diff options
Diffstat (limited to 'gnu/packages/python-science.scm')
| -rw-r--r-- | gnu/packages/python-science.scm | 116 |
1 files changed, 49 insertions, 67 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 393e59896d..8df311baea 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -4,9 +4,9 @@ ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com> ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il> -;;; Copyright © 2016, 2017, 2018, 2019, 2020 Marius Bakke <mbakke@fastmail.com> +;;; Copyright © 2016-2020, 2022 Marius Bakke <marius@gnu.org> ;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr> -;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2019, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org> ;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com> ;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net> @@ -66,13 +66,13 @@ (define-public python-scipy (package (name "python-scipy") - (version "1.6.0") + (version "1.7.3") (source (origin (method url-fetch) (uri (pypi-uri "scipy" version)) (sha256 - (base32 "0rh5b1rwdcvvagld8vpxnpaibszy1skpx39a0fwzd5gx5pwcjvfb")))) + (base32 "1gxsnw6viz2j3sm8ak2a8l7fcn4b2zm3kzfm8w57xxyyrzx7an5b")))) (build-system python-build-system) (propagated-inputs (list python-numpy python-matplotlib python-pyparsing)) @@ -80,8 +80,10 @@ (list openblas pybind11)) (native-inputs (list python-cython + python-pydata-sphinx-theme python-pytest python-sphinx + python-sphinx-panels python-numpydoc gfortran perl @@ -90,11 +92,13 @@ (arguments `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'disable-pythran + (lambda _ + (setenv "SCIPY_USE_PYTHRAN" "0"))) (add-before 'build 'change-home-dir (lambda _ ;; Change from /homeless-shelter to /tmp for write permission. - (setenv "HOME" "/tmp") - #t)) + (setenv "HOME" "/tmp"))) (add-after 'unpack 'disable-broken-tests (lambda _ (substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py" @@ -105,8 +109,7 @@ (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)) + m))))) (add-before 'build 'configure-openblas (lambda* (#:key inputs #:allow-other-keys) (call-with-output-file "site.cfg" @@ -124,8 +127,7 @@ atlas_libs = openblas " (assoc-ref inputs "openblas") (assoc-ref inputs "openblas") - (assoc-ref inputs "openblas")))) - #t)) + (assoc-ref inputs "openblas")))))) (add-after 'install 'install-doc (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((data (string-append (assoc-ref outputs "doc") "/share")) @@ -151,8 +153,7 @@ atlas_libs = openblas (let* ((dir (dirname file)) (tgt-dir (string-append html "/" dir))) (install-file file html))) - (find-files "." ".*"))))) - #t)) + (find-files "."))))))) ;; Tests can only be run after the library has been installed and not ;; within the source directory. (delete 'check) @@ -238,13 +239,7 @@ Cython.") (sha256 (base32 "0bp1n771fj44kdp7a00bcvfwirvv2rc803b7g6yf3va7v0j29c8s")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ - (invoke "nosetests" "-s" "-v" "skfuzzy") - #t))))) + (arguments '(#:tests? #f)) ;XXX: not compatible with newer numpy.testing (native-inputs (list python-nose)) (propagated-inputs @@ -335,13 +330,13 @@ of the SGP4 satellite tracking algorithm.") (define-public python-pandas (package (name "python-pandas") - (version "1.3.4") + (version "1.3.5") (source (origin (method url-fetch) (uri (pypi-uri "pandas" version)) (sha256 - (base32 "1z3gm521wpm3j13rwhlb4f2x0645zvxkgxij37i3imdpy39iiam2")))) + (base32 "1wd92ra8xcjgigbypid53gvby89myg68ica6r8hdw4hhvvsqahhy")))) (build-system python-build-system) (arguments `(#:modules ((guix build utils) @@ -378,23 +373,23 @@ of the SGP4 satellite tracking