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-rw-r--r--gnu/packages/machine-learning.scm146
1 files changed, 64 insertions, 82 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 3185c15aead..ba54e72d12d 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -16,7 +16,7 @@
;;; Copyright © 2020 Konrad Hinsen <konrad.hinsen@fastmail.net>
;;; Copyright © 2020 Edouard Klein <edk@beaver-labs.com>
;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
-;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -222,20 +222,7 @@ classification.")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'enter-dir
- (lambda _ (chdir "ghmm") #t))
- (delete 'check)
- (add-after 'install 'check
- (assoc-ref %standard-phases 'check))
- (add-before 'check 'fix-PYTHONPATH
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((python-version (python-version
- (assoc-ref inputs "python"))))
- (setenv "PYTHONPATH"
- (string-append (getenv "PYTHONPATH")
- ":" (assoc-ref outputs "out")
- "/lib/python" python-version
- "/site-packages")))
- #t))
+ (lambda _ (chdir "ghmm")))
(add-after 'enter-dir 'fix-runpath
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "ghmmwrapper/setup.py"
@@ -246,8 +233,7 @@ classification.")
line
"\"-Wl,-rpath="
(assoc-ref outputs "out")
- "/lib\", ")))
- #t))
+ "/lib\", ")))))
(add-after 'enter-dir 'disable-broken-tests
(lambda _
(substitute* "tests/Makefile.am"
@@ -267,8 +253,7 @@ classification.")
line indent)
(string-append indent
"@unittest.skip(\"Disabled by Guix\")\n"
- line)))
- #t)))))
+ line))))))))
(inputs
`(("python" ,python-2) ; only Python 2 is supported
("libxml2" ,libxml2)))
@@ -946,7 +931,7 @@ computing environments.")
(define-public python-scikit-learn
(package
(name "python-scikit-learn")
- (version "0.24.2")
+ (version "1.0.1")
(source
(origin
(method git-fetch)
@@ -956,7 +941,7 @@ computing environments.")
(file-name (git-file-name name version))
(sha256
(base32
- "0hm92biqwwc87bqnr56lwa5bz77lr7k9q21rdwksnfzq3vsdp2nm"))))
+ "07k92y78sk4074vh5hp8y63pwl592wgl8azrfp0q84chxk8igfx9"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -964,14 +949,17 @@ computing environments.")
(add-after 'build 'build-ext
(lambda _ (invoke "python" "setup.py" "build_ext" "--inplace")))
(replace 'check
- (lambda _
- ;; Restrict OpenBLAS threads to prevent segfaults while testing!
- (setenv "OPENBLAS_NUM_THREADS" "1")
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ ;; Restrict OpenBLAS threads to prevent segfaults while testing!
+ (setenv "OPENBLAS_NUM_THREADS" "1")
- ;; Some tests require write access to $HOME.
- (setenv "HOME" "/tmp")
+ ;; Some tests require write access to $HOME.
+ (setenv "HOME" "/tmp")
- (invoke "pytest" "sklearn" "-m" "not network")))
+ (invoke "pytest" "sklearn" "-m" "not network"
+ ;; This test tries to access the internet.
+ "-k" "not test_load_boston_alternative"))))
(add-before 'reset-gzip-timestamps 'make-files-writable
(lambda* (#:key outputs #:allow-other-keys)
;; Make sure .gz files are writable so that the
@@ -1647,7 +1635,7 @@ automatically.")
(let* ((server (string-append bin "/kaldi-gst-server"))
(client (string-append bin "/kaldi-gst-client"))
(worker (string-append bin "/kaldi-gst-worker"))
- (PYTHONPATH (getenv "PYTHONPATH"))
+ (PYTHONPATH (getenv "GUIX_PYTHONPATH"))
(GST_PLUGIN_PATH (string-append
(assoc-ref inputs "gst-kaldi-nnet2-online")
"/lib/gstreamer-1.0:${GST_PLUGIN_PATH}"))
@@ -1656,7 +1644,7 @@ automatically.")
(lambda _
(format #t
"#!~a
-export PYTHONPATH=~a
+export GUIX_PYTHONPATH=~a
export GST_PLUGIN_PATH=~a
exec ~a ~a/~a \"$@\"~%"
(which "bash") PYTHONPATH GST_PLUGIN_PATH
@@ -1750,7 +1738,7 @@ Python.")
((guix build python-build-system)
#:select (python-version)))
#:imported-modules (,@%cmake-build-system-modules
- (guix build python-build-system))
+ (guix build python-build-system))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'set-source-file-times-to-1980
@@ -1780,10 +1768,9 @@ Python.")
;; https://github.com/tensorflow/tensorflow/issues/34197
(substitute* (find-files "tensorflow/python" ".*\\.cc$")
(("(nullptr,)(\\ +/. tp_print)" _ _ tp_print)
- (string-append "NULL, " tp_print)))
- #t))
+ (string-append "NULL, " tp_print)))))
(add-after 'python3.7-compatibility 'chdir
- (lambda _ (chdir "tensorflow/contrib/cmake") #t))
+ (lambda _ (chdir "tensorflow/contrib/cmake")))
(add-after 'chdir 'disable-downloads
(lambda* (#:key inputs #:allow-other-keys)
(substitute* (find-files "external" "\\.cmake$")
@@ -1798,36 +1785,31 @@ Python.")
