Merge branch 'master' into gnome-team

1 files changed, 904 insertions, 163 deletions

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 47f4ce1e9c..cf1132d571 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7,7 +7,7 @@
 ;;; Copyright © 2014, 2015 Federico Beffa <[email protected]>
 ;;; Copyright © 2015 Omar Radwan <[email protected]>
 ;;; Copyright © 2015 Pierre-Antoine Rault <[email protected]>
-;;; Copyright © 2015-2023 Ricardo Wurmus <[email protected]>
+;;; Copyright © 2015-2024 Ricardo Wurmus <[email protected]>
 ;;; Copyright © 2015, 2016, 2020 Christine Lemmer-Webber <[email protected]>
 ;;; Copyright © 2015 Eric Dvorsak <[email protected]>
 ;;; Copyright © 2015, 2016 David Thompson <[email protected]>
@@ -63,7 +63,7 @@
 ;;; Copyright © 2019, 2020 Alex Griffin <[email protected]>
 ;;; Copyright © 2019, 2020, 2021, 2022, 2023 Pierre Langlois <[email protected]>
 ;;; Copyright © 2019 Jacob MacDonald <[email protected]>
-;;; Copyright © 2019-2021, 2023 Giacomo Leidi <[email protected]>
+;;; Copyright © 2019-2021, 2023, 2024 Giacomo Leidi <[email protected]>
 ;;; Copyright © 2019 Wiktor Żelazny <[email protected]>
 ;;; Copyright © 2019, 2020, 2021, 2022 Tanguy Le Carrour <[email protected]>
 ;;; Copyright © 2019, 2021-2023 Mădălin Ionel Patrașcu <[email protected]>
@@ -80,7 +80,7 @@
 ;;; Copyright © 2020 Josh Holland <[email protected]>
 ;;; Copyright © 2020 Yuval Kogman <[email protected]>
 ;;; Copyright © 2020, 2022 Michael Rohleder <[email protected]>
-;;; Copyright © 2020, 2021, 2022, 2023 Vinicius Monego <[email protected]>
+;;; Copyright © 2020, 2021, 2022, 2023, 2024 Vinicius Monego <[email protected]>
 ;;; Copyright © 2020 Guy Fleury Iteriteka <[email protected]>
 ;;; Copyright © 2020 Hendursaga <[email protected]>
 ;;; Copyright © 2020 Malte Frank Gerdes <[email protected]>
@@ -94,7 +94,7 @@
 ;;; Copyright © 2020, 2021 Zheng Junjie <[email protected]>
 ;;; Copyright © 2020 EuAndreh <[email protected]>
 ;;; Copyright © 2021, 2022 Morgan Smith <[email protected]>
-;;; Copyright © 2021-2023 Sharlatan Hellseher <[email protected]>
+;;; Copyright © 2021-2024 Sharlatan Hellseher <[email protected]>
 ;;; Copyright © 2021 Ellis Kenyő <[email protected]>
 ;;; Copyright © 2021 LibreMiami <[email protected]>
 ;;; Copyright © 2021 Xinglu Chen <[email protected]>
@@ -119,7 +119,7 @@
 ;;; Copyright © 2022 Evgeny Pisemsky <[email protected]>
 ;;; Copyright © 2022 drozdov <[email protected]>
 ;;; Copyright © 2022 Peter Polidoro <[email protected]>
-;;; Copyright © 2022 Wamm K. D. <[email protected]>
+;;; Copyright © 2022, 2023 Wamm K. D. <[email protected]>
 ;;; Copyright © 2022 Jai Vetrivelan <[email protected]>
 ;;; Copyright © 2022 Artyom V. Poptsov <[email protected]>
 ;;; Copyright © 2022 Paul A. Patience <[email protected]>
@@ -258,6 +258,7 @@
   #:use-module (gnu packages shells)
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages ssh)
+  #:use-module (gnu packages statistics)
   #:use-module (gnu packages swig)
   #:use-module (gnu packages tcl)
   #:use-module (gnu packages terminals)
@@ -401,6 +402,35 @@ Jupytext are:
 ")
     (license license:expat)))
 
