diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 294 |
1 files changed, 24 insertions, 270 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9095984811..89be883cda 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -128,6 +128,7 @@ #:use-module (gnu packages python-check) #:use-module (gnu packages python-compression) #:use-module (gnu packages python-crypto) + #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages qt) #:use-module (gnu packages readline) @@ -1154,95 +1155,6 @@ human-friendly syntax.") (define-public python2-schedule (package-with-python2 python-schedule)) -(define-public python-pandas - (package - (name "python-pandas") - (version "0.25.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "pandas" version)) - (sha256 - (base32 "1gp2pvzdiakvgjmykdzdlzrsfbg4vjm49jjdl9s0ha0a3yfs34fa")))) - (build-system python-build-system) - (arguments - `(#:modules ((guix build utils) - (guix build python-build-system) - (ice-9 ftw) - (srfi srfi-26)) - #:phases (modify-phases %standard-phases - (add-after 'unpack 'patch-which - (lambda* (#:key inputs #:allow-other-keys) - (let ((which (assoc-ref inputs "which"))) - (substitute* "pandas/io/clipboard/__init__.py" - (("^CHECK_CMD = .*") - (string-append "CHECK_CMD = \"" which "\"\n")))) - #t)) - (replace 'check - (lambda _ - (let ((build-directory - (string-append - (getcwd) "/build/" - (car (scandir "build" - (cut string-prefix? "lib." <>)))))) - ;; Disable the "strict data files" option which causes - ;; the build to error out if required data files are - ;; not available (as is the case with PyPI archives). - (substitute* "setup.cfg" - (("addopts = --strict-data-files") "addopts = ")) - (with-directory-excursion build-directory - ;; Delete tests that require "moto" which is not yet - ;; in Guix. - (for-each delete-file - '("pandas/tests/io/conftest.py" - "pandas/tests/io/json/test_compression.py" - "pandas/tests/io/parser/test_network.py" - "pandas/tests/io/test_parquet.py")) - (invoke "pytest" "-vv" "pandas" "--skip-slow" - "--skip-network" "-k" - ;; XXX: Due to the deleted tests above. - "not test_read_s3_jsonl")))))))) - (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-openpyxl" ,python-openpyxl) - ("python-pytz" ,python-pytz) - ("python-dateutil" ,python-dateutil) - ("python-xlrd" ,python-xlrd))) - (inputs - `(("which" ,which))) - (native-inputs - `(("python-cython" ,python-cython) - ("python-beautifulsoup4" ,python-beautifulsoup4) - ("python-lxml" ,python-lxml) - ("python-html5lib" ,python-html5lib) - ("python-nose" ,python-nose) - ("python-pytest" ,python-pytest) - ("python-pytest-mock" ,python-pytest-mock))) - (home-page "https://pandas.pydata.org") - (synopsis "Data structures for data analysis, time series, and statistics") - (description - "Pandas is a Python package providing fast, flexible, and expressive data -structures designed to make working with structured (tabular, -multidimensional, potentially heterogeneous) and time series data both easy -and intuitive. It aims to be the fundamental high-level building block for -doing practical, real world data analysis in Python.") - (properties `((python2-variant . ,(delay python2-pandas)))) - (license license:bsd-3))) - -;; Pandas 0.24.x are the last versions that support Python 2. -(define-public python2-pandas - (let ((pandas (package-with-python2 - (strip-python2-variant python-pandas)))) - (package/inherit - pandas - (version "0.24.2") - (source (origin - (method url-fetch) - (uri (pypi-uri "pandas" version)) - (sha256 - (base32 - "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag"))))))) - (define-public python2-mechanize (package (name "python2-mechanize") @@ -3307,42 +3219,6 @@ Mallard using the @command{ducktype} tool. The yelp-tools package provides additional functionality on the produced Mallard documents.") (license license:expat))) -(define-public python-scikit-image - (package - (name "python-scikit-image") - (version "0.14.