From 8fe6d3e8446944294856950ef192cac83e03e58b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Dec 2022 01:00:52 +0100 Subject: gnu: yajl: Drop custom ‘lib-’ prefix. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/web.scm (yajl): New variable, renamed from… (libyajl): …this one, which is now a DEPRECATED-PACKAGE alias of yajl. Adjust all users. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8591423116..9629012a80 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -29784,9 +29784,9 @@ (define-public python-ijson (when tests? (invoke "pytest" "-vv"))))))) (inputs - ;; libyajl is optional, but compiling with it makes faster + ;; yajl is optional, but compiling with it makes faster ;; backends available to ijson: - (list libyajl)) + (list yajl)) (native-inputs (list python-pytest)) (build-system python-build-system) -- cgit v1.2.3 From c4bcb5db49b210097c5452b678e57a0774014814 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 12 Dec 2022 21:40:53 +0100 Subject: gnu: python-typer: Simplify by using pyproject-build-system. * gnu/packages/python-xyz.scm (python-typer)[build-system]: Use pyproject-build-system. [arguments]: Remove extra quoting; remove custom 'build phase; remove custom 'install phase; remove custom 'check phase; add 'pre-check phase. [synopsis]: Pull onto the same line. [description]: Reformat. --- gnu/packages/python-xyz.scm | 74 +++++++++++++++++---------------------------- 1 file changed, 28 insertions(+), 46 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9629012a80..bb25c35caf 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22311,60 +22311,42 @@ (define-public python-typer (file-name (git-file-name name version)) (sha256 (base32 "1knv353qhkl2imav3jfp6bgq47m8wkkqhq1dzmqg2sv8rsy7zgl7")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - `(#:phases - ,#~(modify-phases %standard-phases - ;; Unfortunately, this doesn't seem to be enough to fix these two - ;; tests, but we'll patch this anyway. - (add-after 'unpack 'patch-shell-reference - (lambda _ - (substitute* "tests/test_completion/test_completion.py" - (("\"bash\"") (string-append "\"" (which "bash") "\"")) - (("\"/bin/bash\"") - (string-append "\"" (which "bash") "\""))))) - (replace 'build - (lambda _ - (invoke "flit" "build"))) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (for-each - (lambda (wheel) - (format #true wheel) - (invoke "python" "-m" "pip" "install" - wheel (string-append "--prefix=" #$output))) - (find-files "dist" "\\.whl$")))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "HOME" "/tmp") ; some tests need it - - ;; This is for completion tests - (with-output-to-file "/tmp/.bashrc" - (lambda _ (display "# dummy"))) - - (setenv "GUIX_PYTHONPATH" - (string-append (getcwd) ":" - (getenv "GUIX_PYTHONPATH"))) - (let ((disabled-tests (list "test_show_completion" - "test_install_completion"))) - (invoke "python" "-m" "pytest" "tests/" - "-k" - (string-append "not " - (string-join disabled-tests - " and not ")))))))))) + (list + #:test-flags + '(let ((disabled-tests (list "test_show_completion" + "test_install_completion"))) + (list "-k" (string-append "not " + (string-join disabled-tests + " and not ")))) + #:phases + #~(modify-phases %standard-phases + ;; Unfortunately, this doesn't seem to be enough to fix these two + ;; tests, but we'll patch this anyway. + (add-after 'unpack 'patch-shell-reference + (lambda _ + (substitute* "tests/test_completion/test_completion.py" + (("\"bash\"") (string-append "\"" (which "bash") "\"")) + (("\"/bin/bash\"") + (string-append "\"" (which "bash") "\""))))) + (add-before 'check 'pre-check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp") ; some tests need it + ;; This is for completion tests + (with-output-to-file "/tmp/.bashrc" + (lambda _ (display "# dummy"))))))))) (propagated-inputs (list python-click)) (native-inputs (list python-coverage python-flit python-pytest python-rich python-shellingham)) (home-page "https://github.com/tiangolo/typer") - (synopsis - "Typer builds CLI based on Python type hints") + (synopsis "Typer