algorithm.") (invoke "pytest" "-vv" "pandas" "--skip-slow" "--skip-network" "-k" - ;; These tets access the internet: - ;; pandas/tests/io/xml/test_xml.py::test_wrong_url[lxml] - ;; pandas/tests/io/xml/test_xml.py::test_wrong_url[etree] - ;; TODO: the excel tests fail for unknown reasons - (string-append "not test_wrong_url" - " and not test_excelwriter_fspath" - " and not test_ExcelWriter_dispatch" - ;; TODO: Missing input - " and not TestS3" - " and not s3")))))))))) + (string-append + ;; These test access the internet (see: + ;; https://github.com/pandas-dev/pandas/issues/45085).: + ;; pandas/tests/io/xml/test_xml.py::test_wrong_url[lxml] + ;; pandas/tests/io/xml/test_xml.py::test_wrong_url[etree] + "not test_wrong_url" + ;; TODO: Missing input + " and not TestS3" + " and not s3")))))))))) (propagated-inputs (list python-jinja2 python-numpy python-openpyxl python-pytz python-dateutil - python-xlrd)) + python-xlrd + python-xlsxwriter)) (inputs (list which xclip xsel)) (native-inputs @@ -402,7 +397,6 @@ of the SGP4 satellite tracking algorithm.") python-beautifulsoup4 python-lxml python-html5lib - python-nose python-pytest python-pytest-mock ;; Needed to test clipboard support. @@ -418,33 +412,10 @@ doing practical, real world data analysis in Python.") (properties `((python2-variant . ,(delay python2-pandas)))) (license license:bsd-3))) -(define-public python-pandas-0.25 - (package - (inherit python-pandas) - (version "0.25.3") - (source (origin - (method url-fetch) - (uri (pypi-uri "pandas" version)) - (sha256 - (base32 - "191048m6kdc6yfvqs9w412lq60cfvigrsb57y0x116lwibgp9njj")))) - (arguments - (substitute-keyword-arguments (package-arguments python-pandas) - ((#:phases phases) - `(modify-phases ,phases - (replace '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)) - (delete 'prepare-x))))))) - ;; 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-0.25)))) + (strip-python2-variant python-pandas)))) (package (inherit pandas) (version "0.24.2") @@ -704,26 +675,31 @@ annotations on an existing boxplots and barplots generated by seaborn.") (define-public python-upsetplot (package (name "python-upsetplot") - (version "0.4.1") + (version "0.6.0") (source (origin (method url-fetch) (uri (pypi-uri "UpSetPlot" version)) (sha256 (base32 - "0kwljcmsvrxm33y3ssham2bwv4a5m31mv96y9h18va0cv7s3mqn1")))) + "11zrykwnb00w5spx4mnsnm0f9gwrphdczainpmwkyyi50vipaa2l")) + (modules '((guix build utils))) + (snippet + ;; Patch for compatibility with newer setuptools: + ;; https://github.com/jnothman/UpSetPlot/pull/178 + '(substitute* "upsetplot/data.py" + (("import distutils") + "from distutils.version import LooseVersion") + (("if distutils\\.version\\.LooseVersion") + "if LooseVersion"))))) (build-system python-build-system) (arguments - `(#:phases + '(#:phases (modify-phases %standard-phases - (add-after 'unpack 'fix-versioning - (lambda _ - (substitute* "setup.py" - (("pytest-cov<2.6") "pytest-cov")))) (replace 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "pytest" "-v" "--doctest-modules")))))) + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-v" "--doctest-modules"))))))) (propagated-inputs (list python-matplotlib python-pandas)) (native-inputs @@ -992,6 +968,12 @@ computing in Python. It extends both the @code{concurrent.futures} and (add-after 'unpack 'make-files-writable (lambda _ (for-each make-file-writable (find-files ".")))) + (add-after 'unpack 'loosen-requirements + (lambda _ + (substitute* "setup.py" + ;; Don't depend on a specific version of Pandas. + (("pandas==") + "pandas>=")))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? |