Merge branch 'master' into emacs-team

1 files changed, 170 insertions, 113 deletions

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 6d460e286e..b8e8097c7b 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -61,7 +61,7 @@
 ;;; Copyright © 2019, 2023 Jack Hill <jackhill@jackhill.us>
 ;;; Copyright © 2019-2023, Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2019, 2020 Alex Griffin <a@ajgrf.com>
-;;; Copyright © 2019, 2020, 2021, 2022 Pierre Langlois <pierre.langlois@gmx.com>
+;;; Copyright © 2019, 2020, 2021, 2022, 2023 Pierre Langlois <pierre.langlois@gmx.com>
 ;;; Copyright © 2019 Jacob MacDonald <jaccarmac@gmail.com>
 ;;; Copyright © 2019, 2020, 2021 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
@@ -99,7 +99,7 @@
 ;;; Copyright © 2021 LibreMiami <packaging-guix@libremiami.org>
 ;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz>
 ;;; Copyright © 2021 Raghav Gururajan <rg@raghavgururajan.name>
-;;; Copyright © 2021 jgart <jgart@dismail.de>
+;;; Copyright © 2021, 2023 jgart <jgart@dismail.de>
 ;;; Copyright © 2021 Danial Behzadi <dani.behzi@ubuntu.com>
 ;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
 ;;; Copyright © 2021 Hugo Lecomte <hugo.lecomte@inria.fr>
@@ -2446,7 +2446,7 @@ conventions and aliases in the same expression.")
              (setenv "MAGICK_HOME" (assoc-ref inputs "imagemagick"))
              (setenv "WAND_MAGICK_LIBRARY_SUFFIX" ".Q16")))
          (replace 'check
-           (lambda _
+           (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
                (invoke "pytest" "-vv")))))))
     (native-inputs
@@ -4273,7 +4273,8 @@ processing tasks.")
     (propagated-inputs
      (list python-matplotlib python-numpy python-pandas python-scipy))
     (native-inputs
-     (list python-setuptools python-pytest python-pytest-cov tzdata))
+     (list python-setuptools python-setuptools-scm
+           python-pytest python-pytest-cov tzdata))
     (home-page "https://github.com/has2k1/mizani")
     (synopsis "Create data visualizations in Python")
     (description
@@ -5271,6 +5272,26 @@ recognition library with full Unicode support.  It has features like:
 @end itemize")
     (license license:expat)))
 
+(define-public python-makefun
+  (package
+    (name "python-makefun")
+    (version "1.15.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "makefun" version))
+              (sha256
+               (base32
+                "19a8dga8rnmjn5gy1cy1wdi28swbkdkypwbqikbxil6ynqcg3c20"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-pytest python-setuptools-scm))
+    (home-page "https://github.com/smarie/python-makefun")
+    (synopsis "Library to dynamically create python functions")
+    (description "@code{makefun} helps create functions dynamically with a
+given signature.  It was largely inspired by @code{python-decorator} and
+@code{functools}.")
+    (license license:bsd-3)))
+
 (define-public python-markdown-it-py
   (package
     (name "python-markdown-it-py")
@@ -5743,6 +5764,28 @@ which only supports flat sequences, and allows you to apply a function to each
 leaf preserving the overall structure.")
     (license license:asl2.0)))
 
