diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 391 |
1 files changed, 328 insertions, 63 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 29f2d056f1..6451638afa 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19,7 +19,7 @@ ;;; Copyright © 2015, 2016 Chris Marusich <cmmarusich@gmail.com> ;;; Copyright © 2016 Danny Milosavljevic <dannym+a@scratchpost.org> ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox.org> -;;; Copyright © 2016, 2018, 2019 Hartmut Goebel <h.goebel@crazy-compilers.com> +;;; Copyright © 2016, 2018, 2019, 2021 Hartmut Goebel <h.goebel@crazy-compilers.com> ;;; Copyright © 2016 Daniel Pimentel <d4n1@d4n1.org> ;;; Copyright © 2016 Sou Bunnbu <iyzsong@gmail.com> ;;; Copyright © 2016, 2017 Troy Sankey <sankeytms@gmail.com> @@ -67,7 +67,7 @@ ;;; Copyright © 2019, 2020 Giacomo Leidi <goodoldpaul@autistici.org> ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz> ;;; Copyright © 2019, 2020 Tanguy Le Carrour <tanguy@bioneland.org> -;;; Copyright © 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2019, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2020 Riku Viitanen <riku.viitanen@protonmail.com> ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> ;;; Copyright © 2020 sirgazil <sirgazil@zoho.com> @@ -219,6 +219,49 @@ #:use-module (srfi srfi-1) #:use-module (srfi srfi-26)) +(define-public python-argopt + (package + (name "python-argopt") + (version "0.7.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "argopt" version)) + (sha256 + (base32 + "0ybs7kkp0cpl8zn1lvf7481xhssg1bbhh5la2cjzdm5yibashyxa")))) + (build-system python-build-system) + (native-inputs + `(("python-coverage" ,python-coverage) + ("python-nose" ,python-nose) + ("python-setuptools" ,python-setuptools) ; Won't build without this. + ("python-setuptools-scm" ,python-setuptools-scm))) + (propagated-inputs + `(("python-toml" ,python-toml) + ("python-flake8" ,python-flake8))) + (home-page "https://github.com/casperdcl/argopt") + (synopsis "Generate a command-line interface from a docstring") + (description "This package provides tools to define a command line interface +from a docstring rather than the other way around.") + (license license:mpl2.0))) + +(define-public python-cachetools + (package + (name "python-cachetools") + (version "4.2.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "cachetools" version)) + (sha256 + (base32 + "1zqc098gk6y614lxwqd9z2gm8lldgvrpid133pnlm4m048gfvdb1")))) + (build-system python-build-system) + (home-page "https://github.com/tkem/cachetools/") + (synopsis "Extensible memoizing collections and decorators") + (description "This module provides various memoizing collections and +decorators, including variants of the Python standard library's +@code{lru_cache} function decorator.") + (license license:expat))) + (define-public python-colorful (package (name "python-colorful") @@ -851,9 +894,6 @@ module and then similar looking characters are removed.") and function call return values in a human-readable way.") (license license:asl2.0))) -(define-public python2-shapely - (package-with-python2 python-shapely)) - (define-public python-clyent (package (name "python-clyent") @@ -2129,6 +2169,25 @@ The event dispatch is implicit, which means you can easily use @code{Eventlet} from the Python interpreter, or as a small part of a larger application.") (license license:expat))) +(define-public python-sinfo + (package + (name "python-sinfo") + (version "0.3.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "sinfo" version)) + (sha256 + (base32 + "0kdsp883mx0lfyykv0p12bvs203kdm3skb8bw5wf2pc7kb393sl1")))) + (build-system python-build-system) + (propagated-inputs + `(("python-stdlib-list" ,python-stdlib-list))) + (home-page "https://gitlab.com/joelostblom/session_info") + (synopsis "Output module version information loaded in a Python session") + (description "This package outputs version information for modules loaded +in the current session, Python, and the OS.") + (license license:bsd-3))) + (define-public python-six (package (name "python-six") @@ -4427,7 +4486,7 @@ which can produce feeds in RSS 2.0, RSS 0.91, and Atom formats.") (define-public python-pydantic (package (name "python-pydantic") - (version "1.6.1") + (version "1.8.2") (source (origin (method git-fetch) @@ -4436,24 +4495,39 @@ which can produce feeds in RSS 2.0, RSS 0.91, and Atom formats.