diff options
Diffstat (limited to 'gnu/packages/python.scm')
| -rw-r--r-- | gnu/packages/python.scm | 990 |
1 files changed, 560 insertions, 430 deletions
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 868fa70e19..d9bea45142 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -143,12 +143,13 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system python) #:use-module (guix build-system trivial) - #:use-module (srfi srfi-1)) + #:use-module (srfi srfi-1) + #:use-module (srfi srfi-26)) (define-public python-2.7 (package (name "python2") - (version "2.7.14") + (version "2.7.15") (replacement python-2/fixed) (source (origin @@ -157,7 +158,7 @@ version "/Python-" version ".tar.xz")) (sha256 (base32 - "0rka541ys16jwzcnnvjp2v12m4cwgd2jp6wj4kj511p715pb5zvi")) + "0x2mvz9dp11wj7p5ccvmk9s0hzjk2fa1m462p395l4r6bfnb3n92")) (patches (search-patches "python-2.7-search-paths.patch" "python-2-deterministic-build-info.patch" "python-2.7-site-prefixes.patch" @@ -182,23 +183,7 @@ "tk")) ;tkinter; adds 50 MiB to the closure (build-system gnu-build-system) (arguments - `(;; 356 tests OK. - ;; 6 tests failed: - ;; test_compileall test_distutils test_import test_shutil test_socket - ;; test_subprocess - ;; 39 tests skipped: - ;; test_aepack test_al test_applesingle test_bsddb test_bsddb185 - ;; test_bsddb3 test_cd test_cl test_codecmaps_cn test_codecmaps_hk - ;; test_codecmaps_jp test_codecmaps_kr test_codecmaps_tw test_curses - ;; test_dl test_gdb test_gl test_imageop test_imgfile test_ioctl - ;; test_kqueue test_linuxaudiodev test_macos test_macostools - ;; test_msilib test_ossaudiodev test_scriptpackages test_smtpnet - ;; test_socketserver test_startfile test_sunaudiodev test_timeout - ;; test_tk test_ttk_guionly test_urllib2net test_urllibnet - ;; test_winreg test_winsound test_zipfile64 - ;; 4 skips unexpected on linux2: - ;; test_bsddb test_bsddb3 test_gdb test_ioctl - #:test-target "test" + `(#:test-target "test" #:configure-flags (list "--enable-shared" ;allow embedding "--with-system-ffi" ;build ctypes @@ -223,11 +208,6 @@ "Lib/test/support/__init__.py" "Lib/test/test_subprocess.py")) (("/bin/sh") (which "sh"))) - - ;; Use zero as the timestamp in .pyc files so that builds are - ;; deterministic. TODO: Remove it when this variable is set in - ;; gnu-build-system.scm. - (setenv "SOURCE_DATE_EPOCH" "1") #t)) (add-before 'configure 'do-not-record-configure-flags (lambda* (#:key configure-flags #:allow-other-keys) @@ -281,19 +261,14 @@ ((or "." "..") #f) (file (not + ;; FIXME: Add the 'support' directory + ;; in the next rebuild cycle, since it + ;; moved in 2.7.14. See also + ;; python2-futures below. (string-prefix? "test_support." file)))))) (call-with-output-file "__init__.py" (const #t)) #t))))))) - (add-before 'strip 'make-libraries-writable - (lambda* (#:key outputs #:allow-other-keys) - ;; Make .so files writable so they can be stripped. - (let ((out (assoc-ref outputs "out"))) - (for-each (lambda (file) - (chmod file #o755)) - (find-files (string-append out "/lib") - "\\.so")) - #t))) (add-after 'install 'move-tk-inter (lambda* (#:key outputs #:allow-other-keys) ;; When Tkinter support is built move it to a separate output so @@ -353,9 +328,7 @@ data types.") (inherit (package-source python-2)) (patches (append (origin-patches (package-source python-2)) - (search-patches "python2-CVE-2018-1060.patch" - "python2-CVE-2018-1061.patch" - "python2-CVE-2018-14647.patch" + (search-patches "python2-CVE-2018-14647.patch" "python2-CVE-2018-1000802.patch"))))))) (define-public python2-called-python @@ -367,10 +340,10 @@ data types.") (name "python") (properties `((superseded . ,python-2))))) -(define-public python-3.6 +(define-public python-3.7 (package (inherit python-2) (name "python") - (version "3.6.5") + (version "3.7.0") (replacement python-3/fixed) (source (origin (method url-fetch) @@ -384,66 +357,39 @@ data types.") (patch-flags '("-p0")) (sha256 (base32 - "19l7inxm056jjw33zz97z0m02hsi7jnnx5kyb76abj5ml4xhad7l")) + "0j9mic5c9lbd2b20wka7hily7szz740wy9ilfrczxap63rnrk0h3")) (snippet '(begin (for-each delete-file - '("Lib/ctypes/test/test_structures.py" ; fails on aarch64 - "Lib/ctypes/test/test_win32.py" ; fails on aarch64 - "Lib/test/test_fcntl.py")) ; fails on aarch64 + '(;; This test may hang and eventually run out of + ;; memory on some systems: + ;; <https://bugs.python.org/issue34587> + "Lib/test/test_socket.py" + + ;; These tests fail on AArch64. + "Lib/ctypes/test/test_win32.py" + "Lib/test/test_fcntl.py" + "Lib/test/test_posix.py")) #t)))) (arguments (substitute-keyword-arguments (package-arguments python-2) - ((#:tests? _) #t) ((#:phases phases) - `(modify-phases ,phases - (add-after 'unpack 'patch-timestamp-for-pyc-files - (lambda _ - ;; We set DETERMINISTIC_BUILD to only override the mtime when - ;; building with Guix, lest we break auto-compilation in - ;; environments. - (setenv "DETERMINISTIC_BUILD" "1") - (substitute* "Lib/py_compile.py" - (("source_stats\\['mtime'\\]") - "(1 if 'DETERMINISTIC_BUILD' in os.environ else source_stats['mtime'])")) - - ;; Use deterministic hashes for strings, bytes, and datetime - ;; objects. - (setenv "PYTHONHASHSEED" "0") - - ;; Reset mtime when validating bytecode header. - (substitute* "Lib/importlib/_bootstrap_external.py" - (("source_mtime = int\\(source_stats\\['mtime'\\]\\)") - "source_mtime = 1")) - #t)) - ;; These tests fail because of our change to the bytecode - ;; validation. They fail because expected exceptions do not get - ;; thrown. This seems to be no problem. - (add-after 'unpack 'disable-broken-bytecode-tests - (lambda _ - (substitute* "Lib/test/test_importlib/source/test_file_loader.py" - (("test_bad_marshal") - "disable_test_bad_marshal") - (("test_no_marshal") - "disable_test_no_marshal") - (("test_non_code_marshal") - "disable_test_non_code_marshal")) - #t)) - ;; Unset DETERMINISTIC_BUILD to allow for tests that check that - ;; stale pyc files are rebuilt. - (add-before 'check 'allow-non-deterministic-compilation - (lambda _ (unsetenv "DETERMINISTIC_BUILD") #t)) - ;; We need to rebuild all pyc files for three different - ;; optimization levels to replace all files that were not built - ;; deterministically. - - ;; FIXME: Without this phase we have close to 2000 files that + `(modify-phases ,phases + ;; Unset SOURCE_DATE_EPOCH while running the test-suite and set it + ;; again afterwards. See <https://bugs.python.org/issue34022>. + (add-before 'check 'unset-SOURCE_DATE_EPOCH + (lambda _ (unsetenv "SOURCE_DATE_EPOCH") #t)) + (add-after 'check 'reset-SOURCE_DATE_EPOCH + (lambda _ (setenv "SOURCE_DATE_EPOCH" "1") #t)) + ;; FIXME: Without this phase we have close to 400 files that ;; differ across different builds of this package. With this phase - ;; there are about 500 files left that differ. - (add-after 'install 'rebuild-bytecode + ;; there are 44 files left that differ. + (add-after 'remove-tests 'rebuild-bytecode (lambda* (#:key outputs #:allow-other-keys) - (setenv "DETERMINISTIC_BUILD" "1") (let ((out (assoc-ref outputs "out"))) + ;; Disable hash randomization to ensure the generated .pycs + ;; are reproducible. + (setenv "PYTHONHASHSEED" "0") (for-each (lambda (opt) (format #t "Compiling with optimization level: ~a\n" @@ -455,8 +401,7 @@ data types.") "-m" "compileall" "-f" ; force rebuild ;; Don't build lib2to3, because it's Python 2 code. - ;; Also don't build obviously broken test code. - "-x" "(lib2to3|test/bad.*)" + "-x" "lib2to3/.