _ (setenv "HOME" "/tmp") #t)) - (add-before 'check 'remove-network-tests - (lambda* _ - ;; Remove tests requiring a network connection - (let ((network-tests '("tests/test_upload.py" - "tests/test_authorizations.py" - "tests/test_login.py" - "tests/test_whoami.py" - "utils/notebook/tests/test_data_uri.py" - "utils/notebook/tests/test_base.py" - "utils/notebook/tests/test_downloader.py" - "inspect_package/tests/test_conda.py"))) - (with-directory-excursion "binstar_client" - (for-each delete-file network-tests))) - #t))))) (home-page "https://github.com/Anaconda-Platform/anaconda-client") (synopsis "Anaconda Cloud command line client library") (description -- cgit v1.2.3 From 1a2eb26286c72ac2754969f53f5833b053b96b67 Mon Sep 17 00:00:00 2001 From: Josselin Poiret Date: Tue, 6 Jun 2023 13:18:46 +0200 Subject: services: Check if service is #f before applying clause. * gnu/services.scm (apply-clauses): Check if service is #f before trying to apply clause. Follow up of 181951207339508789b28ba7cb914f983319920f. --- gnu/services.scm | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/services.scm b/gnu/services.scm index 5410d319715..109e050a23e 100644 --- a/gnu/services.scm +++ b/gnu/services.scm @@ -343,12 +343,14 @@ used." ((head . tail) (let ((service clauses (fold2 (lambda (clause service remainder) - (match clause - ((kind proc properties) - (if (eq? kind (service-kind service)) - (values (proc service) remainder) - (values service - (cons clause remainder)))))) + (if service + (match clause + ((kind proc properties) + (if (eq? kind (service-kind service)) + (values (proc service) remainder) + (values service + (cons clause remainder))))) + (values #f (cons clause remainder)))) head '() clauses))) -- cgit v1.2.3 From 2199546a83e521fe3dd78a3014f7ff7b88400191 Mon Sep 17 00:00:00 2001 From: Gruruya Date: Sat, 25 Mar 2023 08:30:28 -0400 Subject: gnu: nim: Update to 1.6.12. Without the attached patch, Nim is broken on Guix as it searches for its stdlib in /lib while it was placed in /lib/nim. * gnu/packages/nim.scm (nim): Update to 1.6.12. [arguments]: In 'patch-installer phase install stdlib source to the right directory. In 'patch-more-shebangs phase edit substitute* to point to the new osproc source. Signed-off-by: Efraim Flashner --- gnu/packages/nim.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/nim.scm b/gnu/packages/nim.scm index 6da382119fa..ebcff26c7b9 100644 --- a/gnu/packages/nim.scm +++ b/gnu/packages/nim.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2020 Tanguy Le Carrour ;;; Copyright © 2022 (unmatched parenthesis ;;; Copyright © 2022 Trevor Richards +;;; Copyright © 2023 Gruruya ;;; ;;; This file is part of GNU Guix. ;;; @@ -36,14 +37,14 @@ (define-public nim (package (name "nim") - (version "1.6.6") + (version "1.6.12") (source (origin (method url-fetch) (uri (string-append "https://nim-lang.org/download/" name "-" version ".tar.xz")) (sha256 - (base32 "0lm4450ig8k4l3rzxv6kcqji5l1lzicsw76ckwxm0q9qdz713cb7")))) + (base32 "1hjd9dxhqzn2ifr988li8q7v6kxpxlcqbdllfd6lsq3knw50pvxc")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; TODO: Investigate tests failures. @@ -55,6 +56,7 @@ (let ((out (assoc-ref outputs "out"))) (substitute* "install.sh" (("/usr/local") out) + (("/lib/nim") "/lib") (("/opt/nimble") (string-append out "/share/nimble")) (("configdir=/etc/nim") (string-append "configdir=" out "/etc/nim")))))) @@ -102,7 +104,7 @@ "lib/pure/osproc.nim" "lib/pure/strscans.nim") (("/bin/sh") sh)) - (substitute* (find-files "c_code" "stdlib_osproc\\.nim\\.c") + (substitute* (find-files "c_code" "@m\\.\\.@slib@spure@sosproc\\.nim\\.c") (("\"/bin/sh\", 7") (format #f "~s, ~s" sh (string-length sh))))))) (replace 'build (lambda* (#:key (parallel-build? #t) #:allow-other-keys) -- cgit v1.2.3 From 72243da2fbc3c590ab17cb7155e68e911ef247f8 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 5 Jun 2023 05:41:39 -0400 Subject: gnu: icecat: Update to 102.12.0-guix0-preview1 [security fixes]. Includes fixes for CVE-2023-34414 and CVE-2023-34416. * gnu/packages/gnuzilla.scm (%icecat-base-version, %icecat-build-id): Update. (icecat-source): Update gnuzilla commit, base version, and hashes. --- gnu/packages/gnuzilla.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index fd7f4565f97..e40d2b89226 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -518,9 +518,9 @@ variable defined below. It requires guile-json to be installed." ;; XXXX: Workaround 'snippet' limitations. (define computed-origin-method (@@ (guix packages) computed-origin-method)) -(define %icecat-base-version "102.11.0") +(define %icecat-base-version "102.12.0") (define %icecat-version (string-append %icecat-base-version "-guix0-preview1")) -(define %icecat-build-id "20230509000000") ;must be of the form YYYYMMDDhhmmss +(define %icecat-build-id "20230606000000") ;must be of the form YYYYMMDDhhmmss ;; 'icecat-source' is a "computed" origin that generates an IceCat tarball ;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat' @@ -540,12 +540,12 @@ variable defined below. It requires guile-json to be installed." "firefox-" upstream-firefox-version ".source.tar.xz")) (sha256 (base32 - "0cyfij00i9m1pwwyfhiq2qasbfr2ykdwziqykj8878kyjvkj1wg7")))) + "189irpd8xkwh3qixbbcmn5jblx7jz80rilcq8ihaawpmdh76safp")))) ;; The upstream-icecat-base-version may be older than the ;; %icecat-base-version. - (upstream-icecat-base-version "102.11.0") - (gnuzilla-commit "5a1894fc966840dc242110ec0459471c637a4675") + (upstream-icecat-base-version "102.12.0") + (gnuzilla-commit "b2d463b0e331795eebe3ee62f2c58c1bd05b9899") (gnuzilla-source (origin (method git-fetch) @@ -557,7 +557,7 @@ variable defined below. It requires guile-json to be installed." (string-take gnuzilla-commit 8))) (sha256 (base32 - "1816lm4cl45l1zbc043827rfnzzzxckhxk16gvj3a8kyg7fxvv3v")))) + "0db03i3xmapdr0xyb9yg6cl66kyxavnl22hhhnf85ffnlfrcdx2r")))) ;; 'search-patch' returns either a valid file name or #f, so wrap it ;; in 'assume-valid-file-name' to avoid 'local-file' warnings. -- cgit v1.2.3 From f056d4f168e18c764ba586de960c00f531ac6d65 Mon Sep 17 00:00:00 2001 From: Navid Afkhami Date: Tue, 6 Jun 2023 18:15:46 +0200 Subject: gnu: Add python-decoupler-py. * gnu/packages/bioinformatics.scm (python-decoupler-py): New variable. Co-authored-by: Ricardo Wurmus . --- gnu/packages/bioinformatics.scm | 63 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 509dc3358b4..9ce28596c29 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1549,6 +1549,69 @@ from high-throughput single-cell RNA sequencing (scRNA-seq) data.") and sequence consensus.") (license license:expat))) +(define-public python-decoupler-py + ;; This latest commit fixes a bug in test_omnip.py. + (let ((commit "b84c524ec4a9280a56c0db963e2c7b010316ce8f") + (revision "1")) + (package + (name "python-decoupler-py") + (version (git-version "1.3.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/saezlab/decoupler-py") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0d74yr5jqc52vcxaca84kxqw7m5rbazpmvnrcp2y4xxrj6yr1sfc")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + '(list "-k" + ;; These tests require internet access + (string-append "not test_get_resource" + " and not test_show_resources" + " and not test_get_dorothea" + " and not test_get_progeny" + ;; XXX This one fails because the "texts" list + ;; is empty, so there are no texts to adjust. + ;; It is not clear whether this a compatibility + ;; problem with our adjusttext package. + " and not test_plot_volcano")) + #:phases + '(modify-phases %standard-phases + (add-before 'check 'set-home + ;; Some tests require a home directory to be set. + (lambda _ (setenv "HOME" "/tmp"))) + ;; Numba needs a writable dir to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs (list python-adjusttext + python-anndata + python-ipython + python-matplotlib + python-nbsphinx + python-numba + python-numpy + python-numpydoc + python-omnipath + python-scanpy + python-scikit-learn + python-scipy + python-skranger + python-tqdm + python-typing-extensions)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/saezlab/decoupler-py") + (synopsis + "Framework for modeling, analyzing and interpreting single-cell RNA-seq data") + (description + "This package provides different statistical methods to extract +biological activities from omics data within a unified framework.") + (license license:gpl3+)))) + (define-public python-demuxem (package (name "python-demuxem") -- cgit v1.2.3 From 2df940ab273a79311e1a7275fb5d491c96b4115f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 6 Jun 2023 22:52:28 +0300 Subject: gnu: kirigami-addons: Update to 0.8.0. * gnu/packages/kde.scm (kirigami-addons): Update to 0.8.0. [source]: Download using git-fetch. --- gnu/packages/kde.scm | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index f9c0a260f03..28b4ce1ee09 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017, 2019, 2020, 2021 Efraim Flashner +;;; Copyright © 2016, 2017, 2019-2021, 2023 Efraim Flashner ;;; Copyright © 2016 David Craven ;;; Copyright © 2016, 2017 Thomas Danckaert ;;; Copyright © 2017, 2018 Mark Meyer @@ -516,15 +516,16 @@ the functionality of the KDE resource and network access abstractions.") (define-public kirigami-addons (package (name "kirigami-addons") - (version "0.3") + (version "0.8.0") (source (origin - (method url-fetch) - (uri (string-append - "https://invent.kde.org/libraries/kirigami-addons/-/archive/v" - version "/kirigami-addons-v" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/libraries/kirigami-addons") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1zr8dpc7bzw6g3y0jaxsr2lqlxqwlcphchpk8iah6g1f3n9fq73r")))) + "1bi6sc1fpycxj1ydd08gkbw1x1pi2ab6p9bk4175hm0mb0rykdir")))) (build-system qt-build-system) (arguments (list #:tests? #f)) ; failing test -- cgit v1.2.3 From 5b3931c2ae62571d856bb1a45470fe843132b9b4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 6 Jun 2023 23:32:24 +0300 Subject: gnu: sonnet: Add support for aspell dictionaries. * gnu/packages/kde-frameworks.scm (sonnet)[inputs]: Add aspell. --- gnu/packages/kde-frameworks.