diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 3554 |
1 files changed, 2425 insertions, 1129 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f6c4ca076f..bdd9810aa5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -155,10 +155,13 @@ #:use-module (gnu packages django) #:use-module (gnu packages djvu) #:use-module (gnu packages docker) + #:use-module (gnu packages documentation) #:use-module (gnu packages enchant) #:use-module (gnu packages file) #:use-module (gnu packages fontutils) + #:use-module (gnu packages fonts) #:use-module (gnu packages freedesktop) + #:use-module (gnu packages gdb) #:use-module (gnu packages gcc) #:use-module (gnu packages geo) #:use-module (gnu packages ghostscript) @@ -173,6 +176,7 @@ #:use-module (gnu packages gtk) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages icu4c) + #:use-module (gnu packages inkscape) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages jupyter) @@ -189,6 +193,7 @@ #:use-module (gnu packages multiprecision) #:use-module (gnu packages networking) #:use-module (gnu packages ncurses) + #:use-module (gnu packages ninja) #:use-module (gnu packages openstack) #:use-module (gnu packages pcre) #:use-module (gnu packages pdf) @@ -364,6 +369,50 @@ library’s logging module. It was designed with both complex and simple applications in mind and the idea to make logging fun.") (license license:bsd-3))) +(define-public python-ubelt + (package + (name "python-ubelt") + (version "1.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Erotemic/ubelt") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0hac9nqqvqfbca2s4g0mp1fnj0ah60bg9fb8234ibna3jww8qs33")))) + (build-system python-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp") ;else the test suite hangs + (invoke "pytest" "-vv" "-k" + (string-append + ;; The builder user home doesn't match HOME, + ;; which causes this test to fail. + "not userhome " + ;; This one pointlessly tries + ;; locating various binaries on + ;; the path. + "and not find_exe")))))))) + (propagated-inputs (list python-ordered-set)) + (native-inputs + (list python-pytest + python-requests + python-xdoctest)) + (home-page "https://github.com/Erotemic/ubelt") + (synopsis "Python library for hashing, caching, timing and more") + (description "Ubelt is a small library of simple functions that extend the +Python standard library. It includes an @acronym{API, Application Programming +Interface} to simplify common problems such as caching, timing, computing +progress, among other things.") + (license license:asl2.0))) + (define-public python-ueberzug (package (name "python-ueberzug") @@ -601,14 +650,18 @@ HTML") (define-public python-mkdocs (package (name "python-mkdocs") - (version "1.1.2") + (version "1.3.0") (source (origin - (method url-fetch) - (uri - (pypi-uri "mkdocs" version)) + ;; The tests suite appears to be incomplete in the PyPI archive. + (method git-fetch) + (uri (git-reference + (url "https://github.com/mkdocs/mkdocs") + (commit version))) + (file-name (git-file-name name version)) (sha256 - (base32 "0fgv5zawpyyv0vd4j5y8m4h058lh9jkwfcm0xy4pg7dr09a1xdph")))) + (base32 + "1n5rdllrxvhnxmdrddf55p3s86dakx0rq2gg6bj6pr6jg2pn932b")))) (build-system python-build-system) (arguments `(#:phases @@ -618,15 +671,27 @@ HTML") (add-after 'unpack 'patch-requirements (lambda _ (substitute* "setup.py" - (("==") ">="))))))) + (("==") ">=")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "unittest" + "discover" "-p" "*tests.py" "mkdocs" + "--top-level-directory" "."))))))) (propagated-inputs - (list python-click + (list python-babel + python-click + python-ghp-import + python-importlib-metadata python-jinja2 - python-livereload - python-lunr python-markdown + python-markupsafe + python-mdx-gh-links + python-mergedeep + python-packaging python-pyyaml - python-tornado)) + python-pyyaml-env-tag + python-watchdog)) (home-page "https://www.mkdocs.org") (synopsis "Project documentation with Markdown") (description "MkDocs is a static site generator geared towards building @@ -657,6 +722,26 @@ configured with a single YAML configuration file.") Markdown. All extensions are found under the module namespace of pymdownx.") (license license:expat))) +(define-public python-mdx-gh-links + (package + (name "python-mdx-gh-links") + (version "0.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "mdx_gh_links" version)) + (sha256 + (base32 "167k1jbp3jifxbnlpi6wy0z1skam7gqv2sixb5bhggb2vypqvysr")))) + (build-system python-build-system) + (arguments (list #:tests? #f)) ;tests connect github + (propagated-inputs (list python-markdown)) + (home-page "https://github.com/Python-Markdown/github-links/") + (synopsis "Python-Markdown extension adding support for shorthand links") + (description "This package is an extension to Python-Markdown which adds +support for shorthand links to GitHub users, repositories, issues and +commits.") + (license license:bsd-3))) + (define-public python-mkdocs-material (package (name "python-mkdocs-material") @@ -1198,7 +1283,37 @@ etc.") (license license:bsd-3))) (define-public python2-babel - (package-with-python2 python-babel)) + (package + (name "python2-babel") + (version "2.9.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "Babel" version)) + (sha256 + (base32 + "018yg7g2pa6vjixx1nx41cfispgfi0azzp0a1chlycbj8jsil0ys")))) + (build-system python-build-system) + (native-inputs + (list python2-freezegun python2-pytest tzdata-for-tests)) + (propagated-inputs + (list python2-pytz)) + (arguments + `(#:python ,python-2 + #:phases (modify-phases %standard-phases + (replace 'check + (lambda _ + (invoke "pytest" "-vv")))))) + (home-page "https://babel.pocoo.org/") + (synopsis + "Tools for internationalizing Python applications") + (description + "Babel is composed of two major parts: +- tools to build and work with gettext message catalogs +- a Python interface to the CLDR (Common Locale Data Repository), providing +access to various locale display names, localized number and date formatting, +etc.") + (license license:bsd-3))) (define-public python2-backport-ssl-match-hostname (package @@ -1798,44 +1913,41 @@ other machines, such as over the network.") (define-public python-setuptools (package (name "python-setuptools") - (version "52.0.0") + (version "62.0.0") (source (origin - (method url-fetch) - (uri (pypi-uri "setuptools" version)) - (sha256 - (base32 - "15ibjdjhkwgj6qbmpsxikkqdfsb1550z46fly7dm15ah4bk1wfpv")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Remove included binaries which are used to build self-extracting - ;; installers for Windows. - ;; TODO: Find some way to build them ourself so we can include them. - (for-each delete-file (find-files "setuptools" "^(cli|gui).*\\.exe$")) - #t)))) + (method url-fetch) + (uri (pypi-uri "setuptools" version)) + (sha256 + (base32 + "0sm8n6y6q640cpac9wjyggidbgi4n9la7vs7pwriyvhvgzccp6br")) + (modules '((guix build utils))) + (snippet + ;; Remove included binaries which are used to build self-extracting + ;; installers for Windows. + ;; TODO: Find some way to build them ourself so we can include them. + '(for-each delete-file (find-files "setuptools" + "^(cli|gui).*\\.exe$"))))) (build-system python-build-system) ;; FIXME: Tests require pytest, which itself relies on setuptools. ;; One could bootstrap with an internal untested setuptools. - (arguments - `(#:tests? #f)) + (arguments (list #:tests? #f)) (home-page "https://pypi.org/project/setuptools/") - (synopsis - "Library designed to facilitate packaging Python projects") - (description - "Setuptools is a fully-featured, stable library designed to facilitate -packaging Python projects, where packaging includes: -Python package and module definitions, -distribution package metadata, -test hooks, -project installation, -platform-specific details, -Python 3 support.") + (synopsis "Library designed to facilitate packaging Python projects") + (description "Setuptools is a fully-featured, stable library designed to +facilitate packaging Python projects, where packaging includes: +@itemize +@item Python package and module definitions +@item distribution package metadata +@item test hooks +@item project installation +@item platform-specific details. +@end itemize") ;; TODO: setuptools now bundles the following libraries: ;; packaging, pyparsing, six and appdirs. How to unbundle? - (license (list license:psfl ; setuptools itself - license:expat ; six, appdirs, pyparsing - license:asl2.0 ; packaging is dual ASL2/BSD-2 + (license (list license:psfl ;setuptools itself + license:expat ;six, appdirs, pyparsing + license:asl2.0 ;packaging is dual ASL2/BSD-2 license:bsd-2)) (properties `((python2-variant . ,(delay python2-setuptools)))))) @@ -1863,7 +1975,17 @@ Python 3 support.") ;; FIXME: Tests require pytest, which itself relies on setuptools. ;; One could bootstrap with an internal untested setuptools. (arguments - `(#:tests? #f)) + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'compatibility-fixes + (lambda _ + ;; HTMLParser no longer exists. + (substitute* "setuptools/py33compat.py" + (("html_parser.HTMLParser\\(\\).unescape") + "html.unescape")) + ;; This needs distutils.msvc9compiler + (delete-file "setuptools/tests/test_msvc.py")))))) (native-inputs (list unzip)) (home-page "https://pypi.org/project/setuptools/") @@ -2063,14 +2185,14 @@ class.") (define-public python-can (package (name "python-can") - (version "3.3.4") + (version "4.0.0") (source (origin (method url-fetch) (uri (pypi-uri "python-can" version)) (sha256 (base32 - "0jclrvyxasaaxr0albq0kqrnrfqdgqxs7m2qw9nd8kfwg8xj4g1d")))) + "0pcbdgdw94lc2sxd56w6wdsshrs9dd5d3wp0x4sfd0drzx32inar")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases @@ -2081,8 +2203,8 @@ class.") (("coverage<5") "coverage") (("pytest~=4\\.6") "pytest") (("pytest-timeout~=1\\.3") "pytest-timeout") - (("hypothesis~=4\\.56") "hypothesis")) - #t)) + (("pytest-cov.*") "pytest-cov\n") + (("hypothesis~=4\\.56") "hypothesis")))) (add-after 'unpack 'fix-broken-tests ;; The tests try to run two scripts it expects should be ;; in PATH, but they aren't at this time (see: @@ -2090,16 +2212,26 @@ class.") (lambda _ (substitute* "test/test_scripts.py" (("\"can_logger\\.py --help\"") "") - (("\"can_player\\.py --help\"") "")) - #t))))) + (("\"can_player\\.py --help\"") "")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" "test" + ;; Disable tests which require specific CAN + ;; drivers we have no package for in Guix. + "--ignore" "test/test_interface_canalystii.py" + ;; These tests fail with "OSError: [Errno 19] + ;; No such device". + "-k" "not BasicTestUdpMulticastBusIPv"))))))) (propagated-inputs - (list python-aenum python-wrapt)) + (list python-msgpack python-typing-extensions python-wrapt)) (native-inputs (list python-codecov python-coverage python-future python-hypothesis python-mock + python-parameterized python-pyserial python-pytest python-pytest-cov @@ -2169,17 +2301,34 @@ a library.") (description "DiskCache is a disk and file backed persistent cache.") (license license:asl2.0))) +(define-public python-argparse-addons + (package + (name "python-argparse-addons") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "argparse_addons" version)) + (sha256 + (base32 "1yx54dmnr3xggjcjk6bbdafvzp6cynrakl56wyz3jglmfvk0znpm")))) + (build-system python-build-system) + (home-page "https://github.com/eerimoq/argparse_addons") + (synopsis "Extensions for Python's @code{argparse} library") + (description "This Python library provides additional types and actions +for the standard @code{argparse} library.") + (license license:expat))) + (define-public python-bitstruct (package (name "python-bitstruct") - (version "8.9.0") + (version "8.14.0") (source (origin (method url-fetch) (uri (pypi-uri "bitstruct" version)) (sha256 (base32 - "1fpc1qh1vss05ap29xvhjp200fm0q4pvgcjl0qpryh7ay6xgr5vx")))) + "149c73yrqbph71bbyf925r2mbh2jdymqxc6d49lnylpiflf1j313")))) (build-system python-build-system) (home-page "https://github.com/eerimoq/bitstruct") (synopsis "Python values to and C bit field structs converter") @@ -2192,7 +2341,7 @@ bits instead of primitive data types like @code{char}, @code{int}, etc.") (define-public python-cantools (package (name "python-cantools") - (version "33.1.1") + (version "37.0.7") (source (origin ;; We take the sources from the Git repository as the documentation is @@ -2204,34 +2353,36 @@ bits instead of primitive data types like @code{char}, @code{int}, etc.") (file-name (git-file-name name version)) (sha256 (base32 - "1aad137yd8b4jkfvlv812qsxmxcgra7g1p4wbxfsjy1cbf8fbq9q")))) + "1qcf1fcwif7w70qmhxw2b8kqh420igbinq60p1chzf98xcb0ansx")))) (build-system python-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'build 'build-doc - (lambda _ - ;; See: https://github.com/eerimoq/cantools/issues/190. - (substitute* "README.rst" - (("https://github.com/eerimoq/cantools/raw/master\ + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'build 'build-doc + (lambda _ + ;; See: https://github.com/eerimoq/cantools/issues/190. + (substitute* "README.rst" + (("https://github.com/eerimoq/cantools/raw/master\ /docs/monitor.png") - "monitor.png")) - (with-directory-excursion "docs" - (invoke "make" "man" "info")))) - (add-after 'install 'install-doc - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (info (string-append out "/share/info")) - (man1 (string-append out "/share/man/man1"))) - (format #t "CWD: ~s~%" (getcwd)) - (install-file "docs/_build/texinfo/cantools.info" info) - (install-file "docs/_build/man/cantools.1" man1) - #t)))))) - (native-inputs - `(("sphinx" ,python-sphinx) - ("texinfo" ,texinfo))) - (propagated-inputs - (list python-bitstruct python-can python-diskcache python-textparser)) + "monitor.png")) + (invoke "make" "-C" "docs" "man" "info"))) + (add-after 'install 'install-doc + (lambda* (#:key outputs #:allow-other-keys) + (let* ((info (string-append #$output "/share/info")) + (man1 (string-append #$output "/share/man/man1"))) + (install-file "docs/_build/texinfo/cantools.info" info) + (install-file "docs/_build/man/cantools.1" man1))))))) + (native-inputs (list python-sphinx texinfo)) + (propagated-inputs + (list python-argparse-addons + python-bitstruct + python-can + python-crccheck + python-diskcache + python-matplotlib + python-parameterized + python-textparser)) (home-page "https://github.com/eerimoq/cantools") (synopsis "Tools for the Controller Area Network (CAN) bus protocol") (description "This package includes Controller Area Network (CAN) related @@ -2912,21 +3063,24 @@ backported for previous versions of Python from 2.4 to 3.3.") (define-public python-parse-type (package (name "python-parse-type") - (version "0.5.2") + (version "0.6.0") (source (origin - (method url-fetch) - (uri (pypi-uri "parse_type" version)) - (sha256 - (base32 - "02wclgiqky06y36b3q07b7ngpks5j0gmgl6n71ac2j2hscc0nsbz")))) + (method url-fetch) + (uri (pypi-uri "parse_type" version)) + (sha256 + (base32 + "07smqnzc9km7sbvxfyx4gdm9njrx58x8grdw6gs4gva81rk3rd10")))) (build-system python-build-system) - (propagated-inputs - (list python-six python-parse)) - (native-inputs - ;; Use setuptools < 58 to work around - ;; https://github.com/jenisys/parse_type/issues/17 - (list python-pytest python-pytest-runner python-setuptools)) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" "-c" "/dev/null"))))))) + (propagated-inputs (list python-six python-parse)) + (native-inputs (list python-pytest)) (home-page "https://github.com/jenisys/parse_type") (synopsis "Extended parse module") (description @@ -3463,30 +3617,23 @@ interfaces.") (define-public python-click (package (name "python-click") - (version "7.1.2") + (version "8.1.2") (source (origin (method url-fetch) (uri (pypi-uri "click" version)) (sha256 (base32 - "06kbzd6sjfkqan3miwj9wqyddfxc2b6hi7p5s4dvqjb3gif2bdfj")))) + "0whs38a2i0561kwbgigs6vic9r0a1887m2v1aw3rmv6r2kz0g5s7")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'fix-paths - (lambda* (#:key inputs #:allow-other-keys) - (let ((glibc (assoc-ref inputs ,(if (%current-target-system) - "cross-libc" "libc")))) - (substitute* "src/click/_unicodefun.py" - (("'locale'") - (string-append "'" glibc "/bin/locale'")))))) (replace 'check - (lambda _ - (invoke "python" "-m" "pytest")))))) - (native-inputs - (list python-pytest)) + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv"))))))) + (native-inputs (list python-pytest)) (home-page "https://palletsprojects.com/p/click/") (synopsis "Command line library for Python") (description @@ -3496,9 +3643,6 @@ composable way with as little code as necessary. Its name stands for with sensible defaults out of the box.") (license license:bsd-3))) -(define-public python2-click - (package-with-python2 python-click)) - (define-public python-click-5 (package (inherit python-click) (name "python-click") @@ -4065,14 +4209,14 @@ for Python.") (define-public python-jinja2 (package (name "python-jinja2") - (version "3.0.1") + (version "3.1.1") (source (origin (method url-fetch) (uri (pypi-uri "Jinja2" version)) (sha256 (base32 - "197ms1wimxql650245v63wkv04n8bicj549wfhp51bx68x5lhgvh")))) + "1saawzys14l1p4kafs7hkihmnvqjq8fwxjmkjiqx3jq1nm5ys2v4")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases @@ -4081,11 +4225,9 @@ for Python.") (if tests? (invoke "pytest" "-vv") (format #t "test suite not run~%"))))))) - (native-inputs - (list python-pytest)) - (propagated-inputs - (list python-markupsafe)) - (home-page "http://jinja.pocoo.org/") + (native-inputs (list python-pytest)) + (propagated-inputs (list python-markupsafe)) + (home-page "https://jinja.palletsprojects.com/") (synopsis "Python template engine") (description "Jinja2 is a small but fast and easy to use stand-alone template engine @@ -4549,14 +4691,14 @@ text styles of documentation.") (define-public python-pygments (package (name "python-pygments") - (version "2.8.1") + (version "2.12.0") (source (origin (method url-fetch) (uri (pypi-uri "Pygments" version)) (sha256 (base32 - "153zyxigm879sk2n71lfv03y2pgxb7dl0dlsbwkz9aydxnkf2mi6")))) + "1sr6iqh21xi6p8aba4wa9pqfhjbbpcvn9jcsx0ggy4lniw8idcay")))) (build-system python-build-system) (arguments ;; FIXME: Tests require sphinx, which depends on this. @@ -5411,58 +5553,27 @@ matching of file paths.") (define-public python-black (package (name "python-black") - (version "21.12b0") + (version "22.3.0") (source (origin (method url-fetch) (uri (pypi-uri "black" version)) (sha256 (base32 - "1czjwr1bx9ax5l64xfi54sxb1ycdy4s9ciaqg592x7jn79lhzf3p")))) + "0yfahlqc7dsdp1js0cbv706apldnfnlbal9b53cww8n0hs40n0im")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - ;; XXX Remove this when updating this package: - ;; https://github.com/psf/black/issues/2703#issuecomment-1004752142 - (add-after 'unpack 'relax-version-requirements - (lambda _ - (substitute* "setup.py" - (("tomli[^\"]*\",") - "tomli\",")))) (add-after 'patch-source-shebangs 'use-absolute-file-names (lambda* (#:key native-inputs inputs #:allow-other-keys) (let* ((inpts (or native-inputs inputs)) - (python3 (search-input-file inpts "/bin/python3")) - (/bin/false (search-input-file inpts "/bin/false")) - (/bin/sleep (search-input-file inpts "/bin/sleep"))) + (python3 (search-input-file inpts "/bin/python3"))) (substitute* (find-files "tests" "\\.py$") (("#!