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1380s9k77g6q15by9fkxndczjk89q6xpz09jdrqip535xws2z3j8")))) + (base32 "06162dss6mvi7wiy2lzxwvzajwxgy8b2fyym7qipaj7zibcqalq2")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases - ;; Reported upstream: - ;; <https://github.com/samuelcolvin/pydantic/issues/1580>. - ;; Disable the faulty test as the fix is unclear. (add-before 'check 'disable-test (lambda _ + ;; Reported upstream: + ;; <https://github.com/samuelcolvin/pydantic/issues/1580>. + ;; Disable the faulty test as the fix is unclear. (substitute* "tests/test_validators.py" (("test_assert_raises_validation_error") "_test_assert_raises_validation_error")) - #t)) + + ;; These fail because of <https://bugs.python.org/issue40398>. + ;; Remove after Python has been upgraded to >= 3.9. + (substitute* "tests/test_generics.py" + (("assert replace_types\\(Callable, \\{T: int\\}\\) == Callable") + "")) + (substitute* "tests/test_schema.py" + (("test_unenforced_constraints_schema") + "_test_unenforced_constraints_schema")) + + ;; Disable tests for the Hypothesis plugin because it is tricky + ;; to configure in the build container. + (delete-file "tests/test_hypothesis_plugin.py"))) (replace 'check - (lambda _ (invoke "pytest" "-vv" "tests")))))) + (lambda _ (invoke "pytest" "-vv")))))) (native-inputs - `(("python-pytest" ,python-pytest))) + `(("python-pytest" ,python-pytest) + ("python-pytest-mock" ,python-pytest-mock))) + (propagated-inputs + `(("python-typing-extensions" ,python-typing-extensions))) (home-page "https://github.com/samuelcolvin/pydantic") (synopsis "Python data validation and settings management") (description @@ -4936,8 +5010,8 @@ capabilities.") (define-public python2-numpy (let ((numpy (package-with-python2 (strip-python2-variant python-numpy)))) - (package/inherit - numpy + (package + (inherit numpy) (version "1.16.5") (source (origin (method url-fetch) @@ -5039,6 +5113,51 @@ objects.") (define-public python2-colormath (package-with-python2 python-colormath)) +(define-public python-sparse + (package + (name "python-sparse") + (version "0.12.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sparse" version)) + (sha256 + (base32 + "05lmzckv69cvxavhdr36k803bgr5dl04cppglid1l880xswc759c")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "pytest" "-v"))))))) + (propagated-inputs + `(("python-numba" ,python-numba) + ("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy))) + (native-inputs + `(("python-dask" ,python-dask) + ("python-pytest" ,python-pytest) + ("python-pytest-black" ,python-pytest-black) + ("python-pytest-cov" ,python-pytest-cov))) + (home-page "https://github.com/pydata/sparse/") + (synopsis "Library for multi-dimensional sparse arrays") + (description + "This package implements sparse arrays of arbitrary dimension on top of +@code{numpy} and @code{scipy.sparse}. Sparse array is a matrix in which most +of the elements are zero. @code{python-sparse} generalizes the +@code{scipy.sparse.coo_matrix} and @code{scipy.sparse.dok_matrix} layouts, but +extends beyond just rows and columns to an arbitrary number of dimensions. +Additionally, this project maintains compatibility with the +@code{numpy.ndarray} interface rather than the @code{numpy.matrix} interface +used in @code{scipy.sparse}. These differences make this project useful in +certain situations where @code{scipy.sparse} matrices are not well suited, but +it should not be considered a full replacement. It lacks layouts that are not +easily generalized like @dfn{compressed sparse row/column}(CSR/CSC) and +depends on @code{scipy.sparse} for some computations.") + (license license:bsd-3))) + (define-public python-spectra (package (name "python-spectra") @@ -5529,8 +5648,11 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc. #t)) (add-before 'install 