Merge remote-tracking branch 'origin/master' into wip-texlive

1 files changed, 169 insertions, 62 deletions

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d5fcc5668c..4541604873 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -2984,38 +2984,44 @@ Language (TOML) configuration files.")
 Server (PLS).")
     (license license:expat)))
 
+;; XXX: We must use a non-release version since the latest release version
+;; requires python-jedi version < 0.15.
 (define-public python-language-server
-  (package
-    (name "python-language-server")
-    (version "0.26.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "python-language-server" version))
-       (sha256
-        (base32
-         "1vs9ckfmm534n1hq3m871916wsjvi5h4gyj6wlzg13ck6506lx0s"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     `(("python-pluggy" ,python-pluggy)
-       ("python-jsonrpc-server" ,python-jsonrpc-server)
-       ("python-jedi" ,python-jedi)
-       ("python-yapf" ,python-yapf)
-       ("python-pyflakes" ,python-pyflakes)
-       ("python-pydocstyle" ,python-pydocstyle)
-       ("python-pycodestyle" ,python-pycodestyle)
-       ("python-mccabe" ,python-mccabe)
-       ("python-rope" ,python-rope)
-       ("python-autopep8" ,python-autopep8)
-       ("python-pylint" ,python-pylint)))
-    (home-page "https://github.com/palantir/python-language-server")
-    (synopsis "Python implementation of the Language Server Protocol")
-    (description
-     "The Python Language Server (pyls) is an implementation of the Python 3
+  (let ((commit "c3cab77a85b1de4af1aec1bafea6a7320d6baec5")
+        (revision "1"))
+    (package
+      (name "python-language-server")
+      (version (git-version "0.28.3" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/palantir/python-language-server.git")
+               (commit commit)))
+         (sha256
+          (base32
+           "1q0xdwgln09sh58j0ryygj92hfgdhwcs57zjvqihya23jr5v0bz4"))))
+      (build-system python-build-system)
+      (propagated-inputs
+       `(("python-pluggy" ,python-pluggy)
+         ("python-jsonrpc-server" ,python-jsonrpc-server)
+         ("python-jedi" ,python-jedi)
+         ("python-yapf" ,python-yapf)
+         ("python-pyflakes" ,python-pyflakes)
+         ("python-pydocstyle" ,python-pydocstyle)
+         ("python-pycodestyle" ,python-pycodestyle)
+         ("python-mccabe" ,python-mccabe)
+         ("python-rope" ,python-rope)
+         ("python-autopep8" ,python-autopep8)
+         ("python-pylint" ,python-pylint)))
+      (home-page "https://github.com/palantir/python-language-server")
+      (synopsis "Python implementation of the Language Server Protocol")
+      (description
+       "The Python Language Server (pyls) is an implementation of the Python 3
 language specification for the Language Server Protocol (LSP).  This tool is
 used in text editing environments to provide a complete and integrated
 feature-set for programming Python effectively.")
-    (license license:expat)))
+      (license license:expat))))
 