/usr/bin/env python3(\\.[0-9]+)?" _ minor-version) (string-append "#!" python3 (if (string? minor-version) minor-version - "")))) - (substitute* "tests/test_primer.py" - (("/bin/false") /bin/false) - (("/bin/sleep") /bin/sleep))))) - (add-after 'unpack 'disable-broken-tests - (lambda* (#:key outputs inputs #:allow-other-keys) - ;; Make installed package available for running the tests - (setenv "PATH" (string-append (assoc-ref outputs "out") "/bin" - ":" (getenv "PATH"))) - - ;; The source formatting test fails because we patch various - ;; files; just disable it. - (substitute* "tests/test_format.py" - (("def test_source_is_formatted" all) - (format #f "@pytest.mark.skip(\"Disabled by Guix.\")\n~a" - all))))) - ;; Remove blackd, because it depends on python-aiohttp and - ;; python-aiohttp-cors. - (add-after 'unpack 'remove-entrypoint - (lambda _ - (substitute* "setup.py" - (("\\s*\"blackd=blackd:patched_main \\[d\\]\",\n") "") - (("\"blackd\", ") "")))) + ""))))))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "pytest" "-vv"))))))) @@ -5690,10 +5801,13 @@ writing C extensions for Python as easy as Python itself.") "17fqacrpis05w1rpi7d7sbimrk20xf8h6d3vrz5nf6ix3899abil")))) (properties '()))) -(define-public python-numpy-next +;; NOTE: when upgrading numpy please make sure that python-numba, +;; python-pandas and python-scipy still build, as these three packages are +;; often used together. +(define-public python-numpy (package - (name "python-numpy-next") - (version "1.22.3") + (name "python-numpy") + (version "1.21.6") (source (origin (method url-fetch) @@ -5702,50 +5816,57 @@ writing C extensions for Python as easy as Python itself.") version "/numpy-" version ".tar.gz")) (sha256 (base32 - "19dw91pqbqcniw2z57kiyqs1qp56g7kqy1bdyv664g8s62sc01m9")))) + "0b0c5y35rd3mvwfk5is1d5ppfw9nl4d2rgx9xkwh1p0w394wdvyl")))) (build-system python-build-system) - (inputs - (list openblas)) - (native-inputs - (list python-cython python-hypothesis-6.23 python-pytest - python-pytest-xdist gfortran)) (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'build 'configure-blas - (lambda* (#:key inputs #:allow-other-keys) - (call-with-output-file "site.cfg" - (lambda (port) - (format port - "\ + (list + #:modules '((guix build utils) + (guix build python-build-system) + (ice-9 format)) + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'parallelize-build + (lambda _ + (setenv "NPY_NUM_BUILD_JOBS" + (number->string (parallel-job-count))))) + (add-before 'build 'configure-blas + (lambda* (#:key inputs #:allow-other-keys) + (call-with-output-file "site.cfg" + (lambda (port) + (format port + "\ [openblas] libraries = openblas library_dirs = ~a/lib -include_dirs = ~a/include -" - (assoc-ref inputs "openblas") - (assoc-ref inputs "openblas")))))) - (add-before 'build 'fix-executable-paths - (lambda* (#:key inputs #:allow-other-keys) - ;; Make /gnu/store/...-bash-.../bin/sh the default shell, - ;; instead of /bin/sh. - (substitute* "numpy/distutils/exec_command.py" - (("(os.environ.get\\('SHELL', ')(/bin/sh'\\))" match match-start match-end) - (string-append match-start (assoc-ref inputs "bash") match-end))) - ;; Use "gcc" executable, not "cc". - (substitute* "numpy/distutils/system_info.py" - (("c = distutils\\.ccompiler\\.new_compiler\\(\\)") - "c = distutils.ccompiler.new_compiler(); c.set_executables(compiler='gcc',compiler_so='gcc',linker_exe='gcc',linker_so='gcc -shared')")))) - (replace 'check - (lambda* (#:key tests? outputs inputs #:allow-other-keys) - (when tests? - ;; Make installed package available for running the tests. - (add-installed-pythonpath inputs outputs) - ;; Make sure "f2py" etc is found. - (setenv "PATH" (string-append (assoc-ref outputs "out") "/bin" - ":" (getenv "PATH"))) - (invoke "./runtests.py" - "-j" (number->string (parallel-job-count))))))))) +include_dirs = ~:*~a/include~%" #$(this-package-input "openblas")))))) + (add-before 'build 'fix-executable-paths + (lambda* (#:key inputs #:allow-other-keys) + ;; Make /gnu/store/...-bash-.../bin/sh the default shell, + ;; instead of /bin/sh. + (substitute* "numpy/distutils/exec_command.py" + (("'/bin/sh'") + (format #f "~s" (search-input-file inputs "bin/bash")))))) + (replace 'check + (lambda* (#:key tests? outputs inputs #:allow-other-keys) + (when tests? + (invoke "./runtests.py" "-vv" "--no-build" "--mode=fast" + "-j" (number->string (parallel-job-count)) + ;; Contrary to scipy, the runtests.py script of numpy + ;; does *not* automatically provide -n when -j is used + ;; (see: https://github.com/numpy/numpy/issues/21359). + "--" "-n" (number->string (parallel-job-count)) + "-k" (string-append + ;; These tests may fail on 32-bit systems (see: + ;; https://github.com/numpy/numpy/issues/18387). + "not test_float_remainder_overflow " + "and not test_pareto")))))))) + (native-inputs + (list python-cython + python-hypothesis-next + python-pytest + python-pytest-xdist + gfortran)) + (inputs (list bash openblas)) (home-page "https://numpy.org") (synopsis "Fundamental package for scientific computing with Python") (description "NumPy is the fundamental package for scientific computing @@ -5756,13 +5877,122 @@ capabilities.") (properties `((python2-variant . ,(delay python2-numpy)))) (license license:bsd-3))) +(define-public python-numpy-next + (package + (inherit python-numpy) + (name "python-numpy-next") + (version "1.22.3") + (source + (origin + (inherit (package-source python-numpy)) + (method url-fetch) + (uri (string-append + "https://github.com/numpy/numpy/releases/download/v" + version "/numpy-" version ".tar.gz")) + (sha256 + (base32 + "19dw91pqbqcniw2z57kiyqs1qp56g7kqy1bdyv664g8s62sc01m9")))))) + +(define-public python-numpy-documentation + (package + (inherit python-numpy) + (name "python-numpy-documentation") + (arguments + (list + #:tests? #f ;we're only generating the documentation + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'add-gnu-freefont-to-texmf + (lambda _ + ;; XXX: The Sphinx-generated tex output specifies the GNU + ;; FreeFont font to be searched via its extension, which uses + ;; kpathsea instead of fontconfig and fail (see: + ;; https://github.com/sphinx-doc/sphinx/issues/10347). Create a + ;; symlink to GNU FreeFont and add it to the TEXMF tree via + ;; GUIX_TEXMF. + (mkdir-p "texmf-dist/fonts/opentype/public") + (symlink (string-append + #$(this-package-native-input "font-gnu-freefont") + "/share/fonts/opentype") + (string-append + (getcwd) "/" + "texmf-dist/fonts/opentype/public/gnu-freefont")) + (setenv "GUIX_TEXMF" (string-append (getenv "GUIX_TEXMF") ":" + (getcwd) "/texmf-dist")))) + (delete 'build) + (replace 'install + (lambda _ + (let* ((data (string-append #$output "/share")) + (doc (string-append data "/doc/numpy")) + (html (string-append doc "/html")) + (info (string-append data "/info")) + (sphinxopts (string-append + "SPHINXOPTS=-j" + (number->string (parallel-job-count))))) + (with-directory-excursion "doc" + ;; Do not treat warnings as errors. + (substitute* "Makefile" + ((" -WT ") " -T ")) + (setenv "HOME" "/tmp") + ;; Build the PDF documentation. + (invoke "make" "latex-build" sphinxopts) + (invoke "make" "-C" "build/latex" "all-pdf" sphinxopts) + ;; Build the HTML documentation + (invoke "make" "html" sphinxopts) + ;; Build the Info documentation. The issues worked around + ;; below can be tracked at + ;; https://github.com/numpy/numpy/issues/12278. + (substitute* "source/conf.py" + ;; The root document should be "index", not "contents". + (("\"contents\"") "'index'") + ;; Disable Sphinx extensions that produce broken Texinfo. + ((".*'numpydoc'.*") "") + ((".*'sphinx.ext.autosummary'.*") "")) + (invoke "make" "info" sphinxopts) + ;; Install the HTML documentation. + (mkdir-p html) + (copy-recursively "build/html" html) + ;; Install the PDF reference and user manuals. + (install-file "build/latex/numpy-ref.pdf" doc) + (install-file "build/latex/numpy-user.pdf" doc) + ;; Install the info manual. + (install-file "build/texinfo/numpy.info" info) + (symlink (string-append html "/_images") + (string-append info "/numpy-figures"))))))))) + (native-inputs + (list font-gnu-freefont + perl + python-breathe + python-ipython + python-matplotlib + python-numpy + python-numpydoc + python-pandas + python-pydata-sphinx-theme + python-scipy ;used by matplotlib + python-sphinx + python-sphinx-panels + texinfo + texlive-bin + texlive-cbfonts + texlive-cm-super + texlive-greek-fontenc + texlive-latex-expdlist + texlive-polyglossia + texlive-xindy)) + (inputs '()) + (propagated-inputs '()) + (synopsis "Documentation for the @code{python-numpy} package") + (description "This package provides the complete NumPy documentation in +the Texinfo, HTML, and PDF formats."))) + ;; Numpy 1.16.x are the last versions that support Python 2. (define-public python2-numpy (let ((numpy (package-with-python2 - (strip-python2-variant python-numpy-next)))) + (strip-python2-variant python-numpy)))) (package (inherit numpy) - (name "python-numpy") + (name "python2-numpy") (version "1.16.5") (source (origin (method url-fetch) @@ -5775,80 +6005,46 @@ capabilities.") (arguments (substitute-keyword-arguments (package-arguments numpy) ((#:phases phases) - `(modify-phases ,phases - (add-after 'unpack 'delete-failing-test - (lambda _ - ;; There's just one failing test here. - (delete-file "numpy/linalg/tests/test_linalg.py") - ;; ...and this one depends on the previous one. - (delete-file "numpy/matrixlib/tests/test_matrix_linalg.py"))))))) + #~(modify-phases #$phases + (add-after 'unpack 'delete-failing-tests + (lambda _ + ;; There's just one failing test here. + (delete-file "numpy/linalg/tests/test_linalg.py") + ;; ...and this one depends on the previous one. + (delete-file "numpy/matrixlib/tests/test_matrix_linalg.py"))) + (replace 'check + ;; Older versions don't cope well with the extra Pytest + ;; options, so remove them. + (lambda* (#:key tests? outputs inputs #:allow-other-keys) + (when tests? + (invoke "./runtests.py" "-vv" "--no-build" "--mode=fast" + "-j" (number->string (parallel-job-count)))))))))) (native-inputs (list python2-cython python2-pytest gfortran))))) -;; Needed by python-numba, see https://github.com/numba/numba/issues/7176 -(define-public python-numpy-1.20 - (package - (inherit python-numpy-next) - (name "python-numpy") - (version "1.20.3") - (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/numpy/numpy/releases/download/v" - version "/numpy-" version ".tar.gz")) - (sha256 - (base32 - "140zq9snx0di4id4g97vaw9zz8x2rfla5lp3a70j666f5030yd5p")))) - ;; python-numpy-next replaced python-hypothesis with - ;; python-hypothesis-6.23. We switch it back here, to prevent - ;; python-numpy-1.20 and its numerous dependents from being rebuilt. - (native-inputs - (list python-cython python-hypothesis python-pytest - python-pytest-xdist gfortran)) - ;; 92 tests fail, many of them because parts of the temp file name - ;; accidentally ends up in a comparison. - (arguments - (substitute-keyword-arguments (package-arguments python-numpy-next) - ((#:tests? _ #t) #f))))) - -;; NOTE: when upgrading numpy please make sure that python-pandas and -;; python-scipy still build, as these three packages are often used together. -(define-public python-numpy python-numpy-1.20) - ;; NOTE: NumPy 1.8 is packaged only for Python 2 because it is of ;; interest only for legacy code going back to NumPy's predecessor ;; Numeric. (define-public python2-numpy-1.8 - (package (inherit python2-numpy) + (package + (inherit python2-numpy) (version "1.8.2") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/numpy/numpy") - (commit (string-append "v" version)))) + (url "https://github.com/numpy/numpy") + (commit (string-append "v" version)))) (file-name (git-file-name "numpy" version)) (sha256 (base32 "0ikgi15rsqwbkfsjjxrwh40lqyal2wvyp3923y6w6ch3dcr82sfk")))) - (arguments - (substitute-keyword-arguments (package-arguments python2-numpy) - ((#:phases phases) - `(modify-phases ,phases - (replace 'configure-blas - (lambda* (#:key inputs #:allow-other-keys) - (call-with-output-file "site.cfg" - (lambda (port) - (format port - "[openblas] -libraries = openblas -library_dirs = ~a/lib -include_dirs = ~a/include -" - (assoc-ref inputs "openblas") - (assoc-ref inputs "openblas")))))))))) - (native-inputs - (list python2-nose)) + (arguments (substitute-keyword-arguments (package-arguments python2-numpy) + ((#:tests? _ #f) #f) ;disable tests + ((#:phases phases) + #~(modify-phases #$phases + (delete 'delete-failing-tests))))) + (native-inputs '()) (description "NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ @@ -6010,129 +6206,16 @@ parser that can be used to decode raw NTLM/SPNEGO/Kerberos tokens into a human readable format.") (license license:expat))) -(define-public python-numpy-documentation - (package - (name "python-numpy-documentation") - (version (package-version python-numpy)) - (source (package-source python-numpy)) - (build-system python-build-system) - (native-inputs - `(("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy) - ("pkg-config" ,pkg-config) - ("python-sphinx" ,python-sphinx) - ("python-numpydoc" ,python-numpydoc) - ("texlive" ,(texlive-updmap.cfg (list - texlive-capt-of - texlive-cm-super - texlive-fonts-ec - texlive-generic-iftex - texlive-pdftex - texlive-amsfonts - texlive-latex-cmap - texlive-latex-environ - texlive-latex-eqparbox - texlive-etoolbox - texlive-latex-expdlist - texlive-latex-fancyhdr - texlive-latex-fancyvrb - texlive-latex-fncychap - texlive-latex-float - texlive-latex-framed - texlive-latex-geometry - texlive-latex-graphics - texlive-hyperref - texlive-latex-mdwtools - texlive-latex-multirow - texlive-latex-needspace - texlive-oberdiek - texlive-latex-parskip - texlive-latex-preview - texlive-latex-tabulary - texlive-latex-threeparttable - texlive-latex-titlesec - texlive-latex-trimspaces - texlive-latex-ucs - texlive-latex-upquote - texlive-url - texlive-latex-varwidth - texlive-wrapfig))) - ("texinfo" ,texinfo) - ("perl" ,perl) - ("scipy-sphinx-theme" - ,(let ((commit "c466764e2231ba132c09826b5b138fffa1cfcec3")) - (origin ;the build script expects scipy-sphinx-theme as a git submodule - (method git-fetch) - (uri (git-reference - (url "https://github.com/scipy/scipy-sphinx-theme") - (commit commit))) - (file-name (git-file-name "python-scipy-sphinx-theme" - (string-take commit 7))) - (sha256 - (base32 - "0q2y87clwlsgc7wvlsn9pzyssybcq10plwhq2w1ydykfsyyqbmkl"))))) - ,@(package-native-inputs python-numpy))) - (arguments - `(#:tests? #f ; we're only generating the documentation - #:phases - (modify-phases %standard-phases - (delete 'build) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((data (string-append (assoc-ref outputs "out") "/share")) - (doc (string-append - data "/doc/" ,name "-" - ,(package-version python-numpy))) - (info-reader (string-append data "/info")) - (html (string-append doc "/html")) - (scipy-sphinx-theme "scipy-sphinx-theme") - (sphinx-theme-checkout (assoc-ref inputs scipy-sphinx-theme)) - (pyver ,(string-append "PYVER="))) - - ;; FIXME: this is needed to for texlive-updmap.cfg to generate - ;; fonts, which are not found. - (setenv "HOME" "/tmp") - - (with-directory-excursion "doc" - (copy-recursively sphinx-theme-checkout scipy-sphinx-theme) - (mkdir-p html) - (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. - ;; (invoke "make" "info" pyver) - ;; (mkdir-p info) - ;; (copy-file "build/texinfo/numpy.info" - ;; (string-append info "/numpy.info")) - (for-each (lambda (file) - (copy-file (string-append "build/latex" file) - (string-append doc file))) - '("/numpy-ref.pdf" "/numpy-user.pdf")) - (with-directory-excursion "build/html" - (for-each (lambda (file) - (let* ((dir (dirname file)) - (tgt-dir (string-append html "/" dir))) - (unless (equal? "." dir) - (mkdir-p tgt-dir)) - (install-file file html))) - (find-files "." ".*"))))) - #t))))) - (home-page (package-home-page python-numpy)) - (synopsis "Documentation for the python-numpy package") - (description (package-description python-numpy)) - (license (package-license python-numpy)))) - (define-public python-pygit2 (package (name "python-pygit2") - (version "1.7.1") + (version "1.9.1") (source (origin (method url-fetch) (uri (pypi-uri "pygit2" version)) (sha256 - (base32 "0p8n25bijirxh31cv99vd1mkdsvpcs6z6441wz1fqva3b2as5ynp")))) + (base32 "1jdr6z1il03nifwgpcdf95w6xzzbfzdkcqq5dcqjaa0rnv1pjr7g")))) (build-system python-build-system) (arguments '(#:tests? #f)) ; tests don't run correctly in our environment @@ -6225,6 +6308,32 @@ to the interactive prompt. It is an extension of the @code{rlcompleter} module from the standard Python library.") (license license:bsd-3))) +(define-public python-ipdb + (package + (name "python-ipdb") + (version "0.13.9") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ipdb" version)) + (sha256 + (base32 "1ibql99agjf2gj7y0svzd5m0h81hailf4p3sj3yl9i1i8ykdj6wm")))) + (build-system python-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "unittest" "discover"))))))) + (propagated-inputs (list python-ipython python-toml python-decorator)) + (home-page "https://github.com/gotcha/ipdb") + (synopsis "IPython-enhanced Python debugger (pdb)") + (description "@code{ipdb} exports functions to access the IPython +debugger, which features tab completion, syntax highlighting, better +tracebacks and better introspection than Python's standard @command{pdb} +debugger, with which it shares the same interface.") + (license license:bsd-3))) + (define-public python-pdbpp (package (name "python-pdbpp") @@ -6365,34 +6474,34 @@ parse and apply unified diffs. It has features such as: (define-public python-numpydoc (package (name "python-numpydoc") - (version "1.1.