diff options
Diffstat (limited to 'gnu/packages/python-science.scm')
| -rw-r--r-- | gnu/packages/python-science.scm | 278 |
1 files changed, 127 insertions, 151 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index eb1f8312cd..d23c56daa6 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -75,20 +75,17 @@ (base32 "0rh5b1rwdcvvagld8vpxnpaibszy1skpx39a0fwzd5gx5pwcjvfb")))) (build-system python-build-system) (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-matplotlib" ,python-matplotlib) - ("python-pyparsing" ,python-pyparsing))) + (list python-numpy python-matplotlib python-pyparsing)) (inputs - `(("openblas" ,openblas) - ("pybind11" ,pybind11))) + (list openblas pybind11)) (native-inputs - `(("python-cython" ,python-cython) - ("python-pytest" ,python-pytest) - ("python-sphinx" ,python-sphinx) - ("python-numpydoc" ,python-numpydoc) - ("gfortran" ,gfortran) - ("perl" ,perl) - ("which" ,which))) + (list python-cython + python-pytest + python-sphinx + python-numpydoc + gfortran + perl + which)) (outputs '("out" "doc")) (arguments `(#:phases @@ -188,14 +185,14 @@ routines such as routines for numerical integration and optimization.") (base32 "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4")))) (native-inputs - `(("python-cython" ,python2-cython) - ("python-pytest" ,python2-pytest) - ("python-sphinx" ,python2-sphinx) - ("python-numpydoc" ,python2-numpydoc) - ("gfortran" ,gfortran-7) - ("gcc" ,gcc-7) - ("perl" ,perl) - ("which" ,which))))) + (list python2-cython + python2-pytest + python2-sphinx + python2-numpydoc + gfortran-7 + gcc-7 + perl + which)))) (define-public python2-weave (package @@ -218,9 +215,9 @@ routines such as routines for numerical integration and optimization.") "--exclude" "test_(user|incorrect_ownership|char_fail|obj_fail)")))))) (propagated-inputs - `(("python-numpy" ,python2-numpy))) + (list python2-numpy)) (native-inputs - `(("python-nose" ,python2-nose))) + (list python2-nose)) (home-page "https://www.scipy.org/") (synopsis "Tools for including C/C++ code within Python code") (description "Weave is the stand-alone version of the obsolete Scipy @@ -249,11 +246,9 @@ Cython.") (invoke "nosetests" "-s" "-v" "skfuzzy") #t))))) (native-inputs - `(("python-nose" ,python-nose))) + (list python-nose)) (propagated-inputs - `(("python-networkx" ,python-networkx) - ("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy))) + (list python-networkx python-numpy python-scipy)) (home-page "https://github.com/scikit-fuzzy/scikit-fuzzy") (synopsis "Fuzzy logic toolkit for SciPy") (description @@ -293,24 +288,24 @@ logic, also known as grey logic.") ;; NOTE: scikit-image has an optional dependency on python-pooch, however ;; propagating it would enable many more tests that require online data. (propagated-inputs - `(("python-cloudpickle" ,python-cloudpickle) - ("python-dask" ,python-dask) - ("python-imageio" ,python-imageio) - ("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-tifffile" ,python-tifffile))) + (list python-cloudpickle + python-dask + python-imageio + python-matplotlib + python-networkx + python-numpy + python-pillow + python-pywavelets + python-scipy + python-tifffile)) (native-inputs - `(("python-codecov" ,python-codecov) - ("python-cython" ,python-cython) - ("python-flake8" ,python-flake8) - ("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-localserver" ,python-pytest-localserver) - ("python-wheel" ,python-wheel))) + (list python-codecov + python-cython + python-flake8 + python-pytest + python-pytest-cov + python-pytest-localserver + python-wheel)) (home-page "https://scikit-image.org/") (synopsis "Image processing in Python") (description @@ -329,7 +324,7 @@ logic, also known as grey logic.") (base32 "0dncp9i5b6afkg7f8mj9j0qzsp008b8v73yc0qkmizhpns7mvwvx")))) (build-system python-build-system) (propagated-inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (home-page "https://github.com/brandon-rhodes/python-sgp4") (synopsis "Track earth satellite TLE orbits using SGP4") (description @@ -394,26 +389,24 @@ of the SGP4 satellite tracking algorithm.") " and not TestS3" " and not s3")))))))))) (propagated-inputs - `(("python-jinja2" ,python-jinja2) - ("python-numpy" ,python-numpy) - ("python-openpyxl" ,python-openpyxl) - ("python-pytz" ,python-pytz) - ("python-dateutil" ,python-dateutil) - ("python-xlrd" ,python-xlrd))) + (list python-jinja2 + python-numpy + python-openpyxl + python-pytz + python-dateutil + python-xlrd)) (inputs - `(("which" ,which) - ("xclip" ,xclip) - ("xsel" ,xsel))) + (list which xclip