+(define-public python-concurrent-log-handler
+  (package
+    (name "python-concurrent-log-handler")
+    (version "0.9.25")
+    ;; No tests in the PyPI tarball.
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Preston-Landers/concurrent-log-handler")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0jp4zkm0idfdsrq3jzb52iqfkh6xzm7sacz1sa34ffnkyqdk3xzh"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-portalocker))
+    (native-inputs (list python-hatchling python-pytest))
+    (home-page "https://github.com/Preston-Landers/concurrent-log-handler")
+    (synopsis
+     "Additional log handler for Python's standard @code{logging} package")
+    (description
+     "This package provides an additional log handler for Python's standard
+@code{logging} package (PEP 282).  This handler will write log events to a log
+file which is rotated when the log file reaches a certain size.  Multiple
+processes can safely write to the same log file concurrently and rotated logs
+can be gzipped if desired.  An optional threaded queue logging handler is
+provided to perform logging in the background.")
+    (license license:asl2.0)))
+
 (define-public python-logzero
   (package
     (name "python-logzero")
@@ -539,6 +569,147 @@ workspaces.
 @end itemize")
     (license license:gpl3+)))
 
+(define-public python-databind-core
+  (package
+    (name "python-databind-core")
+    (version "4.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "databind.core" version))
+       (sha256
+        (base32 "130hr19kbzizx9n2q7cwfzfk20ii3cqmqjrzb16psnafll303k2d"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'install 'fix-name
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (let* ((sitedir (site-packages inputs outputs))
+                     (dist-info
+                      (string-append sitedir "/databind_core-" #$version ".dist-info")))
+                (substitute* (string-append dist-info "/METADATA")
+                  (("Name: databind-core")
+                   "Name: databind.core"))
+                (substitute* (string-append dist-info "/RECORD")
+                  (("databind_core") "databind.core"))
+                (rename-file dist-info
+                             (string-append sitedir
+                                            "/databind.core-"
+                                            #$version ".dist-info"))))))))
+    (propagated-inputs
+     (list python-deprecated
+           python-nr-date
+           python-nr-stream
+           python-typeapi
+           python-typing-extensions))
+    (native-inputs
+     (list python-poetry-core python-pytest))
+    (home-page "https://niklasrosenstein.github.io/python-databind/core/")
+    (synopsis
+     "Library for de-/serializing Python dataclasses")
+    (description
+     "Databind is a library inspired by jackson-databind to de-/serialize
+Python dataclasses.")
+    (license license:expat)))
+
+(define-public python-databind-json
+  (package
+    (name "python-databind-json")
+    (version "4.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "databind.json" version))
+       (sha256
+        (base32 "1lm864d7arfq0pw64hyc83bwn1z94wjg7a22q1xf0qkjynqs70gg"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'install 'fix-name
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (let* ((sitedir (site-packages inputs outputs))
+                     (dist-info
+                      (string-append sitedir "/databind_json-" #$version ".dist-info")))
+                (substitute* (string-append dist-info "/METADATA")
+                  (("Name: databind-json")
+                   "Name: databind.json"))
+                (substitute* (string-append dist-info "/RECORD")
+                  (("databind_json") "databind.json"))
+                (rename-file dist-info
+                             (string-append sitedir
+                                            "/databind.json-"
+                                            #$version ".dist-info"))))))))
+    (propagated-inputs
+     (list python-databind-core python-nr-date
+           python-typeapi python-typing-extensions))
+    (native-inputs (list python-poetry-core python-pytest))
+    (home-page "https://niklasrosenstein.github.io/python-databind/json/")
+    (synopsis
+     "De-/serialize Python dataclasses to or from JSON payloads")
+    (description
+     "The @code{databind.json} package implements the de-/serialization to or
+from JSON payloads using the @code{databind.core} framework.")
+    (license license:expat)))
+
+(define-public python-docspec
+  (package
+    (name "python-docspec")
+    (version "2.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "docspec" version))
+       (sha256
+        (base32 "1zqmdrc6k8pprra8p3wpzq2ml2gph1cfjmsyg07f8b8fvizffm28"))))
+    (build-system pyproject-build-system)
+    (arguments (list #:tests? #false))  ;there are none
+    (propagated-inputs
+     (list python-databind-core
+           python-databind-json
+           python-deprecated))
+    (native-inputs
+     (list python-poetry-core))
+    (home-page "https://github.com/NiklasRosenstein/python-docspec")
+    (synopsis "Represent API documentation of programming languages")
+    (description
+     "Docspec is a JSON object specification for representing API
+documentation of programming languages.")
+    (license license:expat)))
+
+(define-public python-docspec-python
+  (package
+    (name "python-docspec-python")
+    (version "2.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "docspec_python" version))
+       (sha256
+        (base32 "0n8m52vxmlvkj7p5jmd4rfdks65rrp4q4vzak44y6kbg9l5qa6y4"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #false  ;there are none
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'relax-requirements
+           (lambda _
+             ;; We don't have black 23.
+             (substitute* "pyproject.toml"
+               (("23.1.0") "22.3.0")))))))
+    (propagated-inputs (list python-black python-docspec python-nr-util))
+    (native-inputs (list python-poetry-core))
+    (home-page "https://github.com/NiklasRosenstein/docspec/")
+    (synopsis "Produce docspec data from Python source code")
+    (description
+     "This package provides a parser based on @code{lib2to3} producing
+@code{docspec} data from Python source code.")
+    (license license:expat)))
+
 (define-public python-fire
   (package
     (name "python-fire")
@@ -591,6 +762,7 @@ and variables you'll need already imported and created.
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:tests? #false ;there are none
       #:phases
       '(modify-phases %standard-phases
          (add-after 'unpack 'remove-invalid-syntax
@@ -692,6 +864,7 @@ features of the Python's built-in dict.")
                (base32
                 "05zf0xn7ab40dan213fwbp1z4rybih8dphf9mzb2ddmbafxq41mv"))))
     (build-system pyproject-build-system)
+    (arguments (list #:tests? #false)) ;there are none
     (propagated-inputs (list python-matplotlib python-numpy))
     (home-page "https://github.com/Phlya/adjustText")
     (synopsis "Adjust text position in matplotlib plots to minimize overlaps")
@@ -866,6 +1039,46 @@ as functions or string constants to form colored terminal output.")
 into dataclasses.")
     (license license:expat)))
 