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (pypi-uri "numpydoc" version)) (sha256 (base32 - "13j4fvy2p7lc8sn00sxvs0jb19vicaznfgx4cphv9jgxgz5xcvy3")))) + "1xjsli2fqks4iv3524v1d329siad7bbsi4kr174zvhsl1pnjds3w")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "setup.py" + (("'Jinja2>=2.10,<3.1'") + "'Jinja2>=2.10'")))) (replace 'check - (lambda* (#:key tests? inputs outputs #:allow-other-keys) + (lambda* (#:key tests? #:allow-other-keys) (when tests? - (add-installed-pythonpath inputs outputs) (invoke "pytest" "-v" "numpydoc/tests" ;; TODO: unclear why these fail. "-k" "not test_MyClass and not test_my_function"))))))) - (propagated-inputs - (list python-sphinx)) - (native-inputs - (list python-matplotlib python-pytest python-pytest-cov)) + (propagated-inputs (list python-jinja2 python-sphinx)) + (native-inputs (list python-matplotlib python-pytest python-pytest-cov)) (home-page "https://pypi.org/project/numpydoc/") - (synopsis - "Numpy's Sphinx extensions") - (description - "Sphinx extension to support docstrings in Numpy format.") + (synopsis "Numpy's Sphinx extensions") + (description "Sphinx extension to support docstrings in Numpy format.") (license license:bsd-2) (properties `((python2-variant . ,(delay python2-numpydoc)))))) @@ -6546,51 +6655,14 @@ comparison. (define-public python-matplotlib (package (name "python-matplotlib") - (version "3.5.1") + (version "3.5.2") (source (origin (method url-fetch) (uri (pypi-uri "matplotlib" version)) (sha256 - (base32 "076f8qi265x8jy89c03r3vv5h4is4ir5mawwrrrpp96314783sdj")))) - (build-system python-build-system) - (propagated-inputs ; the following packages are all needed at run time - `(("python-cycler" ,python-cycler) - ("python-fonttools" ,python-fonttools) - ("python-kiwisolver" ,python-kiwisolver) - ("python-packaging" ,python-packaging) - ("python-pyparsing" ,python-pyparsing) - ("python-pygobject" ,python-pygobject) - ("python-certifi" ,python-certifi) - ("gobject-introspection" ,gobject-introspection) - ("python-tkinter" ,python "tk") - ("python-dateutil" ,python-dateutil) - ("python-numpy" ,python-numpy) - ("python-pillow" ,python-pillow) - ("python-pytz" ,python-pytz) - ("python-six" ,python-six) - ("python-wxpython" ,python-wxpython) - ;; From version 1.4.0 'matplotlib' makes use of 'cairocffi' instead of - ;; 'pycairo'. However, 'pygobject' makes use of a 'pycairo' 'context' - ;; object. For this reason we need to import both libraries. - ;; https://cairocffi.readthedocs.io/en/stable/cffi_api.html#converting-pycairo-wrappers-to-cairocffi - ("python-pycairo" ,python-pycairo) - ("python-cairocffi" ,python-cairocffi))) - (inputs - (list libpng - freetype - qhull - cairo - glib - tcl - tk)) - (native-inputs - `(("pkg-config" ,pkg-config) - ("python-pytest" ,python-pytest) - ("python-pytest-timeout" ,python-pytest-timeout) - ("python-pytest-xdist" ,python-pytest-xdist) - ("python-setuptools-scm" ,python-setuptools-scm) - ("python-setuptools-scm-git-archive" ,python-setuptools-scm-git-archive))) + (base32 "18h78s5ld1i6mz00w258hy29909nfr3ddq6ry9kq18agw468bks8")))) + (build-system python-build-system) (arguments (list #:phases @@ -6608,8 +6680,8 @@ comparison. (lambda _ (substitute* (append (find-files "lib/matplotlib/tests/" "test_.*\\.py$") - (find-files "lib/mpl_toolkits/tests" - "test_.*\\.py$")) + (find-files "lib/mpl_toolkits/tests" + "test_.*\\.py$")) (("^from matplotlib" match) (string-append "import pytest\n" match)) (("( *)@([^_]+_)*(image_comparison|check_figures_equal)" match @@ -6632,7 +6704,11 @@ reason=\"unknown minor image differences\")\n" match))) ;; different version of FreeType. "lib/matplotlib/tests/test_constrainedlayout.py" ;; Fontconfig returns no fonts. - "lib/matplotlib/tests/test_font_manager.py")))) + "lib/matplotlib/tests/test_font_manager.py" + ;; The images comparison test fails + ;; non-deterministically when run in parallel (see: + ;; https://github.com/matplotlib/matplotlib/issues/22992). + "lib/matplotlib/tests/test_compare_images.py")))) (add-before 'build 'configure-environment (lambda* (#:key inputs #:allow-other-keys) ;; Fix rounding errors when using the x87 FPU. @@ -6662,7 +6738,47 @@ tests = True~%" (assoc-ref inputs "tcl") (assoc-ref inputs "tk")))))) ;; everything gets built in the source directory. (invoke "pytest" "-n" (number->string (parallel-job-count)) - "-m" "not network" "--pyargs" "matplotlib")))))))) + "-m" "not network" "--pyargs" "matplotlib" + ;; The 'test_lazy_auto_backend_selection' fails + ;; because it would require an X server; skip it. + "-k" "not test_lazy_auto_backend_selection")))))))) + (propagated-inputs + (list gobject-introspection + python-cairocffi + python-certifi + python-cycler + python-dateutil + python-fonttools + python-kiwisolver + python-numpy + python-packaging + python-pillow + ;; ;; 'pycairo'. However, 'pygobject' makes use of a 'pycairo' 'context' + ;; ;; From version 1.4.0 'matplotlib' makes use of 'cairocffi' instead of + ;; ;; https://cairocffi.readthedocs.io/en/stable/cffi_api.html#converting-pycairo-wrappers-to-cairocffi + ;; ;; object. For this reason we need to import both libraries. + ;; python-pycairo + python-pygobject + python-pyparsing + python-pytz + python-six + `(,python "tk") + python-wxpython)) + (inputs + (list cairo + freetype + glib + libpng + qhull + tcl + tk)) + (native-inputs + (list pkg-config + python-pytest + python-pytest-timeout + python-pytest-xdist + python-setuptools-scm + python-setuptools-scm-git-archive)) (home-page "https://matplotlib.org/") (synopsis "2D plotting library for Python") (description @@ -6721,87 +6837,65 @@ toolkits.") (define-public python-matplotlib-documentation (package + (inherit python-matplotlib) (name "python-matplotlib-documentation") - (version (package-version python-matplotlib)) - (source (package-source python-matplotlib)) - (build-system python-build-system) - (native-inputs - `(("python-matplotlib" ,python-matplotlib) - ("python-colorspacious" ,python-colorspacious) - ("python-sphinx" ,python-sphinx) - ("python-sphinx-copybutton" ,python-sphinx-copybutton) - ("python-sphinx-gallery" ,python-sphinx-gallery) - ("python-numpydoc" ,python-numpydoc) - ("python-ipython" ,python-ipython) - ("python-ipykernel" ,python-ipykernel) - ("python-mock" ,python-mock) - ("graphviz" ,graphviz) - ("texlive" ,(texlive-updmap.cfg (list texlive-amsfonts - texlive-enumitem - texlive-amsmath - texlive-latex-expdlist - texlive-latex-geometry - texlive-latex-preview - texlive-latex-type1cm - texlive-latex-ucs - - texlive-pdftex - - texlive-fonts-ec - texlive-times - texlive-txfonts))) - ("texinfo" ,texinfo) - ,@(package-native-inputs python-matplotlib))) - (arguments - `(#:tests? #f ; we're only generating documentation - #:phases - (modify-phases %standard-phases - ;; The tests in python-matplotlib are run after the install phase, so - ;; we need to delete the extra phase here. - (delete 'check) - (replace 'build - (lambda _ - (chdir "doc") - (setenv "PYTHONPATH" "../examples/units") - (substitute* "conf.py" - ;; Don't use git. - (("^SHA = check_output.*") - (string-append "SHA = \"" ,version "\"\n")) - ;; Don't fetch intersphinx files from the Internet - (("^explicit_order_folders" m) - (string-append "intersphinx_mapping = {}\n" m)) - (("'sphinx.ext.intersphinx',") "") - ;; Disable URL embedding which requires internet access. - (("'https://docs.scipy.org/doc/numpy'") "None") - (("'https://docs.scipy.org/doc/scipy/reference'") "None")) - (invoke "make" - "SPHINXBUILD=sphinx-build" - "SPHINXOPTS=" ; don't abort on warnings - "html" "texinfo"))) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((data (string-append (assoc-ref outputs "out") "/share")) - (doc (string-append data "/doc/python-matplotlib-" ,version)) - (info (string-append data "/info")) - (html (string-append doc "/html"))) - (mkdir-p html) - (mkdir-p info) - (copy-recursively "build/html" html) - (symlink (string-append html "/_images") - (string-append info "/matplotlib-figures")) - (with-directory-excursion "build/texinfo" - (substitute* "matplotlib.texi" - (("@image\\{([^,]*)" all file) - (string-append "@image{matplotlib-figures/" file))) - (symlink (string-append html "/_images") - "./matplotlib-figures") - (invoke "makeinfo" "--no-split" - "-o" "matplotlib.info" "matplotlib.texi")) - (install-file "build/texinfo/matplotlib.info" info))))))) - (home-page (package-home-page python-matplotlib)) - (synopsis "Documentation for the python-matplotlib package") - (description (package-description python-matplotlib)) - (license (package-license python-matplotlib)))) + (arguments + (list + #:tests? #f ;we're only generating documentation + #:phases + #~(modify-phases %standard-phases + (replace 'build + (lambda _ + (setenv "HOME" "/tmp") + (chdir "doc") + (substitute* "conf.py" + ;; The sphinx_panels extension causes a "TypeError: first + ;; argument must be callable" to be raised when generating the + ;; info target; remove it (see: + ;; https://github.com/executablebooks/sphinx-panels/issues/74). + ((".*'sphinx_panels',.*") "")) + (invoke "make" "html" "info" + ;; Don't abort on warnings; build in parallel. + (format #f "SPHINXOPTS=-j~a" (parallel-job-count))))) + (replace 'install + (lambda _ + (let* ((data (string-append #$output "/share")) + (doc (string-append data "/doc/matplotlib")) + (info (string-append data "/info")) + (html (string-append doc "/html"))) + (mkdir-p html) + (copy-recursively "build/html" html) + (install-file "build/texinfo/matplotlib.info" info) + ;; The "matplotlib-figures" directory contains are a subset of + ;; the images produced for the html target; simply create a + ;; symlink to it, saving about 11 MiB. + (symlink (string-append html "/_images") + (string-append info "/matplotlib-figures")))))))) + (native-inputs + (list graphviz + inkscape + python-colorspacious + python-mpl-sphinx-theme + python-scipy + python-sphinx + python-sphinx-copybutton + python-sphinx-gallery + python-sphinxcontrib-svg2pdfconverter + python-numpydoc + python-ipython + python-ipywidgets + texlive-amsfonts + texlive-amsmath + texlive-babel + texlive-fontspec + texlive-unicode-math + texlive-etoolbox + texlive-latex-expdlist + texlive-underscore + texlive-latex-type1cm + texlive-times + texinfo)) + (synopsis "Documentation for the @code{python-matplotlib} package"))) (define-public python-matplotlib-inline (package @@ -7041,14 +7135,14 @@ Python code against some of the style conventions in (define-public python-multidict (package (name "python-multidict") - (version "4.7.5") + (version "5.2.0") (source (origin (method url-fetch) (uri (pypi-uri "multidict" version)) (sha256 (base32 - "07ikq2c72kd263hpldw55y0px2l3g34hjk66ml9lryh1jv287qmf")))) + "1kjrxav572j45xvr1iy60zb2g8zqvrinzdkl4ax36js4vczckl8d")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases @@ -7089,6 +7183,36 @@ multiple values for the same key. An ordered multivalue dictionary is a multivalue dictionary that retains the order of insertions and deletions.") (license license:unlicense))) +(define-public python-autocommand + (package + (name "python-autocommand") + (version "2.2.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "autocommand" version)) + (sha256 + (base32 "03qp9xx4dq81ljhf56r21gp5j0lpqs1vaw99g0d84i97s3lj1m7y")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; This test fails with an invalid syntax error on 'task1 = + ;; asyncio.async(coro_1())' (see: + ;; https://github.com/Lucretiel/autocommand/issues/20). + (delete-file "test/test_autoasync.py") + (invoke "pytest" "-vv"))))))) + (native-inputs (list python-pytest python-pytest-asyncio)) + (home-page "https://github.com/Lucretiel/autocommand") + (synopsis "Python library to build a command-line from a function") + (description "@code{autocommand} is library to automatically generate and +run simple @code{argparse} parsers from function signatures.") + (license license:lgpl3+))) + (define-public python-autopep8 (package (name "python-autopep8") @@ -8375,19 +8499,41 @@ for older versions of Python.") (define-public python-importlib-metadata (package (name "python-importlib-metadata") - (version "1.5.0") + (version "4.11.3") (source (origin (method url-fetch) (uri (pypi-uri "importlib_metadata" version)) (sha256 (base32 - "00ikdj4gjhankdljnz7g5ggak4k9lql2926x0x117ir9j2lv7x86")))) + "0f951zynlh39yicqnhrs3p1qa5p3g6ajjfcggf12y51ppxz5jk7a")))) (build-system python-build-system) - (propagated-inputs - (list python-zipp)) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; XXX: PEP 517 manual build/install procedures copied from + ;; python-isort. + (replace 'build + (lambda _ + ;; ZIP does not support timestamps before 1980. + (setenv "SOURCE_DATE_EPOCH" "315532800") + (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((whl (car (find-files "dist" "\\.whl$")))) + (invoke "pip" "--no-cache-dir" "--no-input" + "install" "--no-deps" "--prefix" #$output whl)))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" "tests"))))))) + (propagated-inputs (list python-zipp)) (native-inputs - (list python-setuptools-scm python-pyfakefs python-packaging)) + (list python-pypa-build + python-pyfakefs + python-pytest + python-setuptools-scm)) (home-page "https://importlib-metadata.readthedocs.io/") (synopsis "Read metadata from Python packages") (description @@ -8403,19 +8549,29 @@ need to use the older and less efficient @code{pkg_resources} package.") (define-public python2-importlib-metadata (let ((base (package-with-python2 (strip-python2-variant python-importlib-metadata)))) - (package/inherit - base - (name "python2-importlib-metadata") - (native-inputs - `(("python-setuptools-scm" ,python2-setuptools-scm) - ("python-pyfakefs" ,python2-pyfakefs-bootstrap) - ("python-packaging" ,python2-packaging-bootstrap))) - (propagated-inputs - `(("python-configparser" ,python2-configparser) - ("python-contextlib2" ,python2-contextlib2) - ("python-importlib-resources" ,python2-importlib-resources) - ("python-pathlib2" ,python2-pathlib2) - ,@(package-propagated-inputs base)))))) + (package/inherit base + (name "python2-importlib-metadata") + (version "1.5.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "importlib_metadata" version)) + (sha256 + (base32 + "00ikdj4gjhankdljnz7g5ggak4k9lql2926x0x117ir9j2lv7x86")))) + (arguments (substitute-keyword-arguments (package-arguments base) + ((#:phases phases) ;reset standard phases + #~%standard-phases))) + (native-inputs + `(("python-setuptools-scm" ,python2-setuptools-scm) + ("python-pyfakefs" ,python2-pyfakefs-bootstrap) + ("python-packaging" ,python2-packaging-bootstrap))) + (propagated-inputs + `(("python-configparser" ,python2-configparser) + ("python-contextlib2" ,python2-contextlib2) + ("python-importlib-resources" ,python2-importlib-resources) + ("python-pathlib2" ,python2-pathlib2) + ,@(package-propagated-inputs base)))))) ;; This package is used by python2-pytest, and thus must not depend on it. (define-public python2-importlib-metadata-bootstrap @@ -8482,6 +8638,146 @@ finding unresolved symbols in Python code and their corresponding imports.") "@code{inotify-simple} is a simple wrapper around inotify library.") (license license:bsd-3))) +(define-public python-jaraco-classes + (package + (name "python-jaraco-classes") + (version "3.2.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "jaraco.classes" version)) + (sha256 + (base32 "0d6g7qvfv1jlzbzh6asprqdblqd59grvlvr3nwbdqdqrmwlbfm7d")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Do not test the myproject.toml build as it tries to pull + ;; dependencies from the Internet. + (invoke "pytest" "-vv" "-k" "not project"))))))) + (native-inputs + (list python-pytest + python-pytest-black + python-pytest-checkdocs + python-pytest-cov + python-pytest-enabler-bootstrap ;OK since not propagated + python-pytest-flake8 + python-pytest-mypy + python-setuptools-scm + python-wheel)) + (propagated-inputs (list python-more-itertools)) + (home-page "https://github.com/jaraco/jaraco.classes") + (synopsis "Utility functions for Python class constructs") + (description "This Python library contains utility functions for Python +class constructs.") + (license license:expat))) + +;;; Variant used to break a cycle with python-pytest-enabler. +(define-public python-jaraco-context-bootstrap + (hidden-package + (package + (name "python-jaraco-context-bootstrap") + (version "4.1.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "jaraco.context" version)) + (sha256 + (base32 "0hbjm1rpxf4pzmbdp9rh3ali4zqnlcr8m97bhh1nizxvzcpxim7h")))) + (build-system python-build-system) + (arguments (list #:tests? #f)) + (native-inputs (list python-setuptools-scm)) + (home-page "https://github.com/jaraco/jaraco.context") + (synopsis "Context managers Python library") + (description "This Python library provides context managers-related +procedures.") + (license license:expat)))) + +(define-public python-jaraco-context + (package/inherit python-jaraco-context-bootstrap + (name "python-jaraco-context") + (arguments + (substitute-keyword-arguments + (package-arguments python-jaraco-context-bootstrap) + ((#:tests? _ #f) + #t) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Do not test the myproject.toml build as it tries to pull + ;; dependencies from the Internet. + (invoke "pytest" "-vv" "-k" "not project")))))))) + (native-inputs + (modify-inputs + (package-native-inputs python-jaraco-context-bootstrap) + (append python-pytest + python-pytest-black + python-pytest-checkdocs + python-pytest-cov + python-pytest-enabler-bootstrap ;OK since not propagated + python-pytest-flake8 + python-pytest-mypy))) + (properties (alist-delete 'hidden? (package-properties + python-jaraco-context-bootstrap))))) + +;;; Variant used to break a cycle with python-pytest-enabler. +(define-public python-jaraco-functools-bootstrap + (hidden-package + (package + (name "python-jaraco-functools-bootstrap") + (version "3.5.