;; Sqlite
(("include\\(sqlite\\)") "")
(("\\$\\{sqlite_STATIC_LIBRARIES\\}")
- (string-append (assoc-ref inputs "sqlite")
- "/lib/libsqlite3.so"))
+ (search-input-file inputs "/lib/libsqlite3.so"))
(("sqlite_copy_headers_to_destination") "")
;; PNG
(("include\\(png\\)") "")
(("\\$\\{png_STATIC_LIBRARIES\\}")
- (string-append (assoc-ref inputs "libpng")
- "/lib/libpng16.so"))
+ (search-input-file inputs "/lib/libpng16.so"))
(("png_copy_headers_to_destination") "")
;; JPEG
(("include\\(jpeg\\)") "")
(("\\$\\{jpeg_STATIC_LIBRARIES\\}")
- (string-append (assoc-ref inputs "libjpeg")
- "/lib/libjpeg.so"))
+ (search-input-file inputs "/lib/libjpeg.so"))
(("jpeg_copy_headers_to_destination") "")
;; GIF
(("include\\(gif\\)") "")
(("\\$\\{gif_STATIC_LIBRARIES\\}")
- (string-append (assoc-ref inputs "giflib")
- "/lib/libgif.so"))
+ (search-input-file inputs "/lib/libgif.so"))
(("gif_copy_headers_to_destination") "")
;; lmdb
(("include\\(lmdb\\)") "")
(("\\$\\{lmdb_STATIC_LIBRARIES\\}")
- (string-append (assoc-ref inputs "lmdb")
- "/lib/liblmdb.so"))
+ (search-input-file inputs "/lib/liblmdb.so"))
(("lmdb_copy_headers_to_destination") "")
;; Protobuf
@@ -1879,8 +1861,7 @@ set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive "
(("tf_core_cpu grpc") "tf_core_cpu"))
;; This directory is a dependency of many targets.
- (mkdir-p "protobuf")
- #t))
+ (mkdir-p "protobuf")))
(add-after 'configure 'unpack-third-party-sources
(lambda* (#:key inputs #:allow-other-keys)
;; This is needed to configure bundled packages properly.
@@ -1920,8 +1901,7 @@ set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive "
"re2"))
(rename-file "../build/cub/src/cub/cub-1.8.0/"
- "../build/cub/src/cub/cub/")
- #t))
+ "../build/cub/src/cub/cub/")))
(add-after 'unpack 'fix-python-build
(lambda* (#:key inputs outputs #:allow-other-keys)
(mkdir-p "protobuf-src")
@@ -1932,9 +1912,6 @@ set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive "
"-C" "eigen-src" "--strip-components=1")
(substitute* "tensorflow/contrib/cmake/tf_python.cmake"
- ;; Ensure that all Python dependencies can be found at build time.
- (("PYTHONPATH=\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/tf_python" m)
- (string-append m ":" (getenv "PYTHONPATH")))
;; Take protobuf source files from our source package.
(("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/protobuf/src/protobuf/src/google")
(string-append (getcwd) "/protobuf-src/src/google")))
@@ -1946,7 +1923,7 @@ set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive "
(string-append (getcwd) "/eigen-src/"))
;; Take Eigen headers from our own package.
(("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/external/eigen_archive")
- (string-append (assoc-ref inputs "eigen") "/include/eigen3")))
+ (search-input-directory inputs "/include/eigen3")))
;; Correct the RUNPATH of ops libraries generated for Python.
;; TODO: this doesn't work :(
@@ -1960,21 +1937,22 @@ set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive "
(string-append "set_target_properties(${_AT_TARGET} PROPERTIES \
COMPILE_FLAGS ${target_compile_flags} \
INSTALL_RPATH_USE_LINK_PATH TRUE \
-INSTALL_RPATH " (assoc-ref outputs "out") "/lib)\n")))
- #t))
+INSTALL_RPATH " (assoc-ref outputs "out") "/lib)\n")))))
(add-after 'build 'build-pip-package
- (lambda* (#:key outputs #:allow-other-keys)
+ (lambda* (#:key outputs parallel-build? #:allow-other-keys)
(setenv "LDFLAGS"
(string-append "-Wl,-rpath="
(assoc-ref outputs "out") "/lib"))
- (invoke "make" "tf_python_build_pip_package")
- #t))
+ (invoke "make" "-j" (if parallel-build?