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 058f64187dd..1b802922a84 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -40,6 +40,7 @@ #:use-module (gnu packages acl) #:use-module (gnu packages admin) #:use-module (gnu packages aidc) + #:use-module (gnu packages aspell) #:use-module (gnu packages attr) #:use-module (gnu packages avahi) #:use-module (gnu packages base) @@ -1450,7 +1451,8 @@ system.") (native-inputs (list extra-cmake-modules pkg-config qttools-5)) (inputs - (list hunspell + (list aspell + hunspell ;; TODO: hspell (for Hebrew), Voikko (for Finish) qtdeclarative-5 qtbase-5)) -- cgit v1.2.3 From ec9f15b158300da3a77ce02cd2267222f435e80f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 6 Jun 2023 12:12:40 -0400 Subject: gnu: wxwidgets: Add libxtst to inputs. WxWidgets was already built with XTest support, but mostly by luck, via propagation of libxtst from GTK's propagated at-spi2-core package. Make it an explicit input. * gnu/packages/wxwidgets.scm (wxwidgets) [inputs]: Add libxtst. --- gnu/packages/wxwidgets.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/wxwidgets.scm b/gnu/packages/wxwidgets.scm index e6194e6f504..d0c323e30c8 100644 --- a/gnu/packages/wxwidgets.scm +++ b/gnu/packages/wxwidgets.scm @@ -112,6 +112,7 @@ libsecret libsm libtiff + libxtst ;for wxUIActionSimulator mesa pcre2 sdl2 -- cgit v1.2.3 From b775c39b2c9fb820c4832e079a4c6334e738100b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 6 Jun 2023 17:02:57 -0400 Subject: gnu: openconnect: Fix indentation, remove input labels and use gexps. * gnu/packages/vpn.scm (openconnect): Fix indentation. [native-inputs, inputs, propagated-inputs]: Remove input labels. [arguments]: Use gexps. --- gnu/packages/vpn.scm | 56 ++++++++++++++++++++++++---------------------------- 1 file changed, 26 insertions(+), 30 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index 500461fecf9..5c609576d2b 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -20,7 +20,7 @@ ;;; Copyright © 2021 jgart ;;; Copyright © 2022 Josselin Poiret ;;; Copyright © 2022 Lu hui -;;; Copyright © 2022 Maxim Cournoyer +;;; Copyright © 2022, 2023 Maxim Cournoyer ;;; Copyright © 2022 Jean-Pierre De Jesus DIAZ ;;; Copyright © 2022 Arun Isaac ;;; @@ -677,35 +677,31 @@ the user specifically asks to proxy, so the @dfn{VPN} interface no longer (define-public openconnect (package - (name "openconnect") - (version "9.01") - (source (origin - (method url-fetch) - (uri (string-append "ftp://ftp.infradead.org/pub/openconnect/" - "openconnect-" version ".tar.gz")) - (sha256 - (base32 "1iz4j00031a5ircrx30lkiwf58yl9kc827m4ssck4yg963wgmmxk")))) - (build-system gnu-build-system) - (propagated-inputs - (list libxml2 gnutls zlib)) - (inputs - (list lz4 vpnc-scripts)) - (native-inputs - `(("gettext" ,gettext-minimal) - ("pkg-config" ,pkg-config))) - (arguments - `(#:configure-flags - `(,(string-append "--with-vpnc-script=" - (assoc-ref %build-inputs "vpnc-scripts") - "/etc/vpnc/vpnc-script")))) - (synopsis "Client for Cisco VPN") - (description - "OpenConnect is a client for Cisco's AnyConnect SSL VPN, which is -supported by the ASA5500 Series, by IOS 12.4(9)T or later on Cisco SR500, -870, 880, 1800, 2800, 3800, 7200 Series and Cisco 7301 Routers, -and probably others.") - (license license:lgpl2.1) - (home-page "https://www.infradead.org/openconnect/"))) + (name "openconnect") + (version "9.01") + (source (origin + (method url-fetch) + (uri (string-append "ftp://ftp.infradead.org/pub/openconnect/" + "openconnect-" version ".tar.gz")) + (sha256 + (base32 "1iz4j00031a5ircrx30lkiwf58yl9kc827m4ssck4yg963wgmmxk")))) + (build-system gnu-build-system) + (arguments + (list #:configure-flags + #~(list (string-append "--with-vpnc-script=" + (search-input-file %build-inputs + "etc/vpnc/vpnc-script"))))) + (native-inputs (list gettext-minimal pkg-config)) + (inputs (list lz4 vpnc-scripts)) + (propagated-inputs (list libxml2 gnutls zlib)) + (synopsis "Client for Cisco VPN") + (description + "OpenConnect is a client for Cisco's AnyConnect SSL VPN, which is +supported by the ASA5500 Series, by IOS 12.4(9)T or later on Cisco SR500, 870, +880, 1800, 2800, 3800, 7200 Series and Cisco 7301 Routers, and probably +others.") + (license license:lgpl2.1) + (home-page "https://www.infradead.org/openconnect/"))) (define-public openconnect-sso (package -- cgit v1.2.3 From 8f90ab2dd4959fb1bb7f468365822839735fe182 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 6 Jun 2023 17:08:17 -0400 Subject: gnu: openconnect: Update to 9.12. * gnu/packages/vpn.scm (openconnect): Update to 9.12. --- gnu/packages/vpn.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index 5c609576d2b..af070526ec2 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -678,13 +678,13 @@ the user specifically asks to proxy, so the @dfn{VPN} interface no longer (define-public openconnect (package (name "openconnect") - (version "9.01") + (version "9.12") (source (origin (method url-fetch) (uri (string-append "ftp://ftp.infradead.org/pub/openconnect/" "openconnect-" version ".tar.gz")) (sha256 - (base32 "1iz4j00031a5ircrx30lkiwf58yl9kc827m4ssck4yg963wgmmxk")))) + (base32 "0gj1nba1pygvcjasqdakxxnx94dwx3l4hzj0dvipbzjdmbixrgm2")))) (build-system gnu-build-system) (arguments (list #:configure-flags -- cgit v1.2.3 From b3f7f5eb5358747d1aaa8565debe411e7c37d8bc Mon Sep 17 00:00:00 2001 From: Andy Tai Date: Tue, 23 May 2023 23:14:45 -0700 Subject: gnu: fltk: Update to 1.3.8. * gnu/packages/fltk.scm (fltk): Update to 1.3.8. Signed-off-by: Efraim Flashner --- gnu/packages/fltk.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/fltk.scm b/gnu/packages/fltk.scm index 5a1582b1bca..775ede060c4 100644 --- a/gnu/packages/fltk.scm +++ b/gnu/packages/fltk.scm @@ -43,7 +43,7 @@ (define-public fltk (package (name "fltk") - (version "1.3.6") + (version "1.3.8") (source (origin (method url-fetch) @@ -51,7 +51,7 @@ (first (string-split version #\-)) "/fltk-" version "-source.tar.gz")) (sha256 - (base32 "1arp1niiz3qxm8iacpmilwpc5rinsm6hsk4a6fsxfywvkvppbb4s")))) + (base32 "1gyisjwjbdsax4kbdm3hpijp2f0qgh1wk7wgad87l3pb0wmi1hgk")))) (build-system gnu-build-system) (native-inputs (list pkg-config)) -- cgit v1.2.3 From f8b1e50f30eb20b1ce19ba01f4ffd78ca3590d0f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 7 Jun 2023 08:47:05 +0300 Subject: gnu: fltk: Update source uri. * gnu/packages/fltk.scm (fltk)[source]: Update source URI to follow redirect. --- gnu/packages/fltk.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/fltk.scm b/gnu/packages/fltk.scm index 775ede060c4..4518a1e30ad 100644 --- a/gnu/packages/fltk.scm +++ b/gnu/packages/fltk.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2015, 2018 Ricardo Wurmus ;;; Copyright © 2016 Kei Kebreau ;;; Copyright © 2018 Mark H Weaver -;;; Copyright © 2018 Efraim Flashner +;;; Copyright © 2018, 2023 Efraim Flashner ;;; Copyright © 2021 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. @@ -47,7 +47,7 @@ (source (origin (method url-fetch) - (uri (string-append "http://fltk.org/pub/fltk/" + (uri (string-append "https://www.fltk.org/pub/fltk/" (first (string-split version #\-)) "/fltk-" version "-source.tar.gz")) (sha256 -- cgit v1.2.3 From a6e21911bf0dbc3c595d510729a012845d108aa9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 7 Jun 2023 09:30:52 +0300 Subject: gnu: hdf4: Add support for riscv64-linux. * gnu/packages/maths.scm (hdf4)[arguments]: Rename custom phase 'add-more-aarch64-support to 'add-more-architecture-support and add support for riscv64-linux. * gnu/packages/patches/hdf4-architectures.patch: Refresh from upstream. --- gnu/packages/maths.scm | 5 +- gnu/packages/patches/hdf4-architectures.patch | 75 +++++++++++++++++++++++---- 2 files changed, 66 insertions(+), 14 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 4e341244690..4df535f0cbb 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1314,13 +1314,12 @@ computations.") #:phases (modify-phases %standard-phases ;; This is inspired by two of Debian's patches. - (add-before 'configure 'add-more-aarch64-support + (add-before 'configure 'add-more-architecture-support (lambda _ (substitute* '("mfhdf/ncgen/ncgen.l" "mfhdf/ncgen/ncgenyy.c" "mfhdf/libsrc/netcdf.h.in") - (("AIX5L64") "__aarch64__")) - #t)) + (("AIX5L64") "__aarch64__ || ( __riscv && __riscv_xlen == 64)")))) (add-before 'configure 'patchbuild (lambda _ (substitute* diff --git a/gnu/packages/patches/hdf4-architectures.patch b/gnu/packages/patches/hdf4-architectures.patch index 5549f11277f..aa71d5a383a 100644 --- a/gnu/packages/patches/hdf4-architectures.patch +++ b/gnu/packages/patches/hdf4-architectures.patch @@ -21,7 +21,7 @@ Author: Francesco Paolo Lovergine #define DFMT_PC 0x4441 #define DFMT_APPLE 0x1111 #define DFMT_APPLE_INTEL 0x4441 -@@ -75,6 +77,12 @@ +@@ -75,6 +77,13 @@ #define DFMT_IA64 0x4441 #define DFMT_LINUX64 0x4441 #define DFMT_POWERPC64 0x1111 @@ -29,12 +29,13 @@ Author: Francesco Paolo Lovergine +#define DFMT_ARMV4L 0x4441 +#define DFMT_AARCH64 0x4441 +#define DFMT_X86_64 0x4441 -+#define DFMT_SH 0x4441 -+#define DFMT_SHEB 0x1111 ++#define DFMT_SH 0x4441 ++#define DFMT_SHEB 0x1111 ++#define DFMT_RISCV64 0x4441 /* I/O library constants */ #define UNIXUNBUFIO 1 -@@ -288,7 +296,7 @@ typedef int hdf_pint_t; +@@ -288,7 +297,7 @@ typedef int hdf_pint_t; #endif /* IBM6000 */ @@ -43,7 +44,7 @@ Author: Francesco Paolo Lovergine #ifndef HP9000 #define HP9000 -@@ -347,6 +355,10 @@ typedef int hdf_pint_t; +@@ -347,6 +356,10 @@ typedef int hdf_pint_t; /* what each does */ #define JMEMSYS MEM_ANSI @@ -54,7 +55,7 @@ Author: Francesco Paolo Lovergine #endif /* HP9000 */ -@@ -666,6 +678,410 @@ typedef int hdf_pint_t; +@@ -670,6 +683,462 @@ typedef int hdf_pint_t; #endif /* !