diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 187 |
1 files changed, 111 insertions, 76 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 35ac4e69f5..2294b59f33 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -113,6 +113,7 @@ #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages python-check) #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-web) #:use-module (gnu packages qt) @@ -434,42 +435,80 @@ concepts.") (define-public python2-h5py (package-with-python2 python-h5py)) +(define-public python-sh + (package + (name "python-sh") + (version "1.12.14") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sh" version)) + (sha256 + (base32 + "1z2hx357xp3v4cv44xmqp7lli3frndqpyfmpbxf7n76h7s1zaaxm")))) + (build-system python-build-system) + (home-page "https://github.com/amoffat/sh") + (synopsis "Python subprocess replacement") + (description "This package provides a replacement for Python's +@code{subprocess} feature.") + (license license:expat))) + +(define-public python-cftime + (package + (name "python-cftime") + (version "1.0.3.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cftime" version)) + (sha256 + (base32 + "0362dhxbzk593walyjz30dll6y2y79wialik647cbwdsf3ad0x6x")))) + (build-system python-build-system) + (propagated-inputs + `(("python-numpy" ,python-numpy))) + (native-inputs + `(("python-coveralls" ,python-coveralls) + ("python-cython" ,python-cython) + ("python-pytest-cov" ,python-pytest-cov))) + (home-page "https://github.com/Unidata/cftime") + (synopsis "Library for time handling") + (description + "This package provides time-handling functionality that used to be part +of the netcdf4 package before.") + ;; This package claims to include code under the GPLv3 but is released + ;; under ISC. + (license (list license:isc license:gpl3+)))) + (define-public python-netcdf4 (package (name "python-netcdf4") - (version "1.2.9") + (version "1.4.2") (source (origin (method url-fetch) (uri (pypi-uri "netCDF4" version)) (sha256 (base32 - "1h6jq338amlbk0ilzvjyl7cck80i0bah9a5spn9in71vy2qxm7i5")))) + "0c0sklgrmv15ygliin8qq0hp7vanmbi74m6zpi0r1ksr0hssyd5r")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'configure-locations + (lambda* (#:key inputs #:allow-other-keys) + (setenv "HDF5_DIR" (assoc-ref inputs "hdf5")) + #t))))) (native-inputs `(("python-cython" ,python-cython))) (propagated-inputs - `(("python-numpy" ,python-numpy))) + `(("python-numpy" ,python-numpy) + ("python-cftime" ,python-cftime))) (inputs `(("netcdf" ,netcdf) ("hdf4" ,hdf4) ("hdf5" ,hdf5))) - (arguments - '(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ - (setenv "NO_NET" "1") ; disable opendap tests - (with-directory-excursion "test" - (setenv "PYTHONPATH" ; find and add the library we just built - (string-append - (car (find-files "../build" "lib.*" - #:directories? #:t - #:fail-on-error? #:t)) - ":" (getenv "PYTHONPATH"))) - (zero? (system* "python" "run_all.py")))))))) - (home-page - "https://github.com/Unidata/netcdf4-python") + (home-page "https://github.com/Unidata/netcdf4-python") (synopsis "Python/numpy interface to the netCDF library") (description "Netcdf4-python is a Python interface to the netCDF C library. netCDF version 4 has many features not found in earlier @@ -1710,7 +1749,7 @@ version numbers.") (arguments '(#:phases (modify-phases %standard-phases - (replace 'check (lambda _ (zero? (system* "nosetests"))))))) + (replace 'check (lambda _ (invoke "nosetests")))))) (native-inputs `(("python-nose" ,python-nose) ("python-vcversioner" ,python-vcversioner))) @@ -2106,7 +2145,7 @@ logic-free templating system Mustache.") (modify-phases %standard-phases (replace 'check (lambda _ - (zero? (system* "python" "test_pystache.py"))))))))) + (invoke "python" "test_pystache.py")))))))) (define-public python-joblib (package @@ -2855,8 +2894,7 @@ objects.") `(#:phases (modify-phases %standard-phases (replace 'check - (lambda _ - (zero? (system* "nosetests" "-v"))))))) + (lambda _ (invoke "nosetests" "-v")))))) (propagated-inputs `(("python-colormath" ,python-colormath))) (native-inputs @@ -2963,12 +3001,12 @@ color scales, and color space conversion easy. It has support for: (with-directory-excursion "doc" (copy-recursively sphinx-theme-checkout scipy-sphinx-theme) (mkdir-p html) - (system* "make" "html" pyver) - (system* "make" "latex" "PAPER=a4" pyver) - (system* "make" "-C" "build/latex" + (invoke "make" "html" pyver) + (invoke "make" "latex" "PAPER=a4" pyver) + (invoke "make" "-C" "build/latex" "all-pdf" "PAPER=a4" pyver) ;; FIXME: Generation of the info file fails. - ;; (system* "make" "info" pyver) + ;; (invoke "make" "info" pyver) ;; (mkdir-p info) ;; (copy-file "build/texinfo/numpy.info" ;; (string-append info "/numpy.info")) @@ -3193,7 +3231,7 @@ To address this and enable easy cycling over arbitrary @code{kwargs}, the (modify-phases %standard-phases (replace 'check (lambda _ - (zero? (system* "nosetests" "--all-modules" "-v" "colorspacious"))))))) + (invoke "nosetests" "--all-modules" "-v" "colorspacious")))))) (home-page "https://github.com/njsmith/colorspacious") (synopsis "Python library for colorspace conversions") (description "@code{colorspacious} is a Python library that lets you @@ -3376,24 +3414,25 @@ toolkits.") (define-public python2-pysnptools (package (name "python2-pysnptools") - (version "0.3.9") + (version "0.3.13") (source (origin (method url-fetch) - (uri (pypi-uri "pysnptools" version ".zip")) + (uri (pypi-uri "pysnptools" version)) (sha256 (base32 - "1wybggjzz8zw7aav4pjsg2h22xp17a1lghrprza1pxwlm7wf96y2")))) + "0lnis5xsl7bi0hz4f7gbicahzi5zlxkc21nk3g374xv8fb5hb3qm")))) (build-system python-build-system) (arguments - `(#:python ,python-2)) ; only Python 2.7 is supported + `(#:python ,python-2 ; only Python 2.7 is supported + #:tests? #f)) ; test files (e.g. examples/toydata.bim) not included (propagated-inputs `(("python2-numpy" ,python2-numpy) ("python2-scipy" ,python2-scipy) ("python2-pandas" ,python2-pandas))) (native-inputs - `(("unzip" ,unzip))) - (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/") + `(("python2-cython" ,python2-cython))) + (home-page "http://microsoftgenomics.github.io/PySnpTools/") (synopsis "Library for reading and manipulating genetic data") (description "PySnpTools is a library for reading and manipulating genetic data. It @@ -3603,7 +3642,8 @@ where key might be occurred more than once in the container.") ;; The package uses nosetest for running the tests. ;; Adding this initfile allows to run the test suite ;; without requiring nosetest. - (zero? (system* "touch" "tests/__init__.py"))))))) + (with-output-to-file "tests/__init__.py" newline) + #t))))) (propagated-inputs `(("python-six" ,python-six))) (native-inputs @@ -3803,7 +3843,8 @@ a general image processing tool.") (replace 'check (lambda _ (with-directory-excursion "tests" - (zero? (system* "python" "all_tests.py"))))) + (invoke "python" "all_tests.py")) + #t)) (add-after 'install 'install-doc (lambda* (#:key outputs #:allow-other-keys) (let* ((data (string-append (assoc-ref outputs "doc") "/share")) @@ -4145,7 +4186,7 @@ cluster without needing to write any wrapper code yourself.") ;; It's easier to run tests after install. ;; Make installed package available for running the tests (add-installed-pythonpath inputs outputs) - (zero? (system* "py.test" "-v"))))))) + (invoke "py.test" "-v")))))) (home-page "https://github.com/nickstenning/honcho") (synopsis "Manage Procfile-based applications") (description @@ -4854,7 +4895,7 @@ libxml2 and libxslt.") ;; For more information, see the file 'convert-py3k' in the source ;; distribution. (replace 'check - (lambda _ (zero? (system* "./convert-py3k"))))))) + (lambda _ (invoke "./convert-py3k")))))) (home-page "https://www.crummy.com/software/BeautifulSoup/bs4/") (synopsis @@ -5101,8 +5142,7 @@ and statistical routines from scipy and statsmodels.") (modify-phases %standard-phases (replace 'check (lambda _ - (zero? - (system* "python" "mpmath/tests/runtests.py" "-local"))))))) + (invoke "python" "mpmath/tests/runtests.py" "-local")))))) (home-page "http://mpmath.org") (synopsis "Arbitrary-precision floating-point arithmetic in python") (description @@ -5324,7 +5364,7 @@ Python 2 and Python 3.") (modify-phases %standard-phases (replace 'check (lambda _ - (zero? (system* "py.test" "-v"))))))) + (invoke "py.test" "-v")))))) (native-inputs `(("python2-pytest" ,python2-pytest))) (home-page "https://github.com/chrippa/backports.shutil_get_terminal_size") @@ -5668,7 +5708,7 @@ PEP8_PLUGIN('break_before_binary_operator'),")) (setenv "PYTHONPATH" (string-append (getcwd) "/build/lib:" (getenv "PYTHONPATH"))) - (zero? (system* "py.test" "-v"))))))) + (invoke "py.test" "-v")))))) (native-inputs `(("python-flake8" ,python-flake8) ("python-mock" ,python-mock) @@ -5754,8 +5794,7 @@ markdown_py is also provided to convert Markdown files to HTML.") `(#:phases (modify-phases %standard-phases (replace 'check - (lambda _ - (zero? (system* "nosetests"))))))) + (lambda _ (invoke "nosetests")))))) (home-page "https://github.com/pexpect/ptyprocess") (synopsis "Run a subprocess in a pseudo terminal") (description @@ -5809,7 +5848,7 @@ pseudo terminal (pty), and interact with both the process and its pty.") (add-installed-pythonpath inputs outputs) (setenv "PATH" (string-append (getenv "PATH") ":" (assoc-ref outputs "out") "/bin")) - (zero? (system* "make" "test"))))))) + (invoke "make" "test")))))) (build-system python-build-system) (native-inputs `(("python-coverage" ,python-coverage) @@ -6090,7 +6129,7 @@ and MAC network addresses.") (modify-phases %standard-phases ;; Current test in setup.py does not work as of 1.0.0, so use nose to ;; run tests instead for now. - (replace 'check (lambda _ (zero? (system* "nosetests"))))))) + (replace 'check (lambda _ (invoke "nosetests")))))) (native-inputs `(("python-nose" ,python-nose))) (home-page "http://www.python-excel.org/") (synopsis "Library for extracting data from Excel files") @@ -6166,14 +6205,14 @@ printing of sub-tables by specifying a row range.") #t)) (replace 'build (lambda* (#:key inputs #:allow-other-keys) - (zero? (system* "python" "setup.py" "build" - (string-append "--hdf5=" - (assoc-ref inputs "hdf5")))))) + (invoke "python" "setup.py" "build" + (string-append "--hdf5=" + (assoc-ref inputs "hdf5"))))) (replace 'check (lambda* (#:key inputs #:allow-other-keys) - (zero? (system* "python" "setup.py" "check" - (string-append "--hdf5=" - (assoc-ref inputs "hdf5"))))))))) + (invoke "python" "setup.py" "check" + (string-append "--hdf5=" + (assoc-ref inputs "hdf5")))))))) (propagated-inputs `(("python-numexpr" ,python-numexpr) ("python-numpy" ,python-numpy))) @@ -6278,8 +6317,7 @@ implementations of ASN.1-based codecs and protocols.") #:phases (modify-phases %standard-phases (replace 'check - (lambda* _ - (zero? (system* "python" "ipaddr_test.py"))))))) + (lambda _ (invoke "python" "ipaddr_test.py")))))) (home-page "https://github.com/google/ipaddr-py") (synopsis "IP address manipulation library") (description @@ -8489,7 +8527,7 @@ module, adding support for Unicode strings.") (modify-phases %standard-phases (replace 'check ;; Many tests fail, but the installation proceeds. - (lambda _ (zero? (system* "make" "-C" "test" "test"))))))) + (lambda _ (invoke "make" "-C" "test" "test")))))) (native-inputs `(("which" ,which))) ; required for tests (propagated-inputs @@ -9497,8 +9535,7 @@ parsing UK postcodes.") '(#:phases (modify-phases %standard-phases (replace 'check - (lambda _ - (zero? (system* "python" "-m" "unittest" "-v" "tests"))))))) + (lambda _ (invoke "python" "-m" "unittest" "-v" "tests")))))) (native-inputs `(;; For testing ("python-email-validator" ,python-email-validator) @@ -9634,17 +9671,17 @@ characters, mouse support, and auto suggestions.") (define-public python-jedi (package (name "python-jedi") - (version "0.13.1") + (version "0.13.2") (source (origin (method url-fetch) (uri (pypi-uri "jedi" version)) (sha256 (base32 - "0j11q42g5vjkyhhjpyy8nb0gdxs78m3rpjai7p1hvgpyl9rkyjdp")))) + "1za944msp0f8x36qa8l309jhv0kzlsdh7r9nj3z12y8npnsh45sp")))) (build-system python-build-system) (arguments - `( ;; Many tests are failing with Python 3.7.x as of version 0.13.1 (see: + `( ;; Many tests are failing with Python 3.7.x as of version 0.13.2 (see: ;; https://github.com/davidhalter/jedi/issues/1263) #:tests? #f #:phases @@ -9991,9 +10028,9 @@ discovery, monitoring and configuration.") ;; The test runner invokes python2 and python3 for test*.py. ;; To avoid having both in inputs, we replicate it here. (lambda _ - (every (lambda (test-file) - (zero? (system* "python" test-file))) - (find-files "tests" "^test.