xsel)) (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) - ;; Needed to test clipboard support. - ("xorg-server" ,xorg-server-for-tests))) + (list python-cython + python-beautifulsoup4 + python-lxml + python-html5lib + python-nose + python-pytest + python-pytest-mock + ;; Needed to test clipboard support. + xorg-server-for-tests)) (home-page "https://pandas.pydata.org") (synopsis "Data structures for data analysis, time series, and statistics") (description @@ -508,21 +501,18 @@ doing practical, real world data analysis in Python.") ;; XXX: Due to the deleted tests above. "not test_read_s3_jsonl")))))))) (propagated-inputs - `(("python-numpy" ,python2-numpy) - ("python-openpyxl" ,python2-openpyxl) - ("python-pytz" ,python2-pytz) - ("python-dateutil" ,python2-dateutil) - ("python-xlrd" ,python2-xlrd))) + (list python2-numpy python2-openpyxl python2-pytz python2-dateutil + python2-xlrd)) (inputs - `(("which" ,which))) + (list which)) (native-inputs - `(("python-cython" ,python2-cython) - ("python-beautifulsoup4" ,python2-beautifulsoup4) - ("python-lxml" ,python2-lxml) - ("python-html5lib" ,python2-html5lib) - ("python-nose" ,python2-nose) - ("python-pytest" ,python2-pytest) - ("python-pytest-mock" ,python2-pytest-mock)))))) + (list python2-cython + python2-beautifulsoup4 + python2-lxml + python2-html5lib + python2-nose + python2-pytest + python2-pytest-mock))))) (define-public python-pyflow (package @@ -563,11 +553,9 @@ context of a task dependency graph. It has some similarities to make.") (lambda _ (invoke "python" "setup.py" "pytest")))))) (native-inputs - `(("python-hypothesis" ,python-hypothesis) - ("python-pytest" ,python-pytest) - ("python-pytest-runner" ,python-pytest-runner))) + (list python-hypothesis python-pytest python-pytest-runner)) (propagated-inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (home-page "https://github.com/pydata/bottleneck") (synopsis "Fast NumPy array functions written in C") (description @@ -587,9 +575,7 @@ written in C.") (base32 "1c1354a7b3g8slychjgyjxqdm8z40z9kviyl9n4g9kfpdg0p4d64")))) (build-system python-build-system) (propagated-inputs - `(("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy))) + (list python-matplotlib python-numpy python-scipy)) (home-page "https://github.com/janezd/baycomp") (synopsis "Library for comparison of Bayesian classifiers") (description @@ -613,11 +599,9 @@ higher scores.") "1yx8j66b7rn10m2l6gmn8yr9cn38pi5cj0x0wwpy4hdnhy6i7qv4")))) (build-system python-build-system) (native-inputs - `(("python-setuptools-scm" ,python-setuptools-scm) - ("python-pytest" ,python-pytest))) + (list python-setuptools-scm python-pytest)) (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas))) + (list python-numpy python-pandas)) (arguments `(#:phases (modify-phases %standard-phases @@ -649,8 +633,7 @@ and visualization with these data structures.") "0syzy645mwcy7lfjwz6pc8f9p2vv1qk4limc8iina3l5nnf0rjyz")))) (build-system python-build-system) (propagated-inputs - `(("python-msgpack" ,python-msgpack) - ("python-numpy" ,python-numpy))) + (list python-msgpack python-numpy)) (home-page "https://github.com/lebedov/msgpack-numpy") (synopsis "Numpy data serialization using msgpack") @@ -684,7 +667,7 @@ Python's native complex data types is also supported.") (with-directory-excursion "ruffus/test" (invoke "bash" "run_all_unit_tests3.cmd")))))))) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "http://www.ruffus.org.uk") (synopsis "Light-weight computational pipeline management") (description @@ -705,11 +688,8 @@ automated with the minimum of fuss and the least effort.") "1f8c2sylzr7lpjbyqxsqlp9xi8rj3d8c9hfh98x4jbb83zxc4026")))) (build-system python-build-system) (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-seaborn" ,python-seaborn) - ("python-matplotlib" ,python-matplotlib) - ("python-pandas" ,python-pandas) - ("python-scipy" ,python-scipy))) + (list python-numpy python-seaborn python-matplotlib python-pandas + python-scipy)) (home-page "https://github.com/webermarcolivier/statannot") (synopsis "Add annotations to existing plots generated by seaborn") @@ -742,11 +722,9 @@ annotations on an existing boxplots and barplots generated by seaborn.") (add-installed-pythonpath inputs outputs) (invoke "pytest" "-v" "--doctest-modules")))))) (propagated-inputs - `(("python-matplotlib" ,python-matplotlib) - ("python-pandas" ,python-pandas))) + (list python-matplotlib python-pandas)) (native-inputs - `(("python-pytest-runner" ,python-pytest-runner) - ("python-pytest-cov" ,python-pytest-cov))) + (list python-pytest-runner