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "jaraco.functools" version)) + (sha256 + (base32 "186xqzs3bqhjwajnprxy3sc3h0w5vdld8spc1dxjnn9720yykq1i")))) + (build-system python-build-system) + (arguments (list #:tests? #f)) + (native-inputs (list python-setuptools-scm)) + (propagated-inputs (list python-more-itertools)) + (home-page "https://github.com/jaraco/jaraco.functools") + (synopsis "Python library extending Python's @code{functools}") + (description "This library extends the standard @code{functools} Python +module with a few extra procedures.") + (license license:expat)))) + +(define-public python-jaraco-functools + (package/inherit python-jaraco-functools-bootstrap + (name "python-jaraco-functools") + (arguments + (substitute-keyword-arguments + (package-arguments python-jaraco-functools-bootstrap) + ((#:tests? _ #f) + #t) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Do not test the myproject.toml build as it tries to pull + ;; dependencies from the Internet. + (invoke "pytest" "-vv" "-k" "not project")))))))) + (native-inputs + (modify-inputs + (package-native-inputs python-jaraco-functools-bootstrap) + (append python-jaraco-classes + python-pytest + python-pytest-black + python-pytest-checkdocs + python-pytest-cov + python-pytest-enabler-bootstrap ;OK since not propagated + python-pytest-flake8 + python-pytest-mypy))) + (properties (alist-delete 'hidden? (package-properties + python-jaraco-functools-bootstrap))))) + (define-public python-jaraco-packaging (package (name "python-jaraco-packaging") @@ -8510,57 +8806,6 @@ finding unresolved symbols in Python code and their corresponding imports.") releases.") (license license:expat))) -(define-public python-pathpy - (package - (name "python-pathpy") - (version "11.5.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "path.py" version)) - (sha256 - (base32 "0ir9j1haq2jbi7aip6k2fa9l7q1l03k4hp1awxhjhcwzsnwp3ll8")))) - (outputs '("out" "doc")) - (build-system python-build-system) - (propagated-inputs - (list python-appdirs python-importlib-metadata)) - (native-inputs - (list python-setuptools-scm - python-sphinx - python-rst.linker - python-pytest - python-pytest-runner - python-jaraco-packaging)) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'build 'build-doc - (lambda _ - (setenv "LANG" "en_US.UTF-8") - (invoke "python" "setup.py" "build_sphinx"))) - (add-after 'install 'install-doc - (lambda* (#:key 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"))) - (mkdir-p html) - (for-each (lambda (file) - (copy-file file (string-append doc "/" file))) - '("README.rst" "CHANGES.rst")) - (copy-recursively "build/sphinx/html" html) - #t))) - (replace 'check - (lambda _ - ;; The import time test aborts if an import takes longer than - ;; 100ms. It may very well take a little longer than that. - (invoke "pytest" "-v" "-k" "not test_import_time")))))) - (home-page "https://github.com/jaraco/path.py") - (synopsis "Python module wrapper for built-in os.path") - (description - "@code{path.py} implements path objects as first-class entities, allowing -common operations on files to be invoked on those path objects directly.") - (license license:expat))) - (define-public python-simplegeneric (package (name "python-simplegeneric") @@ -8616,47 +8861,43 @@ away.") (define-public python2-ipython-genutils (package-with-python2 python-ipython-genutils)) -(define-public python-ipyparallel - (package - (name "python-ipyparallel") - (version "6.2.4") - (source +;;; Variant used to break a cycle with python-ipykernel. +(define-public python-ipyparallel-bootstrap + (hidden-package + (package + (name "python-ipyparallel-bootstrap") + (version "8.2.1") + (source (origin (method url-fetch) (uri (pypi-uri "ipyparallel" version)) (sha256 (base32 - "0rf0dbpxf5z82bw8lsjj45r3wdd4wc74anz4wiiaf2rbjqlb1ivn")))) - (build-system python-build-system) - (arguments - `(#:tests? #f ; RuntimeError: IO Loop failed to start - #:phases - (modify-phases %standard-phases - (add-before 'check 'prepare-for-tests - (lambda _ - (setenv "HOME" (getcwd)) - #t))))) - (propagated-inputs - (list python-dateutil - python-decorator - python-ipykernel - python-ipython - python-ipython-genutils - python-jupyter-client - python-pyzmq - python-tornado - python-traitlets)) - (native-inputs - (list python-ipython - python-mock - python-nose - python-pytest - python-pytest-cov - python-testpath)) - (home-page "https://ipython.org/") - (synopsis "Interactive Parallel Computing with IPython") - (description - "@code{ipyparallel} is a Python package and collection of CLI scripts for + "0wiwfd7870zbmczzn96jqxxjf2zcbcaxnsl1ddn8hspwa8y4frzj")))) + (build-system python-build-system) + (arguments + (list + #:tests? #f + #:phases #~(modify-phases %standard-phases + ;; The python-ipykernel is normally propagated but is + ;; removed from this package to break the cycle. + (delete 'sanity-check)))) + (propagated-inputs + (list python-dateutil + python-decorator + python-entrypoints + python-ipython + ;; python-ipykernel is omitted here to break a cycle. + python-jupyter-client-bootstrap + python-psutil + python-pyzmq + python-tornado-6 + python-tqdm + python-traitlets)) + (home-page "https://ipython.org/") + (synopsis "Interactive Parallel Computing with IPython") + (description + "@code{ipyparallel} is a Python package and collection of CLI scripts for controlling clusters for Jupyter. @code{ipyparallel} contains the following CLI scripts: @enumerate @@ -8664,7 +8905,32 @@ CLI scripts: @item ipcontroller - start a scheduler @item ipengine - start an engine @end enumerate") - (license license:bsd-3))) + (license license:bsd-3)))) + +(define-public python-ipyparallel + (package + (inherit python-ipyparallel-bootstrap) + (name "python-ipyparallel") + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda _ + (invoke "pytest" "-vv")))))) + (native-inputs + (list python-ipython + python-pytest + python-pytest-asyncio + python-pytest-cov + python-pytest-tornado + python-testpath)) + (propagated-inputs + (modify-inputs (package-propagated-inputs python-ipyparallel-bootstrap) + (replace "python-jupyter-client-bootstrap" python-jupyter-client) + (append python-ipykernel))) + (properties (alist-delete 'hidden? (package-properties + python-ipyparallel-bootstrap))))) (define-public python-ipython-cluster-helper (package @@ -8761,7 +9027,9 @@ connect strings, then issue SQL commands within IPython or IPython Notebook.") (arguments `(#:phases (modify-phases %standard-phases - (replace 'check (lambda _ (invoke "pytest" "-vv" "traitlets")))))) + (replace 'check (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" "traitlets"))))))) (native-inputs (list python-pytest)) (home-page "https://ipython.org") @@ -8778,26 +9046,30 @@ without using the configuration machinery.") (define-public python-jupyter-core (package (name "python-jupyter-core") - (version "4.7.1") + (version "4.10.0") (source (origin (method url-fetch) (uri (string-append (pypi-uri "jupyter_core" version))) (sha256 (base32 - "1d12j5hkff0xiax87pnhmzbsph3jqqzhz16h8xld7z2y4armq0kr")))) + "1v0s31rmwppdmww135hif03hy164j9kimirh24kxfcbvdfql9pm6")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (lambda* (#:key tests? #:allow-other-keys) (when tests? - ; Some tests write to $HOME. + ;; Some tests write to $HOME. (setenv "HOME" "/tmp") - ; Some tests load the installed package. - (add-installed-pythonpath inputs outputs) - (invoke "pytest" "-vv")))) + (invoke "pytest" "-vv" + "-k" + (string-append + ;; XXX: These tests fail with "ModuleNotFoundError: No + ;; module named 'jupyter_core'". + "not test_argv0 and not test_path_priority " + "and not test_not_on_path"))))) (add-after 'unpack 'patch-testsuite (lambda _ ;; test_not_on_path() and test_path_priority() try to run a test @@ -8806,8 +9078,7 @@ without using the configuration machinery.") (("env = \\{'PATH': ''\\}") "env = {'PATH': '', 'PYTHONPATH': os.environ['GUIX_PYTHONPATH']}") (("env = \\{'PATH': str\\(b\\)\\}") - "env = {'PATH': str(b), 'PYTHONPATH': os.environ['GUIX_PYTHONPATH']}")) - #t)) + "env = {'PATH': str(b), 'PYTHONPATH': os.environ['GUIX_PYTHONPATH']}")))) ;; Migration is running whenever etc/jupyter exists, but the ;; Guix-managed directory will never contain any migratable IPython ;; config files and cannot be written to anyway, so just pretend we @@ -8819,10 +9090,8 @@ without using the configuration machinery.") (string-append (assoc-ref outputs "out") "/etc/jupyter/migrated"))))))) - (propagated-inputs - (list python-traitlets)) - (native-inputs - (list python-six python-pytest)) + (propagated-inputs (list python-traitlets)) + (native-inputs (list python-pytest)) ;; This package provides the `jupyter` binary and thus also exports the ;; search paths. (native-search-paths @@ -8838,109 +9107,149 @@ without using the configuration machinery.") "Jupyter core is the base package on which Jupyter projects rely.") (license license:bsd-3))) -(define-public python-jupyter-client - (package - (name "python-jupyter-client") - (version "6.1.12") - (source - (origin - (method url-fetch) - (uri (pypi-uri "jupyter_client" version)) - (sha256 - (base32 - "10p7fcgvv9hvz9zical9wk68ks5ssak2ykbzx65wm1k1hk8a3g64")))) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'set-tool-file-names - (lambda* (#:key inputs #:allow-other-keys) - (let ((iproute (assoc-ref inputs "iproute"))) +;; Bootstrap variant of jupyter-client, which breaks the loop between ipykernel +;; and jupyter-client by removing the former from its native-inputs and +;; disabling tests. +(define-public python-jupyter-client-bootstrap + (hidden-package + (package + (name "python-jupyter-client-bootstrap") + (version "7.2.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "jupyter_client" version)) + (sha256 + (base32 + "12pbp177bfb3710y1a5598mwn8ffhyzmpll67m0nmalb98savnwg")))) + (build-system python-build-system) + (arguments + (list + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-tool-file-names + (lambda* (#:key inputs #:allow-other-keys) (substitute* "jupyter_client/localinterfaces.py" (("'ip'") - (string-append "'" iproute "/sbin/ip'"))) - #t))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - ;; Some tests try to write to $HOME. - (setenv "HOME" "/tmp") - (invoke "pytest" "-vv"))))))) - (inputs - `(("iproute" ,iproute))) - (propagated-inputs - (list python-dateutil python-jupyter-core python-pyzmq - python-tornado-6 python-traitlets)) - (native-inputs - `(("python-pytest" ,python-pytest) - ("python-pytest-timeout" ,python-pytest-timeout) - ("python-async-generator" ,python-async-generator) - ("python-mock" ,python-mock) - ("python-msgpack" ,python-msgpack) - ("python-ipython" ,python-ipython) - ("python-ipykernel" ,python-ipykernel-bootstrap))) - (home-page "https://jupyter.org/") - (synopsis "Jupyter protocol implementation and client libraries") - (description - "The @code{jupyter_client} package contains the reference implementation + (format #f "'~a'" (search-input-file inputs "sbin/ip"))))))))) + (inputs (list iproute)) + (propagated-inputs + (list python-dateutil + python-entrypoints + python-jupyter-core + python-nest-asyncio + python-pyzmq + python-tornado-6 + python-traitlets)) + (home-page "https://jupyter.org/") + (synopsis "Jupyter protocol implementation and client libraries") + (description + "The @code{jupyter_client} package contains the reference implementation of the Jupyter protocol. It also provides client and kernel management APIs for working with kernels, and the @code{jupyter kernelspec} entrypoint for installing @code{kernelspec}s for use with Jupyter frontends.") - (license license:bsd-3))) + (license license:bsd-3)))) -;; Bootstrap variant of jupyter-client, which breaks the loop between ipykernel -;; and jupyter-client by removing the former from its native-inputs and -;; disabling tests. -(define-public python-jupyter-client-bootstrap - (let ((base python-jupyter-client)) - (hidden-package - (package - (inherit base) - (name "python-jupyter-client-bootstrap") - (arguments - `(#:tests? #f - ,@(package-arguments base))) - (native-inputs `()))))) +(define-public python-jupyter-client + (let ((base python-jupyter-client-bootstrap)) + (package + (inherit base) + (name "python-jupyter-client") + (arguments + (substitute-keyword-arguments (package-arguments base) + ((#:tests? _ #f) + #t) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Some tests try to write to $HOME. + (setenv "HOME" "/tmp") + (invoke "pytest" "-vv")))))))) + (native-inputs + (list python-pytest + python-pytest-asyncio + python-pytest-timeout + python-async-generator + python-ipython + python-ipykernel-bootstrap)) + (properties (alist-delete 'hidden? (package-properties base)))))) (define-public python-ipykernel (package (name "python-ipykernel") - (version "5.5.3") + (version "6.13.0") (source (origin - (method url-fetch) - (uri (pypi-uri "ipykernel" version)) - (sha256 - (base32 "02f55cjkp5q64x7ikjxznbxwjpkdmfy237b9kg7dk1pxmzvy90m6")))) + (method url-fetch) + (uri (pypi-uri "ipykernel" version)) + (sha256 + (base32 "0q5yni8h08nadsn53f957p0pjsjhwl2b2lp1hqz3jn0854z2fa0f")))) (build-system python-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "HOME" "/tmp") - (invoke "pytest" "-v")))) - (add-after 'install 'set-python-file-name - (lambda* (#:key outputs #:allow-other-keys) - ;; Record the absolute file name of the 'python' executable in - ;; 'kernel.json'. - (let ((out (assoc-ref outputs "out"))) - (substitute* (string-append out "/share/jupyter" - "/kernels/python3/kernel.json") - (("\"python\"") - (string-append "\"" (which "python") "\""))) - #t)))))) - (propagated-inputs - (list python-ipython python-tornado-6 python-traitlets - ;; imported at runtime during connect - python-jupyter-client)) - (native-inputs - (list python-flaky python-nose python-pytest)) + (list + #:imported-modules `(,@%python-build-system-modules + (guix build syscalls)) + #:modules '((guix build python-build-system) + (guix build syscalls) + (guix build utils) + (ice-9 match)) + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (match (primitive-fork) + (0 ;child process + (set-child-subreaper!) + ;; XXX: Tini provides proper PID1-like signal handling that + ;; reaps zombie processes, necessary for the + ;; 'test_shutdown_subprocesses' test to pass. + + ;; TODO: Complete https://issues.guix.gnu.org/30948. + (setenv "HOME" "/tmp") + (execlp "tini" "--" "pytest" "-vv")) + (pid + (match (waitpid pid) + ((_ . status) + (unless (zero? status) + (error "`pytest' exited with status" + status))))))))) + (add-after 'install 'set-python-file-name + (lambda* (#:key inputs #:allow-other-keys) + ;; Record the absolute file name of the 'python' executable in + ;; 'kernel.json'. + (substitute* (string-append #$output "/share/jupyter" + "/kernels/python3/kernel.json") + (("\"python\"") + (format #f "~s" (search-input-file inputs + "/bin/python3"))))))))) + (propagated-inputs + (list python-debugpy + python-ipython + python-jupyter-client ;imported at runtime during connect + python-matplotlib-inline + ;;python-nest-asyncio + ;;python-packaging + python-psutil + python-tornado-6 + python-traitlets)) + (inputs (list python)) ;for cross compilation + (native-inputs + (list python-flaky + python-ipyparallel-bootstrap + ;; XXX: Our Pytest package captures its native inputs in its + ;; wrapper script (such as python-nose), which is used in the code + ;; and causes deprecation warnings. Using the bootstrap variant + ;; avoids that. + python-pytest-bootstrap + python-pytest-timeout + tini)) (home-page "https://ipython.org") (synopsis "IPython Kernel for Jupyter") - (description - "This package provides the IPython kernel for Jupyter.") + (description "This package provides the IPython kernel for Jupyter.") (license license:bsd-3))) ;; Bootstrap variant of ipykernel, which uses the bootstrap jupyter-client to @@ -8951,10 +9260,16 @@ installing @code{kernelspec}s for use with Jupyter frontends.") (package (inherit parent) (name "python-ipykernel-bootstrap") + (arguments (list #:tests? #f + ;; The package should normally propagate ipykernel, + ;; left out here to break the cycle. + #:phases #~(modify-phases %standard-phases + (delete 'sanity-check)))) + (native-inputs '()) (propagated-inputs - `(("python-jupyter-client" ,python-jupyter-client-bootstrap) - ,@(fold alist-delete (package-propagated-inputs parent) - '("python-jupyter-client")))))))) + (modify-inputs (package-propagated-inputs parent) + (replace "python-jupyter-client" python-jupyter-client-bootstrap) + (append python-ipyparallel-bootstrap))))))) (define-public python-pari-jupyter (package @@ -9000,83 +9315,143 @@ you're careful. The @code{backcall} package provides a way of specifying the callback signature using a prototype function.") (license license:bsd-3))) +(define-public python-pure-eval + (package + (name "python-pure-eval") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pure_eval" version)) + (sha256 + (base32 "1hwsm85cwqwh6d6x4vzcimla2865s6v19ms3ym81ganzyq534i9b")))) + (build-system python-build-system) + (native-inputs (list python-pytest python-setuptools-scm)) + (home-page "https://github.com/alexmojaki/pure_eval") + (synopsis "Python library to evaluate abstract syntax tree nodes") + (description "The @code{pure_eval} Python library can safely evaluate +abstract syntax tree (AST) nodes without side effects.") + (license license:expat))) + +(define-public python-asttokens + (package + (name "python-asttokens") + (version "2.0.