+(define-public python-pyment
+  (package
+    (name "python-pyment")
+    (version "0.3.4")
+    (source
+       (origin
+         (method git-fetch)
+         (uri
+          (git-reference
+           (url "https://github.com/dadadel/pyment")
+           (commit (string-append "v" version))))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0gbx9wmqsxdx85v5sg79lv2zxmy16j5dwi8bip07i1nyvzc5gvn0"))))
+    (build-system python-build-system)
+    (native-inputs (list python-pytest))
+    (home-page "https://github.com/dadadel/pyment/")
+    (synopsis "Convert Python docstrings automatically")
+    (description "Pyment is a command line tool and library that can be
+used to convert between several docstring styles.")
+    (license license:gpl3+)))
+
 (define-public python-docstring-parser
   (package
     (name "python-docstring-parser")
@@ -6334,7 +6377,7 @@ utility, a static analysis tool (linter) for Robot Framework source files.")
            (lambda* (#:key tests? #:allow-other-keys)
              (when tests? (invoke "pytest" "-vv" "tests")))))))
     (propagated-inputs (list python-paramiko))
-    (native-inputs (list openssh python-pytest))
+    (native-inputs (list openssh python-pytest python-mock))
     (home-page "https://github.com/pahaz/sshtunnel")
     (synopsis "Python SSH tunnels library")
     (description "@code{sshtunnel} is a Python module for easily creating SSH
@@ -7226,13 +7269,15 @@ capabilities.")
            python-sphinx-4
            python-sphinx-panels
            texinfo
-           texlive-bin
-           texlive-cbfonts
-           texlive-cm-super
-           texlive-greek-fontenc
-           texlive-latex-expdlist
-           texlive-polyglossia
-           texlive-xindy))
+           (texlive-updmap.cfg
+            (list texlive-cbfonts
+                  texlive-cm-super
+                  texlive-expdlist
+                  texlive-greek-fontenc
+                  texlive-latexmk
+                  texlive-polyglossia
+                  texlive-xetex
+                  texlive-xindy))))
     (inputs '())
     (propagated-inputs '())
     (synopsis "Documentation for the @code{python-numpy} package")
@@ -8011,26 +8056,26 @@ toolkits.")
      (list graphviz
            inkscape/stable
            python-colorspacious
+           python-ipython
+           python-ipywidgets
            python-mpl-sphinx-theme
+           python-numpydoc
            python-scipy
            python-sphinx
            python-sphinx-copybutton
            python-sphinx-gallery
            python-sphinxcontrib-svg2pdfconverter
-           python-numpydoc
-           python-ipython
-           python-ipywidgets
+           texinfo
            texlive-amsfonts
            texlive-amsmath
            texlive-babel
-           texlive-fontspec
-           texlive-unicode-math
            texlive-etoolbox
-           texlive-latex-expdlist
-           texlive-underscore
-           texlive-latex-type1cm
+           texlive-expdlist
+           texlive-fontspec
            texlive-times
-           texinfo))
+           texlive-type1cm
+           texlive-underscore
+           texlive-unicode-math))
     (synopsis "Documentation for the @code{python-matplotlib} package")))
 
 (define-public python-matplotlib-inline
@@ -10826,9 +10871,11 @@ computing.")
            python-sphinx
            python-sphinx-rtd-theme
            texinfo
-           texlive-bin
-           texlive-polyglossia
-           texlive-xindy))))
+           (texlive-updmap.cfg
+            (list texlive-latexmk
+                  texlive-polyglossia
+                  texlive-xetex
+                  texlive-xindy))))))
 
 (define-public python-urwid
   (package
@@ -11418,30 +11465,38 @@ Python style, together with a fast and comfortable execution environment.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "09yrpi9f86r9yvcm2dfjs5zy87c4j31bxama77kfd6y8yfrrjlai"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         ;; For cluster execution Snakemake will call Python.  Since there is
-         ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail.  We
-         ;; fix this by calling the snakemake wrapper instead.
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; For cluster execution Snakemake will call Python.  Since there is
+          ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail.  We
+          ;; fix this by calling the snakemake wrapper instead.
 