(defined(__APPLE__)) */ /*-----------------------------------------------------*/ @@ -461,11 +462,63 @@ Author: Francesco Paolo Lovergine +#define INCLUDES_ARE_ANSI + +#endif /* Linux/aarch64 */ ++ ++#if defined (__linux__) && defined (__riscv) && (__riscv_xlen == 64) ++ ++#ifdef GOT_MACHINE ++If you get an error on this line more than one machine type has been defined. ++Please check your Makefile. ++#endif ++#define GOT_MACHINE 1 ++ ++#include ++#include /* for unbuffered file I/O */ ++#include ++#include ++#include /* for character macros */ ++ ++#define DF_MT DFMT_RISCV64 ++ ++typedef void VOID; ++typedef void * VOIDP; ++typedef char * _fcd; ++typedef char char8; ++typedef unsigned char uchar8; ++typedef signed char int8; ++typedef unsigned char uint8; ++typedef short int int16; ++typedef unsigned short int uint16; ++typedef int int32; ++typedef unsigned int uint32; ++typedef int intn; ++typedef unsigned int uintn; ++typedef float float32; ++typedef double float64; ++typedef int intf; /* size of INTEGERs in Fortran compiler */ ++typedef long hdf_pint_t; /* an integer the same size as a pointer */ ++#define FNAME_POST_UNDERSCORE ++#define _fcdtocp(desc) (desc) ++#define FILELIB UNIXBUFIO ++ ++#ifndef BIG_LONGS ++#define BIG_LONGS ++#endif ++ ++/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ ++ ++/* Determine the memory manager we are going to use. Valid values are: */ ++/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ ++/* what each does */ ++#define JMEMSYS MEM_ANSI ++#define HAVE_STDC ++#define INCLUDES_ARE_ANSI ++ ++#endif /* Linux/riscv64 */ + #if defined(NEXT) || defined(NeXT) #ifndef NEXT -@@ -928,7 +1344,11 @@ Please check your Makefile. +@@ -932,7 +1401,11 @@ Please check your Makefile. #include /* for unbuffered i/o stuff */ #include @@ -478,7 +531,7 @@ Author: Francesco Paolo Lovergine typedef void VOID; typedef void *VOIDP; typedef char *_fcd; -@@ -952,6 +1372,11 @@ typedef long hdf_pint_t; +@@ -956,6 +1429,11 @@ typedef long hdf_pint_t; #define _fcdtocp(desc) (desc) #define FILELIB UNIXBUFIO @@ -490,7 +543,7 @@ Author: Francesco Paolo Lovergine /* JPEG #define's - Look in the JPEG docs before changing - (Q) */ /* Determine the memory manager we are going to use. Valid values are: */ -@@ -1097,6 +1522,8 @@ typedef long hdf_pint_t; +@@ -1101,6 +1579,8 @@ typedef long hdf_pint_t; #define _fcdtocp(desc) (desc) #define FILELIB UNIXBUFIO @@ -499,7 +552,7 @@ Author: Francesco Paolo Lovergine /* JPEG #define's - Look in the JPEG docs before changing - (Q) */ /* Determine the memory manager we are going to use. Valid values are: */ -@@ -1111,6 +1538,66 @@ typedef long hdf_pint_t; +@@ -1115,6 +1595,66 @@ typedef long hdf_pint_t; #endif /* IA64 */ @@ -573,7 +626,7 @@ Author: Francesco Paolo Lovergine /*****************************************************************************/ /* Generally Big-Endian machines */ -#if !defined(INTEL86) && !defined(MIPSEL) && !defined(DEC_ALPHA) && !defined(I860) && !defined(SUN386) && !(defined(__ia64) && !(defined(hpux) || defined(__hpux))) && !defined(__x86_64__) -+#if !defined(INTEL86) && !defined(MIPSEL) && !defined(DEC_ALPHA) && !defined(I860) && !defined(SUN386) && !(defined(__ia64) && !(defined(hpux) || defined(__hpux))) && !defined(__x86_64__) && !(defined(__powerpc__) && defined(__LITTLE_ENDIAN__)) && !defined(__aarch64__) && !defined(__ARM_EABI__) ++#if !defined(INTEL86) && !defined(MIPSEL) && !defined(DEC_ALPHA) && !defined(I860) && !defined(SUN386) && !(defined(__ia64) && !(defined(hpux) || defined(__hpux))) && !defined(__x86_64__) && !(defined(__powerpc__) && defined(__LITTLE_ENDIAN__)) && !defined(__aarch64__) && !defined(__ARM_EABI__) && !defined(__riscv) # define UI8_IN DFKnb1b /* Unsigned Integer, 8 bits */ # define UI8_OUT DFKnb1b # define SI16_IN DFKnb2b /* S = Signed */ -- cgit v1.2.3 From 269fa79398a402ac6344be3b44b4f55a97711e20 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Wed, 10 May 2023 23:12:31 +0100 Subject: gnu: python-can: Update to 4.2.0. * gnu/packages/python-xyz.scm (python-can): Update to 4.2.0. Signed-off-by: Efraim Flashner --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 64139065308..ab2e8b75762 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2688,14 +2688,14 @@ class.") (define-public python-can (package (name "python-can") - (version "4.0.0") + (version "4.2.0") (source (origin (method url-fetch) (uri (pypi-uri "python-can" version)) (sha256 (base32 - "0pcbdgdw94lc2sxd56w6wdsshrs9dd5d3wp0x4sfd0drzx32inar")))) + "1w5sdzxivpd3pw4pypwnjlksvfimdb93qnlddbrh5f13flhsgg8g")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases -- cgit v1.2.3 From 15083a2fc37f4c1b1535281d0f82665e55ebbb72 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Wed, 10 May 2023 23:12:32 +0100 Subject: gnu: python-can: Simplify package style. * gnu/package/python-xyz.scm (python-can): Simplify package style. [build-system]: Use pyproject-build-system. [argument]: Use Gexp. Remove redundant modify-phases procedure. Add {test-flags}. Signed-off-by: Efraim Flashner --- gnu/packages/python-xyz.scm | 44 ++++++++++++++------------------------------ 1 file changed, 14 insertions(+), 30 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ab2e8b75762..c158d9a407f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2696,40 +2696,24 @@ class.") (sha256 (base32 "1w5sdzxivpd3pw4pypwnjlksvfimdb93qnlddbrh5f13flhsgg8g")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'relax-version-requirements - (lambda _ - (substitute* "setup.py" - (("mock~=2\\.0") "mock") - (("coverage<5") "coverage") - (("pytest~=4\\.6") "pytest") - (("pytest-timeout~=1\\.3") "pytest-timeout") - (("pytest-cov.*") "pytest-cov\n") - (("hypothesis~=4\\.56") "hypothesis")))) - (add-after 'unpack 'fix-broken-tests - ;; The tests try to run two scripts it expects should be - ;; in PATH, but they aren't at this time (see: - ;; https://github.com/hardbyte/python-can/issues/805). - (lambda _ - (substitute* "test/test_scripts.py" - (("\"can_logger\\.py --help\"") "") - (("\"can_player\\.py --help\"") "")))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-vv" "test" - ;; Disable tests which require specific CAN - ;; drivers we have no package for in Guix. - "--ignore" "test/test_interface_canalystii.py" - ;; These tests fail with "OSError: [Errno 19] - ;; No such device". - "-k" "not BasicTestUdpMulticastBusIPv"))))))) + (list + #:test-flags + #~(list + ;; TODO: Check if it could be packed: + ;; https://github.com/projectgus/python-canalystii + ;; + ;; Disable tests which require specific CAN drivers we have no + ;; package for in Guix. + "--ignore" "test/test_interface_canalystii.py" + ;; These tests fail with "OSError: [Errno 19] No such device". + "-k" "not BasicTestUdpMulticastBusIPv"))) (propagated-inputs (list python-msgpack python-typing-extensions python-wrapt)) (native-inputs - (list python-codecov + (list ;; python-canalystii ; Not packed yet + python-codecov python-coverage python-future python-hypothesis -- cgit v1.2.3 From 25fdd2e3af12fad0625f16d72d164f3ea84cd06a Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Wed, 10 May 2023 23:12:33 +0100 Subject: gnu: Delete duplicated use-module from (gnu package python-xyz). * gnu/packages/python-xyz.scm: Delete duplicated (gnu packages serialization). Signed-off-by: Efraim Flashner --- gnu/packages/python-xyz.scm | 1 - 1 file changed, 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c158d9a407f..7c15429fa40 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -260,7 +260,6 @@ #:use-module (gnu packages xdisorg) #:use-module (gnu packages tcl) #:use-module (gnu packages bdw-gc) - #:use-module (gnu packages serialization) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) -- cgit v1.2.3 From 4a5bbd293f57e1a6d52953745b1c8d35905fda50 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Wed, 10 May 2023 23:12:34 +0100 Subject: gnu: Sort use-module alphabetically in (gnu packages python-xyz). * gnu/packages/python-xyz.scm: Sort use-module alphabetically to ease maintenance. Signed-off-by: Efraim Flashner --- gnu/packages/python-xyz.scm | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 7c15429fa40..f528da3962c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -156,12 +156,14 @@ (define-module (gnu packages python-xyz) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) - #:use-module (gnu packages algebra) #:use-module (gnu packages adns) #:use-module (gnu packages aidc) + #:use-module (gnu packages algebra) #:use-module (gnu packages attr) #:use-module (gnu packages backup) + #:use-module (gnu packages base) #:use-module (gnu packages bash) + #:use-module (gnu packages bdw-gc) #:use-module (gnu packages check) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) @@ -177,28 +179,28 @@ #:use-module (gnu packages documentation) #:use-module (gnu packages enchant) #:use-module (gnu packages file) - #:use-module (gnu packages fontutils) #:use-module (gnu packages fonts) + #:use-module (gnu packages fontutils) #:use-module (gnu packages freedesktop) - #:use-module (gnu packages gdb) #:use-module (gnu packages gcc) + #:use-module (gnu packages gdb) #:use-module (gnu packages geo) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) #:use-module (gnu packages gnupg) - #:use-module (gnu packages graphviz) #:use-module (gnu packages graphics) + #:use-module (gnu packages graphviz) #:use-module (gnu packages gsasl) #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages icu4c) - #:use-module (gnu packages inkscape) #:use-module (gnu packages image) #:use-module (gnu packages image-processing) #:use-module (gnu packages imagemagick) + #:use-module (gnu packages inkscape) #:use-module (gnu packages java) #:use-module (gnu packages jupyter) #:use-module (gnu packages kerberos) @@ -214,10 +216,10 @@ #:use-module (gnu packages maths) #:use-module (gnu packages monitoring) #:use-module (gnu packages multiprecision) - #:use-module (gnu packages networking) #:use-module (gnu packages ncurses) - #:use-module (gnu packages node) + #:use-module (gnu packages networking) #:use-module (gnu packages ninja) + #:use-module (gnu packages node) #:use-module (gnu packages openstack) #:use-module (gnu packages pcre) #:use-module (gnu packages pdf) @@ -236,14 +238,15 @@ #:use-module (gnu packages rdf) #:use-module (gnu packages readline) #:use-module (gnu packages regex) - #:use-module (gnu packages sdl) #:use-module (gnu packages scanner) + #:use-module (gnu packages sdl) #:use-module (gnu packages search) #:use-module (gnu packages serialization) #:use-module (gnu packages shells) #:use-module (gnu packages sphinx) #:use-module (gnu packages ssh) #:use-module (gnu packages swig) + #:use-module (gnu packages tcl) #:use-module (gnu packages terminals) #:use-module (gnu packages tex) #:use-module (gnu packages texinfo) @@ -254,23 +257,20 @@ #:use-module (gnu packages video) #:use-module (gnu packages web) #:use-module (gnu packages wxwidgets) - #:use-module (gnu packages base) #:use-module (gnu packages xml) - #:use-module (gnu packages xorg) #:use-module (gnu packages xdisorg) - #:use-module (gnu packages tcl) - #:use-module (gnu packages bdw-gc) + #:use-module (gnu packages xorg) #:use-module (guix packages) - #:use-module (guix download) - #:use-module (guix git-download) - #:use-module (guix hg-download) - #:use-module (guix gexp) - #:use-module (guix utils) - #:use-module (guix build-system gnu) #:use-module (guix build-system cargo) #:use-module (guix build-system