 (define-public python-black
   (package
@@ -3800,14 +3806,14 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc.
 (define-public python-matplotlib
   (package
     (name "python-matplotlib")
-    (version "2.2.3")
+    (version "3.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "matplotlib" version))
        (sha256
         (base32
-         "1rcc7x9ig3hpchkc4cwdvym3y451w74275fxr455zkfagrsvymbk"))))
+         "14qc109dibp32xfd9lah54djc0rc76fhbsj9cwyb328lzqmd5sqz"))))
     (build-system python-build-system)
     (propagated-inputs ; the following packages are all needed at run time
      `(("python-cycler" ,python-cycler)
@@ -3824,7 +3830,7 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc.
        ;; 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://pythonhosted.org/cairocffi/cffi_api.html#converting-pycairo
+       ;; https://cairocffi.readthedocs.io/en/stable/cffi_api.html#converting-pycairo-wrappers-to-cairocffi
        ("python-pycairo" ,python-pycairo)
        ("python-cairocffi" ,python-cairocffi)))
     (inputs
@@ -3839,11 +3845,59 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc.
        ("tk" ,tk)))
     (native-inputs
      `(("pkg-config" ,pkg-config)
-       ("python-nose" ,python-nose)
-       ("python-mock" ,python-mock)))
+       ("python-pytest" ,python-pytest)
+       ("python-mock" ,python-mock)
+       ("unzip" ,unzip)
+       ("jquery-ui"
+        ,(origin
+           (method url-fetch)
+           (uri "https://jqueryui.com/resources/download/jquery-ui-1.12.1.zip")
+           (sha256
+            (base32
+             "0kb21xf38diqgxcdi1z3s9ssq36pldvyqxy56hn6pcva6rs3c8zq"))))))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
+         ;; XXX We disable all image comparison tests because we're using a
+         ;; newer version of FreeType than matplotlib expects.  This leads to
+         ;; minor differences throughout the tests.
+         (add-after 'unpack 'fix-and-disable-failing-tests
+           (lambda _
+             (substitute* (append (find-files "lib/matplotlib/tests/"
+                                              "test_.*\\.py$")
+                                  (find-files "lib/mpl_toolkits/tests"
+                                              "test_.*\\.py$"))
+               (("^from matplotlib" match)
+                (string-append "import pytest\n" match))
+               (("( *)@image_comparison" match indent)
+                (string-append indent
+                               "@pytest.mark.skip(reason=\"unknown minor image differences\")\n"
+                               match)))
+             (substitute* "lib/matplotlib/tests/test_animation.py"
+               (("/bin/sh") (which "sh")))
+             (for-each delete-file
+                       ;; test_normal_axes, test_get_tightbbox_polar
+                       '("lib/matplotlib/tests/test_axes.py"
+                         ;; test_outward_ticks
+                         "lib/matplotlib/tests/test_tightlayout.py"
+                         ;; Fontconfig returns no fonts.
+                         "lib/matplotlib/tests/test_font_manager.py"))
+             #t))
+         (add-before 'install 'install-jquery-ui
+           (lambda* (#:key outputs inputs #:allow-other-keys)
+             (let ((dir (string-append (assoc-ref outputs "out")
+                                       "/lib/python3.7/site-packages/matplotlib/backends/web_backend/")))
+               (mkdir-p dir)
+               (invoke "unzip"
+                       (assoc-ref inputs "jquery-ui")
+                       "-d" dir))
+             #t))
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key outputs inputs #:allow-other-keys)
+             (add-installed-pythonpath inputs outputs)
+             (invoke "python" "tests.py" "-v"
+                     "-m" "not network")))
          (add-before 'build 'configure-environment
            (lambda* (#:key outputs inputs #:allow-other-keys)
              (let ((cairo (assoc-ref inputs "cairo")))
@@ -3855,8 +3909,8 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc.
                  (lambda (port)
                    (format port "[directories]~%
 basedirlist = ~a,~a~%
- [rc_options]~%
-backend = TkAgg~%"
+[packages]~%
+tests = True~%"
                         (assoc-ref inputs "tcl")
                         (assoc-ref inputs "tk")))))
              #t)))))
@@ -3875,6 +3929,14 @@ toolkits.")
   (let ((matplotlib (package-with-python2
                      (strip-python2-variant python-matplotlib))))
     (package (inherit matplotlib)
+      (version "2.2.3")
+      (source
+       (origin
+         (method url-fetch)
+         (uri (pypi-uri "matplotlib" version))
+         (sha256
+          (base32
+           "1rcc7x9ig3hpchkc4cwdvym3y451w74275fxr455zkfagrsvymbk"))))
       ;; Make sure to use special packages for Python 2 instead
       ;; of those automatically rewritten by package-with-python2.
       (propagated-inputs
@@ -3898,6 +3960,7 @@ toolkits.")
      `(("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)
@@ -3924,6 +3987,9 @@ toolkits.")
      `(#: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")
@@ -3972,7 +4038,12 @@ toolkits.")
     (license (package-license python-matplotlib))))
 
 (define-public python2-matplotlib-documentation
-  (package-with-python2 python-matplotlib-documentation))
+  (let ((parent (package-with-python2 python-matplotlib-documentation)))
+    (package
+      (inherit parent)
+      (native-inputs
+       (alist-delete "python-sphinx-copybutton"
+                     (package-native-inputs parent))))))
 
 (define-public python-matplotlib-venn
   (package
@@ -4033,14 +4104,14 @@ operators such as union, intersection, and difference.")
 (define-public python-scipy
   (package
     (name "python-scipy")
-    (version "1.2.2")
+    (version "1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "scipy" version))
        (sha256
         (base32
-         "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))
+         "1df113c9i6vazsn6y3n9wc22jh737z1g7dmx3mypkdwpdnscyhr6"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-numpy" ,python-numpy)
@@ -4136,9 +4207,19 @@ routines such as routines for numerical integration and optimization.")
     (properties `((python2-variant . ,(delay python2-scipy))))
     (license license:bsd-3)))
 
+;; Version 1.2.2 is the last version to support Python 2
 (define-public python2-scipy
-  (package-with-python2
-   (strip-python2-variant python-scipy)))
+  (package
+    (inherit (package-with-python2
+              (strip-python2-variant python-scipy)))
+    (version "1.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "scipy" version))
+       (sha256
+        (base32
+         "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
 