python-pytest-cov)) (home-page "https://upsetplot.readthedocs.io") (synopsis "Draw UpSet plots with Pandas and Matplotlib") (description @@ -790,7 +768,7 @@ readable.") ("pkgconfig" ,python-pkgconfig) ("matplotlib" ,python-matplotlib))) (native-inputs ; for python-pkgconfig - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (propagated-inputs `(("numpy" ,python-numpy) ("vtk" ,vtk))) @@ -826,8 +804,7 @@ dependencies.") "12g4av8gpl6l83yza3h97j3f2jblqv69frlidrvdq8ny2rc6awbq")))) (build-system python-build-system) (propagated-inputs - `(("python-pandas" ,python-pandas) - ("python-xarray" ,python-xarray))) + (list python-pandas python-xarray)) (home-page "https://github.com/Zsailer/pandas_flavor") (synopsis "Write your own flavor of Pandas") (description "Pandas 0.23 added a simple API for registering accessors @@ -874,19 +851,18 @@ of Pandas (when tests? (invoke "pytest"))))))) (native-inputs - `(("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov))) + (list python-pytest python-pytest-cov)) (propagated-inputs - `(("python-matplotlib" ,python-matplotlib) - ("python-mpmath" ,python-mpmath) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pandas-flavor" ,python-pandas-flavor) - ("python-scikit-learn" ,python-scikit-learn) - ("python-scipy" ,python-scipy) - ("python-seaborn" ,python-seaborn) - ("python-statsmodels" ,python-statsmodels) - ("python-tabulate" ,python-tabulate))) + (list python-matplotlib + python-mpmath + python-numpy + python-pandas + python-pandas-flavor + python-scikit-learn + python-scipy + python-seaborn + python-statsmodels + python-tabulate)) (home-page "https://pingouin-stats.org/") (synopsis "Statistical package for Python") (description "Pingouin is a statistical package written in Python 3 and @@ -964,21 +940,21 @@ and more ;; "AttributeError: module 'distributed.dashboard' has no attribute 'scheduler'" " and not test_get_client_functions_spawn_clusters")))))))) (propagated-inputs - `(("python-click" ,python-click) - ("python-cloudpickle" ,python-cloudpickle) - ("python-cryptography" ,python-cryptography) - ("python-dask" ,python-dask) - ("python-msgpack" ,python-msgpack) - ("python-psutil" ,python-psutil) - ("python-pyyaml" ,python-pyyaml) - ("python-setuptools" ,python-setuptools) - ("python-sortedcontainers" ,python-sortedcontainers) - ("python-tblib" ,python-tblib) - ("python-toolz" ,python-toolz) - ("python-tornado" ,python-tornado-6) - ("python-zict" ,python-zict))) + (list python-click + python-cloudpickle + python-cryptography + python-dask + python-msgpack + python-psutil + python-pyyaml + python-setuptools + python-sortedcontainers + python-tblib + python-toolz + python-tornado-6 + python-zict)) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://distributed.dask.org") (synopsis "Distributed scheduler for Dask") (description "Dask.distributed is a lightweight library for distributed @@ -1018,31 +994,31 @@ computing in Python. It extends both the @code{concurrent.futures} and (invoke "python" "-m" "pytest" "modin/pandas/test/test_concat.py"))))))) (propagated-inputs - `(("python-cloudpickle" ,python-cloudpickle) - ("python-dask" ,python-dask) - ("python-distributed" ,python-distributed) - ("python-numpy" ,python-numpy) - ("python-packaging" ,python-packaging) - ("python-pandas" ,python-pandas))) + (list python-cloudpickle + python-dask + python-distributed + python-numpy + python-packaging + python-pandas)) (native-inputs - `(("python-coverage" ,python-coverage) - ("python-jinja2" ,python-jinja2) - ("python-lxml" ,python-lxml) - ("python-matplotlib" ,python-matplotlib) - ("python-msgpack" ,python-msgpack) - ("python-openpyxl" ,python-openpyxl) - ("python-psutil" ,python-psutil) - ("python-pyarrow" ,python-pyarrow) - ("python-pytest" ,python-pytest) - ("python-pytest-benchmark" ,python-pytest-benchmark) - ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-xdist" ,python-pytest-xdist) - ("python-scipy" ,python-scipy) - ("python-sqlalchemy" ,python-sqlalchemy) - ("python-tables" ,python-tables) - ("python-tqdm" ,python-tqdm) - ("python-xarray" ,python-xarray) - ("python-xlrd" ,python-xlrd))) + (list python-coverage + python-jinja2 + python-lxml + python-matplotlib + python-msgpack + python-openpyxl + python-psutil + python-pyarrow + python-pytest + python-pytest-benchmark + python-pytest-cov + python-pytest-xdist + python-scipy + python-sqlalchemy + python-tables + python-tqdm + python-xarray + python-xlrd)) (home-page "https://github.com/modin-project/modin") (synopsis "Make your pandas code run faster") (description |