*" ,file))) (find-files out "\\.py$"))) (list '() '("-O") '("-OO"))) @@ -469,7 +414,7 @@ data types.") "/site-packages")))))))) ;; Current 3.x version. -(define-public python-3 python-3.6) +(define-public python-3 python-3.7) (define python-3/fixed (package @@ -477,17 +422,7 @@ data types.") (source (origin (inherit (package-source python-3)) (patches (append (origin-patches (package-source python-3)) - (search-patches "python-CVE-2018-14647.patch"))))) - (arguments - (substitute-keyword-arguments (package-arguments python-3) - ((#:phases phases) - `(modify-phases ,phases - (add-after 'unpack 'delete-broken-test - (lambda _ - ;; Delete test which fails on recent kernels: - ;; <https://bugs.python.org/issue34587>. - (delete-file "Lib/test/test_socket.py") - #t)))))))) + (search-patches "python-CVE-2018-14647.patch"))))))) ;; Current major version. (define-public python python-3) @@ -715,18 +650,24 @@ by @code{binstar}, @code{binstar-build} and @code{chalmers}.") (define-public python-babel (package (name "python-babel") - (version "2.3.4") + (version "2.6.0") (source (origin (method url-fetch) (uri (pypi-uri "Babel" version)) (sha256 (base32 - "0x98qqqw35xllpcama013a9788ly84z8dm1w2wwfpxh2710c8df5")))) + "08rxmbx2s4irp0w0gmn498vns5xy0fagm0fg33xa772jiks51flc")))) (build-system python-build-system) + (native-inputs + `(("python-freezegun" ,python-freezegun) + ("python-pytest" ,python-pytest))) (propagated-inputs `(("python-pytz" ,python-pytz))) - (arguments `(#:tests? #f)) ; no test target + (arguments + `(#:phases (modify-phases %standard-phases + (replace 'check + (lambda _ (invoke "pytest" "-vv")))))) (home-page "http://babel.pocoo.org/") (synopsis "Tools for internationalizing Python applications") @@ -970,14 +911,14 @@ version identifier.") (define-public python-setuptools (package (name "python-setuptools") - (version "31.0.0") + (version "40.0.0") (source (origin (method url-fetch) - (uri (pypi-uri "setuptools" version)) + (uri (pypi-uri "setuptools" version ".zip")) (sha256 (base32 - "0ypybh4hx3bv4vhg2dc74xpj1g56ggnaffm87k4abhwjwq6wq608")) + "0pq116lr14gnc62v76nk0npkm6krb2mpp7p9ab369zgv4n7dnah1")) (modules '((guix build utils))) (snippet '(begin @@ -1273,13 +1214,13 @@ human-friendly syntax.") (define-public python-pandas (package (name "python-pandas") - (version "0.23.1") + (version "0.23.4") (source (origin (method url-fetch) (uri (pypi-uri "pandas" version)) (sha256 - (base32 "142nvwb01r2wv42y2cz40bx33hd8ffh6s6gynapg859fmzr2mdah")))) + (base32 "1x54pd7hr3y7qahx6b5bf2wzj54xvl8r3s1h4pl254pnmi3wl92v")))) (build-system python-build-system) (arguments `(#:modules ((guix build utils) @@ -1294,18 +1235,23 @@ human-friendly syntax.") (getcwd) "/build/" (car (scandir "build" (cut string-prefix? "lib." <>)))))) + ;; Disable the "strict data files" option which causes + ;; the build to error out if required data files are not + ;; available (as is the case with PyPI archives). + (substitute* "setup.cfg" + (("addopts = --strict-data-files") "addopts = ")) (with-directory-excursion build-directory ;; Delete tests that require "moto" which is not yet in Guix. (for-each delete-file '("pandas/tests/io/conftest.py" "pandas/tests/io/json/test_compression.py" + "pandas/tests/io/parser/test_network.py" "pandas/tests/io/test_excel.py" "pandas/tests/io/test_parquet.py")) - (invoke "pytest" "-v" "pandas" "-k" - (string-append - "not network and not disabled" - ;; XXX: Due to the deleted tests above. - " and not test_read_s3_jsonl"))))))))) + (invoke "pytest" "-vv" "pandas" "--skip-slow" + "--skip-network" "-k" + ;; XXX: Due to the deleted tests above. + "not test_read_s3_jsonl")))))))) (propagated-inputs `(("python-numpy" ,python-numpy) ("python-pytz" ,python-pytz) @@ -1816,14 +1762,14 @@ matching them against a list of media-ranges.") (define-public python-py (package (name "python-py") - (version "1.5.3") + (version "1.5.4") (source (origin (method url-fetch) (uri (pypi-uri "py" version)) (sha256 (base32 - "10gq2lckvgwlk9w6yzijhzkarx44hsaknd0ypa08wlnpjnsgmj99")))) + "1xxvwfn82457djf55f5n2c94699rfqnk43br8fif2r2q8gvrmm9z")))) (build-system python-build-system) (arguments ;; FIXME: "ImportError: 'test' module incorrectly imported from @@ -1831,7 +1777,9 @@ matching them against a list of media-ranges.") ;; Expected '/tmp/guix-build-python-py-1.4.31.drv-0/py-1.4.31/py'. ;; Is this module globally installed?" '(#:tests? #f)) - (home-page "https://pylib.readthedocs.io/") + (native-inputs + `(("python-setuptools-scm" ,python-setuptools-scm))) + (home-page "https://github.com/pytest-dev/py") (synopsis "Python library for parsing, I/O, instrospection, and logging") (description "Py is a Python library for file name parsing, .ini file parsing, I/O, @@ -2233,6 +2181,42 @@ easier to build concurrent applications.") (define-public python2-pykka (package-with-python2 python-pykka)) +(define-public python-pympler + (package + (name "python-pympler") + (home-page "https://pythonhosted.org/Pympler/") + (version "0.5") + (source (origin + (method url-fetch) + (uri (pypi-uri "Pympler" version)) + (sha256 + (base32 + "03qwsbilqgvnbl3a1jmpgixbr2kq6m3fvdlzyr3wdp01bwlc85kx")))) + (build-system python-build-system) + (arguments + `(#:phases (modify-phases %standard-phases + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "python" "setup.py" "test")))))) + (synopsis "Measure, monitor and analyze memory behavior") + (description + "Pympler is a development tool to measure, monitor and analyze +the memory behavior of Python objects in a running Python application. + +By pympling a Python application, detailed insight in the size and the +lifetime of Python objects can be obtained. Undesirable or unexpected +runtime behavior like memory bloat and other @samp{pymples} can easily +be identified. + +A web profiling frontend exposes process statistics, garbage +visualisation and class tracker statistics.") + (license license:asl2.0))) + +(define-public python2-pympler + (package-with-python2 python-pympler)) + (define-public python-itsdangerous (package (name "python-itsdangerous") @@ -2321,7 +2305,7 @@ object.") (define-public python-markupsafe (package (name "python-markupsafe") - (version "0.23") + (version "1.0") (source (origin (method url-fetch) @@ -2330,7 +2314,7 @@ object.") version ".tar.gz")) (sha256 (base32 - "1hvip33wva3fnmvfp9x5klqri7hpl1hkgqmjbss18nmrb7zimv54")))) + "0rdn1s8x9ni7ss8rfiacj7x1085lx8mh2zdwqslnw8xc3l4nkgm6")))) (build-system python-build-system) (home-page "https://github.com/mitsuhiko/markupsafe") (synopsis "XML/HTML/XHTML markup safe string implementation for Python") @@ -2345,14 +2329,14 @@ for Python.") (define-public python-jinja2 (package (name "python-jinja2") - (version "2.9.6") + (version "2.10") (source (origin (method url-fetch) (uri (pypi-uri "Jinja2" version)) (sha256 (base32 - "1zzrkywhziqffrzks14kzixz7nd4yh2vc0fb04a68vfd2ai03anx")))) + "190l36hfw3wb2n3n68yacjabxyb1pnxwn7vjx96cmjj002xy2jzq")))) (build-system python-build-system) (propagated-inputs `(("python-markupsafe" ,python-markupsafe))) @@ -2482,26 +2466,17 @@ reStructuredText.") (define-public python-sphinxcontrib-websupport (package (name "python-sphinxcontrib-websupport") - (version "1.0.1") + (version "1.1.0") (source (origin (method url-fetch) (uri (pypi-uri "sphinxcontrib-websupport" version)) (sha256 (base32 - "1f9f0wjpi9nhikbyaz6d19s7qvzdf1nq2g5dsh640fma4q9rd1bs")))) + "1ff3ix76xi1y6m99qxhaq5161ix9swwzydilvdya07mgbcvpzr4x")))) (build-system python-build-system) - (propagated-inputs - `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest) - ("python-xapian-bindings" ,python-xapian-bindings))) - ;; Needed for running the test suite - (native-inputs - `(("python-six" ,python-six) - ("python-jinja2" ,python-jinja2) - ("python-docutils" ,python-docutils) - ("python-sphinx" ,python-sphinx) - ("python-sqlalchemy" ,python-sqlalchemy) - ("python-whoosh" ,python-whoosh))) + (arguments + ;; FIXME: Tests depend on Sphinx, which depends on this. + `(#:tests? #f)) (home-page "http://sphinx-doc.org/") (synopsis "Sphinx API for web applications") (description "This package provides a Python API to easily integrate @@ -2509,17 +2484,20 @@ Sphinx documentation into your web application. It provides tools to integrate Sphinx documents in web templates and to handle searches.") (license license:bsd-3))) +(define-public python2-sphinxcontrib-websupport + (package-with-python2 python-sphinxcontrib-websupport)) + (define-public python-sphinx (package (name "python-sphinx") - (version "1.5.1") + (version "1.7.7") (source (origin (method url-fetch) (uri (pypi-uri "Sphinx" version)) (sha256 (base32 - "1i8p9idnli4gr0y4x67yakbdk5w6a0xjzhrg6bg51y9d1fi7fslf")))) + "0pkkbfj7cl157q550gcs45am5y78ps0h7q6455d64s1zmw01jlvi")))) (build-system python-build-system) (arguments `(#:phases @@ -2528,7 +2506,15 @@ integrate Sphinx documents in web templates and to handle searches.") (lambda _ ;; Requires Internet access. (delete-file "tests/test_build_linkcheck.py") - (zero? (system* "make" "test"))))))) + (substitute* "tests/test_build_latex.py" + (("@pytest.mark.sphinx\\('latex', testroot='images'\\)") + "@pytest.mark.skip()")) + (when (which "python") + ;; XXX: These tests are broken when using Python2: + ;; <https://github.com/sphinx-doc/sphinx/issues/4710>. + (delete-file "tests/test_api_translator.py") + (delete-file "tests/test_setup_command.py")) + (invoke "make" "test")))))) (propagated-inputs `(("python-imagesize" ,python-imagesize) ("python-sphinx-alabaster-theme" @@ -2537,14 +2523,18 @@ integrate Sphinx documents in web templates and to handle searches.") ("python-snowballstemmer" ,python-snowballstemmer) ("python-docutils" ,python-docutils) ("python-jinja2" ,python-jinja2) + ("python-packaging" ,python-packaging) ("python-pygments" ,python-pygments) ("python-requests" ,python-requests) - ("python-six" ,python-six))) + ("python-six" ,python-six) + ("python-sphinxcontrib-websupport" ,python-sphinxcontrib-websupport))) (native-inputs `(("graphviz" ,graphviz) + ("imagemagick" ,imagemagick) ;for "convert" ("python-html5lib" ,python-html5lib) ("python-mock" ,python-mock) - ("python-nose" ,python-nose))) + ("python-nose" ,python-nose) + ("python-pytest" ,python-pytest))) (home-page "http://sphinx-doc.org/") (synopsis "Python documentation generator") (description "Sphinx is a tool that makes it easy to create documentation @@ -2553,62 +2543,6 @@ sources.") (license license:bsd-3) (properties `((python2-variant . ,(delay python2-sphinx)))))) -(define-public python-sphinx-1.6 - (package (inherit python-sphinx) - (name "python-sphinx") - (version "1.6.4") - (source (origin - (method url-fetch) - (uri (pypi-uri "Sphinx" version)) - (sha256 - (base32 - "0gjakw9fv5pwqb5yyclxycs36sapxizk1vx6mkcdizmzgzcfy0gi")))) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ - ;; Requires Internet access. - (delete-file "tests/test_build_linkcheck.py") - (substitute* "tests/test_build_latex.py" - (("@pytest.mark.sphinx\\('latex', testroot='images'\\)") - "@pytest.mark.skip()")) - (zero? (system* "make" "test"))))))) - (propagated-inputs - `(("python-sphinxcontrib-websupport" ,python-sphinxcontrib-websupport) - ,@(package-propagated-inputs python-sphinx))) - (native-inputs - `(("python-pytest" ,python-pytest) - ("imagemagick" ,imagemagick) ; for "convert" - ,@(package-native-inputs python-sphinx))) - (properties `((python2-variant . ,(delay python2-sphinx-1.6)))))) - -(define-public python2-sphinx-1.6 - (let ((base (package-with-python2 (strip-python2-variant python-sphinx-1.6)))) - (package - (inherit base) - (propagated-inputs - `(("python2-typing" ,python2-typing) - ,@(package-propagated-inputs base))) - (native-inputs `(("python2-enum34" ,python2-enum34) - ,@(package-native-inputs base)))))) - -(define-public python-sphinx-1.5.3 - (package - (inherit python-sphinx) - (name "python-sphinx") - (version "1.5.3") - (source - (origin - (method url-fetch) - (uri (pypi-uri "Sphinx" version)) - (sha256 - (base32 - "0kw1axswbvaavr8ggyf4qr6hnisnrzlbkkcdada69vk1x9xjassg")))) - (native-inputs - `(("python-pytest" ,python-pytest) - ,@(package-native-inputs python-sphinx))))) - (define-public python2-sphinx (let ((base (package-with-python2 (strip-python2-variant python-sphinx)))) (package @@ -2617,6 +2551,7 @@ sources.") ("python2-enum34" ,python2-enum34) ,@(package-native-inputs base))) (propagated-inputs `(("python2-pytz" ,python2-pytz) + ("python2-typing" ,python2-typing) ,@(package-propagated-inputs base)))))) (define-public python-sphinx-gallery @@ -2960,7 +2895,11 @@ and is very extensible.") '()) (replace 'check - (lambda _ (invoke "python" "runtests.py" "-vv")))))) + (lambda _ + ;; The "with_outer_raising" test fails with Python 3.7. See + ;; https://github.com/cython/cython/issues/2454 + (delete-file "tests/run/generators_py.py") + (invoke "python" "runtests.py" "-vv")))))) (home-page "http://cython.org/") (synopsis "C extensions for Python") (description "Cython is an optimising static compiler for both the Python @@ -3004,7 +2943,7 @@ between language specification and implementation aspects.") (define-public python-numpy (package (name "python-numpy") - (version "1.14.6") + (version "1.15.4") (source (origin (method url-fetch) @@ -3013,14 +2952,14 @@ between language specification and implementation aspects.") version "/numpy-" version ".tar.gz")) (sha256 (base32 - "1k426vnmmd4pds09zgn75g6w92823ry75zrzwjhzjvg7s63ipc31")))) + "102vcl2qq4pjbm7a3d67vkkvn4466ngia1d8wi5avqwqh8j0jvkn")))) (build-system python-build-system) (inputs `(("openblas" ,openblas) ("lapack" ,lapack))) (native-inputs `(("python-cython" ,python-cython) - ("python-nose" ,python-nose) + ("python-pytest" ,python-pytest) ("gfortran" ,gfortran))) (arguments `(#:phases @@ -3065,9 +3004,12 @@ include_dirs = ~a/include (lambda* (#:key outputs inputs #:allow-other-keys) ;; 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"))) (with-directory-excursion "/tmp" - (zero? (system* "python" "-c" - "import numpy; numpy.test(verbose=2)")))))))) + (invoke "python" "-c" + "import numpy; numpy.test(verbose=2)"))))))) (home-page "http://www.numpy.org/") (synopsis "Fundamental package for scientific computing with Python") (description "NumPy is the fundamental package for scientific computing @@ -3432,25 +3374,14 @@ that client code uses to construct the grammar directly in Python code.") (define-public python-numpydoc (package (name "python-numpydoc") - (version "0.5") + (version "0.8.0") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/n/numpydoc/numpydoc-" - version ".tar.gz")) + (uri (pypi-uri "numpydoc" version)) (sha256 (base32 - "0d4dnifaxkll50jx6czj05y8cb4ny60njd2wz299sj2jxfy51w4k")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Drop a test requiring matplotlib, which we cannot add as an - ;; input since it would create a circular dependency: Extend the - ;; test for Python 3, where it is already dropped, to Python 2. - (substitute* "numpydoc/tests/test_plot_directive.py" - (("3") "2")) - #t)))) + "1zazxg3m8j4fksv3f7v7vpf4bj9qb1vj3r326am0vdip141vzx31")))) (build-system python-build-system) (propagated-inputs `(("python-sphinx" ,python-sphinx))) @@ -3670,7 +3601,7 @@ toolkits.") (native-inputs `(("python-matplotlib" ,python-matplotlib) ("python-colorspacious" ,python-colorspacious) - ("python-sphinx" ,python-sphinx-1.6) + ("python-sphinx" ,python-sphinx) ("python-sphinx-gallery" ,python-sphinx-gallery) ("python-numpydoc" ,python-numpydoc) ("python-ipython" ,python-ipython) @@ -3819,14 +3750,14 @@ functions.") (define-public python-scipy (package (name "python-scipy") - (version "1.0.1") + (version "1.1.0") (source (origin (method url-fetch) (uri (pypi-uri "scipy" version)) (sha256 (base32 - "1fj0r7bg0cfk5clvl57ga06y9bfh05iwlv1dqqs1r6pd89wccfc7")))) + "1lfg686w6vv2m2dfs8v9d0bf2i18z7wz5vgzjnkgmpr4hi0550w7")))) (build-system python-build-system) (propagated-inputs `(("python-numpy" ,python-numpy) @@ -3957,14 +3888,14 @@ as the original project seems to have been abandoned circa 2007.") (define-public python-pycodestyle (package (name "python-pycodestyle") - (version "2.3.1") + (version "2.4.0") (source (origin (method url-fetch) (uri (pypi-uri "pycodestyle" version)) (sha256 (base32 - "0rk78b66p57ala26mdldl9lafr48blv5s659sah9q50qnfjmc8k8")))) + "0fhy4vnlgpjq4qd1wdnl6pvdw7rah0ypmn8c9mkhz8clsndskz6b")))) (build-system python-build-system) (home-page "https://pycodestyle.readthedocs.io/") (synopsis "Python style guide checker") @@ -4117,7 +4048,7 @@ services for your Python modules and applications.") (define-public python-olefile (package (name "python-olefile") - (version "0.44") + (version "0.45.1") (source (origin (method url-fetch) @@ -4126,7 +4057,7 @@ services for your Python modules and applications.