cmake) + #:use-module (guix build-system gnu) #:use-module (guix build-system pyproject) #:use-module (guix build-system python) + #:use-module (guix download) + #:use-module (guix hg-download) + #:use-module (guix git-download) + #:use-module (guix gexp) + #:use-module (guix utils) #:use-module (srfi srfi-1) #:use-module (srfi srfi-26)) -- cgit v1.2.3 From 2a6d2fc1d8e3434e283d6d2e559529b41a242fea Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 7 Jun 2023 09:55:35 +0300 Subject: gnu: sbcl: fix build on riscv64-linux. * gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch: New file. * gnu/local.mk(dist_patch_DATA): register it. * gnu/packages/lisp.scm (sbcl): [source]: Use it here. --- gnu/local.mk | 1 + gnu/packages/lisp.scm | 3 + .../sbcl-riscv-Make-contribs-build-again.patch | 71 ++++++++++++++++++++++ 3 files changed, 75 insertions(+) create mode 100644 gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index f9afb433e6b..254037a3aff 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1895,6 +1895,7 @@ dist_patch_DATA = \ %D%/packages/patches/sbcl-clml-fix-types.patch \ %D%/packages/patches/sbcl-eazy-gnuplot-skip-path-check.patch \ %D%/packages/patches/sbcl-png-fix-sbcl-compatibility.patch \ + %D%/packages/patches/sbcl-riscv-Make-contribs-build-again.patch \ %D%/packages/patches/scalapack-gcc-10-compilation.patch \ %D%/packages/patches/scheme48-tests.patch \ %D%/packages/patches/scons-test-environment.patch \ diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index 9e896cc8a5b..296ed6b5f24 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -23,6 +23,7 @@ ;;; Copyright © 2022 Joeke de Graaf ;;; Copyright © 2021, 2022 jgart ;;; Copyright © 2022 ( +;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -440,6 +441,8 @@ an interpreter, a compiler, a debugger, and much more.") (sha256 (base32 "11ji5n65l31249r0v7hm0wc0yk2ila0y746nj36xn1cxrwh0gjc9")) (modules '((guix build utils))) + ;; backport from upstream. + (patches (search-patches "sbcl-riscv-Make-contribs-build-again.patch")) (snippet '(begin ;; Don't force ARMv5. diff --git a/gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch b/gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch new file mode 100644 index 00000000000..85b96e1b20f --- /dev/null +++ b/gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch @@ -0,0 +1,71 @@ +From 8704f528f227f587d0e06dfd2f807aeca7a69a71 Mon Sep 17 00:00:00 2001 +From: Charles Zhang +Date: Thu, 1 Jun 2023 16:39:26 +0200 +Subject: [PATCH] riscv: Make contribs build again. + +The issue was that the LINKAGE_TEMP_REG being NL3 was a C argument +register, so of course that caused clashing on C call-out, causing +problems with run-program. Going back to NL7 didn't work either +because it wasn't getting saved before entry into the trampoline. The +code here used to have NL7 before the trampoline code was gutted and +then restored, so I'm wondering how this ever worked before, because +it definitely did. Pick LIP as the TEMP_REG now because not only does +it get saved, it's also the least likely thing to get disturbed by +clobbering. + +Fixes #lp2002930. + +Also remove assembly routine printing because it doesn't need to be +part of the build script (unlike the other files in output/ which +can't trivially be recovered from a built image), and because not all +disassembler printers have been written on riscv yet. +--- + NEWS | 3 +++ + make-target-2-load.lisp | 4 ---- + src/runtime/riscv-arch.c | 2 +- + 3 files changed, 4 insertions(+), 5 deletions(-) + +diff --git a/NEWS b/NEWS +index 17537ff92..5c0f7777b 100644 +--- a/NEWS ++++ b/NEWS +@@ -1,5 +1,8 @@ + ;;;; -*- coding: utf-8; fill-column: 78 -*- + ++changes relative to sbcl-2.3.5: ++ * bug fix: riscv can build contribs again. ++ + changes in sbcl-2.3.5 relative to sbcl-2.3.4: + * enhancement: Unicode support has been updated to support version 15.0.0 of + the Unicode standard, including addition of characters and their collation +diff --git a/make-target-2-load.lisp b/make-target-2-load.lisp +index 885ebda74..b9a1a1e36 100644 +--- a/make-target-2-load.lisp ++++ b/make-target-2-load.lisp +@@ -6,10 +6,6 @@ + (defvar *compile-files-p* nil) + (load (merge-pathnames "src/cold/warm.lisp" *load-pathname*)) + +-(with-open-file (stream "output/asm-routines.txt" :direction :output +- :if-does-not-exist :create :if-exists :supersede) +- (sb-c:dis sb-fasl:*assembler-routines* stream)) +- + ;; sb-xref-for-internals is actively harmful to tree-shaking. + ;; Remove some symbols to make the hide-packages test pass. + #+sb-xref-for-internals +diff --git a/src/runtime/riscv-arch.c b/src/runtime/riscv-arch.c +index 6c1994829..062623899 100644 +--- a/src/runtime/riscv-arch.c ++++ b/src/runtime/riscv-arch.c +@@ -159,7 +159,7 @@ arch_install_interrupt_handlers(void) + * Linkage entry size is 8 or 20, because we need 2 instructions for the 32-bit case and we need 3 instructions and an 8 byte address in the 64-bit case. + */ + +-#define LINKAGE_TEMP_REG reg_NL3 ++#define LINKAGE_TEMP_REG reg_LIP // Lisp needs to save before entry. + + void arch_write_linkage_table_entry(int index, void *target_addr, int datap) + { +-- +2.40.1 + -- cgit v1.2.3 From df18bc89005da0a7cbf721e3b3a1024440475d30 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 7 Jun 2023 12:56:33 +0300 Subject: Revert "gnu: sbcl: fix build on riscv64-linux." This reverts commit 2a6d2fc1d8e3434e283d6d2e559529b41a242fea. --- gnu/local.mk | 1 - gnu/packages/lisp.scm | 3 - .../sbcl-riscv-Make-contribs-build-again.patch | 71 ---------------------- 3 files changed, 75 deletions(-) delete mode 100644 gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 254037a3aff..f9afb433e6b 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1895,7 +1895,6 @@ dist_patch_DATA = \ %D%/packages/patches/sbcl-clml-fix-types.patch \ %D%/packages/patches/sbcl-eazy-gnuplot-skip-path-check.patch \ %D%/packages/patches/sbcl-png-fix-sbcl-compatibility.patch \ - %D%/packages/patches/sbcl-riscv-Make-contribs-build-again.patch \ %D%/packages/patches/scalapack-gcc-10-compilation.patch \ %D%/packages/patches/scheme48-tests.patch \ %D%/packages/patches/scons-test-environment.patch \ diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index 296ed6b5f24..9e896cc8a5b 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -23,7 +23,6 @@ ;;; Copyright © 2022 Joeke de Graaf ;;; Copyright © 2021, 2022 jgart ;;; Copyright © 2022 ( -;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -441,8 +440,6 @@ an interpreter, a compiler, a debugger, and much more.") (sha256 (base32 "11ji5n65l31249r0v7hm0wc0yk2ila0y746nj36xn1cxrwh0gjc9")) (modules '((guix build utils))) - ;; backport from upstream. - (patches (search-patches "sbcl-riscv-Make-contribs-build-again.patch")) (snippet '(begin ;; Don't force ARMv5. diff --git a/gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch b/gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch deleted file mode 100644 index 85b96e1b20f..00000000000 --- a/gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch +++ /dev/null @@ -1,71 +0,0 @@ -From 8704f528f227f587d0e06dfd2f807aeca7a69a71 Mon Sep 17 00:00:00 2001 -From: Charles Zhang -Date: Thu, 1 Jun 2023 16:39:26 +0200 -Subject: [PATCH] riscv: Make contribs build again. - -The issue was that the LINKAGE_TEMP_REG being NL3 was a C argument -register, so of course that caused clashing on C call-out, causing -problems with run-program. Going back to NL7 didn't work either -because it wasn't getting saved before entry into the trampoline. The -code here used to have NL7 before the trampoline code was gutted and -then restored, so I'm wondering how this ever worked before, because -it definitely did. Pick LIP as the TEMP_REG now because not only does -it get saved, it's also the least likely thing to get disturbed by -clobbering. - -Fixes #lp2002930. - -Also remove assembly routine printing because it doesn't need to be -part of the build script (unlike the other files in output/ which -can't trivially be recovered from a built image), and because not all -disassembler printers have been written on riscv yet. ---- - NEWS | 3 +++ - make-target-2-load.lisp | 4 ---- - src/runtime/riscv-arch.c | 2 +- - 3 files changed, 4 insertions(+), 5 deletions(-) - -diff --git a/NEWS b/NEWS -index 17537ff92..5c0f7777b 100644 ---- a/NEWS -+++ b/NEWS -@@ -1,5 +1,8 @@ - ;;;; -*- coding: utf-8; fill-column: 78 -*- - -+changes relative to sbcl-2.3.5: -+ * bug fix: riscv can build contribs again. -+ - changes in sbcl-2.3.5 relative to sbcl-2.3.4: - * enhancement: Unicode support has been updated to support version 15.0.0 of - the Unicode standard, including addition of characters and their collation -diff --git a/make-target-2-load.lisp b/make-target-2-load.lisp -index 885ebda74..b9a1a1e36 100644 ---- a/make-target-2-load.lisp -+++ b/make-target-2-load.lisp -@@ -6,10 +6,6 @@ - (defvar *compile-files-p* nil) - (load (merge-pathnames "src/cold/warm.lisp" *load-pathname*)) - --(with-open-file (stream "output/asm-routines.txt" :direction :output -- :if-does-not-exist :create :if-exists :supersede) -- (sb-c:dis sb-fasl:*assembler-routines* stream)) -- - ;; sb-xref-for-internals is actively harmful to tree-shaking. - ;; Remove some symbols to make the hide-packages test pass. - #+sb-xref-for-internals -diff --git a/src/runtime/riscv-arch.c b/src/runtime/riscv-arch.c -index 6c1994829..062623899 100644 ---- a/src/runtime/riscv-arch.c -+++ b/src/runtime/riscv-arch.c -@@ -159,7 +159,7 @@ arch_install_interrupt_handlers(void) - * Linkage entry size is 8 or 20, because we need 2 instructions for the 32-bit case and we need 3 instructions and an 8 byte address in the 64-bit case. - */ - --#define LINKAGE_TEMP_REG reg_NL3 -+#define LINKAGE_TEMP_REG reg_LIP // Lisp needs to save before entry. - - void arch_write_linkage_table_entry(int index, void *target_addr, int datap) - { --- -2.40.1 - -- cgit v1.2.3 From 8504fad80cd4046c33068b89665d16aa697b12a1 Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Wed, 7 Jun 2023 09:55:35 +0300 Subject: gnu: sbcl: fix build on riscv64-linux. * gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch: New file. * gnu/local.mk(dist_patch_DATA): register it. * gnu/packages/lisp.scm (sbcl): [source]: Use it here. --- gnu/local.mk | 1 + gnu/packages/lisp.scm | 3 + .../sbcl-riscv-Make-contribs-build-again.patch | 71 ++++++++++++++++++++++ 3 files changed, 75 insertions(+) create mode 100644 gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index f9afb433e6b..254037a3aff 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1895,6 +1895,7 @@ dist_patch_DATA = \ %D%/packages/patches/sbcl-clml-fix-types.patch \ %D%/packages/patches/sbcl-eazy-gnuplot-skip-path-check.patch \ %D%/packages/patches/sbcl-png-fix-sbcl-compatibility.patch \ + %D%/packages/patches/sbcl-riscv-Make-contribs-build-again.patch \ %D%/packages/patches/scalapack-gcc-10-compilation.patch \ %D%/packages/patches/scheme48-tests.patch \ %D%/packages/patches/scons-test-environment.patch \ diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index 9e896cc8a5b..296ed6b5f24 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -23,6 +23,7 @@ ;;; Copyright © 2022 Joeke de Graaf ;;; Copyright © 2021, 2022 jgart ;;; Copyright © 2022 ( +;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -440,6 +441,8 @@ an interpreter, a compiler, a debugger, and much more.") (sha256 (base32 "11ji5n65l31249r0v7hm0wc0yk2ila0y746nj36xn1cxrwh0gjc9")) (modules '((guix build utils))) + ;; backport from upstream. + (patches (search-patches "sbcl-riscv-Make-contribs-build-again.patch")) (snippet '(begin ;; Don't force ARMv5. diff --git a/gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch b/gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch new file mode 100644 index 00000000000..85b96e1b20f --- /dev/null +++ b/gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch @@ -0,0 +1,71 @@ +From 8704f528f227f587d0e06dfd2f807aeca7a69a71 Mon Sep 17 00:00:00 2001 +From: Charles Zhang +Date: Thu, 1 Jun 2023 16:39:26 +0200 +Subject: [PATCH] riscv: Make contribs build again. + +The issue was that the LINKAGE_TEMP_REG being NL3 was a C argument +register, so of course that caused clashing on C call-out, causing +problems with run-program. Going back to NL7 didn't work either +because it wasn't getting saved before entry into the trampoline. The +code here used to have NL7 before the trampoline code was gutted and +then restored, so I'm wondering how this ever worked before, because +it definitely did. Pick LIP as the TEMP_REG now because not only does +it get saved, it's also the least likely thing to get disturbed by +clobbering. + +Fixes #lp2002930. + +Also remove assembly routine printing because it doesn't need to be +part of the build script (unlike the other files in output/ which +can't trivially be recovered from a built image), and because not all +disassembler printers have been written on riscv yet. +--- + NEWS | 3 +++ + make-target-2-load.lisp | 4 ---- + src/runtime/riscv-arch.c | 2 +- + 3 files changed, 4 insertions(+), 5 deletions(-) + +diff --git a/NEWS b/NEWS +index 17537ff92..5c0f7777b 100644 +--- a/NEWS ++++ b/NEWS +@@ -1,5 +1,8 @@ + ;;;; -*- coding: utf-8; fill-column: 78 -*- + ++changes relative to sbcl-2.3.5: ++ * bug fix: riscv can build contribs again. ++ + changes in sbcl-2.3.5 relative to sbcl-2.3.4: + * enhancement: Unicode support has been updated to support version 15.0.0 of + the Unicode standard, including addition of characters and their collation +diff --git a/make-target-2-load.lisp b/make-target-2-load.lisp +index 885ebda74..b9a1a1e36 100644 +--- a/make-target-2-load.lisp ++++ b/make-target-2-load.lisp +@@ -6,10 +6,6 @@ + (defvar *compile-files-p* nil) + (load (merge-pathnames "src/cold/warm.lisp" *load-pathname*)) + +-(with-open-file (stream "output/asm-routines.txt" :direction :output +- :if-does-not-exist :create :if-exists :supersede) +- (sb-c:dis sb-fasl:*assembler-routines* stream)) +- + ;; sb-xref-for-internals is actively harmful to tree-shaking. + ;; Remove some symbols to make the hide-packages test pass. + #+sb-xref-for-internals +diff --git a/src/runtime/riscv-arch.c b/src/runtime/riscv-arch.c +index 6c1994829..062623899 100644 +--- a/src/runtime/riscv-arch.c ++++ b/src/runtime/riscv-arch.c +@@ -159,7 +159,7 @@ arch_install_interrupt_handlers(void) + * Linkage entry size is 8 or 20, because we need 2 instructions for the 32-bit case and we need 3 instructions and an 8 byte address in the 64-bit case. + */ + +-#define LINKAGE_TEMP_REG reg_NL3 ++#define LINKAGE_TEMP_REG reg_LIP // Lisp needs to save before entry. + + void arch_write_linkage_table_entry(int index, void *target_addr, int datap) + { +-- +2.40.1 + -- cgit v1.2.3 From 433ca5a5c5657d63cd932b5ea10147b4374489ed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Jun 2023 10:26:51 +0200 Subject: gnu: Add python-clickhouse-connect. * gnu/packages/python-xyz.scm (python-clickhouse-connect): New variable. --- gnu/packages/python-xyz.scm | 52 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f528da3962c..894c78296d8 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4397,6 +4397,58 @@ with sensible defaults out of the box.") clickgen is using @code{anicursorgen} and @code{xcursorgen} under the hood.") (license license:expat))) +(define-public python-clickhouse-connect + (package + (name "python-clickhouse-connect") + (version "0.6.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ClickHouse/clickhouse-connect") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1s0lk7xdq8f351cmpbp6jidqi5zdazrdba7w7fxph0w8sd74amry")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; All these tests require docker-compose + '(list "--ignore-glob=tests/integration_tests/*") + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'patch-pyproject + (lambda _ + ;; Our version of pytest is confused by this field. + (substitute* "pyproject.toml" + (("^env_files.*") "")))) + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace")))))) + (propagated-inputs + (list python-arrow + python-certifi + python-lz4 + python-numpy + python-orjson + python-pandas + python-pytz + python-sqlalchemy + python-urllib3 + python-zstandard)) + (native-inputs + (list python-cython + python-pytest)) + (home-page "https://github.com/ClickHouse/clickhouse-connect") + (synopsis + "ClickHouse database core driver for Python, Pandas, and Superset") + (description + "This package provides a high performance core database driver for +connecting ClickHouse to Python, Pandas, and Superset.") + (license license:asl2.0))) + (define-public python-cligj (package (name "python-cligj") -- cgit v1.2.3 From f57acde70b0b91920adf9348447a68845db57228 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Jun 2023 14:27:39 +0200 Subject: gnu: python-flit: Update to 3.8.0. * gnu/packages/python-xyz.scm (python-flit): Update to 3.8.0. [build-system]: Use pyproject-build-system. [arguments]: Run tests, but disable those that need networking; remove custom 'build phase; remove custom 'install phase; replace custom 'check phase with new 'pre-check phase. --- gnu/packages/python-xyz.scm | 25 +++++++++++-------------- 1 file changed, 11 insertions(+), 14 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 894c78296d8..f2a794367f8 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -26681,32 +26681,29 @@ the syntactic logic to configure and launch jobs in an execution environment.") (define-public python-flit (package (name "python-flit") - (version "3.5.1") + (version "3.8.0") ;same as python-flit-core (source (origin (method url-fetch) (uri (pypi-uri "flit" version)) (sha256 - (base32 "04152qj46sqbnlrj7ch9p7svjrrlpzbk0qr39g2yr0s4f5vp6frf")))) - (build-system python-build-system) + (base32 "0dz9sp2zlhkmk6sm5gapbbb30f7xq3n3jn5zxx5pkp25ppsaiwnh")))) + (build-system pyproject-build-system) (arguments (list + #:test-flags + ;; These tests fail when FLIT_NO_NETWORK is set + '(list "-k" "not test_invalid_classifier \ +and not test_install_requires \ +and not test_install_requires_extra \ +and not test_validate_classifiers_private") #:phases #~(modify-phases %standard-phases - ;; XXX: PEP 517 manual build copied from python-isort. - (replace 'build - (lambda _ - (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) - (replace 'check + (add-before 'check 'pre-check (lambda* (#:key tests? inputs outputs #:allow-other-keys) (when tests? (setenv "HOME" "/tmp") - (setenv "FLIT_NO_NETWORK" "1")))) - (replace 'install - (lambda _ - (let ((whl (car (find-files "dist" "\\.whl$")))) - (invoke "pip" "--no-cache-dir" "--no-input" - "install" "--no-deps" "--prefix" #$output whl))))))) + (setenv "FLIT_NO_NETWORK" "1"))))))) (propagated-inputs (list python-pypa-build python-tomli-w -- cgit v1.2.3 From 21696dce059bcb43407e14a1bb162048d821cc11 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Wed, 7 Jun 2023 14:49:13 +0200 Subject: gnu: sbcl-cl-webkit: Update to 3.5.9. * gnu/packages/lisp-xyz.scm (sbcl-cl-webkit): Update to 3.5.9. --- gnu/packages/lisp-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 8031ef53657..16deb85e5e2 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -4978,7 +4978,7 @@ is a library for creating graphical user interfaces.") (define-public sbcl-cl-webkit (package (name "sbcl-cl-webkit") - (version "3.5.7") + (version "3.5.9") (source (origin (method git-fetch) @@ -4988,7 +4988,7 @@ is a library for creating graphical user interfaces.") (file-name (git-file-name "cl-webkit" version)) (sha256 (base32 - "0aqkqcs0n5wkgjx3lb513fvm7f2jw3d5daisc9mw1bmbbcqh2sba")))) + "00h61p5mrvvbycp703isy0wvgqlfb7k0cidw4vg75y7s29m3k6k0")))) (build-system asdf-build-system/sbcl) (inputs `(("cffi" ,sbcl-cffi) -- cgit v1.2.3 From e8f9fb3e03ea8fee0e13f13706a6b16414f74a7b Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Wed, 7 Jun 2023 15:00:10 +0200 Subject: gnu: conky: Update to 1.19.2. * gnu/packages/conky.scm (conky): Update to 1.19.2. --- gnu/packages/conky.