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "asttokens" version)) + (sha256 + (base32 "1mglbkikxvnhrk3inbx0v1qzxwd38qjr6l35sn098yicy0ac2m4s")))) + (build-system python-build-system) + (propagated-inputs (list python-six)) + (native-inputs (list python-astroid python-pytest python-setuptools-scm)) + (home-page "https://github.com/gristlabs/asttokens") + (synopsis "Python library to annotate abstract syntax trees") + (description "The @code{asttokens} module annotates Python abstract syntax +trees (ASTs) with the positions of tokens and text in the source code that +generated them. It makes it possible for tools that work with logical AST +nodes to find the particular text that resulted in those nodes, for example +for automated refactoring or highlighting.") + (license license:asl2.0))) + +(define-public python-littleutils + (package + (name "python-littleutils") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "littleutils" version)) + (sha256 + (base32 "0vwijrylppmk0nbddqvn527r9cg3zw8d6zk6r58hslry42jf7jp6")))) + (build-system python-build-system) + (home-page "https://github.com/alexmojaki/littleutils") + (synopsis "Python utility function collection") + (description "@code{littleutils} is a small collection of Python utility +functions, useful in the context of writing unit tests among other uses.") + (license license:expat))) + +(define-public python-stack-data + (package + (name "python-stack-data") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "stack_data" version)) + (sha256 + (base32 "04lfcj5qrn4qikjw89qbdzqwm0xm4bgm4m8rll1rafk3pm0jssa5")))) + (build-system python-build-system) + (propagated-inputs (list python-asttokens python-executing python-pure-eval)) + (native-inputs + (list python-cython + python-littleutils + python-pygments + python-pytest + python-setuptools-scm + python-typeguard)) + (home-page "https://github.com/alexmojaki/stack_data") + (synopsis "Python stack frame and traceback manipulation library") + (description "The @code{stack_data} Python library extracts data from +stack frames and tracebacks. Is can be used to display more useful tracebacks +than the default.") + (license license:expat))) + (define-public python-ipython (package (name "python-ipython") - (version "7.27.0") + (version "8.2.0") (source (origin (method url-fetch) (uri (pypi-uri "ipython" version ".tar.gz")) (sha256 - (base32 "04xgymypnbfgf2q0d5b0hanjbjsp53f055sh1p8xlq52vyzmxdaq")))) + (base32 "1hcxa713wh3axa57412iy02rj0494ljvv6gpnls4lndc5h9yprbh")))) (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'make-docs-reproducible + (lambda _ + (substitute* "IPython/sphinxext/ipython_directive.py" + ((".*import datetime") "") + ((".*datetime.datetime.now\\(\\)") "") + (("%timeit") "# %timeit")))) + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp/") ;required by some tests + (invoke "python" "-m" "pytest" "-vv"))))))) + (inputs (list readline which)) (propagated-inputs (list python-backcall python-decorator - python-pyzmq - python-prompt-toolkit-2 - python-terminado + python-jedi + python-jinja2 + python-jsonschema python-matplotlib python-matplotlib-inline + python-mistune + python-nbformat python-numpy python-numpydoc - python-jedi - python-jinja2 - python-mistune python-pexpect python-pickleshare + python-prompt-toolkit + python-pygments + python-pyzmq python-simplegeneric - python-jsonschema - python-traitlets - python-nbformat - python-pygments)) - (inputs - (list readline which)) + python-stack-data + python-terminado + python-traitlets)) (native-inputs (list graphviz pkg-config - python-requests ;; for tests - python-testpath - python-nose)) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'make-docs-reproducible - (lambda _ - (substitute* "IPython/sphinxext/ipython_directive.py" - ((".*import datetime") "") - ((".*datetime.datetime.now\\(\\)") "") - (("%timeit") "# %timeit")))) - ;; 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 tests? #:allow-other-keys) - (if tests? - (begin - ;; Make installed package available for running the tests - (add-installed-pythonpath inputs outputs) - (setenv "HOME" "/tmp/") ;; required by a test - ;; We only test the core because one of the other tests - ;; tries to import ipykernel. - (invoke "python" "IPython/testing/iptest.py" - "-v" "IPython/core/tests"))))) - (add-before 'check 'fix-tests - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "./IPython/utils/_process_posix.py" - (("/usr/bin/env', 'which") (which "which"))) - (substitute* "./IPython/core/tests/test_inputtransformer.py" - (("#!/usr/bin/env python") - (string-append "#!" (which "python")))) - ;; This test introduces a circular dependency on ipykernel - ;; (which depends on ipython). - (delete-file "IPython/core/tests/test_display.py") - ;; AttributeError: module 'IPython.core' has no attribute 'formatters' - (delete-file "IPython/core/tests/test_interactiveshell.py") - ;; AttributeError: module 'matplotlib_inline' has no - ;; attribute 'backend_inline' - (delete-file "IPython/core/tests/test_pylabtools.py")))))) + ;; For tests. + python-pytest + python-requests + python-testpath)) (home-page "https://ipython.org") (synopsis "IPython is a tool for interactive computing in Python") (description @@ -9092,79 +9467,78 @@ computing.") (inherit python-ipython) (name "python-ipython-documentation") (version (package-version python-ipython)) + (source + (origin + (inherit (package-source python-ipython)) + (patches (append (search-patches + "python-ipython-documentation-chars.patch" + "python-ipython-documentation-repro.patch") + (origin-patches (package-source python-ipython)))))) (arguments - `(#:phases - (modify-phases %standard-phases - (delete 'build) - (delete 'check) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((data (string-append (assoc-ref outputs "out") "/share")) - (doc (string-append data "/doc/" ,name "-" ,version)) - (html (string-append doc "/html")) - (man1 (string-append data "/man/man1")) - (info (string-append data "/info")) - (examples (string-append doc "/examples")) - (python-arg (string-append "PYTHON=" (which "python")))) - (setenv "LANG" "en_US.utf8") - (with-directory-excursion "docs" - ;; FIXME: pdf fails to build - ;;(system* "make" "pdf" "PAPER=a4") - (system* "make" python-arg "html") - ;; FIXME: the generated texi file contains ^@^@, which trips - ;; up the parser. - ;; (system* "make" python-arg "info") - ) - (copy-recursively "docs/man" man1) - (copy-recursively "examples" examples) - (copy-recursively "docs/build/html" html) - ;; (copy-file "docs/build/latex/ipython.pdf" - ;; (string-append doc "/ipython.pdf")) - (mkdir-p info) - ;; (copy-file "docs/build/texinfo/ipython.info" - ;; (string-append info "/ipython.info")) - (copy-file "COPYING.rst" (string-append doc "/COPYING.rst"))) - #t))))) - (inputs - (list python-ipython python-ipykernel)) - (native-inputs - `(("python-sphinx" ,python-sphinx) - ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme) - ;; FIXME: It's possible that a smaller union would work just as well. - ("texlive" ,(texlive-updmap.cfg (list texlive-amsfonts - texlive-capt-of - texlive-fonts-ec - texlive-generic-iftex - texlive-pdftex - texlive-latex-cmap - texlive-latex-environ - texlive-latex-eqparbox - texlive-etoolbox - texlive-latex-expdlist - texlive-latex-fancyhdr - texlive-latex-fancyvrb - texlive-latex-fncychap - texlive-latex-float - texlive-latex-framed - texlive-latex-geometry - texlive-latex-graphics - texlive-hyperref - texlive-latex-mdwtools - texlive-latex-multirow - texlive-latex-needspace - texlive-oberdiek - texlive-latex-parskip - texlive-latex-preview - texlive-latex-tabulary - texlive-latex-threeparttable - texlive-latex-titlesec - texlive-latex-trimspaces - texlive-latex-ucs - texlive-latex-upquote - texlive-url - texlive-latex-varwidth - texlive-wrapfig))) - ("texinfo" ,texinfo))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-pythonpath + (lambda _ + ;; Ensure this fixed (via the + ;; "python-ipython-documentation-chars.patch" patch) copy of + ;; IPython gets used. + (setenv "PYTHONPATH" (string-append (getcwd))))) + (add-before 'build 'configure-sphinx-for-xelatex + (lambda _ + ;; Use XeLaTeX instead of PDFLaTeX, as it can + ;; cope with the Unicode characters present in the + ;; contributors page, for example. + (substitute* "docs/source/conf.py" + (("project = 'IPython'.*" all) + (string-append all "latex_engine = 'xelatex'\n"))) + ;; XXX: The Sphinx-generated ipython.tex specifies the GNU + ;; FreeFont font to be searched via its extension, which uses + ;; kpathsea instead of fontconfig and fail (see: + ;; https://github.com/sphinx-doc/sphinx/issues/10347). Create a + ;; symlink to GNU FreeFont and add it to the TEXMF tree via + ;; GUIX_TEXMF. + (mkdir-p "texmf-dist/fonts/opentype/public") + (symlink (string-append + #$(this-package-native-input "font-gnu-freefont") + "/share/fonts/opentype") + (string-append + (getcwd) "/" + "texmf-dist/fonts/opentype/public/gnu-freefont")) + (setenv "GUIX_TEXMF" (string-append (getenv "GUIX_TEXMF") ":" + (getcwd) "/texmf-dist")))) + (delete 'build) + (delete 'check) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((data (string-append #$output "/share")) + (doc (string-append data "/doc/" #$name "-" #$version)) + (html (string-append doc "/html")) + (info (string-append data "/info"))) + (invoke "make" "-C" "docs" "info" "html" "pdf" + (string-append "SPHINXOPTS=-j" + (number->string (parallel-job-count)))) + (install-file "COPYING.rst" doc) + (copy-recursively "examples" (string-append doc "/examples")) + ;; Install HTML documentation. + (copy-recursively "docs/build/html" html) + ;; Likewise for the PDF. + (install-file "docs/build/latex/ipython.pdf" doc) + ;; Likewise for the info manual. + (install-file "docs/build/texinfo/ipython.info" info) + (symlink (string-append html "/_images") + (string-append info "/ipython-figures")))))))) + (native-inputs + (list fontconfig ;for XDG_DATA_DIRS to locate fonts + font-gnu-freefont + graphviz + python-docrepr + python-sphinx + python-sphinx-rtd-theme + texinfo + texlive-bin + texlive-polyglossia + texlive-xindy)))) (define-public python-urwid (package @@ -10516,7 +10890,57 @@ plugin for flake8 to check PEP-8 naming conventions.") (arguments `(#:tests? #f ,@(package-arguments base))) - (native-inputs `())))) + (native-inputs `())))) + +(define-public python-pep621 + (package + (name "python-pep621") + (version "0.4.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/FFY00/python-pep621") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0nzig7bmzf0xx5svxlf065mrzihr0ci4p1yaxka9flqjba98flpr")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; XXX: PEP 517 manual build/install procedures copied from + ;; python-isort. + (replace 'build + (lambda _ + ;; ZIP does not support timestamps before 1980. + (setenv "SOURCE_DATE_EPOCH" "315532800") + (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) + (replace 'check + (lambda* (#:key tests? inputs outputs #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" + ;; Two parameterized test_load tests are currently + ;; failing (see: + ;; https://github.com/FFY00/python-pep621/issues/14). + "-k" "not test_load")))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((whl (car (find-files "dist" "\\.whl$")))) + (invoke "pip" "--no-cache-dir" "--no-input" + "install" "--no-deps" "--prefix" #$output whl))))))) + (propagated-inputs (list python-packaging)) + (native-inputs (list python-pypa-build python-pytest python-tomli)) + (home-page "https://github.com/FFY00/python-pep621") + (synopsis "Dataclass for PEP 621 metadata") + (description "This project does not implement the parsing of +@file{pyproject.toml} containing PEP 621 metadata. Instead, given a Python +data structure representing PEP 621 metadata (already parsed), it will +validate this input and generate a PEP 643-compliant metadata +file (e.g. @file{PKG-INFO}).") + (license license:expat))) (define-public python-pyflakes (package @@ -11082,6 +11506,32 @@ output.") (define-public python2-cram (package-with-python2 python-cram)) +(define-public python-crccheck + (package + (name "python-crccheck") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "crccheck" version)) + (sha256 + (base32 "15psg7wjfbpmmry54ffwg6pg63mnv7mkwmb0a7884axnr8qj55j5")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv"))))))) + (native-inputs (list python-pytest)) + (home-page "https://sourceforge.net/projects/crccheck/") + (synopsis "Calculation library for CRCs and checksums") + (description "@code{crccheck} is a calculation library for CRCs and +checksums. It implement more than a hundred checksum routines.") + (license license:gpl3+))) + (define-public python-crashtest (package (name "python-crashtest") @@ -11304,7 +11754,9 @@ from an XML-based format.") (license license:expat) (properties `((python2-variant . ,(delay python2-fonttools))))))) -(define-public python-fonttools-with-tests +;;; Rename 'python-fonttools' in next cycle, renaming the current +;;; 'python-fonttools' to 'python-fonttools-minimal'. +(define-public python-fonttools-full (package/inherit python-fonttools (arguments (substitute-keyword-arguments (package-arguments python-fonttools) @@ -11329,11 +11781,15 @@ from an XML-based format.") " and not ")))))))))) (native-inputs (modify-inputs (package-native-inputs python-fonttools) - (append python-pytest ;FIXME: indentation is broken - python-brotli - python-fs - python-scipy - python-zopfli))) + (append python-pytest))) + (propagated-inputs + (list python-brotli + python-fs + python-lxml + python-lz4 + python-scipy + python-unicodedata2 + python-zopfli)) (properties (alist-delete 'hidden? (package-properties python-fonttools))))) ;; Fonttools 4.x dropped support for Python 2, so stick with 3.x here. @@ -11349,6 +11805,18 @@ from an XML-based format.") (base32 "0v6399g755f2hn1ry62i5b6gdinf2fpx2966v3bxh6bjw1accb5p"))))))) +(define-public python-fonttools-next + (package + (inherit python-fonttools-full) + (version "4.32.0") + (source (origin + (inherit (package-source python-fonttools-full)) + (method url-fetch) + (uri (pypi-uri "fonttools" version ".zip")) + (sha256 + (base32 + "14nk43z0dmznypm3zp4sdc04x1y608jawlnmwdkk32a947khvaar")))))) + (define-public python-ly (package (name "python-ly") @@ -11957,14 +12425,14 @@ asyncio.") (define-public python-pytest-black (package (name "python-pytest-black") - (version "0.3.8") + (version "0.3.12") (source (origin (method url-fetch) (uri (pypi-uri "pytest-black" version)) (sha256 (base32 - "04lppqydxm0f3f3x0l8hj7v0j6d8syj34jc37yzqwqcyqsnaga81")))) + "19bmbcnaq02md8nnj6pywri3vps8sxnhysbfy386qkbn9w09ncqx")))) (build-system python-build-system) (propagated-inputs (list python-pytest python-black python-toml)) @@ -12428,6 +12896,83 @@ is binding LibSass.") domains support.") (license license:expat))) +;;; Variant used to break a cycle with python-pip-run-bootstrap. +(define-public python-path-bootstrap + (hidden-package + (package + (name "python-path-bootstrap") + (version "16.4.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "path" version)) + (sha256 + (base32 "0lig13gxnfv98v790db1smvsbd3mnj7y8rwyiwhfi6xiqibygwms")))) + (build-system python-build-system) + (arguments + (list + #:tests? #f + #:phases + #~(modify-phases %standard-phases + ;; XXX: PEP 517 manual build/install procedures copied from + ;; python-isort. + (replace 'build + (lambda _ + ;; ZIP does not support timestamps before 1980. + (setenv "SOURCE_DATE_EPOCH" "315532800") + (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((whl (car (find-files "dist" "\\.whl$")))) + (invoke "pip" "--no-cache-dir" "--no-input" + "install" "--no-deps" "--prefix" #$output whl))))))) + (native-inputs (list python-pypa-build python-setuptools-scm)) + (home-page "https://github.com/jaraco/path") + (synopsis "Object-oriented file system path manipulation library") + (description "@code{path} (formerly @code{path.py}) implements path +objects as first-class entities, allowing common operations on files to be +invoked on those path objects directly.") + (license license:expat)))) + +(define-public python-path + (package/inherit python-path-bootstrap + (name "python-path") + (arguments + (substitute-keyword-arguments + (package-arguments python-path-bootstrap) + ((#:tests? _ #f) + #t) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Do not test the myproject.toml build as it tries to pull + ;; dependencies from the Internet. + (invoke "pytest" "-vv" "-k" + (string-append + "not project " + ;; This tests assumes a root user exists. + "and not test_get_owner"))))))))) + (native-inputs + (modify-inputs (package-native-inputs python-path-bootstrap) + (append python-appdirs + python-packaging + python-pygments + python-pytest + python-pytest-black + python-pytest-checkdocs + python-pytest-cov + python-pytest-enabler + python-pytest-flake8 + python-pytest-mypy))) + (properties (alist-delete 'hidden? + (package-properties + python-path-bootstrap))))) + +(define-public python-pathpy + (deprecated-package "python-pathpy" python-path)) + (define-public python-pretend (package (name "python-pretend") @@ -12476,6 +13021,87 @@ Python Package Index (PyPI).") (define-public python2-pip (package-with-python2 python-pip)) +;;; Variant used to break a dependency cycle with +;;; python-pytest-perf-bootstrap. +(define-public python-pip-run-bootstrap + (hidden-package + (package + (name "python-pip-run-bootstrap") + (version "8.8.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jaraco/pip-run") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ycrjj3jgqcr9c2k7y8vprq65iblg0q0hvwz8zwi13gmb0ffds0c")))) + (build-system python-build-system) + (arguments + (list + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'pretend-version + ;; The version string is usually derived via setuptools-scm, but + ;; without the git metadata available this fails. + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))))) + (native-inputs (list python-setuptools-scm)) + (propagated-inputs (list python-autocommand python-path-bootstrap + python-packaging)) + (home-page "https://github.com/jaraco/pip-run") + (synopsis "Dynamic dependency loader for Python") + (description "The @command{pip-run} command provides on-demand temporary +package installation for a single interpreter run. It replaces this series of +commands: +@example +$ virtualenv --python pythonX.X --system-site-packages /tmp/env +$ /tmp/env/bin/pip install pkg1 pkg2 -r reqs.txt +$ /tmp/env/bin/python ... +$ rm -rf /tmp/env +@end example") + (license license:expat)))) + +(define-public python-pip-run + (package/inherit python-pip-run-bootstrap + (name "python-pip-run") + (arguments + (substitute-keyword-arguments (package-arguments python-pip-run-bootstrap) + ((#:tests? _ #f) + #t) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-k" + (string-append + ;; Do not test the myproject.toml build as it tries + ;; to pull dependencies from the internet. + "not project " + ;; These tests attempt to install dependencies from + ;; the network and fail. + "and not test_pkg_imported " + "and not test_pkg_loaded_from_alternate_index "))))))))) + (propagated-inputs + (modify-inputs (package-propagated-inputs python-pip-run-bootstrap) + (replace "python-path-bootstrap" python-path))) + (native-inputs + (modify-inputs (package-native-inputs python-pip-run-bootstrap) + (append python-nbformat + python-pygments + python-pytest + python-pytest-black + python-pytest-checkdocs + python-pytest-cov + python-pytest-enabler + python-pytest-flake8 + python-pytest-mypy))) + (properties (alist-delete 'hidden? (package-properties + python-pip-run-bootstrap))))) + (define-public python-tlsh (package (name "python-tlsh") @@ -12639,6 +13265,179 @@ libmagic."))) (define-public python2-file (package-with-python2 python-file)) +(define-public python-pydevd + ;; Use the latest commit, which includes cleanups that removes Python 2 + ;; syntax that would fail to build. + (let ((revision "0") + (commit "47e298499ef19563bb2ef5941a57046a35ae6868")) + (package + (name "python-pydevd") + (version (git-version "2.8.