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1wmxbrhyqjry2000zx0zdhqdqxhgi06nz7sbzjlh222q2zjv1gpj")))) + "18ai19zwagm6nli14k8bii31ipbab2rp7plrvsm6gmfql551a8ai")))) (build-system python-build-system) (home-page "https://www.decalage.info/python/olefileio") @@ -4143,19 +4074,17 @@ the OleFileIO module from PIL, the Python Image Library.") (define-public python-pillow (package (name "python-pillow") - (version "4.3.0") + (version "5.2.0") (source (origin (method url-fetch) (uri (pypi-uri "Pillow" version)) (sha256 (base32 - "09xmn7rl6840sli2iz1k3fgxfgmri2nqz6vkinmb9mgg8ifp2z59")) - (patch-flags '("-p1" "--binary")) - (patches (search-patches "python-pillow-fix-failing-tests.patch")))) + "1ary9mj2ddllq3lkxgn6aac7qxqiwbcg2pacrl94py58ql9x9czq")))) (build-system python-build-system) (native-inputs - `(("python-nose" ,python-nose))) + `(("python-pytest" ,python-pytest))) (inputs `(("freetype" ,freetype) ("lcms" ,lcms) @@ -4176,9 +4105,8 @@ the OleFileIO module from PIL, the Python Image Library.") ;; Make installed package available for running the ;; tests (add-installed-pythonpath inputs outputs) - (and (zero? (system* "python" "selftest.py" - "--installed")) - (zero? (system* "python" "test-installed.py")))))) + (invoke "python" "selftest.py" "--installed") + (invoke "python" "-m" "pytest" "-vv")))) (delete 'check)))) (home-page "https://pypi.python.org/pypi/Pillow") (synopsis "Fork of the Python Imaging Library") @@ -4199,14 +4127,14 @@ a general image processing tool.") (define-public python-pycparser (package (name "python-pycparser") - (version "2.17") + (version "2.18") (source (origin (method url-fetch) (uri (pypi-uri "pycparser" version)) (sha256 (base32 - "1dkkjri0miidqb1zcqhqljfa34fcy9k5akasgwsv6k622zlk3b0a")))) + "09mjyw82ibqzl449g7swy8bfxnfpmas0815d2rkdjlcqw81wma4r")))) (outputs '("out" "doc")) (build-system python-build-system) (native-inputs @@ -4243,14 +4171,14 @@ a front-end for C compilers or analysis tools.") (define-public python-xcffib (package (name "python-xcffib") - (version "0.5.1") + (version "0.6.0") (source (origin (method url-fetch) (uri (pypi-uri "xcffib" version)) (sha256 (base32 - "09gbnmr5vn58mm8xi3fmd7fz6743cks6c46dphnxzwax6zsxmy60")))) + "04k91yxyb3pgc5lvxmivh8w71yjrap2g57yk3s73x4rm4nvjq51n")))) (build-system python-build-system) (inputs `(("libxcb" ,libxcb))) @@ -4289,17 +4217,14 @@ support for Python 3 and PyPy. It is based on cffi.") (define-public python-cairocffi (package (name "python-cairocffi") - (version "0.8.0") + (version "0.9.0") (source (origin (method url-fetch) - ;; The archive on pypi is missing the 'utils' directory! - (uri (string-append "https://github.com/Kozea/cairocffi/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (pypi-uri "cairocffi" version)) (sha256 (base32 - "1rk2dvy3fxrga6bvvxc2fi5lbaynm5h4a0w0aaxyn3bc77rszjg9")) + "0dq3k4zhqd8cwsf3nyjqvjqm8wkvrjn1wjf44rl3v0h8kqx6qf0m")) (patches (search-patches "python-cairocffi-dlopen-path.patch")))) (build-system python-build-system) (outputs '("out" "doc")) @@ -4312,14 +4237,14 @@ support for Python 3 and PyPy. It is based on cffi.") (native-inputs `(("pkg-config" ,pkg-config) ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-runner" ,python-pytest-runner) ("python-sphinx" ,python-sphinx) ("python-docutils" ,python-docutils))) (propagated-inputs `(("python-xcffib" ,python-xcffib))) ; used at run time (arguments - `(;; FIXME: Tests cannot find 'libcairo.so.2'. - #:tests? #t - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'unpack 'patch-paths (lambda* (#:key inputs outputs #:allow-other-keys) @@ -4535,13 +4460,13 @@ displayed.") (define-public python-pexpect (package (name "python-pexpect") - (version "4.2.1") + (version "4.6.0") (source (origin (method url-fetch) (uri (pypi-uri "pexpect" version)) (sha256 - (base32 "14ls7k99pwvl21zqv65kzrhccv50j89m5ij1hf0slmsvlxjj84rx")))) + (base32 "1fla85g47iaxxpjhp9vkxdnv4pgc7rplfy6ja491smrrk0jqi3ia")))) (build-system python-build-system) (arguments `(#:phases @@ -4584,13 +4509,13 @@ child application and control it as if a human were typing commands.") (define-public python-setuptools-scm (package (name "python-setuptools-scm") - (version "1.15.6") + (version "3.1.0") (source (origin (method url-fetch) (uri (pypi-uri "setuptools_scm" version)) (sha256 (base32 - "0pzvfmx8s20yrgkgwfbxaspz2x1g38qv61jpm0ns91lrb22ldas9")))) + "0h4bglwfz8b9prqljv8z3w9rgydfyxzaj05bm1y6zs5m6shz548i")))) (build-system python-build-system) (home-page "https://github.com/pypa/setuptools_scm/") (synopsis "Manage Python package versions in SCM metadata") @@ -4713,25 +4638,25 @@ away.") (define-public python-traitlets (package (name "python-traitlets") - (version "4.2.0") + (version "4.3.2") (source (origin (method url-fetch) (uri (pypi-uri "traitlets" version)) (sha256 (base32 - "1afy08sa5n9gnkvh3da49c16zkyv598vchv0p1hp7zzjy8895hz4")))) + "0dbq7sx26xqz5ixs711k5nc88p8a0nqyz6162pwks5dpcz9d4jww")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (replace 'check (lambda _ (zero? (system* "nosetests"))))))) + (replace 'check (lambda _ (invoke "pytest" "-vv" "traitlets")))))) (propagated-inputs `(("python-ipython-genutils" ,python-ipython-genutils) - ("python-decorator" ,python-decorator))) + ("python-decorator" ,python-decorator))) ;not needed for >4.3.2 (native-inputs - `(("python-mock" ,python-mock) - ("python-nose" ,python-nose))) + `(("python-pytest" ,python-pytest))) + (properties `((python2-variant . ,(delay python2-traitlets)))) (home-page "https://ipython.org") (synopsis "Configuration system for Python applications") (description @@ -4744,7 +4669,12 @@ without using the configuration machinery.") (license license:bsd-3))) (define-public python2-traitlets - (package-with-python2 python-traitlets)) + (let ((traitlets (package-with-python2 (strip-python2-variant python-traitlets)))) + (package + (inherit traitlets) + (propagated-inputs + `(("python2-enum34" ,python2-enum34) + ,@(package-propagated-inputs traitlets)))))) (define-public python-jupyter-core (package @@ -5094,15 +5024,15 @@ parsing (browser/HTTP) user agent strings.") (define-public python-dbus (package (name "python-dbus") - (version "1.2.0") + (version "1.2.8") (source (origin (method url-fetch) - (uri (string-append - "https://dbus.freedesktop.org/releases/dbus-python/dbus-python-" - version ".tar.gz")) + (uri (string-append "https://dbus.freedesktop.org/releases/dbus-python/" + "dbus-python-" version ".tar.gz")) (sha256 - (base32 "1py62qir966lvdkngg0v8k1khsqxwk5m4s8nflpk1agk5f5nqb71")))) + (base32 + "0vvvjmiwnc9cjlks3gcdk43ap7llhlpz7cm1wbw0nc2yfsxjpwdb")))) (build-system gnu-build-system) (arguments '(#:phases @@ -5118,7 +5048,7 @@ parsing (browser/HTTP) user agent strings.") (native-inputs `(("pkg-config" ,pkg-config))) (inputs - `(("python" ,python) + `(("python" ,python-wrapper) ("dbus-glib" ,dbus-glib))) (synopsis "Python bindings for D-bus") (description "python-dbus provides bindings for libdbus, the reference @@ -5140,14 +5070,14 @@ implementation of D-Bus.") (define-public python-lxml (package (name "python-lxml") - (version "3.8.0") + (version "4.2.4") (source (origin (method url-fetch) (uri (pypi-uri "lxml" version)) (sha256 (base32 - "15nvf6n285n282682qyw3wihsncb0x5amdhyi4b83bfa2nz74vvk")))) + "1jk336k0kw616gfhqk1wwxsjjwz0flld0n294lz8kxch610bxbz2")))) (build-system python-build-system) (inputs `(("libxml2" ,libxml2) @@ -5168,14 +5098,14 @@ libxml2 and libxslt.") (define-public python-beautifulsoup4 (package (name "python-beautifulsoup4") - (version "4.5.3") + (version "4.6.3") (source (origin (method url-fetch) (uri (pypi-uri "beautifulsoup4" version)) (sha256 (base32 - "0glaw1vyxnbp03fni7h5496n6iib0n5iim4gax1n0ngscs9s075j")))) + "041dhalzjciw6qyzzq7a2k4h1yvyk76xigp35hv5ibnn448ydy4h")))) (build-system python-build-system) (arguments `(#:phases @@ -5256,25 +5186,6 @@ of the structure, dynamics, and functions of complex networks.") (define-public python2-networkx (package-with-python2 python-networkx)) -;; Define new package, because the current version of python-colormath does -;; not build against 2.0. -(define-public python-networkx2 - (package (inherit python-networkx) - (name "python-networkx2") - (version "2.