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* gnu: augeas: Update to 1.14.1.•••* gnu/packages/augeas.scm (augeas): Update to 1.14.1. [source]: Use tarballs from GitHub. [inputs]: Change to "native-inputs". Add readline. Change-Id: I9ca46b8a50d11c75ff6d816f2f15e1f005877244 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Artyom V. Poptsov2024-05-221-8/+14
* gnu: Add r-tglkmeans.•••* gnu/packages/cran.scm (r-tglkmeans): New variable. Change-Id: I13aa0e8c4ab062993d84c99811971ebf6e9179bd Marco Baggio2024-05-221-0/+40
* gnu: Add r-slanter.•••* gnu/packages/cran.scm (r-slanter): New variable. Change-Id: I3b6c76431940f5e6be6a86344029552dded54e54 Marco Baggio2024-05-221-0/+22
* gnu: Add r-shinydashboardplus.•••* gnu/packages/cran.scm (r-shinydashboardplus): New variable. Change-Id: Ie50bd8a0234af0fb5ea63377aa005655acad01bd Ricardo Wurmus2024-05-221-0/+83
* gnu: Add r-waiter.•••* gnu/packages/cran.scm (r-waiter): New variable. Change-Id: I98b27630eba86ab700ac30a361baf14a5d58dae8 Ricardo Wurmus2024-05-221-0/+169
* gnu: Add esbuild-node.•••* gnu/packages/web.scm (esbuild-node): New variable. Change-Id: I5e1a353a13ef7b4018fcf4aef4832af25f3dabe2 Ricardo Wurmus2024-05-221-0/+59
* gnu: ensembl-vep: Update to 112.•••* gnu/packages/bioinformatics.scm (ensembl-vep): Update to 112. [propagated-inputs]: Add perl-list-moreutils. [native-inputs]: Add perl-test-deep and perl-test-warnings. Change-Id: I8c7de9f3dbc8c6fe4d1383f9dc215aeba018af0d Ricardo Wurmus2024-05-221-8/+11
* gnu: Add r-chameleon.•••* gnu/packages/cran.scm (r-chameleon): New variable. Change-Id: I9e0f3c27e434bb802c86ef9e2877f4d810397158 Signed-off-by: Ricardo Wurmus <rekado@elephly.net> guix@mawumag.com2024-05-221-0/+21
* doc: Make changes to the handling of branches.•••Require that you create a "Request to merge" issue when you create a branch, rather than when you wish to merge it. This should help avoid this step being missed. Also, add information on how to manage these branches: 1. Suggest creating the branch from patches, rather than having a stateful branch, since this should help to reduce complexity and avoid merges. 2. Require that branches don't have unnecessary changes, since this increases the risks of conflicts with other branches. 3. Suggest that the branch not be stateful, and it's just a combination of patches. 4. Suggest avoiding merges since these create a more complicated Git history. 5. Suggest that the branch be up to date before merging, as this helps avoid the combination of master plus the branch differing significantly from the branch alone. 6. Document how to manage branches without commit access. Finally, require that the branch be deleted once they're merged. This prepares for the branch being created again. * doc/contributing.texi (Managing Patches and Branches): Make changes to the handling of branches. Change-Id: Ib9419c6df94f485475bd6f147e82ea254e76cec2 Christopher Baines2024-05-221-17/+51
* gnu: python-pandera: Update to 0.18.0, fix build.•••* gnu/packages/python-science.scm (python-pandera): Update to 0.18.0. [arguments] <#:test-flags>: Disable one more failing test. Change-Id: I4d3f59dae8d90ea0afbe9cc932fc6163def282c9 Sharlatan Hellseher2024-05-221-3/+4
* gnu: python-pymysql: Propagate python-cryptography.•••* gnu/packages/databases.scm (python-pymysql) [inputs]: Swap to [propagated-inputs]. [propagated-inputs]: Add python-pynacl (mycli, sqlcrush): Remove propagated python-cryptography. Change-Id: I40ee51087cd14cb98bd2390095fa9f6f0d144b47 Sharlatan Hellseher2024-05-221-5/+3
* gnu: python-pymysql: Update to 1.1.1 [fixes CVE-2024-36039].•••* gnu/packages/databases.scm (python-pymysql): Update to 1.1.1. [source]: Refresh archive name as seen on <https://pypi.org/project/PyMySQL/#files>. [build-system]: Swap to pyproject-build-system. Change-Id: I20d06f6d1d252f501df001120ee44520e6e5d785 Sharlatan Hellseher2024-05-221-4/+4