builds CLI based on Python type hints") (description - "Typer is a library for building CLI applications. It's based on -Python 3.6+ type hints.") + "Typer is a library for building CLI applications. It's based on Python +3.6+ type hints.") ;; MIT license (license license:expat))) -- cgit v1.2.3 From 8b9c9051ba798572577cef474085cc88adb73ae4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 12 Dec 2022 23:45:52 +0100 Subject: gnu: python-numcodecs: Update to 0.10.2. * gnu/packages/python-xyz.scm (python-numcodecs): Update to 0.10.2. [build-system]: Use pyproject-build-system. [arguments]: Enable tests; add phase 'build-extensions; remove custom 'check phase. [propagated-inputs]: Add python-entrypoints and python-typing-extensions-next. --- gnu/packages/python-xyz.scm | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index bb25c35caf..ef3043f09c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23473,14 +23473,14 @@ (define-public python-numba (define-public python-numcodecs (package (name "python-numcodecs") - (version "0.6.4") + (version "0.10.2") (source (origin (method url-fetch) (uri (pypi-uri "numcodecs" version)) (sha256 (base32 - "0kbfr8pl3x9glsypbq8hzim003f16ml1b1cvgrh4w1sdvgal6j7g")) + "1i2rvm1f23dapcf6w3mj4877jzq5f24bhfa0fafbv1nr7xmqr0r2")) (modules '((guix build utils))) (snippet '(begin @@ -23490,11 +23490,11 @@ (define-public python-numcodecs "numcodecs/lz4.c" "numcodecs/vlen.c" "numcodecs/zstd.c")))))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - `(#:tests? #false ; TODO: unclear why numcodecs.* are not found - #:phases - (modify-phases %standard-phases + (list + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'disable-avx2 (lambda _ (setenv "DISABLE_NUMCODECS_AVX2" "1"))) @@ -23511,16 +23511,18 @@ (define-public python-numcodecs "'numcodecs.lz4', libraries=['lz4'], ") (("'numcodecs.blosc',") "'numcodecs.blosc', libraries=['blosc'], ")))) - (replace 'check - (lambda* (#:key tests? inputs outputs #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "pytest" "-vv"))))))) + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace")))))) (inputs (list c-blosc lz4 zlib `(,zstd "lib"))) (propagated-inputs - (list python-numpy python-msgpack)) + (list python-entrypoints + python-numpy + python-msgpack + python-typing-extensions-next)) (native-inputs (list python-cython python-pytest python-setuptools-scm)) (home-page "https://github.com/zarr-developers/numcodecs") -- cgit v1.2.3 From 2c65106cf5bc591ecf8d2303fdfd48d578f47b62 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 12 Dec 2022 23:47:19 +0100 Subject: gnu: python-zarr: Update to 2.13.3. * gnu/packages/python-xyz.scm (python-zarr): Update to 2.13.3. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ef3043f09c..579105e263 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23552,14 +23552,14 @@ (define-public python-asciitree (define-public python-zarr (package (name "python-zarr") - (version "2.4.0") + (version "2.13.3") (source (origin (method url-fetch) (uri (pypi-uri "zarr" version)) (sha256 (base32 - "026n3sjzjv2gmwx6y72b8ij0hk42bc8zdbvfj5gdqzd4i6wj3ajk")))) + "135ls2q7zc98pk61a5cnh88j4hnnavcwasrswdjqyqvcc68b096v")))) (build-system python-build-system) (arguments `(#:phases -- cgit v1.2.3 From 75331dc6e690e790cccfa7ec0b936ff60e7f517d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 12 Dec 2022 23:47:27 +0100 Subject: gnu: python-anndata: Use pyproject-build-system. * gnu/packages/python-xyz.scm (python-anndata)[build-system]: Use pyproject-build-system. [arguments]: Replace custom 'build phase with 'set-version phase; remove custom 'install phase; disable doctest via build phase 'disable-doctests and the #:test-flags property. [propagated-inputs]: Add python-scikit-learn. [native-inputs]: Add python-boltons. --- gnu/packages/python-xyz.scm | 49 ++++++++++++++++++++++++--------------------- 1 file changed, 26 insertions(+), 23 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 579105e263..f5c4e3e9f7 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -201,6 +201,7 @@ (define-module (gnu