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "networkx" version ".zip")) - (sha256 - (base32 - "1ajl2jp8qry9nyjzzkqpy0vmsr14d23z1qk7y0vr5iwjbpvzhpyd")) - (patches - (search-patches "python-networkx2-reproducible-build.patch")))))) - -(define-public python2-networkx2 - (package-with-python2 python-networkx2)) - (define-public python-datrie (package (name "python-datrie") @@ -5287,6 +5198,14 @@ of the structure, dynamics, and functions of complex networks.") (base32 "08r0if7dry2q7p34gf7ffyrlnf4bdvnprxgydlfxgfnvq8f3f4bs")))) (build-system python-build-system) + (arguments + `(#:phases (modify-phases %standard-phases + (add-before 'build 'cythonize + (lambda _ + ;; Regenerate Cython classes to solve ABI issues with Python + ;; 3.7.0. See <https://github.com/pytries/datrie/issues/52>. + (invoke "cython" "src/datrie.pyx" "src/cdatrie.pxd" + "src/stdio_ext.pxd" "-a")))))) (native-inputs `(("python-cython" ,python-cython) ("python-hypothesis" ,python-hypothesis) @@ -5673,14 +5592,14 @@ so it might be a tiny bit slower.") (define-public python-waf (package (name "python-waf") - (version "1.9.8") + (version "2.0.11") (source (origin (method url-fetch) (uri (string-append "https://waf.io/" "waf-" version ".tar.bz2")) (sha256 (base32 - "0wl4cnmp06lfxqjxaan58bqxn27smhydz0sg5prrfbl3bsw4gv6q")))) + "13zrniwkmfqgsgzi9v5m1367fppp9yzrz6z2ny6hy8dmpb8mj4z4")))) (build-system python-build-system) (arguments '(#:phases @@ -5711,13 +5630,13 @@ applications.") (define-public python-pyzmq (package (name "python-pyzmq") - (version "15.1.0") + (version "17.1.2") (source (origin (method url-fetch) (uri (pypi-uri "pyzmq" version)) (sha256 - (base32 "13fhwnlvsvxv72kfhqbpn6qi7msh8mc8377mpabv32skk2cjfnxx")))) + (base32 "1pyxxrz60f88ffm0y6vpbx3q8jcr9ybz8fcilihwzwhh36n84ax7")))) (build-system python-build-system) (arguments `(#:configure-flags @@ -5767,14 +5686,14 @@ PEP 8.") (define-public python-pyflakes (package (name "python-pyflakes") - (version "1.5.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (pypi-uri "pyflakes" version)) (sha256 (base32 - "1x1pcca4a24k4pw8x1c77sgi58cg1wl2k38mp8a25k608pzls3da")))) + "0jba28czyvimdc72llms3f17swp3i8jdcabf5w0j00adfbn64xls")))) (build-system python-build-system) (home-page "https://github.com/pyflakes/pyflakes") @@ -5869,52 +5788,93 @@ complexity of Python source code.") (define-public python2-pyflakes-0.8.1 (package-with-python2 python-pyflakes-0.8.1)) -(define-public python-flake8 +;; This package is used by hypothesis which has thousands of dependent packages. +;; FIXME: Consolidate this with "python-flake8" below in the next rebuild cycle. +(define-public python-flake8-3.5 (package (name "python-flake8") - (version "3.4.1") + (version "3.5.0") (source (origin (method url-fetch) (uri (pypi-uri "flake8" version)) (sha256 (base32 - "1n0i38592vy3q0x2a9bf8z6rhhn04i30wsn5i5zzcj7qkxvl8062")))) + "184b33grvvjmiwlv9kyd7yng9qv5ld24154j70z332xxg9gjclvj")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases + ;; Two errors don't seem to have assigned codes. + (add-after 'unpack 'delete-broken-test + (lambda _ (delete-file "tests/unit/test_pyflakes_codes.py") #t)) + (add-after 'unpack 'fix-problem-with-pycodestyle + (lambda _ + ;; See https://gitlab.com/pycqa/flake8/merge_requests/230 + ;; This should no longer be needed with the next release. + (substitute* "setup.py" + (("PEP8_PLUGIN\\('break_around_binary_operator'\\),") + "PEP8_PLUGIN('break_after_binary_operator'),\ +PEP8_PLUGIN('break_before_binary_operator'),")) + #t)) (delete 'check) (add-after 'install 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (zero? (system* "pytest" "-v"))))))) + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "-v") + #t))))) (propagated-inputs - `(("python-pycodestyle" ,python-pycodestyle) - ("python-pyflakes" ,python-pyflakes) - ;; flake8 depends on a newer setuptools than provided by python. - ("python-setuptools" ,python-setuptools) - ("python-mccabe" ,python-mccabe))) + `(("python-pycodestyle" ,python-pycodestyle) + ("python-pyflakes" ,python-pyflakes) + ("python-mccabe" ,python-mccabe))) (native-inputs - `(("python-mock" ,python-mock) ; TODO: only required for < 3.3 - ("python-pytest" ,python-pytest-bootstrap) - ("python-pytest-runner" ,python-pytest-runner))) + `(("python-mock" ,python-mock) + ("python-pytest" ,python-pytest-bootstrap) + ("python-pytest-runner" ,python-pytest-runner))) (home-page "https://gitlab.com/pycqa/flake8") (synopsis "The modular source code checker: pep8, pyflakes and co") (description "Flake8 is a wrapper around PyFlakes, pep8 and python-mccabe.") - (properties `((python2-variant . ,(delay python2-flake8)))) + (properties `((python2-variant . ,(delay python2-flake8-3.5)))) (license license:expat))) -(define-public python2-flake8 - (let ((base (package-with-python2 (strip-python2-variant python-flake8)))) +(define-public python2-flake8-3.5 + (let ((base (package-with-python2 (strip-python2-variant python-flake8-3.5)))) (package (inherit base) (propagated-inputs `(("python2-configparser" ,python2-configparser) ("python2-enum34" ,python2-enum34) ,@(package-propagated-inputs base)))))) +;; Version 3.5.0 has compatibility issues with Pyflakes 2.0, so we need +;; this newer version. Keep it as a separate variable for now to avoid +;; rebuilding "python-hypothesis"; this should be removed in the next +;; rebuild cycle. +(define-public python-flake8 + (package + (inherit python-flake8-3.5) + (version "3.6.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "flake8" version)) + (sha256 + (base32 + "0w0nprx22rbvrrkbfx9v5jc5gskbm08g219l7r8wai8zfswgadba")))) + (arguments + (substitute-keyword-arguments (package-arguments python-flake8-3.5) + ((#:phases phases) + `(modify-phases ,phases + (delete 'delete-broken-test) + (delete 'fix-problem-with-pycodestyle))))) + (properties `((python2-variant . ,(delay python2-flake8)))))) + +(define-public python2-flake8 + (let ((base (package-with-python2 (strip-python2-variant python-flake8)))) + (package (inherit base) + (propagated-inputs + (package-propagated-inputs python2-flake8-3.5))))) + ;; python-hacking requires flake8 <2.6.0. (define-public python-flake8-2.5 (package @@ -6143,28 +6103,18 @@ add functionality and customization to your projects with their own plugins.") (define-public python-fonttools (package (name "python-fonttools") - (version "3.15.1") + (version "3.28.0") (source (origin (method url-fetch) (uri (pypi-uri "fonttools" version ".zip")) (sha256 (base32 - "1hhj97izwliy0vybmza72d90l5d4mcn50y8akq7kyccfl82vdx4d")))) + "0vsvjhidpb5kywpjgz1j3fywzkddxkb0afqai18qa3h6lqjyxwpb")))) (build-system python-build-system) - (arguments - '(#:test-target "check" - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-setuppy - ;; Remove the undocumented "extra_path" argument, which adds an - ;; intervening directories between site-packages and the package - ;; directory. - (lambda _ - (substitute* "setup.py" - (("^[ \t]*extra_path *= *'FontTools',") "")) - #t))))) (native-inputs - `(("unzip" ,unzip))) + `(("unzip" ,unzip) + ("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner))) (home-page "https://github.com/behdad/fonttools") (synopsis "Tools to manipulate font files") (description @@ -6173,9 +6123,7 @@ supports reading and writing of TrueType/OpenType fonts, reading and writing of AFM files, reading (and partially writing) of PS Type 1 fonts. The package also contains a tool called “TTX” which converts TrueType/OpenType fonts to and from an XML-based format.") - (license (license:non-copyleft - "file://LICENSE.txt" - "See LICENSE.txt in the distribution.")))) + (license license:expat))) (define-public python2-fonttools (package-with-python2 python-fonttools)) @@ -6228,13 +6176,13 @@ should be stored on various operating systems.") (define-public python-llfuse (package (name "python-llfuse") - (version "1.3.3") + (version "1.3.5") (source (origin (method url-fetch) (uri (pypi-uri "llfuse" version ".tar.bz2")) (sha256 (base32 - "1rqww632y2zz71xmr6ch7yq80kvza9mhqr2z773k0d8l1lwzl575")))) + "1n7a90jww3ly49fm7x27m3xw3la3qfrnykcakga654g6kcyjlhbf")))) (build-system python-build-system) (inputs `(("fuse" ,fuse) @@ -6547,13 +6495,13 @@ implementations of ASN.1-based codecs and protocols.") (define-public python-ipaddress (package (name "python-ipaddress") - (version "1.0.19") + (version "1.0.22") (source (origin (method url-fetch) (uri (pypi-uri "ipaddress" version)) (sha256 (base32 - "10agaa1cys1bk1ycpl2w8lky9vjx8h1xh1z29mg0niqx0638c390")))) + "0b570bm6xqpjwqis15pvdy6lyvvzfndjvkynilcddjj5x98wfimi")))) (build-system python-build-system) (home-page "https://github.com/phihag/ipaddress") (synopsis "IP address manipulation library") @@ -6599,14 +6547,14 @@ versions of Python.") (define-public python-idna (package (name "python-idna") - (version "2.6") + (version "2.7") (source (origin (method url-fetch) (uri (pypi-uri "idna" version)) (sha256 (base32 - "13qaab6d0s15gknz8v3zbcfmbj6v86hn9pjxgkdf62ch13imssic")))) + "05jam7d31767dr12x0rbvvs8lxnpb1mhdb2zdlfxgh83z6k3hjk8")))) (build-system python-build-system) (home-page "https://github.com/kjd/idna") (synopsis "Internationalized domain names in applications") @@ -7407,25 +7355,26 @@ be set via config files and/or environment variables.") @code{ArgumentParser} object.") (license license:asl2.0))) -(define-public python-contextlib2 +(define-public python2-contextlib2 (package - (name "python-contextlib2") - (version "0.4.0") + (name "python2-contextlib2") + (version "0.5.5") (source (origin (method url-fetch) (uri (pypi-uri "contextlib2" version)) (sha256 (base32 - "0cmp131dlh0d0zvw0aza1zd13glvngzk8lb4avks0hm7yxwdr9am")))) + "0j6ad6lwwyc9kv71skj098v5l7x5biyj2hs4lc5x1kcixqcr97sh")))) (build-system python-build-system) (arguments - `(#:phases + `(#:python ,python-2 + #:phases (modify-phases %standard-phases (replace 'check - (lambda _ (zero? - (system* - "python" "test_contextlib2.py" "-v"))))))) + (lambda _ (invoke "python" "test_contextlib2.py" "-v")))))) + (native-inputs + `(("python2-unittest2" ,python2-unittest2))) (home-page "http://contextlib2.readthedocs.org/") (synopsis "Tools for decorators and context managers") (description "This module is primarily a backport of the Python @@ -7435,9 +7384,6 @@ managers. It also contains additional features that are not part of the standard library.") (license license:psfl))) -(define-public python2-contextlib2 - (package-with-python2 python-contextlib2)) - (define-public python-texttable (package (name "python-texttable") @@ -7581,13 +7527,13 @@ minimal and fast API targeting the following uses: (define-public python-icalendar (package (name "python-icalendar") - (version "4.0.2") + (version "4.0.3") (source (origin (method url-fetch) (uri (pypi-uri "icalendar" version)) (sha256 (base32 - "13003kw2vbas1ha146vv3x2rdg9k7w38rdzxj63vi1i67jgjldl0")))) + "0mk3dk1dxkcm46jy48v27j2w2349iv4sbimqj1yb5js43mx49hh7")))) (build-system python-build-system) (propagated-inputs `(("python-dateutil" ,python-dateutil) @@ -7815,16 +7761,20 @@ otherwise matches 3.2’s API.") (define-public python2-futures (package (name "python2-futures") - (version "3.0.5") + (version "3.2.0") (source (origin (method url-fetch) (uri (pypi-uri "futures" version)) (sha256 (base32 - "1pw1z4329xvlabdpwqa6b7v2fxf7hl64m4cgr22ckbym8m8m4hh5")))) + "0rdjmmsab550kxsssdq49jcniz77zlkpw4pvi9hvib3lsskjmh4y")))) (build-system python-build-system) - (arguments `(#:python ,python-2)) + (arguments `(#:python ,python-2 + ;; FIXME: Python 2.7.14 moved the test.support library, + ;; but our package has not yet been adjusted. Enable + ;; tests when the python2 package has been fixed. + #:tests? #f)) (home-page "https://github.com/agronholm/pythonfutures") (synopsis "Backport of the concurrent.futures package from Python 3.2") @@ -7916,15 +7866,17 @@ library as well as on the command line.") (define-public python-pluggy (package (name "python-pluggy") - (version "0.6.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (pypi-uri "pluggy" version)) (sha256 (base32 - "1zqckndfn85l1cd8pndw212zg1bq9fkg1nnj32kp2mppppsyg2kz")))) + "1qbn70mksmr03hac6jgp6fiqc4l7859z8dchx2x950vhlij87swm")))) (build-system python-build-system) + (native-inputs + `(("python-setuptools-scm" ,python-setuptools-scm))) (synopsis "Plugin and hook calling mechanism for Python") (description "Pluggy is an extraction of the plugin manager as used by Pytest but stripped of Pytest specific details.") @@ -8632,6 +8584,15 @@ ambiguities (forward vs. backward slashes, etc.). @end enumerate") (license license:expat))) +(define-public python2-pathlib2-bootstrap + (hidden-package + (package + (inherit python2-pathlib2) + (name "python2-pathlib2-bootstrap") + (propagated-inputs + `(("python2-scandir" ,python2-scandir) + ("python2-six" ,python2-six-bootstrap)))))) + (define-public python-jellyfish (package (name "python-jellyfish") @@ -8880,23 +8841,10 @@ LDFLAGS and parse the output to build extensions with setup.py.") files. It contains a drop-in replacement for the I/O interface in the standard library's @code{bz2} module, including features from the latest development version of CPython that are not available in older releases.") - (license license:asl2.0) - (properties `((python2-variant . ,(delay python2-bz2file)))))) + (license license:asl2.0))) (define-public python2-bz2file - (let ((base (package-with-python2 - (strip-python2-variant python-bz2file)))) - (package - (inherit base) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - ;; 'python setup.py test' does not work as of 0.98. - ;; There is only the one test file, so we run it directly. - (replace 'check - (lambda _ (zero? (system* "python" - "test_bz2file.py")))))))))) + (package-with-python2 python-bz2file)) (define-public python-future (package @@ -9081,6 +9029,14 @@ own code, responding to click events and updating clock every second.") (arguments `(#:phases (modify-phases %standard-phases + (add-before 'check 'adjust-tests + (lambda _ + (when (which "python3") + ;; Adjust the example output to match that of Python 3.7: + ;; <https://github.com/ionelmc/python-tblib/issues/36>. + (substitute* "README.rst" + (("Exception\\('fail',") "Exception('fail'")) + #t))) (replace 'check (lambda _ ;; Upstream runs tests after installation and the package itself @@ -9113,13 +9069,13 @@ multiple processes (imagine multiprocessing, billiard, futures, celery etc). (define-public python-greenlet (package (name "python-greenlet") - (version "0.4.11") + (version "0.4.14") (source (origin (method url-fetch) (uri (pypi-uri "greenlet" version)) (sha256 (base32 - "1xhik26j4f3kc4qw9xmj0c567rb5h1zryb4ijwqnqwwjvfhbv59h")))) + "1bsij3bwdhz2chq4ar2v6jqbh69yc7k9ymh41jd8vrdd2n52dk7i")))) (build-system python-build-system) (home-page "https://greenlet.readthedocs.io/") (synopsis "Lightweight in-process concurrent programming") @@ -9133,16 +9089,40 @@ are synchronized with data exchanges on \"channels\".") (define-public python2-greenlet (package-with-python2 python-greenlet)) +(define-public python-objgraph + (package + (name "python-objgraph") + (version "3.4.