* gnu: schmutz: update to commit f8043e.•••* gnu/packages/guile-xyz.scm (schmutz): Update to commit f8043e. [inputs]: Switch guile-2.2 to guile-3.0. Change-Id: Ibd3e5a5074119e3d2a9affcd7c98f47cb9f1f677 Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn> Andy Tai2024-05-221-4/+4
* gnu: axel: Update to 2.17.14.•••* gnu/packages/networking.scm (axel): Update to 2.17.14. Change-Id: I62ce6e62d7f50662e13e89baff8658ae49224f56 Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn> Artyom V. Poptsov2024-05-221-3/+3
* gnu: gcc-13: Update to 13.3.0.•••* gnu/packages/gcc.scm (gcc-13): Update to 13.3.0. Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn> Change-Id: Ia2dc3185acbb6671b2719e2d88d55b7d2b8fb92e Michael Ford2024-05-221-2/+2
* import/elpa: Add proper file-name to origin.•••This avoids the lint "the source file name should contain the package name" with generated packages. Change-Id: I61c81203d9f3cdd035e2b64a4c7a8d86d1f3dd50 Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn> Nicolas Graves via Guix-patches via2024-05-221-0/+1
* gnu: emacs-denote: Update to 2.3.0.•••* gnu/packages/emacs-xyz.scm (emacs-denote): Update source location and bump version to 2.3.0. Change-Id: I573db7f285832bf27659b33274e1d592d1c5aa45 Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> David Wilson2024-05-221-3/+3
* gnu: wlsunset: Update to 0.4.0.•••* gnu/packages/xdisorg.scm (wlsunset): Update to 0.4.0. Change-Id: I4638d89c29fd4da2ae9850955bb43875fb00d416 Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn> Wilko Meyer2024-05-221-2/+2
* gnu: wlsunset: Install man pages.•••* gnu/packages/xdisorg.scm (wlsunset)[native-inputs]: Add scdoc. Reviewed-by: Dale Mellor <guix-devel-0brg6a@rdmp.org> Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn> Change-Id: Iffeb9427a1fd625f9dac4098107336cba639f5e9 Sören Tempel2024-05-221-1/+1
* gnu: btop: Update to 1.3.2.•••* gnu/packages/admin.scm (btop): Update to 1.3.2. Change-Id: I503bc5730dd498640cff76e252825c7b47cd5d11 Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn> Artyom V. Poptsov2024-05-221-2/+2
* gnu: LLVM, Clang, libomp, lld: Update to 18.1.6.•••* gnu/packages/llvm.scm (llvm-18, clang-18, libomp-18, lld-18): Update to 18.1.6. Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn> Change-Id: Ifd5ab99f4195c93e9b8d67aa26caead26c8dd5bc Michael Ford2024-05-221-4/+4
* gnu: yambar-wayland: Update to 1.11.0.•••* gnu/packages/wm.scm (yambar-wayland): Update to 1.11.0. Change-Id: I8ee9726a665a97e9dccaead32f1272ab98289c8f Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn> dan2024-05-221-2/+2
* gnu: fnott: Update to 1.6.0.•••* gnu/packages/wm.scm (fnott): Update to 1.6.0. [arguments]<#:phases>: Patch dbus service file install directory. Change-Id: I0a64c93b0e1ed43f101cb5a77ecfce5025a2b4b0 Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn> dan2024-05-221-3/+9
* system: images: Add visionfive2 module.•••* gnu/system/images/visionfive2.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. Change-Id: I8831f1148bcddb0d604e1174034fca85cd2887a1 Zheng Junjie2024-05-222-0/+123
* bootloader: Add u-boot-starfive-visionfive2-bootloader.•••* gnu/bootloader/u-boot.scm (u-boot-starfive-visionfive2-bootloader): New variable. Change-Id: I4b73906fe18d481644102c271f5e0883167b3a50 Zheng Junjie2024-05-221-0/+29
* gnu: Add u-boot-starfive-visionfive2.•••* gnu/packages/bootloaders.scm (u-boot-starfive-visionfive2): New variable. Change-Id: I2a7d2275b1a0f4253ffc3152c892687aae11a471 Zheng Junjie2024-05-221-0/+25
* gnu: Add opensbi-for-visionfive2.•••* gnu/packages/firmware.scm (opensbi-for-visionfive2): New variable. Change-Id: I27963937410a3900a63193ce2a1033ac20a79919 Zheng Junjie2024-05-221-0/+14
* gnu: shepherd-0.10: When target riscv64, use guile-fibers-1.1.•••* gnu/packages/admin.scm (shepherd-0.10)[native-inputs]: When target-riscv64? is true, use guile-fibers-1.1. Change-Id: I89d2e1a7bd6cbc69d19230d9b1c45ce6e339a13d Zheng Junjie2024-05-221-2/+3
* image: Raise error when use both grub-efi* bootloader and not gpt image.•••* gnu/system/image.scm: Switch Inversion logic, it allow we use customize bootloader with gpt image. Change-Id: I801327f6e826a37588b8f0f5246ca820e742f721 Zheng Junjie2024-05-221-3/+3