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "scikit-image" version)) - (sha256 - (base32 "07qchljkyxvg5nrm12fvszi7pmjk4m01qp0w0z8syxzxxs20pz8s")))) - (build-system python-build-system) - (arguments - ;; TODO: Some tests require running X11 server. Disable them? - '(#:tests? #f)) - ;; See DEPENDS.txt for the list of build and run time requiremnts - (propagated-inputs - `(("python-cloudpickle" ,python-cloudpickle) - ("python-dask" ,python-dask) - ("python-matplotlib" ,python-matplotlib) - ("python-networkx" ,python-networkx) - ("python-numpy" ,python-numpy) - ("python-pillow" ,python-pillow) - ("python-pywavelets" ,python-pywavelets) - ("python-scipy" ,python-scipy) - ("python-six" ,python-six))) - (native-inputs - `(("python-cython" ,python-cython))) - (home-page "http://scikit-image.org/") - (synopsis "Image processing in Python") - (description - "Scikit-image is a collection of algorithms for image processing.") - (license license:bsd-3))) - -(define-public python2-scikit-image - (package-with-python2 python-scikit-image)) - (define-public python-cython (package (name "python-cython") @@ -4312,125 +4188,6 @@ those files. It can also efficiently manipulate ranges of integers using set operators such as union, intersection, and difference.") (license license:asl2.0))) -(define-public python-scipy - (package - (name "python-scipy") - (version "1.3.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "scipy" version)) - (sha256 - (base32 "192d8dsybvhv19igkrsafbdafx198nz7pibkjgrqjhlr66s3jfd0")))) - (build-system python-build-system) - (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-matplotlib" ,python-matplotlib) - ("python-pyparsing" ,python-pyparsing))) - (inputs - `(("lapack" ,lapack) - ("openblas" ,openblas))) - (native-inputs - `(("python-cython" ,python-cython) - ("python-pytest" ,python-pytest) - ("python-sphinx" ,python-sphinx) - ("python-numpydoc" ,python-numpydoc) - ("gfortran" ,gfortran) - ("perl" ,perl) - ("which" ,which))) - (outputs '("out" "doc")) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'disable-broken-tests - (lambda _ - (substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py" - (("^( +)def test_threads_parallel\\(self\\):" m indent) - (string-append indent - "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" - m))) - (substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py" - (("^def test_parallel_threads\\(\\):" m) - (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" - m))) - #t)) - (add-before 'build 'configure-openblas - (lambda* (#:key inputs #:allow-other-keys) - (call-with-output-file "site.cfg" - (lambda (port) - (format port - "[blas] -libraries = openblas -library_dirs = ~a/lib -include_dirs = ~a/include - -# backslash-n to make emacs happy -\n[atlas] -library_dirs = ~a/lib -atlas_libs = openblas -" - (assoc-ref inputs "openblas") - (assoc-ref inputs "openblas") - (assoc-ref inputs "openblas")))) - #t)) - (add-after 'install 'install-doc - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((data (string-append (assoc-ref outputs "doc") "/share")) - (doc (string-append data "/doc/" ,name "-" ,version)) - (html (string-append doc "/html")) - (pyver ,(string-append "PYVER=" (version-major+minor - (package-version python)))) - ;; By default it tries to run sphinx-build through the Python - ;; interpreter which won't work with our shell wrapper. - (sphinxbuild "SPHINXBUILD=LANG=C sphinx-build")) - ;; Make installed package available for building the - ;; documentation - (add-installed-pythonpath inputs outputs) - (with-directory-excursion "doc" - ;; Fix generation of images for mathematical expressions. - (substitute* (find-files "source" "conf\\.py") - (("pngmath_use_preview = True") - "pngmath_use_preview = False")) - (mkdir-p html) - (invoke "make" "html" pyver sphinxbuild) - (with-directory-excursion "build/html" - (for-each (lambda (file) - (let* ((dir (dirname file)) - (tgt-dir (string-append html "/" dir))) - (install-file file html))) - (find-files "." ".*"))))) - #t)) - ;; Tests can only be run after the library has been installed and not - ;; within the source directory. - (delete 'check) - (add-after 'install 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (with-directory-excursion "/tmp" - (invoke "python" "-c" - "import scipy; scipy.test(verbose=2)"))))))) - (home-page "https://www.scipy.org/") - (synopsis "The Scipy library provides efficient numerical routines") - (description "The SciPy library is one of the core packages that make up -the SciPy stack. It provides many user-friendly and efficient numerical -routines such as routines for numerical integration and optimization.") - (properties `((python2-variant . ,(delay python2-scipy)))) - (license license:bsd-3))) - -;; Version 1.2.2 is the last version to support Python 2 -(define-public python2-scipy - (package - (inherit (package-with-python2 - (strip-python2-variant python-scipy))) - (version "1.2.