+ (number->string (parallel-job-count))
+ "1")
+ "tf_python_build_pip_package")))
(add-after 'build-pip-package 'install-python
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(wheel (car (find-files "../build/tf_python/dist/" "\\.whl$")))
(python-version (python-version
- (assoc-ref inputs "python"))))
+ (assoc-ref inputs "python"))))
(invoke "python" "-m" "pip" "install" wheel
(string-append "--prefix=" out))
@@ -1983,8 +1961,7 @@ INSTALL_RPATH " (assoc-ref outputs "out") "/lib)\n")))
(string-append
out "/lib/python" python-version
"/site-packages/tensorflow/contrib/"
- "seq2seq/python/ops/lib_beam_search_ops.so"))
- #t))))))
+ "seq2seq/python/ops/lib_beam_search_ops.so"))))))))
(native-inputs
`(("pkg-config" ,pkg-config)
("protobuf:native" ,protobuf-3.6) ; protoc
@@ -2244,7 +2221,7 @@ advanced research.")
(install-file file target-dir)))
(find-files "." "\\.h$")))))))))
(inputs
- `(("abseil-cpp" ,abseil-cpp)
+ `(("abseil-cpp" ,abseil-cpp-20200923.3)
("eigen" ,eigen-for-tensorflow-lite)
("flatbuffers" ,flatbuffers)
("python" ,python)))
@@ -2552,24 +2529,31 @@ with image data, text data, and sequence data.")
(delete-file "keras/backend/theano_backend.py")
(delete-file "keras/backend/cntk_backend.py")
(delete-file "tests/keras/backend/backend_test.py")
-
;; FIXME: This doesn't work because Tensorflow is missing the
;; coder ops library.
- (delete-file "tests/keras/test_callbacks.py")
- #t))
+ (delete-file "tests/keras/test_callbacks.py")))
(replace 'check
- (lambda _
- ;; These tests attempt to download data files from the internet.
- (delete-file "tests/integration_tests/test_datasets.py")
- (delete-file "tests/integration_tests/imagenet_utils_test.py")
- ;; Backport https://github.com/keras-team/keras/pull/12479.
- (substitute* "tests/keras/engine/test_topology.py"
- (("np.ones\\(\\(3, 2\\)\\)")
- "1."))
- (invoke "python" "-m" "pytest"
- ;; The following test fail only in the build container;
- ;; skip it.
- "-k" "not test_selu"))))))
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ ;; These tests attempt to download data files from the internet.
+ (delete-file "tests/integration_tests/test_datasets.py")
+ (delete-file "tests/integration_tests/imagenet_utils_test.py")
+ ;; Backport https://github.com/keras-team/keras/pull/12479.
+ (substitute* "tests/keras/engine/test_topology.py"
+ (("np.ones\\(\\(3, 2\\)\\)")
+ "1."))
+ (invoke "python" "-m" "pytest" "tests"
+ "-p" "no:pep8"
+ ;; FIXME: python-build-system lacks PARALLEL-TESTS?
+ "-n" (number->string (parallel-job-count))
+ "-k"
+ (string-append
+ ;; The following test fails only in the build
+ ;; container; skip it.
+ "not test_selu "
+ ;; The following test was found flaky and removed in
+ ;; recent versions.
+ "and not test_stateful_metrics"))))))))
(propagated-inputs
`(("python-h5py" ,python-h5py)
("python-keras-applications" ,python-keras-applications)
@@ -2596,7 +2580,6 @@ with image data, text data, and sequence data.")
and capable of running on top of TensorFlow. It was developed with a focus on
enabling fast experimentation. Use Keras if you need a deep learning library
that:
-
@itemize
@item Allows for easy and fast prototyping (through user friendliness,
modularity, and extensibility).
@@ -2836,13 +2819,10 @@ TensorFlow.js, PyTorch, and MediaPipe.")
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
;; Run the test suite following the instructions in
;; 'CONTRIBUTING.md'. XXX: Unfortunately this doesn't
- ;; work, unless you set PYTHONPATH presumably.
+ ;; work, unless you set GUIX_PYTHONPATH presumably.
(when tests?
- (let ((python-site (site-packages inputs outputs)))
- (setenv "PYTHONPATH"
- (string-append python-site ":"
- (getenv "PYTHONPATH")))
- (invoke "python" "test/run_test.py")))))
+ (add-installed-pythonpath inputs outputs)
+ (invoke "python" "test/run_test.py"))))
(add-after 'install 'remove-test-executables
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Remove test executables, but keep other executables
@@ -2855,6 +2835,7 @@ TensorFlow.js, PyTorch, and MediaPipe.")
;; XXX: Tests attempt to download data such as
;; <https://raw.githubusercontent.com/pytorch/test-infra/master/stats/slow-tests.json>.
+ ;; We're also missing some Python modules, such as expecttest.
#:tests? #f))
(native-inputs
`(("cmake" ,cmake)
@@ -2878,6 +2859,7 @@ TensorFlow.js, PyTorch, and MediaPipe.")
("zstd" ,zstd)))
(propagated-inputs
`(("python-astunparse" ,python-astunparse)
+ ("python-click" ,python-click)
("python-numpy" ,python-numpy)
("python-pyyaml" ,python-pyyaml)
("python-cffi" ,python-cffi)
generated by cgit v1.2.3 (git 2.47.1) at 2025-01-30 23:45:01 +0000