+(define-public python-contourpy
+  (package
+    (name "python-contourpy")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "contourpy" version))
+       (sha256
+        (base32 "088bhyh6m6q0h637wiq2paqhwn76hqvvbhqwacfx4a1qhv1lcc75"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; All these tests require matplotlib, but matplotlib requires contourpy
+      ;; now.
+      '(list "-k" "not test_mypy"
+             "--ignore=tests/test_config.py"
+             "--ignore=tests/test_filled.py"
+             "--ignore=tests/test_lines.py"
+             "--ignore=tests/test_renderer.py")))
+    (propagated-inputs (list python-mypy
+                             python-numpy
+                             python-pillow
+                             python-pytest
+                             python-pytest-cov
+                             python-pytest-xdist
+                             python-selenium
+                             python-sphinx
+                             python-sphinx-copybutton
+                             python-wurlitzer))
+    (native-inputs (list meson-python pybind11-2.10 pkg-config))
+    (home-page "https://contourpy.readthedocs.io/")
+    (synopsis
+     "Python library for calculating contours of 2D quadrilateral grids")
+    (description
+     "ContourPy is a Python library for calculating contours of 2D
+quadrilateral grids.  It is written in C++11 and wrapped using pybind11.")
+    (license license:bsd-3)))
+
 (define-public python-yaspin
   (package
     (name "python-yaspin")
@@ -1127,10 +1340,26 @@ variables into the markdown template")
                 (substitute* "tests/test_bugs.py"
                   (("def test_change_user") "def _do_not_test_change_user")
                   (("def test_lost_connection") "def _do_not_test_lost_connection")
-                  (("def test_kill_query") "def _do_not_test_kill_query"))
+                  (("def test_kill_query") "def _do_not_test_kill_query")
+                  ;; These all fail because of expired certificates.
+                  (("def test_cext_verify_server_certificate")
+                   "def _do_not_test_cext_verify_server_certificate")
+                  (("def test_pure_verify_server_certificate")
+                   "def _do_not_test_pure_verify_server_certificate")
+                  (("def test_verify_server_name_cext_cnx")
+                   "def _do_not_test_verify_server_name_cext_cnx")
+                  (("def test_verify_server_name_pure_cnx")
+                   "def _do_not_test_verify_server_name_pure_cnx"))
                 (substitute* "tests/test_connection.py"
                   (("def test_allow_local_infile_in_path")
-                   "def _do_not_test_allow_local_infile_in_path"))
+                   "def _do_not_test_allow_local_infile_in_path")
+                  ;; This fails because of expired certificates.
+                  (("def test_connect_with_unix_socket")
+                   "def _do_not_test_connect_with_unix_socket"))
+                (substitute* "tests/test_mysqlx_connection.py"
+                  ;; This fails because of expired certificates.
+                  (("def test_ssl_connection")
+                   "def _do_not_test_ssl_connection"))
                 (substitute* "tests/test_constants.py"
                   (("def test_deprecated")
                    "def _do_not_test_deprecated"))
@@ -1226,30 +1455,30 @@ Markdown.  All extensions are found under the module namespace of pymdownx.")
 (define-public python-pint
   (package
     (name "python-pint")
-    (version "0.22")
+    (version "0.23")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "Pint" version))
               (sha256
                (base32
-                "0cs4lsvngrkfzpnrmxcwz728m47y0xbw1knksz51cc6gpdm9y4rd"))))
+                "1d69dqs0j907x4hgz2k8f3zjzhgs9zvlw2k0gi955g3dc28rnl71"))))
     (build-system pyproject-build-system)
     (arguments
-     ;; This single test tries to write to $HOME/.cache/pint.
-     (list #:test-flags #~'("-k" "not test_auto")))
-    (native-inputs
-     (list python-dask
-           python-distributed
-           python-importlib-metadata
-           python-pytest                ;for pytest-subtests
-           python-pytest-cov
-           python-pytest-mpl
-           python-pytest-subtests
-           python-setuptools-scm
-           python-sparse
-           python-uncertainties
-           python-xarray))
-    (propagated-inputs (list python-typing-extensions))
+     (list
+      #:test-flags
+      '(list "-k" (string-append
+                   ;; This test tries to write to $HOME/.cache/pint.
+                   "not test_auto"
+                   ;; Fails with "Group USCSLengthInternational already
+                   ;; present in registry"
+                   " and not test_load_definitions_stage_2"))))
+    (native-inputs
+     (list python-pytest python-pytest-benchmark python-pytest-cov
+           python-pytest-mpl python-pytest-subtests
+           python-setuptools-scm))
+    (propagated-inputs
+     (list python-typing-extensions
+           python-uncertainties))
     (home-page "https://github.com/hgrecco/pint")
     (synopsis "Physical quantities module")
     (description
@@ -1432,6 +1661,87 @@ generator MkDocs.")
 bindings to the C++ random forest implementation, ranger, using Cython.")
     (license license:gpl3+)))
 