-         ;; XXX: There is another instance of sys.executable on line 692, but
-         ;; it is not clear how to patch it.
-         (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
-           (lambda* (#:key outputs #:allow-other-keys)
-             (substitute* "snakemake/executors/__init__.py"
-               (("\\{sys.executable\\} -m snakemake")
-                (string-append (assoc-ref outputs "out")
-                               "/bin/snakemake")))))
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (setenv "HOME" "/tmp")
-               ;; This test attempts to change S3 buckets on AWS and fails
-               ;; because there are no AWS credentials.
-               (delete-file "tests/test_tibanna.py")
-               (invoke "pytest")))))))
+          ;; XXX: There is another instance of sys.executable on line 692, but
+          ;; it is not clear how to patch it.
+          (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
+            (lambda* (#:key outputs #:allow-other-keys)
+              (substitute* "snakemake/executors/__init__.py"
+                (("\\{sys.executable\\} -m snakemake")
+                 (string-append #$output "/bin/snakemake")))))
+          (add-after 'unpack 'patch-version
+            (lambda _
+              (substitute* "setup.py"
+                (("version=versioneer.get_version\\(\\)")
+                 (format #f "version=~s" #$version)))
+              (substitute* '("snakemake/_version.py"
+                             "versioneer.py")
+                (("0\\+unknown") #$version))))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (setenv "HOME" "/tmp")
+                ;; This test attempts to change S3 buckets on AWS and fails
+                ;; because there are no AWS credentials.
+                (delete-file "tests/test_tibanna.py")
+                (invoke "pytest")))))))
     (propagated-inputs
      (list python-appdirs
            python-configargparse
@@ -11486,32 +11541,41 @@ Python style, together with a fast and comfortable execution environment.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "1qrqbmx4cbis0wxr6dl2rdjv9v627sbirsz6v5c31vlbqwkvs04q"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         ;; For cluster execution Snakemake will call Python.  Since there is
-         ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail.  We
-         ;; fix this by calling the snakemake wrapper instead.
-         (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
-           (lambda* (#:key outputs #:allow-other-keys)
-             (substitute* "snakemake/executors/__init__.py"
-               (("self\\.get_python_executable\\(\\),")
-                "")
-               (("\"-m snakemake\"")
-                (string-append "\"" (assoc-ref outputs "out")
-                               "/bin/snakemake" "\"")))))
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (setenv "HOME" "/tmp")
-               ;; This test attempts to change S3 buckets on AWS and fails
-               ;; because there are no AWS credentials.
-               (delete-file "tests/test_tibanna.py")
-               ;; It's a similar story with this test, which requires access
-               ;; to the Google Storage service.
-               (delete-file "tests/test_google_lifesciences.py")
-               (invoke "pytest")))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; For cluster execution Snakemake will call Python.  Since there is
+          ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail.  We
+          ;; fix this by calling the snakemake wrapper instead.
+          (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
+            (lambda* (#:key outputs #:allow-other-keys)
+              (substitute* "snakemake/executors/__init__.py"
+                (("self\\.get_python_executable\\(\\),")
+                 "")
+                (("\"-m snakemake\"")
+                 (string-append "\"" #$output
+                                "/bin/snakemake" "\"")))))
+          (add-after 'unpack 'patch-version
+            (lambda _
+              (substitute* "setup.py"
+                (("version=versioneer.get_version\\(\\)")
+                 (format #f "version=~s" #$version)))
+              (substitute* '("snakemake/_version.py"
+                             "versioneer.py")
+                (("0\\+unknown") #$version))))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (setenv "HOME" "/tmp")
+                ;; This test attempts to change S3 buckets on AWS and fails
+                ;; because there are no AWS credentials.
+                (delete-file "tests/test_tibanna.py")
+                ;; It's a similar story with this test, which requires access
+                ;; to the Google Storage service.
+                (delete-file "tests/test_google_lifesciences.py")
+                (invoke "pytest")))))))
     (propagated-inputs
      (list python-appdirs
            python-configargparse
@@ -13272,16 +13336,16 @@ third-party code.")
 (define-public python-llfuse
   (package
     (name "python-llfuse")
-    (version "1.4.1")
+    (version "1.4.4")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "llfuse" version))
               (sha256
                (base32
-                "1jaf790rsxvz3hs9fbr3hrnmg0xzl6a2bqfa10bbbsjsdbcpk762"))))
+                "1jb4c9avvb0v3830xlbj1r9kj05i98vv6nq05105ppg57y7lq14j"))))
     (build-system python-build-system)
     (inputs
-     (list fuse attr))
+     (list fuse-2 attr))
     (native-inputs
      (list pkg-config python-pytest))
     (synopsis "Python bindings for FUSE")
@@ -15159,37 +15223,38 @@ time.")