 (define-public python-socksipy-branch
   (package
@@ -4956,7 +5037,8 @@ releases.")
     (outputs '("out" "doc"))
     (build-system python-build-system)
     (propagated-inputs
-     `(("python-appdirs" ,python-appdirs)))
+     `(("python-appdirs" ,python-appdirs)
+       ("python-importlib-metadata" ,python-importlib-metadata)))
     (native-inputs
      `(("python-setuptools-scm" ,python-setuptools-scm)
        ("python-sphinx" ,python-sphinx)
@@ -5389,6 +5471,13 @@ computing.")
     (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"))
+             #t))
          ;; Tests can only be run after the library has been installed and not
          ;; within the source directory.
          (delete 'check)
@@ -7480,17 +7569,31 @@ serve the same purpose: provide Python bindings for libmagic.")))
   (package
     (name "python-debian")
     (home-page "https://salsa.debian.org/python-debian-team/python-debian")
-    (version "0.1.28")
+    (version "0.1.36")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri name version))
+       ;; Use git-fetch, as pypi doesn't include test suite.
+       (method git-fetch)
+       (uri (git-reference
+             (url home-page)
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0i15f0xzx679sd0ldq2sls9pnnps9fv6vhqvnv9dzf4qhma42i0y"))))
+         "0qy6x28bj6yfikhjww932v5xq4mf5bm1iczl7acy4c7zm6mwhqfa"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'remove-debian-specific-tests
+                    ;; python-apt, apt and dpkg are not yet available in guix,
+                    ;; and these tests heavily depend on them.
+                    (lambda _
+                      (delete-file "lib/debian/tests/test_deb822.py")
+                      (delete-file "lib/debian/tests/test_debfile.py")
+                      #t)))))
     (propagated-inputs
-     `(("python-six" ,python-six)))
+     `(("python-six" ,python-six)
+       ("python-chardet" ,python-chardet)))
     (synopsis "Debian package related modules")
     (description
      ;; XXX: Use @enumerate instead of @itemize to work around
@@ -10532,25 +10635,29 @@ characters, mouse support, and auto suggestions.")
 (define-public python-jedi
   (package
     (name "python-jedi")
-    (version "0.13.3")
+    (version "0.15.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "jedi" version))
        (sha256
         (base32
-         "0nsrjlb57njqppxmi8wjsb1dkad7qa7svx67jbkhixq66lz61c1b"))))
+         "0bp4pxhsynaarbvzblsn5x32lzp29svy3sxfy8i6m5iwz9s9r1ds"))))
     (build-system python-build-system)
     (arguments
-     `( ;; Many tests are failing with Python 3.7.x as of version 0.13.3 (see:
-        ;; https://github.com/davidhalter/jedi/issues/1263)
-       #:tests? #f
-       #:phases
+     `(#:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'disable-file-completion-test
+           ;; A single parameterized test currently fail (see:
+           ;; https://github.com/davidhalter/jedi/issues/1395).  Remove it.
+           (lambda _
+             (substitute* "test/test_api/test_completion.py"
+               ((".*'example.py', 'rb\"' \\+ join\\('\\.\\.'.*") ""))
+             #t))
          (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (invoke "py.test" "-vv")))))))
+           (lambda _
+             (setenv "HOME" "/tmp")
+             (invoke "python" "-m" "pytest"))))))
     (native-inputs
      `(("python-pytest" ,python-pytest)
        ("python-docopt" ,python-docopt)))
@@ -10568,11 +10675,7 @@ well.")
     (license license:expat)))
 
 (define-public python2-jedi
-  (let ((base (package-with-python2 (strip-python2-variant python-jedi))))
-    (package
-      (inherit base)
-      (arguments (substitute-keyword-arguments (package-arguments base)
-                   ((#:tests? _) #t))))))
+  (package-with-python2 python-jedi))
 
 (define-public ptpython
   (package
@@ -14720,17 +14823,21 @@ time-based (TOTP) passwords.")
 (define-public python-parso
   (package
     (name "python-parso")
-    (version "0.3.1")
+    (version "0.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "parso" version))
        (sha256
         (base32
-         "18p89iwcm8mnf380f92g9w0bhx5km8wxp392vvjcq4y1ld1llw1m"))))
+         "171a9ivhxwsd52h1cgsz40zgzpgzscn7yqb7sdjhy8m1lzj0wsv6"))))
     (native-inputs
      `(("python-pytest" ,python-pytest)))
     (build-system python-build-system)
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (replace 'check
+                    (lambda _ (invoke "pytest" "-vv"))))))
     (home-page "https://github.com/davidhalter/parso")
     (synopsis "Python Parser")
     (description "Parso is a Python parser that supports error recovery and