+(define-public python-nr-date
+  (package
+    (name "python-nr-date")
+    (version "2.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "nr_date" version))
+       (sha256
+        (base32 "1rnjyykjp41mqz6h1vx18jblq97gi5m5x7dgasyaihnd7fhswhq6"))))
+    (build-system pyproject-build-system)
+    (arguments (list #:tests? #false)) ;there are none
+    (propagated-inputs (list python-dataclasses))
+    (native-inputs (list python-poetry-core))
+    (home-page "https://github.com/NiklasRosenstein/python-nr.date")
+    (synopsis "Fast, regex-based date parsing library in plain Python")
+    (description "This package provides a fast, regex-based date parsing
+library in pure Python.")
+    (license license:expat)))
+
+(define-public python-nr-stream
+  (package
+    (name "python-nr-stream")
+    (version "1.1.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "nr_stream" version))
+       (sha256
+        (base32 "0rag4vbjnalkyfcarx6yipn11ih2hmc3pfldava4c6n6pz31c0pb"))))
+    (build-system pyproject-build-system)
+    (arguments (list #:tests? #false))  ;there are none
+    (native-inputs (list python-poetry-core))
+    (home-page "https://github.com/NiklasRosenstein/python-nr.stream")
+    (synopsis "Stream and Optional classes for Python")
+    (description "This package provides a @code{Stream} and @code{Optional}
+class.")
+    (license license:expat)))
+
+(define-public python-nr-util
+  (package
+    (name "python-nr-util")
+    (version "0.8.12")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "nr.util" version))
+       (sha256
+        (base32 "1x0l4811dskwrk83l2xzdcldx2iazlrx5wxkg41jz7fr6ch9qm54"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #false                   ;there are none
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-build-system
+            (lambda _
+              (substitute* "pyproject.toml"
+                (("^config =.*") "config = []\n"))))
+          (add-after 'install 'fix-name
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (let* ((sitedir (site-packages inputs outputs))
+                     (dist-info
+                      (string-append sitedir "/nr_util-" #$version ".dist-info")))
+                (substitute* (string-append dist-info "/METADATA")
+                  (("Name: nr-util")
+                   "Name: nr.util"))
+                (substitute* (string-append dist-info "/RECORD")
+                  (("nr_util") "nr.util"))
+                (rename-file dist-info
+                             (string-append sitedir
+                                            "/nr.util-"
+                                            #$version ".dist-info"))))))))
+    (propagated-inputs (list python-deprecated python-typing-extensions))
+    (native-inputs (list python-poetry-core))
+    (home-page "https://github.com/NiklasRosenstein/python-nr.util")
+    (synopsis "General purpose Python utility library")
+    (description "This package provides a general purpose Python utility
+library.")
+    (license license:expat)))
+
 (define-public python-slixmpp
   (package
     (name "python-slixmpp")
@@ -1580,6 +1890,32 @@ progress bar and a percentage indicator object that let you track the progress
 of a loop structure or other iterative computation.")
     (license license:bsd-3)))
 