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "objgraph" version)) + (sha256 + (base32 + "184m09am5gpbqfaiy7l0hwh476mczbrly1dffs0rw2p1d1i2q32a")))) + (build-system python-build-system) + (propagated-inputs + `(("python-graphviz" ,python-graphviz))) + (native-inputs + `(("python-mock" ,python-mock) + ("graphviz" ,graphviz))) + (home-page "https://mg.pov.lt/objgraph/") + (synopsis "Draw Python object reference graphs with graphviz") + (description + "This package provides tools to draw Python object reference graphs with +graphviz.") + (license license:expat))) + (define-public python-gevent (package (name "python-gevent") - (version "1.2.2") + (version "1.3.7") (source (origin (method url-fetch) (uri (pypi-uri "gevent" version)) (sha256 (base32 - "0bbbjvi423y9k9xagrcsimnayaqymg6f2dj76m9z3mjpkjpci4a7")) + "0b0fr04qdk1p4sniv87fh8z5psac60x01pv054kpgi94520g81iz")) (modules '((guix build utils))) (snippet '(begin @@ -9174,11 +9154,14 @@ are synchronized with data exchanges on \"channels\".") (find-files "src/greentest" "\\.py$")) #t)) (add-before 'build 'do-not-use-bundled-sources - (lambda _ + (lambda* (#:key inputs #:allow-other-keys) (setenv "CONFIG_SHELL" (which "bash")) (setenv "LIBEV_EMBED" "false") (setenv "CARES_EMBED" "false") (setenv "EMBED" "false") + (setenv "CPATH" + (string-append (assoc-ref inputs "python-greenlet") + "/include/python3.7m")) #t)) (replace 'check (lambda _ @@ -9199,7 +9182,8 @@ are synchronized with data exchanges on \"channels\".") (make-regexp "test_+(subprocess|core)") <>))))))))) (propagated-inputs - `(("python-greenlet" ,python-greenlet))) + `(("python-greenlet" ,python-greenlet) + ("python-objgraph" ,python-objgraph))) (native-inputs `(("libev-source" ,(package-source libev)) ("python-six" ,python-six))) @@ -9273,14 +9257,14 @@ focus on event-based network programming and multiprotocol integration.") (define-public python-pika (package (name "python-pika") - (version "0.10.0") + (version "0.12.0") (source (origin (method url-fetch) (uri (pypi-uri "pika" version)) (sha256 (base32 - "0nb4h08di432lv7dy2v9kpwgk0w92f24sqc2hw2s9vwr5b8v8xvj")))) + "0ld7akgm93s8pfa4dsx9qlzlhj76zspbr5m9ms0ns09yd2w4aq9h")))) (build-system python-build-system) (native-inputs `(("python-pyev" ,python-pyev) @@ -9847,32 +9831,25 @@ etc.") (define-public python-stem (package (name "python-stem") - (version "1.6.0") + (version "1.7.0") (source (origin (method url-fetch) (uri (pypi-uri "stem" version)) (sha256 (base32 - "1va9p3ij7lxg6ixfsvaql06dn11l3fgpxmss1dhlvafm7sqizznp")))) + "1awiglfiajnx2hva9aqpj3fmdvdb4qg7cwnlfyih827m68y3cq8v")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (add-before 'check 'fix-test-environment - (lambda _ - ;; Fixes: FileNotFoundError: [Errno 2] No such file or directory: - ;; '/tmp/guix-build-python-stem-1.6.0.drv-0/stem-1.6.0/.gitignore'. - (with-output-to-file ".gitignore" - (lambda _ (format #t "%"))) - #t)) (replace 'check (lambda _ (invoke "./run_tests.py" "--unit") #t))))) (native-inputs `(("python-mock" ,python-mock) - ("python-pep8" ,python-pep8) + ("python-pycodestyle" ,python-pycodestyle) ("python-pyflakes" ,python-pyflakes))) (home-page "https://stem.torproject.org/") (synopsis @@ -10629,21 +10606,17 @@ Record Format (DWARF).") (define-public python-imagesize (package (name "python-imagesize") - (version "0.7.1") + (version "1.0.0") (source (origin (method url-fetch) (uri (pypi-uri "imagesize" version)) (sha256 (base32 - "0qk07k0z4241lkzzjji7z4da04pcvg7bfc4xz1934zlqhwmwdcha")))) + "05b3p62r7rbcvvbk5vknr3bhcq9b2airysn6ric534mng136wcjv")))) (build-system python-build-system) - (arguments - '(;; Test files are not distributed on PyPi: - ;; https://github.com/shibukawa/imagesize_py/issues/7 - #:tests? #f)) (home-page "https://github.com/shibukawa/imagesize_py") - (synopsis "Gets image size of files in variaous formats in Python") + (synopsis "Gets image size of files in various formats in Python") (description "This package allows determination of image size from PNG, JPEG, JPEG2000 and GIF files in pure Python.") @@ -10733,23 +10706,53 @@ possible on all supported Python versions.") (propagated-inputs `(("python2-bz2file" ,python2-bz2file) ,@(package-propagated-inputs base)))))) -(define-public python2-cheetah +(define-public python-cheetah (package - (name "python2-cheetah") - (version "2.4.4") + (name "python-cheetah") + (version "3.1.0") (source (origin (method url-fetch) - (uri (pypi-uri "Cheetah" version)) + (uri (pypi-uri "Cheetah3" version)) (sha256 (base32 - "0l5mm4lnysjkzpjr95q5ydm9xc8bv43fxmr79ypybrf1y0lq4c5y")))) + "1ihag9cxll6b86fc8v5lkhmr3brdbi4yiz16zpgw79yylmv8fgr9")))) (build-system python-build-system) (arguments - `(#:python ,python-2)) - (propagated-inputs - `(("python2-markdown" ,python2-markdown))) - (home-page "https://pythonhosted.org/Cheetah/") + `(#:modules ((guix build utils) + (guix build python-build-system) + (ice-9 ftw) + (srfi srfi-1) + (srfi srfi-26)) + #:phases (modify-phases %standard-phases + (add-after 'unpack 'use-absolute-python + (lambda _ + (substitute* "Cheetah/CheetahWrapper.py" + (("#!/usr/bin/env python") + (string-append "#!" (which "python")))) + #t)) + (replace 'check + (lambda _ + (let ((cwd (getcwd))) + (setenv "PYTHONPATH" + (string-append + cwd "/build/" + (find (cut string-prefix? "lib" <>) + (scandir (string-append cwd "/build"))) + ":" (getenv "PYTHONPATH"))) + (setenv "PATH" + (string-append (getenv "PATH") + ":" cwd "/bin")) + (setenv "TMPDIR" "/tmp") + + (substitute* "Cheetah/Tests/Test.py" + (("unittest.TextTestRunner\\(\\)") + "unittest.TextTestRunner(verbosity=2)")) + + (invoke "python" "Cheetah/Tests/Test.py"))))))) + (propagated-inputs + `(("python-markdown" ,python-markdown))) ;optional + (home-page "http://cheetahtemplate.org/") (synopsis "Template engine") (description "Cheetah is a text-based template engine and Python code generator. @@ -10777,6 +10780,9 @@ Features: @end enumerate") (license (license:x11-style "file://LICENSE")))) +(define-public python2-cheetah + (package-with-python2 python-cheetah)) + (define-public python-dulwich (package (name "python-dulwich") @@ -11110,6 +11116,32 @@ projects.") (define-public python2-incremental (package-with-python2 python-incremental)) +(define-public python-invoke + (package + (name "python-invoke") + (home-page "http://www.pyinvoke.org/") + (version "1.1.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "invoke" version)) + (sha256 + (base32 + "0aiy1xvk1f91246zxd1zqrm679vdvd10h843a2na41cqr3cflpi6")))) + (build-system python-build-system) + (arguments + ;; XXX: Requires many dependencies that are not yet in Guix. + `(#:tests? #f)) + (synopsis "Pythonic task execution") + (description + "Invoke is a Python task execution tool and library, drawing inspiration +from various sources to arrive at a powerful and clean feature set. It is +evolved from the Fabric project, but focuses on local and abstract concerns +instead of servers and network commands.") + (license license:bsd-3))) + +(define-public python2-invoke + (package-with-python2 python-invoke)) + (define-public python-automat (package (name "python-automat") @@ -11193,17 +11225,36 @@ and bit flag values.") (define-public python-attrs (package (name "python-attrs") - (version "17.4.0") + (version "18.2.0") (source (origin (method url-fetch) (uri (pypi-uri "attrs" version)) (sha256 (base32 - "1jafnn1kzd6qhxgprhx6y6ik1r5m2rilx25syzcmq03azp660y8w")))) + "0s9ydh058wmmf5v391pym877x4ahxg45dw6a0w4c7s5wgpigdjqh")))) (build-system python-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build python-build-system) + (ice-9 ftw) + (srfi srfi-1) + (srfi srfi-26)) + #:phases (modify-phases %standard-phases + (replace 'check + (lambda _ + (let ((cwd (getcwd))) + (setenv "PYTHONPATH" + (string-append + cwd "/build/" + (find (cut string-prefix? "lib" <>) + (scandir (string-append cwd "/build"))) + ":" + (getenv "PYTHONPATH"))) + (invoke "python" "-m" "pytest"))))))) (native-inputs `(("python-coverage" ,python-coverage) ("python-hypothesis" ,python-hypothesis) + ("python-pympler" ,python-pympler) ("python-pytest" ,python-pytest) ("python-six" ,python-six) ("python-sphinx" ,python-sphinx) @@ -11222,6 +11273,15 @@ protocols.") (package (inherit python-attrs) (name "python-attrs-bootstrap") + ;; Keep this on a fixed version so python-attrs can be updated without + ;; triggering a mass-rebuild. FIXME: Update this in the next rebuild cycle. + (version "17.4.