*\\.py$"))))))) + (for-each (lambda (test-file) (invoke "python" test-file)) + (find-files "tests" "^test.*\\.py$")) + #t))))) (build-system python-build-system) (home-page "https://github.com/eea/odfpy") (synopsis "Python API and tools to manipulate OpenDocument files") @@ -10392,7 +10429,7 @@ is used by PostgreSQL and the OpenSSH Server for example.") (setenv "PYTHONPATH" (string-append (getcwd) "/build/lib:" (getenv "PYTHONPATH"))) - (zero? (system* "py.test" "-vv" ))))))) + (invoke "py.test" "-vv" )))))) (native-inputs `(("python-pytest" ,python-pytest))) (home-page @@ -10512,7 +10549,7 @@ PNG, JPEG, JPEG2000 and GIF files in pure Python.") (modify-phases %standard-phases (replace 'check (lambda _ - (zero? (system* "python" "test3.py"))))))) + (invoke "python" "test3.py")))))) (home-page "https://github.com/gfxmonk/termstyle") (synopsis "Console text coloring for Python") (description "This package provides console text coloring for Python.") @@ -10720,7 +10757,7 @@ protocols written in pure Python.") (setenv "PYTHONPATH" (string-append (getcwd) "/build/lib:" (getenv "PYTHONPATH"))) - (zero? (system* "python" "test/test_pbkdf2.py"))))))) + (invoke "python" "test/test_pbkdf2.py")))))) (propagated-inputs `(("python-pycrypto" ,python-pycrypto))) ; optional (home-page "https://www.dlitz.net/software/python-pbkdf2/") @@ -10928,7 +10965,7 @@ Problem} (SAT) solver.") (add-after 'install 'check (lambda* (#:key inputs outputs #:allow-other-keys) (add-installed-pythonpath inputs outputs) - (zero? (system* "python" "test/testordereddict.py"))))))) + (invoke "python" "test/testordereddict.py")))))) (home-page "https://bitbucket.org/ruamel/ordereddict") (synopsis "Version of dict that keeps keys in insertion order") (description @@ -11185,7 +11222,7 @@ protocols.") ;; Disable python3 tests (substitute* "check" (("python3") "# python3")) - (zero? (system* "./check"))))))) + (invoke "./check")))))) (native-inputs `(("python2-coverage-test-runner" ,python2-coverage-test-runner) ("python2-pep8" ,python2-pep8))) @@ -11225,8 +11262,7 @@ iterating over input files.") ;; and fails. (delete 'check) (add-before 'build 'check - (lambda _ - (zero? (system* "make" "check"))))))) + (lambda _ (invoke "make" "check")))))) (home-page "https://liw.fi/ttystatus/") (synopsis "Python library for showing progress reporting and status updates on terminals") @@ -11288,8 +11324,7 @@ happens using the @code{logging} library.") ;; and fails. (delete 'check) (add-before 'build 'check - (lambda _ - (zero? (system* "make" "check"))))))) + (lambda _ (invoke "make" "check")))))) (native-inputs `(("cmdtest" ,cmdtest) ("python2-coverage-test-runner" ,python2-coverage-test-runner))) @@ -12303,7 +12338,7 @@ Swagger 2.0).") (setenv "PYTHONPATH" (string-append (getcwd) ":" (getenv "PYTHONPATH"))) - (zero? (system* "py.test"))))))) + (invoke "py.test")))))) (propagated-inputs `(("python-flask" ,python-flask) ("python-pyyaml" ,python-pyyaml) @@ -13149,9 +13184,9 @@ is the new Pyro version that is actively developed.") (modify-phases %standard-phases (replace 'build (lambda* (#:key inputs #:allow-other-keys) - (zero? (system* "python" "setup.py" "build" - (string-append "--netcdf_prefix=" - (assoc-ref inputs "netcdf"))))))))) + (invoke "python" "setup.py" "build" + (string-append "--netcdf_prefix=" + (assoc-ref inputs "netcdf")))))))) (home-page "https://bitbucket.org/khinsen/scientificpython") (synopsis "Python modules for scientific computing") (description "ScientificPython is a collection of Python modules that are |