* gnu: linux-libre-6.8: Add riscv config.•••* gnu/packages/aux-files/linux-libre/6.8-riscv.conf: New files. * Makefile.am (AUX_FILES): Add it. Change-Id: I293912d4f7fe09e281432b0f973999d9d8db582a Zheng Junjie2024-05-222-0/+7682
* gnu: buildah: Switch to gnu-build-system.•••Buildah is fundamentally similar to podman and provides its own Makefile. This commit switches from go-build-system to gnu-build-system so that the build can be done using `make' instead of reinvention some parts (like documentation) in the guile. The package pretty much follows how podman package looks like. * gnu/packages/containers.scm (buildah)[source]: Reformat. [build-system]: Use gnu-build-system. [arguments]<#:import-path, #:unpack-path, #:go, #:install-source?>: Delete. <#:make-flags>: Set make flags. <#:test-target>: Set, even though the tests are disabled. <#:imported-modules>: Also import (guix build go-build-system) for the remove-go-references phase. <#:phases>{'prepare-install-docs, 'build-docs, 'install-docs}: Delete. {'configure}: Delete. {'set-env, 'check, 'symlink-helpers, 'wrap-buildah, 'remove-go-references} {'install-completions}: New phases. [inputs]: Remove no longer used cni-plugins, conmon, runc. Add bash-minimal. [native-inputs]: Remove gnu-make, add go-1.21 and bats. Change-Id: I0ddd5febb0116a71a857e2a98a9951dbe8bd40d9 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Tomas Volf2024-05-211-37/+62
* gnu: podman: Revamp the package.•••Substantial rework of the podman package. The source is no longer patched (at all) and all necessary modifications were moved into wrap-program and phases. Not everything is supported out of the box, but description mentions what packages to install to get additional functionality working. * gnu/packages/containers.scm (podman)[source]: Remove snippet and patches. [arguments]<#:make-flags>: Add HELPER_BINARIES_DIR. Add GOMD2MAN to actually use go-github-com-go-md2man package instead of the bundled version. <#:imported-modules>: Add (guix build go-build-system). <#:phases>{'set-env}: Set `CC' as an environment variable due to bug in make before 4.4. {'fix-hardcoded-paths}: Remove everything except patching `libexec' and `lib' locations. {'symlink-helpers}: New phase symlinking tools not discoverable via $PATH into one directory (`HELPER_BINARIES_DIR'). {'wrap-podman}: New phase wrapping `podman' to set correct $PATH. {'remove-go-references}: New phase stripping references to the golang toolchain from the binaries. [inputs]: Remove no longer needed cni-plugins, slirp4netns. Remove referenced in 'wrap-podman conmon, crun, iptables, passt. Move go-github-com-go-md2man into native-inputs. Add bash-minimal. [native-inputs]: Add custom grep with supported -P. Use newer go. Add mandoc. [description]: Explain how to get `podman compose' and `podman machine' working. * gnu/packages/patches/podman-program-lookup.patch: Delete file. Change-Id: Ifc28971a68751831d781517b041eec951a617087 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Tomas Volf2024-05-213-166/+74
* gnu: buildah: Update to 1.35.3.•••* gnu/packages/containers.scm (buildah): Update to 1.35.3. Change-Id: I0a00d6a73079ddaa38a454856781adfc2d7f158f Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Tomas Volf2024-05-211-10/+10
* gnu: gvisor-tap-vsock: Remove references to go.•••This is handled automatically by go-build-system, but (obviously) not by the gnu-build-system, so add the phase manually. * gnu/packages/containers.scm (gvisor-tap-vsock)[arguments]<#:phases>: Add 'remove-go-references phase. Change-Id: I5cef0bc03dfa7f219bdfec4226d0e7772401a5a5 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Tomas Volf2024-05-211-1/+7
* gnu: Add podman-compose.•••* gnu/packages/containers.scm (podman-compose): New variable. Change-Id: Ieb5ee4b6e82464599a17ec950be8a7dbb2efa842 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Tomas Volf2024-05-211-0/+31