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/conky.scm b/gnu/packages/conky.scm index 9843cbe3c0e..afc6374554c 100644 --- a/gnu/packages/conky.scm +++ b/gnu/packages/conky.scm @@ -40,7 +40,7 @@ (package (name "conky") (home-page "https://github.com/brndnmtthws/conky") - (version "1.12.2") + (version "1.19.2") (source (origin (method git-fetch) @@ -49,7 +49,7 @@ (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1grxapl4q37fzk2rsijwz2rrl0aj520y8daki6bg48jb9vjd39n7")))) + (base32 "196wqr477fch1152cqmf11ckwrgkk2wmhl56ms6jk19hfs83d980")))) (build-system cmake-build-system) (arguments `(#:configure-flags -- cgit v1.2.3 From b9eb74d6559deaa83b8bf32d778fe623f76f78f1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Jun 2023 20:16:07 +0200 Subject: gnu: python-pyarrow: Include dataset support. * gnu/packages/databases.scm (python-pyarrow)[arguments]: Remove obsolete build phase 'make-git-checkout-writable; rename phase 'set-PYARROW_WITH_PARQUET to 'set-pyarrow-build-options and also enable building of dataset extension. --- gnu/packages/databases.scm | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 43f5f9c0727..74483d27f78 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -4677,13 +4677,11 @@ algorithm implementations.") (delete 'build) ; XXX the build is performed again during the install phase (add-after 'unpack 'enter-source-directory (lambda _ (chdir "python"))) - (add-after 'unpack 'make-git-checkout-writable - (lambda _ - (for-each make-file-writable (find-files ".")))) - (add-before 'install 'set-PYARROW_WITH_PARQUET + (add-before 'install 'set-pyarrow-build-options (lambda _ (setenv "PYARROW_BUNDLE_ARROW_CPP_HEADERS" "0") - (setenv "PYARROW_WITH_PARQUET" "1")))))) + (setenv "PYARROW_WITH_PARQUET" "1") + (setenv "PYARROW_WITH_DATASET" "1")))))) (propagated-inputs (list (list apache-arrow "lib") (list apache-arrow "include") -- cgit v1.2.3 From d7e0306aa5e7c8ac2f8794ab5839424911d62d52 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Jun 2023 20:16:00 +0200 Subject: gnu: Add python-duckdb. * gnu/packages/python-xyz.scm (python-duckdb): New variable. --- gnu/packages/python-xyz.scm | 53 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f2a794367f8..1aad8b90ca4 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20515,6 +20515,59 @@ from the header, as well as section details and data available.") Mustache templating language renderer.") (license license:expat))) +(define-public python-duckdb + (package + (name "python-duckdb") + (version "0.8.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "duckdb" version)) + (sha256 + (base32 + "13y1gs565q51li5fi9m7fpf0sqns8frsaii6v95acwjhmdds73f6")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + '(list "--ignore=tests/slow/test_h2oai_arrow.py" + ;; Don't install anything, thank you. + "-k" "not test_install_non_existent_extension") + #:phases + #~(modify-phases %standard-phases + ;; Tests need this + (add-before 'check 'set-HOME + (lambda _ (setenv "HOME" "/tmp"))) + (add-before 'build 'set-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version) + (substitute* "setup.py" + (("\"setuptools_scm<7.0.0\",") "")))) + ;; Later versions of pybind replace "_" with "const_name". + (add-after 'unpack 'pybind-compatibility + (lambda _ + (with-directory-excursion "src/include/duckdb_python" + (substitute* '("python_objects.hpp" + "pyfilesystem.hpp" + "pybind11/conversions/pyconnection_default.hpp") + (("const_name") "_")))))))) + (native-inputs + (list pybind11 + python-fsspec + python-google-cloud-storage + python-mypy + python-numpy + python-pandas + python-psutil + python-pyarrow + python-pytest + python-pytest-runner + python-setuptools-scm)) + (home-page "https://www.duckdb.org") + (synopsis "DuckDB embedded database") + (description "DuckDB is an in-process SQL OLAP database management +system.") + (license license:expat))) + (define-public python-dulwich (package (name "python-dulwich") -- cgit v1.2.3 From ffcd2315e4d65f41fdf593ecbda14ce6dff8c722 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Jun 2023 20:20:47 +0200 Subject: gnu: Add python-pubmed-parser. * gnu/packages/python-xyz.scm (python-pubmed-parser): New variable. --- gnu/packages/python-xyz.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1aad8b90ca4..e48172de280 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10335,6 +10335,36 @@ you're careful. The @code{backcall} package provides a way of specifying the callback signature using a prototype function.") (license license:bsd-3))) +(define-public python-pubmed-parser + (package + (name "python-pubmed-parser") + (version "0.3.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/titipata/pubmed_parser") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "195cmjjg7xdwjj5455h78q7jnxnccia07a19xwndhlkxv7vk9v60")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-lxml + python-numpy + python-requests + python-six + python-unidecode)) + (native-inputs + (list python-pytest + python-pytest-cov)) + (home-page "https://github.com/titipata/pubmed_parser") + (synopsis "Parser for Pubmed Open-Access Subset and MEDLINE XML repository") + (description + "This package provides a Python parser for Pubmed Open-Access Subset and +MEDLINE XML repository.") + (license license:expat))) + (define-public python-pure-eval (package (name "python-pure-eval") -- cgit v1.2.3 From d8dcd1200a9ce5cfb2333b7f43a72c40f8fc80bb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Jun 2023 21:10:32 +0200 Subject: gnu: Add python-srsly. * gnu/packages/python-xyz.scm (python-srsly): New variable. --- gnu/packages/python-xyz.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e48172de280..a6c2cfbb730 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -31881,6 +31881,40 @@ uses the parsed regular expression, so you get a much more accurate result than trying to just split strings.") (license license:asl2.0))) +(define-public python-srsly + (package + (name "python-srsly") + (version "2.4.6") + (source (origin + (method url-fetch) + (uri (pypi-uri "srsly" version)) + (sha256 + (base32 + "0vsafkvk4g0p5m0dqrczqvlyza837i20xxmb24rrqk5s78r1zd27")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace")))))) + (propagated-inputs (list python-catalogue)) + (native-inputs + (list python-cython + python-pytest + python-pytest-timeout + python-mock + python-numpy + python-psutil)) + (home-page "https://github.com/explosion/srsly") + (synopsis "Serialization utilities for Python") + (description "This package bundles some of the best Python serialization +libraries into one standalone package, with a high-level API that makes it +easy to write code that's correct across platforms and Pythons.") + (license license:expat))) + (define-public python-pyperf (package (name "python-pyperf") -- cgit v1.2.3 From 0836c0769d46a45955600ed42dbdd36a4ce298bb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Jun 2023 21:12:07 +0200 Subject: gnu: Add python-confection. * gnu/packages/python-xyz.scm (python-confection): New variable. --- gnu/packages/python-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a6c2cfbb730..cb323b5279f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15411,6 +15411,27 @@ provide an easy to use, pythonic and comprehensive Python interface to dialog. This allows one to make simple text-mode user interfaces on Unix-like systems") (license license:lgpl2.1))) +(define-public python-confection + (package + (name "python-confection") + (version "0.0.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "confection" version)) + (sha256 + (base32 + "1ksfn10zhnpkcj3y0c3xs4dznvc062bk62x4c3ig0dd6bn4gbpdi")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-pydantic python-srsly + python-typing-extensions)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/explosion/confection") + (synopsis "Config system for Python") + (description "Confection is a lightweight library that offers a +configuration system letting you conveniently describe arbitrary trees of +objects.") + (license license:expat))) + (define-public python-configobj (package (name "python-configobj") -- cgit v1.2.3 From 28d5ec153cf509135326720360628a02b2d096db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Jun 2023 21:51:07 +0200 Subject: gnu: blis: Update to 0.9.0. * gnu/packages/maths.scm (blis): Update to 0.9.0. [arguments]: Use G-expression; remove trailing #T from build phases. --- gnu/packages/maths.scm | 133 ++++++++++++++++++++++++------------------------- 1 file changed, 64 insertions(+), 69 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 4df535f0cbb..395db2ba3f3 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4681,90 +4681,85 @@ library.") (define-public blis (package (name "blis") - (version "0.8.1") + (version "0.9.0") (home-page "https://github.com/flame/blis") (source (origin (method git-fetch) (uri (git-reference (url home-page) (commit version))) (sha256 (base32 - "05ifil6jj9424sr8kmircl8k4bmxnl3y12a79vwj1kxxva5gz50g")) + "14v2awhxma6nzas42hq97702672f2njrskqhsv9kl23hvrvci8fm")) (file-name (git-file-name "blis" version)))) (native-inputs (list python perl)) (build-system gnu-build-system) (arguments - `(#:modules - ((guix build gnu-build-system) + (list + #:modules + '((guix build gnu-build-system) (guix build utils) (srfi srfi-1)) - #:test-target "test" - #:phases - (modify-phases %standard-phases - (replace 'configure - (lambda* (#:key outputs - target - system - (configure-flags '()) - #:allow-other-keys) - ;; This is a home-made 'configure' script. - (let* ((out (assoc-ref outputs "out")) - ;; Guix-specific support for choosing the configuration + #:test-target "test" + #:phases + #~(modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs target system (configure-flags '()) + #:allow-other-keys) + ;; This is a home-made 'configure' script. + (let* (;; Guix-specific support for choosing the configuration ;; via #:configure-flags: see below for details. - (config-flag-prefix "--blis-config=") - (maybe-config-flag (find - (lambda (s) - (string-prefix? config-flag-prefix s)) - configure-flags)) - (configure-flags (if maybe-config-flag - (delete maybe-config-flag - configure-flags) + (config-flag-prefix "--blis-config=") + (maybe-config-flag (find + (lambda (s) + (string-prefix? config-flag-prefix s)) configure-flags)) - ;; Select the "configuration" to build. - ;; The "generic" configuration is non-optimized but - ;; portable (no assembly). - ;; The "x86_64" configuration family includes - ;; sub-configurations for all supported - ;; x86_64 microarchitectures. - ;; BLIS currently lacks runtime hardware detection - ;; for other architectures: see - ;; . - ;; Conservatively, we stick to "generic" on armhf, - ;; aarch64, and ppc64le for now. (But perhaps - ;; "power9", "cortexa9", and "cortexa57" might be - ;; general enough to use?) - ;; Another approach would be to use the "auto" - ;; configuration and make this package - ;; non-substitutable. - ;; The build is fairly intensive, though. - (blis-config - (cond - (maybe-config-flag - (substring maybe-config-flag - (string-length config-flag-prefix))) - ((string-prefix? "x86_64" (or target system)) - "x86_64") - (else - "generic"))) - (configure-args - `("-p" ,out - "-d" "opt" - "--disable-static" - "--enable-shared" - "--enable-threading=openmp" - "--enable-verbose-make" - ,@configure-flags - ,blis-config))) - (format #t "configure args: ~s~%" configure-args) - (apply invoke - "./configure" - configure-args) - #t))) - (add-before 'check 'show-test-output - (lambda _ - ;; By default "make check" is silent. Make it verbose. - (system "tail -F output.testsuite &") - #t))))) + (configure-flags (if maybe-config-flag + (delete maybe-config-flag + configure-flags) + configure-flags)) + ;; Select the "configuration" to build. + ;; The "generic" configuration is non-optimized but + ;; portable (no assembly). + ;; The "x86_64" configuration family includes + ;; sub-configurations for all supported + ;; x86_64 microarchitectures. + ;; BLIS currently lacks runtime hardware detection + ;; for other architectures: see + ;; . + ;; Conservatively, we stick to "generic" on armhf, + ;; aarch64, and ppc64le for now. (But perhaps + ;; "power9", "cortexa9", and "cortexa57" might be + ;; general enough to use?) + ;; Another approach would be to use the "auto" + ;; configuration and make this package + ;; non-substitutable. + ;; The build is fairly intensive, though. + (blis-config + (cond + (maybe-config-flag + (substring maybe-config-flag + (string-length config-flag-prefix))) + ((string-prefix? "x86_64" (or target system)) + "x86_64") + (else + "generic"))) + (configure-args + `("-p" ,#$output + "-d" "opt" + "--disable-static" + "--enable-shared" + "--enable-threading=openmp" + "--enable-verbose-make" + ,@configure-flags + ,blis-config))) + (format #t "configure args: ~s~%" configure-args) + (apply invoke + "./configure" + configure-args)))) + (add-before 'check 'show-test-output + (lambda _ + ;; By default "make check" is silent. Make it verbose. + (system "tail -F output.testsuite &")))))) (synopsis "High-performance basic linear algebra (BLAS) routines") (description "BLIS is a portable software framework for instantiating high-performance -- cgit v1.2.3 From 069618522d3ee040e0b0f2d9f24ceb763ce434aa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Jun 2023 09:59:45 +0200 Subject: gnu: Add python-blis. * gnu/packages/maths.scm (python-blis): New variable. --- gnu/packages/maths.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 395db2ba3f3..a1a051c52e0 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -96,6 +96,7 @@ #:use-module (guix build-system meson) #:use-module (guix build-system ocaml) #:use-module (guix build-system perl) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (guix build-system ruby) #:use-module (gnu packages algebra) @@ -4773,6 +4774,35 @@ access to BLIS implementations via traditional BLAS routine calls.") (define ignorance blis) +;; It is unfortunate that we cannot just link with the existing blis package. +(define-public python-blis + (package + (name "python-blis") + (version "0.9.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "blis" version)) + (sha256 + (base32 + "0vrnzk9jx7fcl56q6zpa4w4mxkr4iknxs42fngn9g78zh1kc9skw")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'build 'build-ext + (lambda _ + (invoke "python" "setup.py" "build_ext" "--inplace" + "-j" (number->string (parallel-job-count)))))))) + (propagated-inputs (list python-numpy)) + (native-inputs (list python-cython python-pytest)) + (home-page "https://github.com/explosion/cython-blis") + (synopsis "Blis as a self-contained C-extension for Python") + (description + "This package provides the Blis BLAS-like linear algebra library, as a +self-contained C-extension for Python.") + (license license:bsd-3))) + (define-public openlibm (package (name "openlibm") -- cgit v1.2.3 From 2ab53074881c98b615b571cd4f7389b329b5774f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Jun 2023 10:00:14 +0200 Subject: gnu: yoshimi: Update to 2.3.0. * gnu/packages/music.scm (yoshimi): Update to 2.3.0. --- gnu/packages/music.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 7e4a7d11693..b7369391db9 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -3215,7 +3215,7 @@ capabilities, custom envelopes, effects, etc.") (define-public yoshimi (package (name "yoshimi") - (version "2.2.2.1") + (version "2.3.0") (source (origin (method url-fetch) @@ -3223,7 +3223,7 @@ capabilities, custom envelopes, effects, etc.") (version-major+minor version) "/yoshimi-" version ".tar.bz2")) (sha256 - (base32 "1axrbk1qwsiq77g5957db744481zb2v158psnk2w530wxhls2442")))) + (base32 "0rkwz545bipanyl8kcp6rgdqppiad7s0j409a4n8dd97maislsa0")))) (build-system cmake-build-system) (arguments (list -- cgit v1.2.3 From e3f148a6df106902bbd4bc943a70c46065d80505 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Jun 2023 10:00:33 +0200 Subject: gnu: Add python-spacy-legacy. * gnu/packages/machine-learning.scm (python-spacy-legacy): New variable. --- gnu/packages/machine-learning.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index c9bc5e8b68d..b2429625a25 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -727,6 +727,27 @@ depend on language-specific pre- or post-processing.") unsupervised text tokenizer.") (license license:asl2.0))) +(define-public python-spacy-legacy + (package + (name "python-spacy-legacy") + (version "3.0.12") + (source (origin + (method url-fetch) + (uri (pypi-uri "spacy-legacy" version)) + (sha256 + (base32 + "0x57aw1qgjrzgapsv1cwymqlck2anqm1bisvryhpq7bfkc66wzdk")))) + (build-system pyproject-build-system) + ;; This package depends on spacy, which depends on this package. + (arguments (list #:tests? #false)) + (native-inputs (list python-pytest)) + (home-page "https://spacy.io") + (synopsis "Legacy registered functions for spaCy backwards compatibility") + (description + "This package contains legacy registered functions for spaCy backwards +compatibility.") + (license license:expat))) + (define-public shogun (package (name "shogun") -- cgit v1.2.3 From db8cf18517c0aa83a78102f3a9491f9b87f46024 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Jun 2023 10:00:56 +0200 Subject: gnu: Add python-spacy-loggers. * gnu/packages/machine-learning.scm (python-spacy-loggers): New variable. --- gnu/packages/machine-learning.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index b2429625a25..e29f5fe691e 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -748,6 +748,26 @@ unsupervised text tokenizer.") compatibility.") (license license:expat))) +(define-public python-spacy-loggers + (package + (name "python-spacy-loggers") + (version "1.0.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "spacy-loggers" version)) + (sha256 + (base32 + "0a5zjfxd0mci7pwda24ihg55whalpmjby4bvpgar2013f6zq7yg6")))) + (build-system pyproject-build-system) + ;; This package depends on spacy, which depends on this package. + (arguments (list #:tests? #false)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/explosion/spacy-loggers") + (synopsis "Logging utilities for SpaCy") + (description "This package provides logging utilities for the SpaCy +natural language processing framework.") + (license license:expat))) + (define-public shogun (package (name "shogun") -- cgit v1.2.3 From c3f78236707edb1f7e648574387dc5c7c8c9dfe4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Jun 2023 10:11:10 +0200 Subject: gnu: Add python-blis-for-thinc. * gnu/packages/maths.scm (python-blis-for-thinc): New variable. --- gnu/packages/maths.scm | 12 ++++++++++++ 1 file changed, 12 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index a1a051c52e0..f89e70c0bb7 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4803,6 +4803,18 @@ access to BLIS implementations via traditional BLAS routine calls.") self-contained C-extension for Python.") (license license:bsd-3))) +(define-public python-blis-for-thinc + (package + (inherit python-blis) + (name "python-blis") + (version "0.7.8") + (source (origin + (method url-fetch) + (uri (pypi-uri "blis" version)) + (sha256 + (base32 + "0mvcif9g69424bk8xiflacxzpvz802ns791v2r8a6fij0sxl3mgp")))))) + (define-public openlibm (package (name "openlibm") -- cgit v1.2.3 From 7a78dd1e39bd6e9a41047f28a101e9c1baf29a86 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Jun 2023 10:14:04 +0200 Subject: gnu: Add python-thinc. * gnu/packages/machine-learning.scm (python-thinc): New variable. --- gnu/packages/machine-learning.scm | 40 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index e29f5fe691e..261911c4fec 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1317,6 +1317,46 @@ computing environments.") data analysis.") (license license:bsd-3))) +(define-public python-thinc + (package + (name "python-thinc") + (version "8.1.10") + (source (origin + (method url-fetch) + (uri (pypi-uri "thinc" version)) + (sha256 + (base32 + "14drmwa2sh8fqszv1fm2jl4lky1j5yrbkjv89bl49q07vbblhjkc")))) + (build-system pyproject-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'build 'build-ext + (lambda _ + (invoke "python" "setup.py" "build_ext" "--inplace" + "-j" (number->string (parallel-job-count)))))))) + (propagated-inputs (list python-blis-for-thinc + python-catalogue + python-confection + python-contextvars + python-cymem + python-dataclasses + python-murmurhash + python-numpy + python-packaging + python-preshed + python-pydantic + python-srsly + python-typing-extensions + python-wasabi)) + (native-inputs (list python-cython python-mock python-pytest)) + (home-page "https://github.com/explosion/thinc") + (synopsis "Functional take on deep learning") + (description + "This package provides a functional take on deep learning, compatible +with your favorite libraries.") + (license license:expat))) + (define-public python-threadpoolctl (package (name "python-threadpoolctl") -- cgit v1.2.3 From d3934c7cc250cf9bc539504fcdb7cd3717b8a6bd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Jun 2023 10:22:41 +0200 Subject: gnu: Add python-pathy. * gnu/packages/python-xyz.scm (python-pathy): New variable. --- gnu/packages/python-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index cb323b5279f..98abf038a5b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9441,6 +9441,28 @@ all the newest features of the standard @code{pathlib} can be used also on older Python versions.") (license license:expat))) +(define-public python-pathy + (package + (name "python-pathy") + (version "0.10.