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/fabioz/PyDev.Debugger") + (commit commit))) + (modules '((guix build utils))) + (snippet '(begin + ;; Delete pre-built binaries. + (for-each delete-file (find-files "." "\\.(so|dylib|dll)")) + ;; This source is generated via Cython. + (delete-file "_pydevd_bundle/pydevd_cython.c"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1yd017dh6xgxrqcyf8kk8jrr0a3zw895yfjih0z5jghyf0rck38q")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-tests + (lambda _ + (substitute* "tests_python/test_convert_utilities.py" + ;; Add missing trailing '/'. + (("'\\\\\\\\usr\\\\\\\\bin\\\\\\\\') == '/usr/bin" all) + (string-append all "/"))))) + (add-after 'unpack 'patch-command-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "_pydevd_bundle/pydevd_api.py" + (("'kill'") + (format #f "~s" (search-input-file inputs "bin/kill"))) + (("'pgrep'") + (format #f "~s" (search-input-file inputs "bin/pgrep")))))) + (add-after 'unpack 'generate-sources + (lambda _ + (setenv "PYTHONPATH" (getcwd)) + (invoke "python" "build_tools/build.py"))) + (add-after 'unpack 'adjust-attach-binary-name + (lambda _ + (substitute* + '("pydevd_tracing.py" + "pydevd_attach_to_process/add_code_to_python_process.py") + (("def get_(target|python_helper_lib)_filename.*" all) + (format #f "~a return ~s~%" all + (string-append #$output "/lib/attach.so")))))) + (add-after 'unpack 'patch-gdb + (lambda* (#:key inputs #:allow-other-keys) + (substitute* + "pydevd_attach_to_process/add_code_to_python_process.py" + (("'gdb',") + (format #f "~s," (search-input-file inputs "bin/gdb")))))) + (add-after 'build 'build-attach-linux-binary + (lambda _ + (invoke #+(cxx-for-target) "-shared" "-o" "attach.so" + "-fPIC" "-nostartfiles" + "pydevd_attach_to_process/linux_and_mac/attach.cpp"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "PYDEVD_USE_CYTHON" "YES") + (invoke "pytest" "-vv" + "-n" (number->string (parallel-job-count)) + "-k" + (string-append + ;; the GUI event loop requires an X server. + "not test_gui_event_loop_custom " + ;; This test validates that 'pydevd' is not in the + ;; exception message, but it is due to being part + ;; of the build file name present in the message. + "and not test_evaluate_exception_trace"))))) + (add-after 'install 'install-attach-binary + (lambda _ + (install-file "attach.so" + (string-append #$output "/lib")))) + ;; Some modules aren't designed to be loadable by themselves, such + ;; as 'pydev_app_engine_debug_startup' and fail. + (delete 'sanity-check)))) + (native-inputs + (list python-cython + python-numpy + python-psutil + python-pytest + python-pytest-xdist + python-trio + python-untangle)) + (inputs (list coreutils gdb procps)) + (home-page "https://github.com/fabioz/PyDev.Debugger/") + (synopsis "Python debugger") + (description "PyDev.Debugger is a capable Python debugger used in PyDev +and other @acronym{IDEs, Integrated Development Environments}.") + (license license:epl1.0)))) + +(define-public python-debugpy + (package + (name "python-debugpy") + (version "1.6.0") + (source + (origin + (method git-fetch) + (uri (git-reference ;no tests in PyPI archive + (url "https://github.com/microsoft/debugpy") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (modules '((guix build utils))) + ;; Remove the bundled PyDev-Debugger copy, including its pre-built + ;; attach binary. + (snippet '(delete-file-recursively "src/debugpy/_vendored")) + (patches (search-patches "python-debugpy-unbundle-pydevd.patch")) + (sha256 + (base32 + "1dpfzs3p51648i7f3fz8dw5d0vrj39iwn1jhn0226idc02ybyqih")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-sh-in-tests + (lambda _ + (substitute* "tests/debugpy/test_run.py" + (("#!/bin/sh") + (string-append "#!" (which "sh")))))) + (add-after 'unpack 'fix-version + ;; Versioneer is useless when there is no git metadata. + (lambda _ + (substitute* "setup.py" + (("version=versioneer.get_version\\(),") + (format #f "version=~s," #$version))))) + (add-before 'build 'configure + (lambda _ + ;; This adjusts the behavior of debugpy to load pydevd from + ;; Python site packages. + (setenv "DEBUGPY_BUNDLING_DISABLED" "1"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (invoke "pytest" "-vv" + "-n" (number->string (parallel-job-count)) + "-k" + (string-append + ;; These tests cannot be run in parallel because their + ;; test data would not be copied by xdist and lead to + ;; import errors. (see: + ;; https://github.com/microsoft/debugpy/issues/342 and + ;; https://github.com/microsoft/debugpy/issues/880). + "not test_custom_python_args " + "and not test_autokill "))))))) + (native-inputs + ;; See: https://raw.githubusercontent.com/microsoft/debugpy/ + ;; main/tests/requirements.txt. + (list python-django + python-gevent + python-flask + python-psutil + python-pytest + python-pytest-cov + python-pytest-timeout + python-pytest-xdist + python-requests)) + (propagated-inputs (list python-pydevd)) + (home-page "https://aka.ms/debugpy") + (synopsis "Debug Adapter Protocol Python implementation") + (description "An implementation of the Debug Adapter Protocol for +Python.") + (license license:expat))) + (define-public python-debian (package (name "python-debian") @@ -12751,16 +13550,16 @@ drafts 04, 06 and 07.") (define-public python-nbformat (package (name "python-nbformat") - (version "5.1.3") + (version "5.3.0") ;; The PyPi release tarball lacks some test cases and test data. (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/jupyter/nbformat.git") + (url "https://github.com/jupyter/nbformat") (commit version))) (sha256 (base32 - "033v16cfmxzh3jn5phnil4p3silr49iwh9wiigzhv0crc6sanvwz")) + "114c5c6cvpxhxj8zrw74351gcfzyzjh1jq3py4xf8wk9rahfay9z")) (file-name (git-file-name name version)))) (build-system python-build-system) (arguments @@ -12771,13 +13570,10 @@ drafts 04, 06 and 07.") (when tests? (invoke "pytest" "-vv"))))))) (propagated-inputs - (list python-ipython-genutils python-jsonschema python-jupyter-core + (list python-fastjsonschema python-jsonschema python-jupyter-core python-traitlets)) (native-inputs (list python-pytest - python-fastjsonschema ; This is only active - ; when setting NBFORMAT_VALIDATOR="fastjsonschema", so include it for - ; testing only. python-testpath)) (home-page "https://jupyter.org") (synopsis "Jupyter Notebook format") @@ -12809,23 +13605,21 @@ systems, as a command line tool, and as a Python library.") (define-public python-bleach (package (name "python-bleach") - (version "4.1.0") + (version "5.0.0") (source (origin (method url-fetch) (uri (pypi-uri "bleach" version)) (sha256 - (base32 "1nkibazmw1ry4cfxs9qrkkidxdf2z1hh1b20xq1ahqdsgsrxh009")))) + (base32 "0rc5avysbsl3w3i2qvb6522263zhwlvf50w0ifs8776w9c2wrmn6")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "pytest" "-vv"))))))) - (propagated-inputs - (list python-packaging python-six python-webencodings)) - (native-inputs - (list python-pytest)) + (propagated-inputs (list python-tinycss2 python-webencodings)) + (native-inputs (list python-pytest)) (home-page "https://github.com/mozilla/bleach") (synopsis "Whitelist-based HTML-sanitizing tool") (description "Bleach is an easy whitelist-based HTML-sanitizing tool.") @@ -12957,70 +13751,71 @@ time.") (define-public python-nbconvert (package (name "python-nbconvert") - (version "6.0.7") + (version "6.5.0") (source (origin (method url-fetch) (uri (pypi-uri "nbconvert" version)) (sha256 (base32 - "00lhqaxn481qvk2w5568asqlsnvrw2fm61p1vssx3m7vdnl17g6b")))) + "17g9xq4za7vvzml6l6d8zrzknhxsvgx02hymmsw9d1dygbi4cgi2")))) (build-system python-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-paths-and-tests - (lambda _ - ;; Use pandoc binary from input. - (substitute* "nbconvert/utils/pandoc.py" - (("'pandoc'") (string-append "'" (which "pandoc") "'"))) - ;; Same for LaTeX. - (substitute* "nbconvert/exporters/pdf.py" - (("\"xelatex\"") (string-append "\"" (which "xelatex") "\"")) - (("\"bibtex\"") (string-append "\"" (which "bibtex") "\""))) - ;; Make sure tests are not skipped. - (substitute* (find-files "." "test_.+\\.py$") - (("@onlyif_cmds_exist\\(('(pandoc|xelatex)'(, )?)+\\)") "")) - ;; Pandoc is never missing, disable test. - (substitute* "nbconvert/utils/tests/test_pandoc.py" - (("import os" all) (string-append all "\nimport pytest")) - (("(.+)(def test_pandoc_available)" all indent def) - (string-append indent "@pytest.mark.skip('disabled by guix')\n" - indent def))) - ;; Not installing pyppeteer, delete test. - (delete-file "nbconvert/exporters/tests/test_webpdf.py") - (substitute* "nbconvert/tests/test_nbconvertapp.py" - (("(.+)(def test_webpdf_with_chromium)" all indent def) - (string-append indent "@pytest.mark.skip('disabled by guix')\n" - indent def))))) - (replace 'check - (lambda* (#:key tests? inputs outputs #:allow-other-keys) - (when tests? - ;; Some tests invoke the installed nbconvert binary. - (add-installed-pythonpath inputs outputs) - ;; Tests depend on templates installed to output. - (setenv "JUPYTER_PATH" - (string-append - (assoc-ref outputs "out") - "/share/jupyter:" - (getenv "JUPYTER_PATH"))) - ;; Some tests need HOME - (setenv "HOME" "/tmp") - (invoke "pytest" "-vv"))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-paths + (lambda* (#:key inputs #:allow-other-keys) + ;; Use pandoc binary from input. + (substitute* "nbconvert/utils/pandoc.py" + (("'pandoc'") + (format #f "~s" (search-input-file inputs "bin/pandoc")))) + ;; Same for LaTeX. + (substitute* "nbconvert/exporters/pdf.py" + (("\"xelatex\"") + (format #f "~s" (search-input-file inputs "bin/xelatex"))) + (("\"bibtex\"") + (format #f "~s" (search-input-file inputs "bin/bibtex")))) + ;; Likewise for Inkscape. + (substitute* "nbconvert/preprocessors/svg2pdf.py" + (("inkscape_path = which\\(\"inkscape\")") + (format #f "inkscape_path = ~s" + (search-input-file inputs "bin/inkscape")))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Tests depend on templates installed to output. + (setenv "JUPYTER_PATH" + (string-append #$output "/share/jupyter:" + (getenv "JUPYTER_PATH"))) + ;; Step outside of the source directory to avoid having both + ;; the installed package *and* the package from the source on + ;; Python's path. + (with-directory-excursion "/tmp" + (invoke "pytest" "--pyargs" "nbconvert" + "-vv" "-n" (number->string (parallel-job-count)) + "-k" + (string-append + ;; These tests require pyppeteer, not yet + ;; available in Guix. + "not test_webpdf_with_chromium " + "and not test_webpdf.py " + ;; These tests require ipywidgets, which would + ;; introduce a dependency cycle. + "and not test_execute_widgets_from_nbconvert " + "and not test_execute_multiple_notebooks "))))))))) (inputs - (list pandoc - ;; XXX: Disabled, needs substitute*. - ;;("inkscape" ,inkscape) - )) - (native-inputs - `(("python-ipykernel" ,python-ipykernel) - ;; XXX: Disabled, not in guix. - ;;("python-pyppeteer" ,python-pyppeteer) - ("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-dependency" ,python-pytest-dependency))) + (list inkscape pandoc)) + (native-inputs + (list python-ipykernel + ;; Adding ipywidgets would create a cycle. + ;;python-ipywidgets + ;;python-pyppeteer ;TODO: package me + python-pytest + python-pytest-xdist)) (propagated-inputs - (list python-bleach + (list python-beautifulsoup4 + python-bleach python-defusedxml python-entrypoints python-jinja2 @@ -13036,37 +13831,39 @@ time.") ;; Required, even if [serve] is not used. python-tornado-6 ;; Required at runtime for `jupyter nbconvert --to=pdf`. - (texlive-updmap.cfg (list texlive-adjustbox - texlive-amsfonts - texlive-booktabs - texlive-caption - texlive-enumitem + texlive-adjustbox + texlive-booktabs + texlive-caption + texlive-enumitem + texlive-fontspec + texlive-generic-iftex + texlive-grffile + texlive-hyperref + texlive-latex-fancyvrb + texlive-latex-float + texlive-latex-geometry + texlive-latex-jknapltx + texlive-latex-ms + texlive-latex-parskip + texlive-latex-trimspaces + texlive-latex-upquote + texlive-stringenc + texlive-tcolorbox + texlive-titling + texlive-tools + texlive-ulem + texlive-unicode-math + texlive-xcolor + (texlive-updmap.cfg (list texlive-amsfonts + texlive-amsmath texlive-eurosym texlive-fonts-rsfs - texlive-generic-iftex texlive-jknappen - texlive-amsmath - texlive-latex-fancyvrb - texlive-latex-float - texlive-fontspec - texlive-latex-geometry - texlive-grffile - texlive-hyperref - texlive-latex-jknapltx - texlive-latex-ms - texlive-oberdiek - texlive-latex-parskip - texlive-latex-trimspaces - texlive-latex-upquote texlive-latex-ucs texlive-lm + texlive-lm-math texlive-mathpazo - texlive-stringenc - texlive-tcolorbox - texlive-titling - texlive-tools - texlive-ulem - texlive-xcolor + texlive-oberdiek texlive-zapfding)))) (home-page "https://jupyter.org") (synopsis "Converting Jupyter Notebooks") @@ -13088,13 +13885,13 @@ convert an @code{.ipynb} notebook file into various static formats including: (define-public python-notebook (package (name "python-notebook") - (version "6.3.0") + (version "6.4.10") (source (origin (method url-fetch) (uri (pypi-uri "notebook" version)) (sha256 (base32 - "0zfwr87ndjzmdp9adpc9lby1hdqdkjp2q7c9vff3wiw1dj6kkjfb")))) + "03p976xq1l9xf4djwk0snmywd0zck3i6gjngxsl874i8qrmsf214")))) (build-system python-build-system) (arguments `(#:phases @@ -13113,10 +13910,9 @@ convert an @code{.ipynb} notebook file into various static formats including: (setenv "HOME" (getcwd)))) (replace 'check (lambda* (#:key tests? inputs outputs #:allow-other-keys) - ;; These tests require a browser + ;; These tests require a browser. (delete-file-recursively "notebook/tests/selenium") (when tests? - (add-installed-pythonpath inputs outputs) ;; Interferes with test expectations. (unsetenv "JUPYTER_CONFIG_PATH") ;; Some tests do not expect all files to be installed in the @@ -13133,6 +13929,7 @@ convert an @code{.ipynb} notebook file into various static formats including: python-jinja2 python-jupyter-client python-jupyter-core + python-nest-asyncio python-nbconvert python-nbformat python-prometheus-client @@ -13256,13 +14053,13 @@ Jupyter kernels such as IJulia and IRKernel.") (define-public python-qtconsole (package (name "python-qtconsole") - (version "4.7.7") + (version "5.3.0") (source (origin (method url-fetch) (uri (pypi-uri "qtconsole" version)) (sha256 - (base32 "013qgpsm8jzcz3prhq7sxs36l8f7fgagmn3xa010gfhxf7cfldpj")))) + (base32 "09anp8g7vqi8z8wyi2lv21a2frd2dyhyrzvcrk2anijyqzyj0dcf")))) (build-system python-build-system) (arguments `(#:phases @@ -13279,7 +14076,7 @@ Jupyter kernels such as IJulia and IRKernel.") python-jupyter-core python-pygments python-pyqt python-pyzmq python-qtpy python-traitlets)) (native-inputs - (list python-flaky python-pytest)) + (list python-flaky python-pytest python-pytest-qt)) (home-page "https://jupyter.org") (synopsis "Jupyter Qt console") (description "This package provides a Qt-based console for Jupyter with @@ -14549,9 +15346,6 @@ document.") (home-page "https://github.com/jmespath/jmespath.py") (license license:expat))) -(define-public python2-jmespath - (package-with-python2 python-jmespath)) - (define-public python-symengine (package (name "python-symengine") @@ -14601,6 +15395,23 @@ numbers with uncertainties. It can also yield the derivatives of any expression.") (license license:bsd-3))) +(define-public python-unicodedata2 + (package + (name "python-unicodedata2") + (version "14.0.