packages python-xyz) #:use-module (gnu packages libusb) #:use-module (gnu packages linux) #:use-module (gnu packages llvm) + #:use-module (gnu packages machine-learning) #:use-module (gnu packages man) #:use-module (gnu packages markup) #:use-module (gnu packages maths) @@ -23601,29 +23602,26 @@ (define-public python-anndata (sha256 (base32 "0v7npqrg1rdm8jzw22a45c0mqrmsv05r3k88i3lhzi0pzzxca1i1")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (delete 'check) - (replace 'build - (lambda _ - (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" ,version) - (substitute* "anndata/_metadata.py" - (("__version__ =.*") - (string-append "__version__ = \"" ,version "\"\n"))) - ;; ZIP does not support timestamps before 1980. - (setenv "SOURCE_DATE_EPOCH" "315532800") - (invoke "flit" "build"))) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (let ((out (assoc-ref outputs "out"))) - (for-each (lambda (wheel) - (format #true wheel) - (invoke "python" "-m" "pip" "install" - wheel (string-append "--prefix=" out))) - (find-files "dist" "\\.whl$")))))))) + (list + #:test-flags + '(list "-k" "not concatenation.rst") + #:phases + #~(modify-phases %standard-phases + ;; Doctests require scanpy from (gnu packages bioinformatics) + (add-after 'unpack 'disable-doctests + (lambda _ + (substitute* "pyproject.toml" + (("--doctest-modules") "")))) + (add-before 'build 'set-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version) + (substitute* "anndata/_metadata.py" + (("__version__ =.*") + (string-append "__version__ = \"" #$version "\"\n"))) + ;; ZIP does not support timestamps before 1980. + (setenv "SOURCE_DATE_EPOCH" "315532800")))))) (propagated-inputs (list python-h5py python-importlib-metadata @@ -23632,9 +23630,14 @@ (define-public python-anndata python-packaging python-pandas python-scipy + python-scikit-learn python-zarr)) (native-inputs - (list python-joblib python-pytest python-toml python-flit + (list python-boltons + python-joblib + python-pytest + python-toml + python-flit python-setuptools-scm)) (home-page "https://github.com/theislab/anndata") (synopsis "Annotated data for data analysis pipelines") -- cgit v1.2.3 From 08b9e29d4672d2209026f4b7fa592abb958cbd34 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 10 Dec 2022 22:03:45 +0100 Subject: gnu: python-bokeh: Skip failing PIL test. The test compares base64-encoded gifs; the gifs look identical but the base64-encoded data differs. Since the result seems fine, disabling this PIL test is probably okay. * gnu/packages/python-xyz.scm (python-bokeh)[arguments]: Ignore failing test_transform_PIL test. --- gnu/packages/python-xyz.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f5c4e3e9f7..2acba1fa39 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15466,7 +15466,10 @@ (define-public python-bokeh (delete-file "tests/unit/bokeh/models/test_sources.py") (delete-file "tests/unit/bokeh/embed/test_bundle.py") - (invoke "pytest" "-v"))))))) + ;; XXX: This one test transforms a gif of a red box. It + ;; transforms it all right but the base64 doesn't look as + ;; expected, probably because of a change in pillow. + (invoke "pytest" "-v" "-k" "not test_transform_PIL"))))))) (propagated-inputs (list node-lts python-jinja2 -- cgit v1.2.3 From 0fcba8b01c23af756dba5f863db8712d6f840f36 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 11 Dec 2022 13:44:29 +0100 Subject: gnu: python-marshmallow: Update to 3.19.0. * gnu/packages/python-xyz.scm (python-marshmallow): Update to 3.19.0. [build-system]: Use pyproject-build-system. [propagated-inputs]: Remove python-dateutil and python-simplejson; add python-packaging. [native-inputs]: Add python-flake8, python-flake8-bugbear, python-mypy, python-pre-commit, and python-simplejson. --- gnu/packages/python-xyz.scm | 31 ++++++++++++++++++------------- 1 file changed, 18 insertions(+), 13 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2acba1fa39..2d013054ec 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20954,24 +20954,29 @@ (define-public python-flex (define-public python-marshmallow (package (name "python-marshmallow") - (version "3.9.1") + (version "3.19.0") (source (origin - (method url-fetch) - (uri (pypi-uri "marshmallow" version)) - (sha256 - (base32 - "0kizhh3mnhpa08wfnsv1gagy22bpxzxszgbiylkhpz1d8qvwrykk")))) - (build-system python-build-system) + (method url-fetch) + (uri (pypi-uri "marshmallow" version)) + (sha256 + (base32 + "0y6vpq2p5841kcw2qil68la0rx9z1vmxzj3dxjv99kjhsq7jq0wh")))) + (build-system pyproject-build-system) (propagated-inputs - (list python-dateutil python-simplejson)) + (list python-packaging)) (native-inputs - (list python-pytest python-pytz)) + (list python-flake8 + python-flake8-bugbear + python-mypy + python-pre-commit + python-pytest + python-pytz + python-simplejson)) (home-page "https://github.com/marshmallow-code/marshmallow") - (synopsis "Convert complex datatypes to and from native - Python datatypes") - (description "@code{marshmallow} provides a library for converting - complex datatypes to and from native Python datatypes.") + (synopsis "Convert complex datatypes to and from native Python datatypes") + (description "@code{marshmallow} provides a library for converting complex +datatypes to and from native Python datatypes.") (license license:expat))) (define-public python-marshmallow-jsonapi -- cgit v1.2.3 From 99a29b4933144599c29bd54a0eb654b20cbe6500 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 11 Dec 2022 13:45:51 +0100 Subject: gnu: python-apispec: Update to 6.0.2. * gnu/packages/python-xyz.scm (python-apispec): Update to 6.0.2. [build-system]: Use pyproject-build-system. [arguments]: Disable test through test-flags, not by replacing the 'check phase. [propagated-inputs]: Remove python-pyyaml; add python-packaging. [native-inputs]: Add python-flake8, python-flake8-bugbear, python-mypy, python-pre-commit, and python-pyyaml. --- gnu/packages/python-xyz.scm | 39 +++++++++++++++++++++------------------ 1 file changed, 21 insertions(+), 18 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2d013054ec..0ddb91cf79 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21012,33 +21012,36 @@ (define-public python-marshmallow-jsonapi (define-public python-apispec (package (name "python-apispec") - (version "4.0.0") + (version "6.0.2") (source (origin - (method url-fetch) - (uri (pypi-uri "apispec" version)) - (sha256 + (method url-fetch) + (uri (pypi-uri "apispec" version)) + (sha256 (base32 - "12n4w5zkn4drcn8izq68vmixmqvz6abviqkdn4ip0kaax3jjh3in")))) - (build-system python-build-system) + "11vqxwdxmm7qmyhdbxk4gnx37nbzmn266ah92gi4pvzd76vq0vg7")))) + (build-system pyproject-build-system) (arguments - '(#:phases (modify-phases %standard-phases - (replace 'check - (lambda _ - (invoke "pytest" "-vv" - ;; Disable validation tests since they require - ;; the optional 'prance' library which is not - ;; yet in Guix. - "-k" "not openapi_tools_validate")))))) + (list + ;; Disable validation tests since they require + ;; the optional 'prance' library which is not + ;; yet in Guix. + #:test-flags '(list "-k" "not openapi_tools_validate"))) (propagated-inputs - (list python-pyyaml)) + (list python-packaging)) (native-inputs - (list python-pytest python-marshmallow)) + (list python-flake8 + python-flake8-bugbear + python-marshmallow + python-mypy + python-pre-commit + python-pytest + python-pyyaml)) (home-page "https://github.com/marshmallow-code/apispec") (synopsis "Swagger/OpenAPI specification generator") (description "@code{python-apispec} is a pluggable API specification - generator. It currently supports the OpenAPI specification, formerly known - as Swagger.") +generator. It currently supports the OpenAPI specification, formerly known as +Swagger.") (license license:expat))) (define-public python-apispec-webframeworks -- cgit v1.2.3 From 8c197f990b7ab60e4524567d628d78ea62973c11 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 11 Dec 2022 15:01:42 +0100 Subject: gnu: python-pyjwt: Update to 2.6.0. * gnu/packages/python-xyz.scm (python-pyjwt): Update to 2.6.0. [build-system]: Use pyproject-build-system. [arguments]: Remove. [native-inputs]: Add pytohn-coverage, python-pre-commit, python-sphinx, and python-sphinx-rtd-theme. --- gnu/packages/python-xyz.scm | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0ddb91cf79..0f7903bdfb 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4088,23 +4088,22 @@ (define-public python-text-unidecode (define-public python-pyjwt (package (name "python-pyjwt") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (pypi-uri "PyJWT" version)) (sha256 (base32 - "1fmbcwfw1463wjzwbcgg3s16rad6kfb1mc5y7jbkp6v9ihh0hafl")))) - (build-system python-build-system) - (arguments - '(#:phases (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-vv"))))))) + "1z85kwr945rbzrn5wabrsmck5x8disa9wc7b3y5gci7w65z5qa39")))) + (build-system pyproject-build-system) (native-inputs - (list python-cryptography python-pytest)) + (list python-coverage + python-cryptography + python-pre-commit + python-pytest + python-sphinx + python-sphinx-rtd-theme)) (home-page "https://github.com/progrium/pyjwt") (synopsis "JSON Web Token implementation in Python") (description -- cgit v1.2.3 From 9bf2101049eb79430a6b15f0017a6027ad37a1f2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 11 Dec 2022 15:37:40 +0100 Subject: gnu: python-flasgger: Update to 0.9.5. * gnu/packages/python-xyz.scm (python-flasgger): Update to 0.9.5. [build-system]: Use pyproject-build-system. [arguments]: Remove custom 'check phase; add 'prepare-check phase; disable "test_swag" test via #:test-flags. [native-inputs]: Add python-apispec-webframeworks and python-flask-jwt. --- gnu/packages/python-xyz.scm | 36 +++++++++++++++++++++--------------- 1 file changed, 21 insertions(+), 15 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0f7903bdfb..2279503d63 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21074,7 +21074,7 @@ (define-public python-apispec-webframeworks (define-public python-flasgger (package (name "python-flasgger") - (version "0.6.3") + (version "0.9.5") (source (origin (method git-fetch) @@ -21083,29 +21083,35 @@ (define-public python-flasgger (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0yydxsyjnc0clbrjqb1n7587l6cdqvwdagwxk5hkx01qwdfbkvpn")))) - (build-system python-build-system) + (base32 "0a2djgfq905a4in16068qz0ikg88dm4nbckaamhaz2v9khllr0bi")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (substitute* "Makefile" - (("flake8 flasgger --ignore=F403") - "flake8 flasgger --ignore=E731,F403")) - (invoke "py.test")))))) + (list + ;; This test fails due to missing fixtures + #:test-flags '(list "-k" "not test_swag") + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'prepare-check + (lambda _ + ;; This requires a dummy package "flasgger_package" to be installed. + (delete-file "examples/package_example.py") + ;; These fail with an internal server error + (for-each delete-file '("examples/marshmallow_apispec.py" + "examples/validation.py"))))))) (propagated-inputs (list python-flask python-pyyaml python-jsonschema python-mistune python-six)) (native-inputs - (list python-decorator + (list python-apispec + python-apispec-webframeworks + python-decorator python-flake8 + python-flask-jwt python-flask-restful python-flex - python-pytest - python-pytest-cov python-marshmallow - python-apispec)) + python-pytest + python-pytest-cov)) (home-page "https://github.com/rochacbruno/flasgger/") (synopsis "Extract Swagger specs from your Flask project") (description "@code{python-flasgger} allows extracting Swagger specs -- cgit v1.2.3 From 0682e7c2e36933c5447678549c8e61bd1271d92c Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Mon, 5 Dec 2022 22:59:12 +0000 Subject: gnu: python-h5netcdf: Update to 1.1.0. * gnu/packages/python-xyz.scm (python-h5netcdf): Update to 1.1.0. [build-system]: Use pyproject-build-system, to simplify package. [description]: Style content and add links to referenced projects. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 21 ++++++++------------- 1 file changed, 8 insertions(+), 13 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2279503d63..3ea2763b49 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1759,21 +1759,14 @@ (define-public python-hdf4 (define-public python-h5netcdf (package (name "python-h5netcdf") - (version "1.0.1") + (version "1.1.0") (source (origin (method url-fetch) (uri (pypi-uri "h5netcdf" version)) (sha256 - (base32 "1b2dcgf5rwy7pb7hr4prkc5vgcw9qc2was20dmnj90lbrpx08rvp")))) - (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" "h5netcdf/tests"))))))) + (base32 "0mmzfr6k55zqxxpb64gvdqisak8s1zb2r04yzkmp0wzd7dbknb4k")))) + (build-system pyproject-build-system) (native-inputs (list python-netcdf4 python-pytest @@ -1782,9 +1775,11 @@ (define-public python-h5netcdf (list python-h5py python-packaging)) (home-page "https://h5netcdf.org") (synopsis "Python interface for the netCDF4 file-format based on h5py") - (description "This package provides Python interface for the netCDF4 -file-format that reads and writes local or remote HDF5 files directly via h5py -or h5pyd, without relying on the Unidata netCDF library") + (description "This package provides a Python interface for the netCDF4 +file-format that reads and writes local or remote HDF5 files directly via +@url{h5py, https://www.h5py.org/} or @url{h5pyd, +https://github.com/HDFGroup/h5pyd}, without relying on the Unidata netCDF +library.") (license license:bsd-3))) (define-public python-h5py -- cgit v1.2.3 From 7833acab0da02335941974608510c02e2d1d8069 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 21 Dec 2022 11:17:44 +0100 Subject: gnu: pyzo: Update to 4.12.4. * gnu/packages/python-xyz.scm (pyzo): Update to 4.12.4. --- gnu/packages/python-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3ea2763b49..ee25a2d655 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -27002,17 +27002,17 @@ (define-public python-dictpath (define-public pyzo (package (name "pyzo") - (version "4.12.3") + (version "4.12.4") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/pyzo/pyzo.git") + (url "https://github.com/pyzo/pyzo") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 - "0v6rgp52bf9za2spxx9c1yc6wmskvlsj81iw0gipjy7y8vpypgn2")))) + "10qqilbh7n4z2656qbr9gllvgi7xq11xcm2bv64h02jmkb7m4m6n")))) (build-system python-build-system) (arguments `(#:phases -- cgit v1.2.3 From bae13578f7b03735c1cfcd1addb31a05fa413c44 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sat, 24 Dec 2022 00:43:20 +0100 Subject: gnu: python-scikit-build: Depend on 'git-minimal/fixed'. * gnu/packages/python-xyz.scm (python-scikit-build)[native-inputs]: Replace 'git-minimal' with 'git-minimal/fixed'. --- gnu/packages/python-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ee25a2d655..6b71d6872e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -28550,7 +28550,7 @@ (define-public python-scikit-build (native-inputs (list cmake-minimal gfortran - git-minimal + git-minimal/fixed ;for tests ninja python-coverage python-cython -- cgit v1.2.3 From 0cb8f7125b19264b01962c1249c3df4c5ce85aa9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 27 Dec 2022 21:46:46 +0100 Subject: gnu: python-bitarray: Update to 2.6.1. * gnu/packages/python-xyz.scm (python-bitarray): Update to 2.6.1. [arguments]: Override check phase. --- gnu/packages/python-xyz.scm | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 6b71d6872e..d0cedf696a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1675,14 +1675,24 @@ (define-public python-bip39 (define-public python-bitarray (package (name "python-bitarray") - (version "1.4.0") + (version "2.6.1") (source (origin (method url-fetch) (uri (pypi-uri "bitarray" version)) (sha256 (base32 - "177fj6wbw5jln54wpp6plcqy2329wjkwqwvgz7022rrg3xfrq49g")))) + "0c4jli872nzix81n1xirnrghlq2fdsxb570d9rnfvxi1694sah44")))) (build-system python-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Step out of the source directory to avoid interference. + (with-directory-excursion "/tmp" + (invoke "python" "-c" + "import bitarray; bitarray.test()")))))))) (home-page "https://github.com/ilanschnell/bitarray") (synopsis "Efficient arrays of booleans") (description "This package provides an object type which efficiently -- cgit v1.2.3