'install-jquery-ui (lambda* (#:key outputs inputs #:allow-other-keys) - (let ((dir (string-append (assoc-ref outputs "out") - "/lib/python3.7/site-packages/matplotlib/backends/web_backend/"))) + (let* ((python-version (python-version + (assoc-ref inputs "python"))) + (dir (string-append (assoc-ref outputs "out") + "/lib/python" python-version "/site-packages" + "/matplotlib/backends/web_backend/"))) (mkdir-p dir) (invoke "unzip" (assoc-ref inputs "jquery-ui") @@ -7506,9 +7628,6 @@ profile, launches a cluster and returns a view. On program exit it shuts the cluster down and deletes the throwaway profile.") (license license:expat))) -(define-public python2-ipython-cluster-helper - (package-with-python2 python-ipython-cluster-helper)) - (define-public python-traitlets (package (name "python-traitlets") @@ -8042,7 +8161,8 @@ features useful for text console applications.") (define-public python2-urwid (let ((base (package-with-python2 (strip-python2-variant python-urwid)))) - (package/inherit base + (package + (inherit base) (version "2.1.0") (source (origin @@ -9477,8 +9597,8 @@ markdown_py is also provided to convert Markdown files to HTML.") ;; Markdown 3.2 dropped support for Python 2. (define-public python2-markdown (let ((base (package-with-python2 (strip-python2-variant python-markdown)))) - (package/inherit - base + (package + (inherit base) (version "3.1.1") (source (origin (method url-fetch) @@ -9596,6 +9716,26 @@ output.") "Python library that makes exceptions handling and inspection easier.") (license license:expat))) +(define-public python-stdlib-list + (package + (name "python-stdlib-list") + (version "0.8.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "stdlib-list" version)) + (sha256 + (base32 + "17vdn4q0sdlndc2fr9svapxx6366hnrhkn0fswp1xmr0jxqh7rd1")))) + (build-system python-build-system) + (arguments + `(#:tests? #f)) ; Tests require more dependencies. + (native-inputs + `(("python-sphinx" ,python-sphinx))) + (home-page "https://github.com/jackmaney/python-stdlib-list") + (synopsis "Python Standard Libraries") + (description "This package contains a list of Python Standard Libraries.") + (license license:expat))) + (define-public python-straight-plugin (package (name "python-straight-plugin") @@ -9646,8 +9786,8 @@ from an XML-based format.") ;; Fonttools 4.x dropped support for Python 2, so stick with 3.x here. (define-public python2-fonttools (let ((base (package-with-python2 (strip-python2-variant python-fonttools)))) - (package/inherit - base + (package + (inherit base) (version "3.44.0") (source (origin (method url-fetch) @@ -10269,6 +10409,30 @@ implementations of ASN.1-based codecs and protocols.") module to older versions of Python.") (license license:psfl))) +(define-public python-asn1tools + (package + (name "python-asn1tools") + (version "0.158.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "asn1tools" version)) + (sha256 + (base32 "1k88a1azmyvp2ab6qcf2i40dig5abhyn7cmlyhmwwh8kr3syvma0")))) + (build-system python-build-system) + (propagated-inputs + `(("python-bitstruct" ,python-bitstruct) + ("python-diskcache" ,python-diskcache) + ("python-prompt-toolkit" ,python-prompt-toolkit) + ("python-pyparsing" ,python-pyparsing))) + (home-page "https://github.com/eerimoq/asn1tools") + (synopsis "ASN.1 parsing, encoding and decoding") + (description "This package provides ASN.1 parsing, encoding and decoding +for Python, including constraints checking. It supports several +codecs (e.g. BER, PER, UPER, XER) as well as limited C source code generating +for OER and UPER.") + (license license:expat))) + (define-public python2-ipaddr (package (name "python2-ipaddr") @@ -10686,14 +10850,13 @@ JSON Reference and JSON Pointer.") (define-public python-fastjsonschema (package (name "python-fastjsonschema") - (version "2.15.0") + (version "2.15.1") (source (origin (method url-fetch) (uri (pypi-uri "fastjsonschema" version)) (sha256 - (base32 - "0xknp399gpdjf08lrq2yvv66s7nsc51fgbm6vph7vyyg1ckbmv71")))) + (base32 "1ln2j60jzyn6p8i8ljygfgrji58hc23452g7nllkcjdk4p93c7v7")))) (build-system python-build-system) (arguments `(#:tests? #f ; Fail with a strange backtrace ending in importlib. @@ -11140,29 +11303,8 @@ convert an @code{.ipynb} notebook file into various static formats including: (description "The Jupyter HTML notebook is a web-based notebook environment for interactive computing.") - (properties `((python2-variant . ,(delay python2-notebook)))) (license license:bsd-3))) -(define-public python2-notebook - (let ((base (package-with-python2 - (strip-python2-variant python-notebook)))) - (package/inherit base - (native-inputs - `(("python2-mock" ,python2-mock) - ,@(package-native-inputs base))) - (arguments - (substitute-keyword-arguments (package-arguments base) - ((#:phases phases) - `(modify-phases ,phases - (add-before 'check 'disable-test-case - ;; The test requires network access to localhost. Curiously it - ;; fails with Python 2 only. Simply make the test-case return - ;; immediately. - (lambda _ - (substitute* - "notebook/services/nbconvert/tests/test_nbconvert_api.py" - (("formats = self.nbconvert_api") "return #"))))))))))) - (define-public python-widgetsnbextension (package (name "python-widgetsnbextension") @@ -12768,14 +12910,13 @@ designed to work across multiple versions of Python.") (define-public python-cookiecutter (package (name "python-cookiecutter") - (version "1.7.2") + (version "1.7.3") (source (origin (method url-fetch) (uri (pypi-uri "cookiecutter" version)) (sha256 - (base32 - "1b2xa5dypk1vf8aq599fd8zw4y0pwvq3hgl7ia8aiv8gg3ab5dpg")))) + (base32 "0mx49whhwcxmvcak27zr7p7ndzkn3w7psfd7fzh3n91fi1r4v6kb")))) (build-system python-build-system) (native-inputs `(("python-freezegun" ,python-freezegun) @@ -15421,6 +15562,11 @@ extracting firmware images") '(;; The tests require some extra resources to be downloaded. ;; TODO Try packaging these resources. #:tests? #f)) + (propagated-inputs + `(("python-click" ,python-click) + ("python-joblib" ,python-joblib) + ("python-regex" ,python-regex) + ("python-tqdm" ,python-tqdm))) (native-inputs `(("unzip" ,unzip))) (home-page "http://nltk.org/") @@ -15442,7 +15588,8 @@ reasoning, wrappers for natural language processing libraries.") (method url-fetch) (uri (pypi-uri "nltk" version ".zip")) (sha256 - (base32 "153x2clrnigs74jdgnn3qmljdjj4gprmvpdvh49i18ls4m8mbm5y")))))) + (base32 "153x2clrnigs74jdgnn3qmljdjj4gprmvpdvh49i18ls4m8mbm5y")))) + (propagated-inputs `(("python-six" ,python-six))))) (define-public python2-nltk (package-with-python2 python-nltk)) @@ -16410,6 +16557,30 @@ converting text with ANSI color codes to HTML or LaTeX.") (define-public python2-ansi2html (package-with-python2 python-ansi2html)) +(define-public python-easy-ansi + (package + (name "python-easy-ansi") + (version "0.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/joeysbytes/easy-ansi") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0albh55ynzs98qy9pln4qaxw5qhhh3lk09jy9bx19gycrp1c3lc3")))) + (build-system python-build-system) + (home-page "https://gitlab.com/joeysbytes/easy-ansi") + (synopsis "Terminal framework API") + (description + "Easy ANSI is a terminal framework API to give you an easy way to use +colors, cursor control movements, and line/box drawing. It is not meant as a +replacement to more full-featured frameworks (such as curses or urwid), but as +a tool to quickly create nice-looking screens in your terminal window. You +can even create animations with the cursor controls.") + (license license:expat))) + (define-public python-ddt (package (name "python-ddt") @@ -20867,28 +21038,41 @@ N-dimensional arrays for Python.") (define-public python-anndata (package (name "python-anndata") - (version "0.7.1") + (version "0.7.6") (source (origin (method url-fetch) (uri (pypi-uri "anndata" version)) (sha256 (base32 - "0rnfbpr55j1a1bi2kd4mz444741hrn74kz90h5rnjr59jmpfnh09")))) + "1ch8yp0xmag6z0kl01pljm35lbbwax7lrimfhiclpkd4m6xngk53")))) (build-system python-build-system) (arguments - `(#:phases + `(#:tests? #f ; The tarball from PyPi doesn't include tests. + #:phases (modify-phases %standard-phases - (add-after 'unpack 'delete-inconvenient-tests - (lambda _ - ;; This test depends