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "unicodedata2" version)) + (sha256 + (base32 "110nnvh02ssp92xbmswy39aa186jrmb7m41x4220wigl8c0dzxs1")))) + (build-system python-build-system) + (home-page "https://github.com/fonttools/unicodedata2") + (synopsis "Python unicodedata backport") + (description "This package corresponds to the latest @code{unicodedata} +standard Python module.") + (license license:asl2.0))) + (define-public python-asteval (package (name "python-asteval") @@ -14803,6 +15614,36 @@ python-xdo for newer bindings.)") (define-public python2-xdo (package-with-python2 python-xdo)) +(define-public python-xdoctest + (package + (name "python-xdoctest") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "xdoctest" version)) + (sha256 + (base32 "0bgbmb9nqv95f9gfxqifqff1qaz5fnanjqy4hv7ygrjp2kksgfvy")))) + (build-system python-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; A writable HOME is needed by the + ;; 'import_module_from_path' test. + (setenv "HOME" "/tmp") + (invoke "pytest" "-vv"))))))) + (propagated-inputs (list python-six)) + (native-inputs (list python-pytest which)) + (home-page "https://github.com/Erotemic/xdoctest") + (synopsis "Rewrite of the Python builtin doctest module") + (description "This package provides a rewrite of the builtin doctest +module which leverages the Python @acronym{AST, Abstract Syntax Tree} instead +of @acronym{REGEXPs, regular expressions}.") + (license license:asl2.0))) + (define-public python-mako (package (name "python-mako") @@ -14977,18 +15818,27 @@ and provides a uniform API regardless of which JSON implementation is used.") (define-public python-amqp (package (name "python-amqp") - (version "5.0.7") + (version "5.1.1") (source (origin (method url-fetch) (uri (pypi-uri "amqp" version)) (sha256 - (base32 "0p9alyinl24z699w4gpd8wvn90sm2il1p0gfwdhbpinksy7vfmyp")))) + (base32 "1qmmffiy48nady7is8529vxcyqbq88v5zgawqr3fk4q8rkz166rc")))) (build-system python-build-system) (arguments - `(#:tests? #f)) ; not compatible with pytest>=6 as of 5.0.7 - (propagated-inputs - (list python-vine)) + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" + "-c" "/dev/null" ;take control over pytest options + ;; Integration tests require network connectivity. + "--ignore" "t/integration"))))))) + (native-inputs (list python-pytest)) + (propagated-inputs (list python-vine)) (home-page "https://github.com/celery/py-amqp") (synopsis "Low-level AMQP client for Python (fork of amqplib)") (description @@ -15046,23 +15896,28 @@ applications.") (define-public python-kombu (package (name "python-kombu") - (version "5.2.2") + (version "5.2.4") (source (origin (method url-fetch) (uri (pypi-uri "kombu" version)) (sha256 - (base32 "0256915q3z4pjrkqxw16a31np3p25dxnk1mq2zv0hs4izdihfp8g")))) + (base32 "044ng79gj04668kf5fmy7fjkw8302xyapskkn65ym52zfbpf7kip")))) (build-system python-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'delete-transport-tests - (lambda _ ; this tests message passing to many different databases - (delete-file-recursively "t/unit/transport")))))) + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" + ;; The transport tests attempt to pass messages to + ;; many different databases. + "--ignore" "t/unit/transport"))))))) (native-inputs - (list python-case python-mock python-pyro4 python-pytest-sugar - python-pytz)) + (list python-case python-pyro4 python-pytest-sugar + python-pytest python-pytz)) (propagated-inputs (list python-amqp python-cached-property python-vine)) (home-page "https://kombu.readthedocs.io") @@ -15111,31 +15966,37 @@ Python 2.4 and 2.5, and will draw its fixes/improvements from python-trunk.") (define-public python-celery (package (name "python-celery") - (version "5.1.2") ;newer versions require python-click>=8 + (version "5.2.6") (source (origin (method url-fetch) (uri (pypi-uri "celery" version)) (sha256 - (base32 "1c6lw31i3v81fyj4yn37lbvv70xdgb389iccirzyjr992vlkv6ld")))) + (base32 "109lcqarrbmh95sk1dm4yxayq1h3i27f4w23ndk64mqgyfnqqffi")))) (build-system python-build-system) (arguments - '(#:tests? #f - #:phases + '(#:phases (modify-phases %standard-phases - (add-after 'unpack 'delete-integration-tests + (add-after 'unpack 'relax-requirements (lambda _ - (delete-file-recursively "t/integration"))) ;hangs tests + (substitute* "requirements/default.txt" + (("pytz.*") + "pytz\n")))) (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (lambda* (#:key tests? #:allow-other-keys) (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "python" "-m" "pytest" "t" "-k" - (string-append ; AssertionErrors - "not test_check_privileges_no_fchown" - " and not test_all_reqs_enabled_in_tests")))))))) + (invoke "python" "-m" "pytest" "t" + "--ignore" "t/integration" ;hangs tests + ;; The MongoDB backend test appears to expect an older + ;; version of MongoDB which provided its own bson + ;; module, fails with " AttributeError: module 'bson' + ;; has no attribute 'encode'". + "--ignore" "t/unit/backends/test_mongodb.py" + ;; AssertionErrors + "-k" "not test_check_privileges_no_fchown "))))))) (native-inputs (list python-case + python-dnspython python-flaky python-iniconfig python-moto @@ -15147,12 +16008,10 @@ Python 2.4 and 2.5, and will draw its fixes/improvements from python-trunk.") python-toml)) (propagated-inputs (list python-billiard - python-boto3 python-click python-click-didyoumean python-click-plugins python-click-repl - python-cryptography python-kombu python-pytz python-vine)) @@ -16138,13 +16997,13 @@ library. It can be used to act both as a TFTP client or TFTP server.") (define-public python-greenlet (package (name "python-greenlet") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (pypi-uri "greenlet" version)) (sha256 (base32 - "10gllbrcbazxck84nr7dw3js3gq0rxrsr4kkvy5hg542rms2gwn0")))) + "0jkln5bf6rq7dbvpv7ypin3pp9jqd2jr91yyxlnfcii3msj5w3z3")))) (build-system python-build-system) (home-page "https://greenlet.readthedocs.io/") (synopsis "Lightweight in-process concurrent programming") @@ -16697,6 +17556,28 @@ daemon. It is the client side software which allows storing values in one or more, possibly remote, memcached servers.") (license license:psfl))) +(define-public python-mergedeep + (package + (name "python-mergedeep") + (version "1.3.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/clarketm/mergedeep") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1msvvdzk33sxzgyvs4fs8dlsrsi7fjj038z83s0yw5h8m8d78469")))) + (build-system python-build-system) + (native-inputs (list python-pytest)) + (home-page "https://github.com/clarketm/mergedeep") + (synopsis "Deep merge function for Python") + (description "This package provides a deep merge function for Python, +useful to combine multiple data objects as one.") + (license license:expat))) + (define-public python-clikit (package (name "python-clikit") @@ -17105,28 +17986,28 @@ parsing UK postcodes.") (define-public python-faker (package (name "python-faker") - (version "9.3.1") + (version "13.3.4") (source (origin (method url-fetch) (uri (pypi-uri "Faker" version)) (sha256 (base32 - "0lpfdc4ndvk7chgqrfd2b1my4n54pccq9b645vp9cp5s5ypyknfd")))) + "04855dqvvi2mr739l5x3qf82rxq0a7spc8gl76k8xixmbw36328q")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases (replace 'check - (lambda _ (invoke "python" "-m" "pytest" "-v")))))) + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "pytest" "-v"))))))) (native-inputs - (list ;; For testing - python-freezegun - python-pytest-6 + (list python-freezegun + python-pytest python-random2 python-ukpostcodeparser python-validators)) - (propagated-inputs - (list python-dateutil python-text-unidecode)) + (propagated-inputs (list python-dateutil)) (home-page "https://github.com/joke2k/faker") (synopsis "Python package that generates fake data") (description @@ -17159,6 +18040,24 @@ YAML-serialized data.") (define-public python2-pyaml (package-with-python2 python-pyaml)) +(define-public python-pyyaml-env-tag + (package + (name "python-pyyaml-env-tag") + (version "0.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pyyaml_env_tag" version)) + (sha256 + (base32 "1nsva88jsmwn0cb9jnrfiz4dvs9xakkpgfii7g1xwkx1pmsjc2bh")))) + (build-system python-build-system) + (propagated-inputs (list python-pyyaml)) + (home-page "https://github.com/waylan/pyyaml-env-tag") + (synopsis "Custom YAML tag for environment variables") + (description "This package provides a custom YAML tag for referencing +environment variables in YAML files.") + (license license:expat))) + (define-public python-backpack (package (name "python-backpack") @@ -17187,25 +18086,24 @@ collections of data.") (define-public python-prompt-toolkit (package (name "python-prompt-toolkit") - (version "3.0.18") + (version "3.0.29") (source (origin (method url-fetch) (uri (pypi-uri "prompt_toolkit" version)) (sha256 - (base32 "1g1kq1aimhm23k2dmlmnznfzc83l6ly65g0h32hqz8injcdz3d71")))) + (base32 "19vf5cahp3imdpwhgvk55g3dvqmc6ga175r4vkq79kffx1h0yr5x")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (delete 'check) - (add-after 'install 'post-install-check - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; HOME is needed for the test - ;; "test_pathcompleter_can_expanduser". - (setenv "HOME" "/tmp") - (add-installed-pythonpath inputs outputs) - (invoke "py.test")))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; HOME is needed for the test + ;; "test_pathcompleter_can_expanduser". + (setenv "HOME" "/tmp") + (invoke "pytest" "-vv"))))))) (propagated-inputs (list python-wcwidth)) (native-inputs @@ -17715,6 +18613,35 @@ multitouch applications.") (define-public python-binwalk (deprecated-package "python-binwalk" binwalk)) +(define-public python-bson + (package + (name "python-bson") + (version "0.5.10") + (source + (origin + (method git-fetch) ;for tests + (uri (git-reference + (url "https://github.com/py-bson/bson") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1vpy4rsvm3hhawvbg9rbw4j36ck8qylkhm8cjy0q6imvinkd2als")))) + (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "./test.py"))))))) + (propagated-inputs (list python-dateutil python-six)) + (home-page "https://github.com/py-bson/bson") + (synopsis "BSON (Binary JSON) codec for Python") + (description "@code{bson} is a Python library implementing a BSON (Binary +JSON) codec.") + (license license:asl2.0))) + (define-public python-nltk (package (name "python-nltk") @@ -19126,21 +20053,19 @@ multitouch applications.") (base32 "19iiys4233cicpm48fd7lrkm31kk47qiv44wvk952rqbcn4rd2dh")))) (build-system python-build-system) (propagated-inputs - (list python-lazy-object-proxy python-wrapt)) + (list python-lazy-object-proxy python-typing-extensions python-wrapt)) (native-inputs - (list python-pytest python-pytest-runner python-typing-extensions)) + (list python-pytest python-pytest-runner)) (home-page "https://github.com/PyCQA/astroid") - (synopsis "Common base representation of python source code for pylint and - other projects") + (synopsis "Python source code base representation") (description "@code{python-astroid} provides a common base representation - of python source code for projects such as pychecker, pyreverse, pylint, etc. - - It provides a compatible representation which comes from the _ast module. It - rebuilds the tree generated by the builtin _ast module by recursively walking - down the AST and building an extended ast. The new node classes have - additional methods and attributes for different usages. They include some - support for static inference and local name scopes. Furthermore, astroid - builds partial trees by inspecting living objects.") +of Python source code for projects such as pychecker, pyreverse, pylint, etc. +It provides a compatible representation which comes from the _ast module. It +rebuilds the tree generated by the builtin _ast module by recursively walking +down the AST and building an extended ast. The new node classes have +additional methods and attributes for different usages. They include some +support for static inference and local name scopes. Furthermore, astroid +builds partial trees by inspecting living objects.") (license license:lgpl2.1+))) (define-public python-isbnlib @@ -19606,30 +20531,26 @@ point is the point of maximum curvature.") (define-public python-factory-boy (package (name "python-factory-boy") - (version "2.8.1") + (version "3.2.1") (source (origin (method url-fetch) (uri (pypi-uri "factory_boy" version)) (sha256 - (base32 "1fvin6san5xsjh2c4y18caj2lnmwxlylyqm8mh1yc6rp38wlwr56")))) + (base32 "0pm5lbvnwm0kg5i6z611rg907yw1gy551f2advmpaz041ixjg3d9")))) (build-system python-build-system) (arguments ;; Tests are not included in the tarball. `(#:tests? #f)) - (propagated-inputs - `(("faker" ,python-faker))) + (propagated-inputs (list python-faker)) (home-page "https://github.com/benhoyt/scandir") (synopsis "Versatile test fixtures replacement") - (description - "Factory_boy is a fixtures replacement based on thoughtbot’s factory_girl. - - As a fixtures replacement tool, it aims to replace static, hard to maintain - fixtures with easy-to-use factories for complex object. - - Instead of building an exhaustive test setup with every possible combination - of corner cases, factory_boy allows you to use objects customized for the - current test, while only declaring the test-specific fields") + (description "Factory_boy is a fixtures replacement based on thoughtbot’s +factory_girl. As a fixtures replacement tool, it aims to replace static, hard +to maintain fixtures with easy-to-use factories for complex object. Instead +of building an exhaustive test setup with every possible combination of corner +cases, factory_boy allows you to use objects customized for the current test, +while only declaring the test-specific fields.") (license license:expat))) (define-public python-translate-toolkit @@ -21110,6 +22031,60 @@ particularly convenient for use in tests.") (define-public python2-tempdir (package-with-python2 python-tempdir)) +(define-public python-tempora + (package + (name "python-tempora") + (version "5.0.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "tempora" version)) + (sha256 + (base32 "09wirlk5vmxlhl9rnxp7g5qz2nsd6b0gnzk5fczbz0s8lsbz386b")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; XXX: PEP 517 manual build copied from python-isort. + (replace 'build + (lambda _ + (setenv "SOURCE_DATE_EPOCH" "315532800") + (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) + (replace 'install + (lambda _ + (let ((whl (car (find-files "dist" "\\.whl$")))) + (invoke "pip" "--no-cache-dir" "--no-input" + "install" "--no-deps" "--prefix" #$output whl)))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Do not test the myproject.toml build as it tries to pull + ;; dependencies from the Internet. + (invoke "pytest" "-k" "not project"))))))) + (native-inputs + (list python-pypa-build + python-freezegun + python-pytest + python-pytest-black + python-pytest-checkdocs + python-pytest-cov + python-pytest-enabler + python-pytest-flake8 + python-pytest-freezegun + python-pytest-mypy + python-setuptools-scm + python-types-freezegun + python-types-pytz)) + (propagated-inputs (list python-jaraco-functools python-pytz)) + (home-page "https://github.com/jaraco/tempora") + (synopsis "Python date and time objects and routines") + (description "The @code{tempora} Python library contains miscellaneous +date and time related utilities and constants, routines for measuring, +profiling, and getting datetime-aware @acronym{UTC, Coordinated Universal +Time} values as well as an event scheduler.") + (license license:expat))) + (define-public python-activepapers (package (name "python-activepapers") @@ -21413,46 +22388,35 @@ systems policies.") (define-public python-send2trash (package (name "python-send2trash") - (version "1.5.0") + (version "1.8.0") (source (origin (method git-fetch) ;; Source tarball on PyPI doesn't include tests. (uri (git-reference - (url "https://github.com/hsoft/send2trash") + (url "https://github.com/arsenetar/send2trash") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 - "1c76zldhw2ay7q7r00nnzcampjz9lkqfcbzqpm0iqp5i6bmmv30v")))) + "1k7dfypaaq4f36fbciaasv72j6wgjihw8d88axmz9c329bz8v5qx")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-before 'check 'pre-check (lambda _ - (mkdir-p "/tmp/foo") - (setenv "HOME" "/tmp/foo") - #t))))) - (home-page "https://github.com/hsoft/send2trash") + (setenv "HOME" "/tmp"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv"))))))) + (native-inputs (list python-pytest)) + (home-page "https://github.com/arsenetar/send2trash") (synopsis "Send files to the user's @file{~/Trash} directory") (description "This package provides a Python library to send files to the user's @file{~/Trash} directory.") - (properties `((python2-variant . ,(delay python2-send2trash)))) (license license:bsd-3))) -(define-public python2-send2trash - (let ((base (package-with-python2 - (strip-python2-variant python-send2trash)))) - (package/inherit base - (arguments - (substitute-keyword-arguments (package-arguments python-send2trash) - ((#:phases phases) - `(modify-phases ,phases - (add-before 'check 'setenv - (lambda _ - (setenv "GUIX_PYTHONPATH" - (string-append (getcwd) ":" (getenv "GUIX_PYTHONPATH")))))))))))) - (define-public python-pyfavicon (package (name "python-pyfavicon") @@ -22973,14 +23937,14 @@ validation testing and application logic.") (define-public python-numba (package (name "python-numba") - (version "0.54.1") + (version "0.55.1") (source (origin (method url-fetch) (uri (pypi-uri "numba" version)) (sha256 (base32 - "0gzl2hz9azav9mny4mga19096rrnpw5816r1h4iwrvb4r01wipzr")))) + "18rf8i32m1045zxglvicpgldvzmqdxqvs3dhjd7wilb64sd0ds83")))) (build-system python-build-system) (arguments `(#:phases @@ -23271,6 +24235,49 @@ which supports the spawning of processes using the API of the standard library's @code{threading} module.") (license license:bsd-3))) +(define-public python-toolrack + (package + (name "python-toolrack") + (version "3.