* gnu: Add catatonit.•••* gnu/packages/containers.scm (catatonit): New variable. Change-Id: Ib6948bde8204426a8cb008982cb7cc9302f9e6d6 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Wilke Schwiedop2024-05-211-0/+28
* gnu: passt: Update to 2024_03_20.71dd405.•••* gnu/packages/containers.scm (passt): Update to 2024_03_20.71dd405. Change-Id: I089b7e9364058e59139bdb7cb942fad693254c1f Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Tomas Volf2024-05-211-2/+2
* gnu: conmon: Update to 2.1.11.•••* gnu/packages/containers.scm (conmon): Update to 2.1.11. Change-Id: I2a46b2dcd344909da34199145fef4ad3fa4418de Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Tomas Volf2024-05-211-2/+2
* gnu: podman: Update to 5.0.2.•••* gnu/packages/containers.scm (podman): Update to 5.0.2. Change-Id: Id12c017e68f30db4ea99547beca54dbd01e3b029 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Tomas Volf2024-05-211-3/+6
* gnu: podman: Drop obsolete comment.•••cgroup2 is now the default type. * gnu/packages/containers.scm (podman): Drop the comment. Change-Id: I197ed7e4901b26ad820295ed7adcaffd7bf533f5 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Tomas Volf2024-05-211-3/+0
* gnu: crun: Update to 1.15.•••* gnu/packages/containers.scm (crun): Update to 1.15. Change-Id: I769c15663bf668a967cf32243dd8139b6c949953 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Tomas Volf2024-05-211-2/+2
* gnu: Add cl-in-memory-streams.•••* gnu/packages/lisp-xyz.scm (cl-in-memory-streams, ecl-in-memory-streams, sbcl-in-memory-streams): New variables. Change-Id: I5f55f1185dfc396d7287b1a402541ad68f355b56 Guillaume Le Vaillant2024-05-211-0/+33
* gnu: Add cl-cf.•••* gnu/packages/lisp-xyz.scm (cl-cf, ecl-cf, sbcl-cf): New variables. Change-Id: Ic377597dceaf4f4d0c71319056185a958df06155 Guillaume Le Vaillant2024-05-211-0/+29
* gnu: cl-for: Update to 1.2.0-1.a397829.•••* gnu/packages/lisp-xyz.scm (sbcl-for): Update to 1.2.0-1.a397829. Change-Id: I521ed1cf56bf13934996ba35304cb842c394cdac Guillaume Le Vaillant2024-05-211-4/+4
* gnu: julia-fixedpointnumbers: Update to 0.8.5.•••* gnu/packages/julia-xyz.scm (julia-fixedpointnumbers): Update to 0.8.5. (julia-colortypes)[arguments]: Remove 'skip-failing-test phase. Change-Id: I18cee60a90311af0a052e5d49e4f2b43b54e7e14 Efraim Flashner2024-05-211-32/+21
* gnu: perl-dbix-class: Update to 0.082843.•••* gnu/packages/databases.scm (perl-dbix-class): Update to 0.082843. [propagated-inputs]: Remove perl-moo, perl-scalar-list-utils, and perl-text-balanced; add perl-moo-2. [native-inputs]: Remove perl-file-temp. [properties]: New field. Change-Id: I67f00f7e4f5b1bc71d9632bb90213df3c0a20ce5 Efraim Flashner2024-05-211-6/+6
* gnu: abseil-cpp: Fix build on i686-linux.•••* gnu/packages/cpp.scm (abseil-cpp)[source]: Add patch. (abseil-cpp-20220623.1)[source]: Same. * gnu/packages/patches/abseil-cpp-20220623.1-no-kepsilon-i686.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. Change-Id: I27b9abc2c44ff6dc313209f4b0b12542a92d6fcd Efraim Flashner2024-05-213-2/+30
* gnu: abseil-cpp-20200923.3: Fix test suite on some architectures.•••* gnu/packages/cpp.scm (abseil-cpp-20200923.3)[source]: Add patches. * gnu/packages/patches/abseil-cpp-20200923.3-adjust-sysinfo.patch, gnu/packages/patches/abseil-cpp-20200923.3-duration-test.patch: New files. * gnu/local.mk (dist_patch_DATA): Register them. Change-Id: I3a0a6c3396a7c2854236c68ec77a68bbdd6af1f4 Efraim Flashner2024-05-214-1/+151
* gnu: labwc: Build with librsvg-for-system.•••* gnu/packages/wm.scm (labwc)[inputs]: Replace librsvg with librsvg-for-system. Change-Id: I46505b3f041f46b42b403f9b7fbba5737c128f3f Efraim Flashner2024-05-211-1/+1
* gnu: enblend-enfuse: Build with librsvg-for-system.•••* gnu/packages/photo.scm (enblend-enfuse)[native-inputs]: Replace librsvg with librsvg-for-system. Change-Id: I04e046191abf1e36cdbb42d50a5c5abab029edf1 Efraim Flashner2024-05-211-2/+2
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