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "scipy" version)) - (sha256 - (base32 - "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4")))))) - (define-public python-socksipy-branch (package (name "python-socksipy-branch") @@ -4462,7 +4219,7 @@ as the original project seems to have been abandoned circa 2007.") (define-public python-socksipychain (package (name "python-socksipychain") - (version "2.0.15") + (version "2.1.0") (source (origin (method git-fetch) @@ -4472,7 +4229,7 @@ as the original project seems to have been abandoned circa 2007.") (file-name (git-file-name name version)) (sha256 (base32 - "1pkljnh9hfwla8sg7mil4f9zrnsqj0dbhr3crxjw3k8dnjz70dvk")))) + "0idm9a050rd2kbgbz2sk9ib9589kj4xh1xdnggs6xbq2v2y8f6zn")))) (build-system python-build-system) (arguments `(#:tests? #f)) ; Tests try to access the network. @@ -4485,9 +4242,6 @@ TLS/SSL encryption. It was developed for use in PageKite, and also includes a simple netcat replacement with chaining support.") (license license:bsd-3))) -(define-public python2-socksipychain - (package-with-python2 python-socksipychain)) - (define-public python-pycodestyle (package (name "python-pycodestyle") @@ -4677,25 +4431,25 @@ the OleFileIO module from PIL, the Python Image Library.") (define-public python-pillow (package (name "python-pillow") - (version "6.1.0") + (version "6.2.1") (source (origin (method url-fetch) (uri (pypi-uri "Pillow" version)) (sha256 (base32 - "1pnrsz0f0n0c819v1pdr8j6rm8xvhc9f3kh1fv9xpdp9n5ygf108")))) + "1c8wkzc58f5wdh006jvmwdk3wxld1xgagcbdvj7iv17qi0m9fkmz")))) (build-system python-build-system) (native-inputs `(("python-pytest" ,python-pytest))) (inputs `(("freetype" ,freetype) ("lcms" ,lcms) - ("zlib" ,zlib) ("libjpeg" ,libjpeg) - ("openjpeg" ,openjpeg) ("libtiff" ,libtiff) - ("libwebp" ,libwebp))) + ("libwebp" ,libwebp) + ("openjpeg" ,openjpeg) + ("zlib" ,zlib))) (propagated-inputs `(("python-olefile" ,python-olefile))) (arguments @@ -4705,15 +4459,16 @@ the OleFileIO module from PIL, the Python Image Library.") (lambda _ (substitute* "setup.py" (("\\['/sbin/ldconfig', '-p'\\]") "['true']")))) - (delete 'check) ; We must run checks after python-pillow is installed. - (add-after 'install 'check-installed - (lambda* (#:key outputs inputs #:allow-other-keys) - (begin - (setenv "HOME" (getcwd)) - ;; Make installed package available for running the tests. - (add-installed-pythonpath inputs outputs) - (invoke "python" "selftest.py" "--installed") - (invoke "python" "-m" "pytest" "-vv"))))))) + (replace 'check + (lambda* (#:key outputs inputs tests? #:allow-other-keys) + (if tests? + (begin + (setenv "HOME" (getcwd)) + ;; Make installed package available for running the tests. + (add-installed-pythonpath inputs outputs) + (invoke "python" "selftest.py" "--installed") + (invoke "python" "-m" "pytest" "-vv")) + #t)))))) (home-page "https://python-pillow.org") (synopsis "Fork of the Python Imaging Library") (description @@ -8660,13 +8415,13 @@ minimal and fast API targeting the following uses: (define-public python-icalendar (package (name "python-icalendar") - (version "4.0.3") + (version "4.0.4") (source (origin (method url-fetch) (uri (pypi-uri "icalendar" version)) (sha256 (base32 - "0mk3dk1dxkcm46jy48v27j2w2349iv4sbimqj1yb5js43mx49hh7")))) + "16gjvqv0n05jrb9g228pdjgzd3amz2pdhvcgsn1jypszjg5m2w9l")))) (build-system python-build-system) (propagated-inputs `(("python-dateutil" ,python-dateutil) @@ -12476,13 +12231,13 @@ projects.") (package (name "python-invoke") (home-page "http://www.pyinvoke.org/") - (version "1.1.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (pypi-uri "invoke" version)) (sha256 (base32 - "0aiy1xvk1f91246zxd1zqrm679vdvd10h843a2na41cqr3cflpi6")))) + "1nn7gad0rvy492acpyhkrp01zsk86acf34qhsvq4xmm6x39788n5")))) (build-system python-build-system) (arguments ;; XXX: Requires many dependencies that are not yet in Guix. @@ -14381,14 +14136,13 @@ Git.") (define-public python-pyclipper (package (name "python-pyclipper") - (version "1.1.0.post1") + (version "1.1.0.post3") (source (origin (method url-fetch) (uri (pypi-uri "pyclipper" version ".zip")) (sha256 - (base32 - "0ldbkbnx94an4zzrwb1sxmg6k0jgk4cwmvcdyy8y5k1zslc612wa")) + (base32 "164yksvqwqvwzh8f8lq92asg87hd8rvcy2xb5vm4y4ccvd5xgb7i")) (modules '((guix build utils))) (snippet '(begin |