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/albertodonato/toolrack") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ych11b7nchnkhqgf7dgivbvn2lzafjsi7nhb1an5zjjyns39gpx")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-/bin/sh + (lambda _ + (substitute* "toolrack/aio/tests/test_process.py" + (("/bin/sh") + (which "sh"))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" "--pyargs" "toolrack" + "-k" + (string-append + ;; These tests fail for unknown reason comparing the + ;; expected output of shell scripts. + "not test_parse_stderr " + "and not test_parse_no_ending_newline " + "and not test_parse_stdout")))))))) + (native-inputs (list python-pytest python-pytest-asyncio + python-pytest-mock)) + (home-page "https://github.com/albertodonato/toolrack") + (synopsis "Collection of Python utility functions and classes") + (description "This package provides a collection of miscellaneous utility +functions and classes.") + (license license:lgpl3+))) + (define-public python-toolz (package (name "python-toolz") @@ -23983,26 +24990,32 @@ project.") (define-public python-trio (package (name "python-trio") - (version "0.19.0") + (version "0.20.0") (source (origin (method url-fetch) (uri (pypi-uri "trio" version)) (sha256 - (base32 "1qgg4zhca81dxc1nlmcr5pl1bclmvdp3niqbyslwxs65bs732pl9")))) + (base32 "0w30cwmdwfa8zq2agqv3h62jzwwsk7ms8f683ag8f3jx279m42k7")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'patch-sleep + (lambda _ + (substitute* "trio/tests/test_subprocess.py" + (("/bin/sleep") + (which "sleep"))))) (add-before 'check 'change-home (lambda _ ;; Tests require a writable home. - (setenv "HOME" "/tmp") - #t)) + (setenv "HOME" "/tmp"))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? - (invoke "pytest" "-vv" "-k" + (invoke "pytest" "-vv" + "-n" (number->string (parallel-job-count)) + "-k" (string-append ;; This test times out. "not test_ki_protection_works" @@ -24011,7 +25024,10 @@ project.") " and not test_run_in_trio_thread_ki" " and not test_simple_cancel_scope_usage_doesnt_create_cyclic_garbage" " and not test_nursery_cancel_doesnt_create_cyclic_garbage" + " and not test_cancel_scope_exit_doesnt_create_cyclic_garbage" " and not test_locals_destroyed_promptly_on_cancel" + " and not test_ipython_exc_handler" + " and not test_for_leaking_fds" ;; These try to raise KeyboardInterrupt which does not work ;; in the build environment. " and not test_ki_self" @@ -24020,7 +25036,9 @@ project.") " and not test_getnameinfo" " and not test_SocketType_resolve" ;; OSError: protocol not found. - " and not test_getprotobyname")))))))) + " and not test_getprotobyname" + ;; EOFError: Ran out of input. + " and not test_static_tool_sees_all_symbols")))))))) (native-inputs (list python-astor python-ipython @@ -24028,6 +25046,7 @@ project.") python-pylint python-pyopenssl python-pytest + python-pytest-xdist python-pytest-cov python-trustme)) (propagated-inputs @@ -24210,16 +25229,15 @@ processes may share the same data.") (define-public python-croniter (package (name "python-croniter") - (version "0.3.34") + (version "1.3.4") (source (origin (method url-fetch) (uri (pypi-uri "croniter" version)) (sha256 (base32 - "0r79cx4v2dw4hzr0annkkxxis46c8hivq61sr39z6p7lcjsbk1ki")))) + "1whbm26m9kpn0klgr9dqiqpp83ki9nhpxifaq9afcjw32rckcs9i")))) (build-system python-build-system) - (propagated-inputs - (list python-dateutil python-natsort)) + (propagated-inputs (list python-dateutil)) (home-page "https://github.com/kiorky/croniter") (synopsis "Iterate datetime objects with cron-like syntax") (description @@ -24913,43 +25931,44 @@ standard error channel (stderr) in your program.") `(#:phases (modify-phases %standard-phases (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (lambda* (#:key tests? #:allow-other-keys) (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "pytest" "-vv" "-p" "no:asyncio" - "-m" "not network" - "-k" - (string-append - "not test_is_block_device" - - ;; These fail because of network (or specifically - ;; IPv6 network) access. - " and not test_accept" - " and not test_accept_after_close" - " and not test_close_during_receive" - " and not test_close_from_other_task" - " and not test_concurrent_receive" - " and not test_concurrent_send" - " and not test_connect_tcp_with_tls" - " and not test_connect_tcp_with_tls_cert_check_fail" - " and not test_connection_refused" - " and not test_extra_attributes" - " and not test_getaddrinfo" - " and not test_getnameinfo" - " and not test_happy_eyeballs" - " and not test_iterate" - " and not test_receive_after_close" - " and not test_receive_timeout" - " and not test_reuse_port" - " and not test_run_process" - " and not test_send_after_close" - " and not test_send_after_eof" - " and not test_send_after_peer_closed" - " and not test_send_eof" - " and not test_send_large_buffer" - " and not test_send_receive" - " and not test_socket_options" - " and not test_unretrieved_future_exception_server_crash")))))))) + (invoke + "pytest" "-vv" "-p" "no:asyncio" + "-m" "not network" + "-k" + (string-append + "not test_is_block_device" + + ;; These fail because of network (or specifically IPv6 + ;; network) access (see: + ;; https://github.com/agronholm/anyio/issues/417). + " and not test_accept" + " and not test_accept_after_close" + " and not test_close_during_receive" + " and not test_close_from_other_task" + " and not test_concurrent_receive" + " and not test_concurrent_send" + " and not test_connect_tcp_with_tls" + " and not test_connect_tcp_with_tls_cert_check_fail" + " and not test_connection_refused" + " and not test_extra_attributes" + " and not test_getaddrinfo" + " and not test_getnameinfo" + " and not test_happy_eyeballs" + " and not test_iterate" + " and not test_receive_after_close" + " and not test_receive_timeout" + " and not test_reuse_port" + " and not test_run_process" + " and not test_send_after_close" + " and not test_send_after_eof" + " and not test_send_after_peer_closed" + " and not test_send_eof" + " and not test_send_large_buffer" + " and not test_send_receive" + " and not test_socket_options" + " and not test_unretrieved_future_exception_server_crash")))))))) (propagated-inputs (list python-contextvars python-dataclasses @@ -24961,9 +25980,8 @@ standard error channel (stderr) in your program.") python-coverage python-hypothesis python-mock - python-pytest-6 + python-pytest python-pytest-mock - python-pytest-trio python-setuptools-scm python-trio python-trustme @@ -26396,6 +27414,25 @@ cryptographically signed ones).") dictionaries.") (license license:expat))) +(define-public python-dictpath + (package + (name "python-dictpath") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "dictpath" version)) + (sha256 + (base32 "1n4hq4wbgaw59bbb16nhkgg5wk8sl4iw940vjrgx4xmifqxxw73m")))) + (build-system python-build-system) + (native-inputs (list python-pytest python-pytest-cov python-pytest-flake8)) + (home-page "https://github.com/p1c2u/pathable") + (synopsis "Object-oriented path library for Python") + (description "This object-oriented dictionary path Python library enables +traversing resources like paths or accessing resources on demand with separate +accessor layer.") + (license license:asl2.0))) + (define-public pyzo (package (name "pyzo") @@ -26691,14 +27728,14 @@ positioning, and keyboard input.") (define-public python-readme-renderer (package (name "python-readme-renderer") - (version "32.0") + (version "34.0") (source (origin (method url-fetch) (uri (pypi-uri "readme_renderer" version)) (sha256 (base32 - "11av194kgq6mvp2afpapkb6vyn3y14gingmgsp3n10krlspvw4mm")))) + "1c75h9znffc2lh4j56yg23l5ifj5l8fbdq3kfigi8vbh45zx3d6z")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases @@ -26710,7 +27747,12 @@ positioning, and keyboard input.") "cmarkgfm>=0.5.0")))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) - (when tests? (invoke "pytest" "-vv"))))))) + (when tests? + ;; The GFM tests fail due to slight differences in the + ;; generated vs expected HTML due to using a more + ;; recent bleach version (see: + ;; https://github.com/pypa/readme_renderer/issues/234). + (invoke "pytest" "-vv" "-k" "not GFM"))))))) (propagated-inputs (list python-bleach python-docutils python-pygments @@ -27226,14 +28268,14 @@ a text editor and easily understood and used by both programmers and non-program (define-public python-nest-asyncio (package (name "python-nest-asyncio") - (version "1.5.1") + (version "1.5.5") (source (origin (method url-fetch) (uri (pypi-uri "nest_asyncio" version)) (sha256 (base32 - "1anha29fcijminn5bh2icnx8x7nk39lna9wkc72262i12p2s3idg")))) + "0rbdw7lry66yj13hh4w63yzflnapdal1ffl237k8nsa2v4f2jhp4")))) (build-system python-build-system) (home-page "https://github.com/erdewit/nest_asyncio") (synopsis "Patch asyncio to allow nested event loops") @@ -27854,6 +28896,94 @@ and frame grabber interface.") ;; Yet another variant of the X/MIT license. "https://github.com/python-pillow/Sane/blob/master/COPYING")))) +(define-public python-scikit-build + (package + (name "python-scikit-build") + (version "0.14.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "scikit-build" version)) + (sha256 + (base32 "1wx1m9vnxnnz59lyaisgyxldp313kciyd4af8lf112vb8vbjy9yk")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-cmake-executable + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "skbuild/constants.py" + (("^(CMAKE_DEFAULT_EXECUTABLE = ).*" _ head) + (format #f "~a ~s~%" head + (search-input-file inputs "bin/cmake")))))) + ;; XXX: PEP 517 manual build copied from python-isort. + (replace 'build + (lambda _ + (setenv "SOURCE_DATE_EPOCH" "315532800") + (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; These tests attempt to pull dependencies from the Internet. + (delete-file "tests/test_distribution.py") + (delete-file "tests/test_pep518.py") + (invoke "pytest" "-vv" + "-n" (number->string (parallel-job-count)) + "-k" (string-append + ;; These tests attempt to write to read-only + ;; Python install directory. + "not test_install_command " + "and not test_test_command " + "and not test_hello_develop " + ;; These sdist-related tests fail for unknown + ;; reasons (see: + ;; https://github.com/scikit-build/scikit-build/issues/689). + "and not test_hello_sdist_with_base " + "and not test_manifest_in_sdist " + "and not test_hello_sdist " + "and not test_sdist_with_symlinks " + ;; These are not parallel safe and fail + ;; nondeterministically (see: + ;; https://github.com/scikit-build/scikit-build/issues/711). + "and not test_generator_cleanup " + "and not test_generator_selection "))))) + (replace 'install + (lambda _ + (let ((whl (car (find-files "dist" "\\.whl$")))) + (invoke "pip" "--no-cache-dir" "--no-input" + "install" "--no-deps" "--prefix" #$output whl))))))) + (native-inputs + (list cmake-minimal + gfortran + git-minimal + ninja + python-coverage + python-cython + python-mock + python-packaging + python-path + python-pypa-build + python-pytest + python-pytest-cov + python-pytest-mock + python-pytest-virtualenv + python-pytest-xdist + python-requests + python-setuptools-scm + python-wheel)) + (propagated-inputs + (list python-distro python-packaging python-wheel)) + (home-page "https://github.com/scikit-build/scikit-build") + (synopsis "Build system generator for Python C/C++/Fortran/Cython extensions") + (description "Scikit-build is an improved build system generator for +CPython C/C++/Fortran/Cython extensions. It has support for additional +compilers, build systems, cross compilation, and locating dependencies and +determining their build requirements. The scikit-build package is +fundamentally just glue between the @code{setuptools} Python module and +CMake.") + (license license:expat))) + (define-public python-screenkey (package (name "python-screenkey") @@ -28723,6 +29853,69 @@ from multiple sources. Online trading accounts also often provide account statements in OFX files.") (license license:expat))) +(define-public python-rfc3339-validator + (package + (name "python-rfc3339-validator") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "rfc3339_validator" version)) + (sha256 + (base32 "0srg0b89aikzinw72s433994k5gv5lfyarq1adhas11kz6yjm2hk")))) + (build-system python-build-system) + (native-inputs (list python-hypothesis + python-pytest + python-pytest-runner + python-strict-rfc3339)) + (propagated-inputs (list python-six)) + (home-page "https://github.com/naimetti/rfc3339-validator") + (synopsis "Python RFC3339 validator") + (description "This package provides a pure Python RFC3339 validator.") + (license license:expat))) + +(define-public python-strict-rfc3339 + (package + (name "python-strict-rfc3339") + (version "0.7") + (source + (origin + (method git-fetch) ;no tests in pypi release + (uri (git-reference + (url "https://github.com/danielrichman/strict-rfc3339") + (commit (string-append "version-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0b12bh9v9gwkm89kxbidxw2z81lg8fx1v5fzgs313v1wgx6qb09p")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" + ;; The timestamp to local offset tests fail due to + ;; missing timezone data (see: + ;; https://github.com/danielrichman/strict-rfc3339/issues/9). + "-k" "not LocalOffset"))))))) + (native-inputs (list python-pytest)) + (home-page "https://github.com/danielrichman/strict-rfc3339") + (synopsis "RFC3339 procedures library") + (description "The @code{strict_rfc3339} Python module provides strict, +simple, lightweight RFC3339 procedures. It enables or aims to: +@itemize +@item Convert UNIX timestamps to and from RFC3339. +@item Produce RFC3339 strings with a UTC offset (Z) or with the offset that +the C time module reports is the local timezone offset. +@item Be simple with minimal dependencies/libraries. +@item Avoid timezones as much as possible. +@item Be very strict and follow RFC3339. +@end itemize") + (license license:gpl3+))) + (define-public python-stripe (package (name "python-stripe") @@ -28977,6 +30170,32 @@ simple mock/record and a complete capture/replay framework.") interfaces.") (license license:bsd-3))) +(define-public python-ordered-set + (package + (name "python-ordered-set") + (version "4.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ordered-set" version)) + (sha256 + (base32 "1a34fg3r3480nfm6652kyqql3lwixf8jirzdja9camvnr128wjk9")))) + (build-system python-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv"))))))) + (native-inputs (list python-cython python-pytest)) + (home-page "https://github.com/simonpercivall/orderedset") + (synopsis "Ordered Set implementation in Cython") + (description "This library provides an @code{OrderedSet} data type that +works like a regular set, but remembers insertion order. It supports the full +Python @code{set} interface.") + (license license:asl2.0))) + (define-public python-orgparse (package (name "python-orgparse") @@ -29031,12 +30250,14 @@ interfaces.") (arguments `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'patch-for-click-8 + (lambda _ + (substitute* "dynaconf/cli.py" + (("click.get_os_args\\()") ;deprecated from Click 8.1+ + "sys.argv[1:]")))) (replace 'check (lambda* (#:key tests? outputs #:allow-other-keys) (when tests? - (setenv "PATH" - (string-append (assoc-ref outputs "out") "/bin:" - (getenv "PATH"))) ;; These tests depend on hvac and a live Vault process. (delete-file "tests/test_vault.py") (invoke "make" "test_only"))))))) @@ -29044,7 +30265,7 @@ interfaces.") (list python-click python-configobj python-dotenv-0.13.0 python-ruamel.yaml python-toml)) (native-inputs - (list python-django python-flask python-pytest-6 python-pytest-cov + (list python-django python-flask python-pytest python-pytest-cov python-pytest-mock)) (home-page "https://www.dynaconf.com/") (synopsis "The dynamic configurator for your Python project") @@ -29068,32 +30289,29 @@ development, testing, production]}; @end itemize") (license license:expat))) -(define-public pudb +(define-public python-pudb (package - (name "pudb") - (version "2021.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "pudb" version)) - (sha256 - (base32 "0p16pvzfa3w02ybg3n0iy5rs23z4rz4a42lb8wh3mcq62y9ik2w7")))) + (name "python-pudb") + (version "2022.1.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "pudb" version)) + (sha256 + (base32 + "0gq82hwnibby9qdyv7ri11phvg94nby4jb0w9h3jk79w89kdsfyv")))) (build-system python-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'check 'fix-read-only-home - (lambda _ - (setenv "HOME" "/tmp"))) - (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "pytest"))))))) - (native-inputs - (list python-numpy python-pytest python-pytest-mock)) - (propagated-inputs - (list python-jedi python-pygments python-urwid python-urwid-readline)) + `(#:phases (modify-phases %standard-phases + (add-before 'check 'fix-read-only-home + (lambda _ + (setenv "HOME" "/tmp"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv"))))))) + (native-inputs (list python-pytest python-pytest-mock)) + (propagated-inputs (list python-jedi python-pygments python-urwid + python-urwid-readline)) (home-page "https://documen.tician.de/pudb/") (synopsis "Console-based Python debugger") (description @@ -29102,6 +30320,9 @@ all the niceties of modern GUI-based debuggers in a more lightweight and keyboard-friendly package.") (license license:expat))) +(define-public pudb + (deprecated-package "pudb" python-pudb)) + (define-public python-iwlib (package (name "python-iwlib") @@ -29390,10 +30611,27 @@ multipurpose analysis in Python.") (home-page "https://github.com/python/typeshed") (synopsis "Typing stubs for dataclasses") (description - "This packages provides a collection of library stubs for Python, with + "This package provides a collection of library stubs for Python, with static types.") (license license:asl2.0))) +(define-public python-types-docutils + (package + (name "python-types-docutils") + (version "0.18.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "types-docutils" version)) + (sha256 + (base32 "14ypv0x6fk1pjw0bvvr1lkb2g6dvq2pwvbd5b5pzjl6182fhmaim")))) + (build-system python-build-system) + (home-page "https://github.com/python/typeshed") + (synopsis "Typing stubs for docutils") + (description "This package provides a collection of library stubs for +Python, with static types.") + (license license:asl2.0))) + (define-public python-psycopg2-binary (package (name "python-psycopg2-binary") @@ -29471,6 +30709,60 @@ async I/O support.") "This package adds ANSI colors and decorations to your strings.") (license license:isc))) +(define-public python-types-freezegun + (package + (name "python-types-freezegun") + (version "1.1.8") + (source + (origin + (method url-fetch) + (uri (pypi-uri "types-freezegun" version)) + (sha256 + (base32 "08g926s8343zwq140zcfwly3qfgmahm7lp0vgb3ics549b2hifzl")))) + (build-system python-build-system) + (home-page "https://github.com/python/typeshed") + (synopsis "Typing stubs for @code{freezegun}") + (description "This package contains typing stubs for for @code{freezegun}, a +very small subset the Python stubs contained in the complete @code{typeshed} +collection.") + (license license:asl2.0))) + +(define-public python-types-pytz + (package + (name "python-types-pytz") + (version "2021.3.6") + (source + (origin + (method url-fetch) + (uri (pypi-uri "types-pytz" version)) + (sha256 + (base32 "14yr5hg2ww8s4a0mz2bkd549fv8qgm538fnzxvqv92ld1pcpym3l")))) + (build-system python-build-system) + (home-page "https://github.com/python/typeshed") + (synopsis "Typing stubs for pytz") + (description "This package contains typing stubs for @code{pytz}, a very +small subset the Python stubs contained in the complete @code{typeshed} +collection.") + (license license:asl2.0))) + +(define-public python-types-toml + (package + (name "python-types-toml") + (version "0.10.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "types-toml" version)) + (sha256 + (base32 "10400bd3yv6rjfnq8galskkbpqz1sfx9sfgr5qwvw04270x4cjgr")))) + (build-system python-build-system) + (home-page "https://github.com/python/typeshed") + (synopsis "Typing stubs for TOML") + (description "This package contains typing stubs for TOML, a very small +subset the Python stubs contained in the complete @code{typeshed} +collection.") + (license license:asl2.0))) + (define-public python-types-ujson (package (name "python-types-ujson") @@ -29554,6 +30846,10 @@ writing STL files. It supports both the text and binary forms of STL.") ;; There is a bug in the test_suit specification. (add-after 'unpack 'patch-test-suite (lambda _ + ;; Make compatible with PyYAML 6. + (substitute* "multipart/tests/test_multipart.py" + (("yaml.load") + "yaml.safe_load")) (substitute* "setup.py" (("test_suite = 'multipart.tests.suite'") "test_suite = 'multipart.tests.test_multipart.suite'")) |