on python-scikit-learn. - (delete-file "anndata/tests/test_inplace_subset.py") - #t)) (delete 'check) - (add-after 'install 'check + (add-before 'build 'relax-dependency-requirements + (lambda _ + ;; We need to upgrade python-pandas to avoid + ;; https://github.com/pandas-dev/pandas/issues/35446 + (substitute* "pyproject.toml" + (("pandas>=1.1.1") "pandas>=1.0.5")))) + (replace 'build + (lambda _ + ;; ZIP does not support timestamps before 1980. + (setenv "SOURCE_DATE_EPOCH" "315532800") + (invoke "flit" "build"))) + (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) (add-installed-pythonpath inputs outputs) - (invoke "pytest" "-vv")))))) + (let ((out (assoc-ref outputs "out"))) + (for-each (lambda (wheel) + (format #true wheel) + (invoke "python" "-m" "pip" "install" + wheel (string-append "--prefix=" out))) + (find-files "dist" "\\.whl$"))) + #t))))) (propagated-inputs `(("python-h5py" ,python-h5py) ("python-importlib-metadata" ,python-importlib-metadata) @@ -20901,6 +21085,8 @@ N-dimensional arrays for Python.") (native-inputs `(("python-joblib" ,python-joblib) ("python-pytest" ,python-pytest) + ("python-toml" ,python-toml) + ("python-flit" ,python-flit) ("python-setuptools-scm" ,python-setuptools-scm))) (home-page "https://github.com/theislab/anndata") (synopsis "Annotated data for data analysis pipelines") @@ -24812,6 +24998,41 @@ module patches @code{asyncio} to allow nested use of @code{asyncio.run} and @code{loop.run_until_complete}.") (license license:bsd-3))) +(define-public python-simpervisor + (package + (name "python-simpervisor") + (version "0.4") + (source + (origin + ;; Tests not included in release. + (method git-fetch) + (uri (git-reference + (url "https://github.com/yuvipanda/simpervisor") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1brsisx7saf4ic0dih1n5y7rbdbwn1ywv9pl32bch3061r46prvv")))) + (build-system python-build-system) + (arguments + `(#:tests? #f ; Test suite can't find aiohttp. + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "--maxfail" "3" "--verbose")) + #t))))) + (native-inputs + `(("python-aiohttp" ,python-aiohttp) + ("python-pytest" ,python-pytest) + ("python-pytest-asyncio" ,python-pytest-asyncio))) + (home-page "https://github.com/yuvipanda/simpervisor") + (synopsis "Simple async process supervisor") + (description + "This package provides a simple async process supervisor in Python.") + (license license:bsd-3))) + (define-public python-parallel (package (name "python-parallel") @@ -25071,6 +25292,50 @@ query Watchman to discover file changes.") environment.") (license license:expat))) +(define-public python-logutils + (package + (name "python-logutils") + (version "0.3.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "logutils" version)) + (sha256 + (base32 + "10lsi5wv5ysnvf9ya4ncbix6mmipnv5067sf2cglc2f2sljql1dw")))) + (build-system python-build-system) + (home-page "https://bitbucket.org/vinay.sajip/logutils/") + (synopsis "Logging utilities") + (description "This package provides a set of handlers for the Python +standard library logging package. Some of these handlers are out-of-scope +for the standard library, and so they are packaged here. Others are updated +versions which have appeared in recent Python releases, but are usable with +older versions of Python and so are packaged here.") + (license license:bsd-3))) + +(define-public python-helper + (package + (name "python-helper") + (version "2.5.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "helper" version)) + (sha256 + (base32 + "1d2j64wgbggzv5rhvil10zndp2w78wa5np5w0psj122ws9qr9wsa")))) + (build-system python-build-system) + (native-inputs + `(("python-mock" ,python-mock))) + (propagated-inputs + `(("python-logutils" ,python-logutils) + ("python-pyyaml" ,python-pyyaml))) + (home-page "https://github.com/gmr/helper") + (synopsis "Library for writing configurable applications and daemons") + (description + "This package provides procedures for quickly writing configurable +applications and daemons.") + (license license:bsd-3))) + (define-public python-qtsass (package (name "python-qtsass") |