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "attrs" version)) + (sha256 + (base32 + "1jafnn1kzd6qhxgprhx6y6ik1r5m2rilx25syzcmq03azp660y8w")))) (native-inputs `()) (arguments `(#:tests? #f)))) @@ -11381,28 +11441,37 @@ clone, while other processes access the original tree.") (define-public python-astroid (package (name "python-astroid") - (version "1.5.3") + (version "2.0.4") (source (origin (method url-fetch) - (uri (string-append - "https://github.com/PyCQA/astroid/archive/astroid-" - version ".tar.gz")) + (uri (pypi-uri "astroid" version)) (sha256 (base32 - "0isn5p7f9n48hmksgbrj7dkm9dyglnayzn5jngk37qywg8a74ngn")))) + "138svbm88w5k0y2nvl4svyas1jfhcc5iy0d2ywkbcpn9kq8ks0f7")))) (build-system python-build-system) (propagated-inputs `(("python-lazy-object-proxy" ,python-lazy-object-proxy) ("python-six" ,python-six) ("python-wrapt" ,python-wrapt))) + (native-inputs + `(("python-dateutil" ,python-dateutil) + ("python-nose" ,python-nose) + ("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner))) (arguments `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'remove-spurious-test + (lambda _ + ;; This can be removed after upgrading from python-3.7 + ;; https://github.com/PyCQA/astroid/issues/593 + ;; https://bugs.python.org/issue34056 + (delete-file "astroid/tests/unittest_modutils.py") + #t)) (replace 'check - (lambda _ - (zero? (system* "python" "-m" "unittest" "discover" - "-p" "unittest*.py"))))))) + (lambda _ + (invoke "pytest" "astroid")))))) (home-page "https://github.com/PyCQA/astroid") (synopsis "Common base representation of python source code for pylint and other projects") @@ -11422,12 +11491,35 @@ builds partial trees by inspecting living objects.") (let ((base (package-with-python2 (strip-python2-variant python-astroid)))) (package (inherit base) - (propagated-inputs - `(("python2-backports-functools-lru-cache" - ,python2-backports-functools-lru-cache) - ("python2-enum34" ,python2-enum34) - ("python2-singledispatch" ,python2-singledispatch) - ,@(package-propagated-inputs base)))))) + ;; Version 2.x removes python2 support. + (version "1.6.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "astroid" version)) + (sha256 + (base32 + "0fir4b67sm7shcacah9n61pvq313m523jb4q80sycrh3p8nmi6zw")))) + (arguments + (substitute-keyword-arguments (package-arguments base) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'unpack 'remove-spurious-test + (lambda _ + ;; https://github.com/PyCQA/astroid/issues/276 + (delete-file "astroid/tests/unittest_brain.py") + #t)) + (replace 'check + (lambda _ + (invoke"python" "-m" "unittest" "discover" + "-p" "unittest*.py"))))))) + (native-inputs `()) + (propagated-inputs + `(("python2-backports-functools-lru-cache" + ,python2-backports-functools-lru-cache) + ("python2-enum34" ,python2-enum34) + ("python2-singledispatch" ,python2-singledispatch) + ,@(package-propagated-inputs base)))))) (define-public python-isort (package @@ -11724,13 +11816,13 @@ It supports both normal and Unicode strings.") (define-public python-scandir (package (name "python-scandir") - (version "1.7") + (version "1.9.0") (source (origin (method url-fetch) (uri (pypi-uri "scandir" version)) (sha256 - (base32 "0gbnhjzg42rj87ljv9kb648rfxph69ly3c8r9841dxy4d7l5pmdj")))) + (base32 "0r3hvf1a9jm1rkqgx40gxkmccknkaiqjavs8lccgq9s8khh5x5s4")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases @@ -11850,15 +11942,19 @@ several utilities, as well as an API for building localization tools.") (define-public python-packaging (package (name "python-packaging") - (version "16.8") + (version "17.1") (source (origin (method url-fetch) (uri (pypi-uri "packaging" version)) (sha256 (base32 - "17k1xbjshackwvbsnxqixbph8rbqhz4bf4g3al5xyzhavxgq6l2x")))) + "0nrpayk8kij1zm9sjnk38ldz3a6705ggvw8ljylqbrb4vmqbf6gh")))) (build-system python-build-system) + (arguments + `(#:phases (modify-phases %standard-phases + (replace 'check + (lambda _ (invoke "py.test" "-vv")))))) (native-inputs `(("python-pretend" ,python-pretend) ("python-pytest" ,python-pytest))) @@ -12899,26 +12995,40 @@ belong to tagged versions.") (define-public python-pyclipper (package (name "python-pyclipper") - (version "1.0.6") + (version "1.1.0.post1") (source (origin (method url-fetch) (uri (pypi-uri "pyclipper" version ".zip")) (sha256 (base32 - "1zpmwv3bya3j984y5cf9x9d5108kf6mxldcba68wiq0frv5qrssw")))) + "0ldbkbnx94an4zzrwb1sxmg6k0jgk4cwmvcdyy8y5k1zslc612wa")) + (modules '((guix build utils))) + (snippet + '(begin + ;; This file is generated by Cython. + (delete-file "pyclipper/pyclipper.cpp") #t)))) (build-system python-build-system) (arguments - `(#:tests? #f)); 8 Tests fail, 37 succeed + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'cythonize-sources + (lambda _ + (with-directory-excursion "pyclipper" + (invoke "cython" "--cplus" "pyclipper.pyx"))))))) (propagated-inputs `(("python-setuptools-scm-git-archive" ,python-setuptools-scm-git-archive))) (native-inputs - `(("unzip" ,unzip))) + `(("python-cython" ,python-cython) + ("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner) + ("python-unittest2" ,python-unittest2) + ("unzip" ,unzip))) (home-page "https://github.com/greginvm/pyclipper") (synopsis "Wrapper for Angus Johnson's Clipper library") (description "Pyclipper is a Cython wrapper for the C++ translation of the - Angus Johnson's polygon clipping Clipper library (ver. 6.2.1).") +Angus Johnson's polygon clipping Clipper library (ver. 6.4.2).") (license license:expat))) (define-public python2-pyclipper @@ -13261,14 +13371,14 @@ user's @file{~/Trash} directory.") (define-public python-yapf (package (name "python-yapf") - (version "0.21.0") + (version "0.24.0") (source (origin (method url-fetch) (uri (pypi-uri "yapf" version)) (sha256 (base32 - "144gc7d6b1415vh02409rnb8qd5kxi6mxlr7y64d5cizgxbf72kx")))) + "0anwby0ydmyzcsgjc5dn1ryddwvii4dq61vck447q0n96npnzfyf")))) (build-system python-build-system) (home-page "https://github.com/google/yapf") (synopsis "Formatter for Python code") @@ -13658,15 +13768,29 @@ file system events on Linux.") (define-public python-more-itertools (package (name "python-more-itertools") - (version "4.1.0") + (version "4.3.0") (source (origin (method url-fetch) (uri (pypi-uri "more-itertools" version)) (sha256 (base32 - "0i3ch700g5fyjp692gprlnzbysl8w0sa2vijbp3s40drvk67xkn9")))) + "17h3na0rdh8xq30w4b9pizgkdxmm51896bxw600x84jflg9vaxn4")))) (build-system python-build-system) + (arguments + `(,@(if (any (cute string-prefix? <> (or (%current-system) + (%current-target-system))) + '("armhf" "i686")) + '(#:phases + (modify-phases %standard-phases + ;; This is required for 32-bit hardware. + ;; TODO: Try to remove this when upgrading. + (add-after 'unpack 'patch-test + (lambda _ + (substitute* "more_itertools/tests/test_more.py" + (("10 \\*\\* 10") "9 ** 9")) + #t)))) + '()))) (propagated-inputs `(("python-six" ,python-six-bootstrap))) (home-page "https://github.com/erikrose/more-itertools") @@ -14000,10 +14124,16 @@ introspection.") @item Inter-process locks @item Generic helpers @end itemize\n") + (properties `((python2-variant . ,(delay python2-fasteners)))) (license license:asl2.0))) (define-public python2-fasteners - (package-with-python2 python-fasteners)) + (let ((base (package-with-python2 (strip-python2-variant python-fasteners)))) + (package + (inherit base) + (propagated-inputs + `(("python2-futures" ,python2-futures) + ,@(package-propagated-inputs base)))))) (define-public python-requests-file (package |