            texlive-adjustbox
            texlive-booktabs
            texlive-caption
+           texlive-collection-basic
            texlive-enumitem
+           texlive-environ
+           texlive-eurosym
+           texlive-fancyvrb
+           texlive-float
            texlive-fontspec
-           texlive-iftex
+           texlive-geometry
            texlive-grffile
            texlive-hyperref
-           texlive-fancyvrb
-           texlive-latex-float
-           texlive-latex-geometry
-           texlive-latex-jknapltx
+           texlive-jknapltx
+           texlive-jknapltx
+           texlive-lm
+           texlive-lm-math
+           texlive-mathpazo
            texlive-ms
-           texlive-latex-parskip
-           texlive-latex-trimspaces
-           texlive-latex-upquote
+           texlive-parskip
+           texlive-pdfcol
+           texlive-pgf
+           texlive-rsfs
            texlive-stringenc
            texlive-tcolorbox
            texlive-titling
            texlive-tools
+           texlive-trimspaces
+           texlive-ucs
            texlive-ulem
            texlive-unicode-math
+           texlive-upquote
            texlive-xcolor
-           (texlive-updmap.cfg (list texlive-amsfonts
-                                     texlive-amsmath
-                                     texlive-eurosym
-                                     texlive-fonts-rsfs
-                                     texlive-jknappen
-                                     texlive-latex-ucs
-                                     texlive-lm
-                                     texlive-lm-math
-                                     texlive-mathpazo
-                                     texlive-oberdiek
-                                     texlive-zapfding))))
+           texlive-xetex
+           texlive-zapfding))
     (home-page "https://jupyter.org")
     (synopsis "Converting Jupyter Notebooks")
     (description "The @code{nbconvert} tool, @code{jupyter nbconvert}, converts
@@ -24361,10 +24426,9 @@ commit, but it also includes some other useful statistics.")
              (let ((fuse (assoc-ref inputs "fuse")))
                (substitute* "fuse.py"
                  (("find_library\\('fuse'\\)")
-                  (string-append "'" fuse "/lib/libfuse.so'")))
-               #t))))))
+                  (string-append "'" fuse "/lib/libfuse.so'")))))))))
     (propagated-inputs
-     (list fuse))
+     (list fuse-2))
     (home-page "https://github.com/fusepy/fusepy")
     (synopsis "Simple ctypes bindings for FUSE")
     (description "Python module that provides a simple interface to FUSE and
@@ -24391,10 +24455,9 @@ MacFUSE.  The binding is created using the standard @code{ctypes} library.")
              (let ((fuse (assoc-ref inputs "fuse")))
                (substitute* "fusepyng.py"
                  (("os.environ.get\\('FUSE_LIBRARY_PATH'\\)")
-                  (string-append "\"" fuse "/lib/libfuse.so\""))))
-             #t)))))
+                  (string-append "\"" fuse "/lib/libfuse.so\"")))))))))
     (inputs
-     (list fuse))
+     (list fuse-2))
     (propagated-inputs
      (list python-paramiko))
     (home-page "https://github.com/rianhunter/fusepyng")
@@ -25570,16 +25633,16 @@ decisions with any given backend.")
 (define-public python-dask
   (package
     (name "python-dask")
-    (version "2023.4.1")
+    (version "2023.7.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/dask/dask/")
-             (commit "a69a808f75a961504a9ba18058bff5e458be97fb")))
+             (commit "8523b3bae2ec0183d9d92cc536a3405f15189b7e")))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "089kz6hcgl4yxwx99br1124sg1gkdy554hf120z9a5cfbrf0ah9y"))))
+        (base32 "1x617m0jlc63v938kqga9mhflhac3aj1ylq5mkpf2g9pd9x2hcbz"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -29169,13 +29232,7 @@ By default it uses the open Python vulnerability database Safety DB.")
     (propagated-inputs
      `(("wheel" ,python-wheel)))
     (native-inputs
-     `(("texlive" ,(texlive-updmap.cfg (list texlive-amsfonts
-                                        texlive-fonts-ec
-                                        texlive-iftex
-                                        texlive-hyperref
-                                        texlive-oberdiek
-                                        texlive-lm
-                                        texlive-xcolor)))))
+     `(("texlive" ,(texlive-updmap.cfg (list texlive-lm texlive-xcolor)))))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -31942,10 +31999,10 @@ Psycopg 2 is both Unicode and Python 3 friendly.")
           (base32 "0cvybynv9igssfa4l13q09gb6m7afmwk34wsbq8jk14sqpd4dl92"))))
     (build-system python-build-system)
     (native-inputs (list pkg-config))
-    (inputs (list fuse-3))
+    (inputs (list fuse))
     (propagated-inputs (list python-pytest-trio))
     (home-page "https://github.com/libfuse/pyfuse3")
-    (synopsis "Python bindings FUSE 3")
+    (synopsis "Python bindings to FUSE 3")
     (description "This package provides Python 3 bindings for libfuse 3 with
 async I/O support.")
     (license license:gpl2+)))
@@ -32269,13 +32326,13 @@ than trying to just split strings.")
 (define-public python-srsly
   (package
     (name "python-srsly")
-    (version "2.4.6")
+    (version "2.4.7")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "srsly" version))
               (sha256
                (base32
-                "0vsafkvk4g0p5m0dqrczqvlyza837i20xxmb24rrqk5s78r1zd27"))))
+                "022x0djlkl6pgh9yrd4avlai1n6y4hxm9l1xnb6630kpi12wrhlk"))))
     (build-system pyproject-build-system)
     (arguments
      (list