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "pathy" version)) + (sha256 + (base32 + "12v196q3rai33cfzrmb9pqfqv7ailngssjdrzdf8gzym9hdygmjc")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-dataclasses python-smart-open python-typer)) + (native-inputs (list python-mock python-pytest)) + (home-page "https://github.com/justindujardin/pathy") + (synopsis "Path interface for local and cloud bucket storage") + (description "Pathy is a python package (with type annotations) for +working with Cloud Bucket storage providers using a @code{pathlib} interface. +It provides @code{pathlib.Path} subclasses for local and cloud bucket +storage.") + (license license:asl2.0))) + (define-public python-importlib-resources (package (name "python-importlib-resources") -- cgit v1.2.3 From 266e54d7cbe7b8e72212fcd672f9001635ae98fe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Jun 2023 10:15:00 +0200 Subject: gnu: Add python-spacy. * gnu/packages/machine-learning.scm (python-spacy): New variable. --- gnu/packages/machine-learning.scm | 65 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 261911c4fec..827bcd597b7 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -768,6 +768,71 @@ compatibility.") natural language processing framework.") (license license:expat))) +(define-public python-spacy + (package + (name "python-spacy") + (version "3.5.3") + (source (origin + (method url-fetch) + (uri (pypi-uri "spacy" version)) + (sha256 + (base32 + "13141hc966d8nxbnlwj01vhndgq0rq4nmii3qkb3hrap45kiv5rm")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + '(list "-k" + (string-append + ;; We don't do that around here. + "not test_download_compatibility" + ;; This needs to download a model. + " and not test_validate_compatibility_table" + ;; This tries to run the application with typer, which fails + ;; with an unspecified error, possibly because the build + ;; container doesn't have /bin/sh. + " and not test_project_assets")) + #:phases + '(modify-phases %standard-phases + (add-after 'build 'build-ext + (lambda _ + (invoke "python" "setup.py" "build_ext" "--inplace" + "-j" (number->string (parallel-job-count)))))))) + (propagated-inputs (list python-catalogue + python-cymem + python-jinja2 + python-langcodes + python-murmurhash + python-numpy + python-packaging + python-pathy + python-preshed + python-pydantic + python-requests + python-setuptools + python-smart-open + python-spacy-legacy + python-spacy-loggers + python-srsly + python-thinc + python-tqdm + python-typer + python-typing-extensions + python-wasabi)) + (native-inputs + (list python-cython python-pytest python-mock)) + (home-page "https://spacy.io") + (synopsis "Natural Language Processing (NLP) in Python") + (description + "SpaCy is a library for advanced Natural Language Processing in Python +and Cython. It comes with pretrained pipelines and currently supports +tokenization and training for 70+ languages. It features state-of-the-art +speed and neural network models for tagging, parsing, named entity +recognition, text classification and more, multi-task learning with pretrained +transformers like BERT, as well as a production-ready training system and easy +model packaging, deployment and workflow management.") + (license license:expat))) + (define-public shogun (package (name "shogun") -- cgit v1.2.3 From 2d9601ed3d77c9d2c0b68812e60cb1b3bf045584 Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Sat, 3 Jun 2023 11:26:41 +0800 Subject: gnu: libxfce4ui: Update to 4.18.4. * gnu/packages/xfce.scm (libxfce4ui): Update to 4.18.4. --- gnu/packages/xfce.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index 2eb90ed4b2e..edafde8ed49 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -185,7 +185,7 @@ storage system.") (define-public libxfce4ui (package (name "libxfce4ui") - (version "4.18.3") + (version "4.18.4") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/xfce/" @@ -193,7 +193,7 @@ storage system.") name "-" version ".tar.bz2")) (sha256 (base32 - "1g8a067xbazgh0qc25nc7k1zc6aqmznhh4vy5wnn3aykxrpa98xg")))) + "0k6b8al8cy2w5zi8iywkzjsz2cgiz9r8ir2dflzxw9kdgiwzxvl7")))) (build-system gnu-build-system) (arguments `(#:configure-flags -- cgit v1.2.3 From 0a8fbee0d1e2cf804ed7a4b673512dbe35f44a08 Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Sat, 3 Jun 2023 11:26:42 +0800 Subject: gnu: xfce4-panel: Update to 4.18.4. * gnu/packages/xfce.scm (xfce4-panel): Update to 4.18.4. --- gnu/packages/xfce.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index edafde8ed49..cea538edb72 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -398,7 +398,7 @@ management D-Bus specification.") (define-public xfce4-panel (package (name "xfce4-panel") - (version "4.18.3") + (version "4.18.4") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/xfce/" @@ -406,7 +406,7 @@ management D-Bus specification.") name "-" version ".tar.bz2")) (sha256 (base32 - "06sy6vjydx1p8rx8z94ya6szvmvyarijl5x0pm5ij4cqbihviq2a")) + "0m7vmk7rc2sjfqba0flgnw77kn1j222xqs7r86bpg8sf1614yc1j")) (patches (search-patches "xfce4-panel-plugins.patch")))) (build-system gnu-build-system) (arguments -- cgit v1.2.3 From cbeb3204effff4a56d5f942c2a4b53378b2fc202 Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Sat, 3 Jun 2023 11:26:43 +0800 Subject: gnu: xfce4-screenshooter: Update to 1.10.4. * gnu/packages/xfce.scm (xfce4-screenshooter): Update to 1.10.4. --- gnu/packages/xfce.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index cea538edb72..b4205ff75b2 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -1453,7 +1453,7 @@ of data to either CD/DVD/BD.") (define-public xfce4-screenshooter (package (name "xfce4-screenshooter") - (version "1.10.3") + (version "1.10.4") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/apps/" @@ -1463,7 +1463,7 @@ of data to either CD/DVD/BD.") version ".tar.bz2")) (sha256 (base32 - "061qixpz8krvpixs6ickl9ha5m0pb078rdd5fjifrkxy8yc1am54")))) + "1534h1a3a8b9pl20zpccaifrlsrbsihdcdjndn9nmqalgrl9kwd2")))) (build-system gnu-build-system) (native-inputs (list pkg-config intltool -- cgit v1.2.3 From 756ccd920275e30c50505a03b1201aae75876f86 Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Sat, 3 Jun 2023 11:26:44 +0800 Subject: gnu: xfce4-pulseaudio-plugin: Update to 0.4.7. * gnu/packages/xfce.scm (xfce4-pulseaudio-plugin): Update to 0.4.7. --- gnu/packages/xfce.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index b4205ff75b2..a717e710173 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -498,7 +498,7 @@ matching them against regular expressions.") (define-public xfce4-pulseaudio-plugin (package (name "xfce4-pulseaudio-plugin") - (version "0.4.6") + (version "0.4.7") (source (origin (method url-fetch) @@ -507,7 +507,7 @@ matching them against regular expressions.") (version-major+minor version) "/" "xfce4-pulseaudio-plugin-" version ".tar.bz2")) (sha256 - (base32 "05k02ilvffddgbp6in9wpjvg6vzlcxxw09nmj29hzba44klc04bf")))) + (base32 "0b4fjvrrah0b97cbv8ds7r6cwnj392ya2r7703ixf724f43hkpah")))) (build-system gnu-build-system) (native-inputs (list intltool pkg-config dbus-glib dbus)) -- cgit v1.2.3 From 60c09c3b5ea536440a634f0ddc72f28a6d091ef9 Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Sat, 3 Jun 2023 11:26:45 +0800 Subject: gnu: xfce4-session: Update to 4.18.3. * gnu/packages/xfce.scm (xfce4-session): Update to 4.18.3. --- gnu/packages/xfce.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index a717e710173..65274ce5583 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -630,7 +630,7 @@ your system in categories, so you can quickly find and launch them.") (define-public xfce4-session (package (name "xfce4-session") - (version "4.18.2") + (version "4.18.3") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/xfce/" @@ -638,7 +638,7 @@ your system in categories, so you can quickly find and launch them.") "xfce4-session-" version ".tar.bz2")) (sha256 (base32 - "12pbppyhg0jdwswwk59fffh2n5ckpfvwc999zkg1l2f2skl7zzq1")) + "1v4lfgz7az8iqp01a1ww8sxxjfmr676bijhrhw4r6r7cjvh96brq")) (modules '((guix build utils))) (snippet '(begin -- cgit v1.2.3 From 47085b3ea07d6e525fd32d0ae143180378af90b1 Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Sat, 3 Jun 2023 11:26:46 +0800 Subject: gnu: xfce4-power-manager: Update to 4.18.2. * gnu/packages/xfce.scm (xfce4-power-manager): Update to 4.18.2. --- gnu/packages/xfce.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index 65274ce5583..b8336314a3c 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -1222,7 +1222,7 @@ system resources, while still being visually appealing and user friendly.") (define-public xfce4-power-manager (package (name "xfce4-power-manager") - (version "4.18.1") + (version "4.18.2") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/xfce/" @@ -1230,7 +1230,7 @@ system resources, while still being visually appealing and user friendly.") "xfce4-power-manager-" version ".tar.bz2")) (sha256 (base32 - "00zz9bhzsf2vww8mym9c093sz7va5716qb6kvdvn6ldp9h6b223b")))) + "0kfzvhb1hnr16fcplm7bdpp4fcxr3irzq3w4q0lpbc5n6kaqyq71")))) (build-system gnu-build-system) (native-inputs (list pkg-config intltool)) -- cgit v1.2.3 From 91454f54a4bf07030b51d718482416518ba5c9a7 Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Sat, 3 Jun 2023 11:26:47 +0800 Subject: gnu: xfce4-screensaver: Update to 4.18.2. * gnu/packages/xfce.scm (xfce4-screensaver): Update to 4.18.2. --- gnu/packages/xfce.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index b8336314a3c..31dc7501012 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -1482,7 +1482,7 @@ A plugin for the Xfce panel is also available.") (define-public xfce4-screensaver (package (name "xfce4-screensaver") - (version "4.18.1") + (version "4.18.2") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/apps/" @@ -1492,7 +1492,7 @@ A plugin for the Xfce panel is also available.") version ".tar.bz2")) (sha256 (base32 - "0p2an3g5jlhmr60if319cfgkqacziym52csj7dfwq64assmyhcdp")))) + "161bdsvkbknaf9fpz4b1r4amnm72hzfmx9c6krg2396k2k2d5z74")))) (build-system gnu-build-system) (arguments `(#:phases -- cgit v1.2.3 From 872b2487451c39020a78ed3227992fb02a7ed5e5 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Thu, 8 Jun 2023 13:25:14 +0200 Subject: gnu: sbcl: Fix build on armhf. * gnu/packages/lisp.scm (sbcl)[source]: Update snippet. --- gnu/packages/lisp.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index 296ed6b5f24..a7e06dd34cf 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -447,7 +447,7 @@ an interpreter, a compiler, a debugger, and much more.") '(begin ;; Don't force ARMv5. (substitute* "src/runtime/Config.arm-linux" - (("-march=armv5") "")))))) + (("-march=armv5t") "")))))) (build-system gnu-build-system) (outputs '("out" "doc")) (native-inputs -- cgit v1.2.3