+(define-public python-gh-md-to-html
+  (package
+    (name "python-gh-md-to-html")
+    (version "1.21.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "gh_md_to_html" version))
+       (sha256
+        (base32 "1cnaqnckpcrpc4b8ba18s5ds05w1yfiszcp7ql7pmx0jnrj25qax"))))
+    (build-system pyproject-build-system)
+    (arguments (list #:tests? #false))  ;there are none
+    (propagated-inputs
+     (list python-beautifulsoup4
+           python-emoji
+           python-pillow
+           python-requests
+           python-shellescape
+           python-webcolors))
+    (home-page "https://github.com/phseiff/github-flavored-markdown-to-html/")
+    (synopsis "Github-flavored Markdown")
+    (description
+     "This package provides a feature-rich Github-flavored Markdown to HTML
+Python library and command line interface.")
+    (license license:expat)))
+
 (define-public python-glymur
   (package
     (name "python-glymur")
@@ -2387,6 +2723,7 @@ Unicode-to-LaTeX conversion.")
        (file-name (git-file-name name version))
        (sha256
         (base32 "0bkhfnlik89j3yamr20br4wm8975f20v33wabi2nyxvj10whr5dj"))
+       (patches (search-patches "python-pyls-black-41.patch"))
        ;; Patch to work with python-lsp-server.  Taken from
        ;; <https://github.com/rupert/pyls-black/pull/37>.
        (modules '((guix build utils)))
@@ -2402,9 +2739,11 @@ Unicode-to-LaTeX conversion.")
               "pylsp_format_range")
              (("from pyls([ \\.])" _ char)
               (string-append "from pylsp" char)))))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:test-target "pytest"))
+     (list
+      #:test-flags
+      '(list "-k" "not test_load_config_target_version")))
     (propagated-inputs
      (list python-black python-lsp-server python-tomli))
     (native-inputs
@@ -3764,6 +4103,46 @@ lossless but can be tweaked for more aggressive cleaning.")
 after Andy Lester’s Perl module WWW::Mechanize.")
     (license license:bsd-3)))
 
+(define-public python-mediapy
+  (package
+    (name "python-mediapy")
+    (version "1.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/google/mediapy")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "14hmwib0dmy9h1w7allwsp0cgrfdv8f2sm9qlvy65yxai68v6vnl"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'fix-references
+           (lambda _
+             (substitute* "mediapy_test.py"
+               (("'/bin/bash")
+                (string-append "'" (which "bash")))))))))
+    (inputs (list ffmpeg-5))
+    (propagated-inputs (list python-absl-py
+                             python-ipython
+                             python-matplotlib
+                             python-numpy
+                             python-pillow))
+    (native-inputs
+     (list python-flit-core
+           python-pylint
+           python-pytest
+           python-pytest-xdist))
+    (home-page "https://github.com/google/mediapy")
+    (synopsis "Read/write/show images and videos in an IPython notebook")
+    (description "This Python library makes it easy to display images and
+videos in a notebook.")
+    (license license:asl2.0)))
+
 (define-public python-simpleaudio
   (package
     (name "python-simpleaudio")
@@ -6991,6 +7370,51 @@ errors when data is invalid.")
 Interfaces} via data models provided in the JSON format.")
     (license license:expat)))
 
+(define-public python-pydoc-markdown
+  (package
+    (name "python-pydoc-markdown")
+    (version "4.8.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pydoc_markdown" version))
+       (sha256
+        (base32 "02vzlrd18r8wi0b64vq2gnbhaadysg9rnbylf9sf2v9q65z94v7v"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #false ;there are none
+      #:phases
+      '(modify-phases %standard-phases
+         ;; This is probably not a good idea, but it wants a rather old
+         ;; version of docstring-parser.
+         (add-after 'unpack 'relax-requirements
+           (lambda _
+             (substitute* "pyproject.toml"
+               (("docstring-parser = .*")
+                "docstring-parser = \"^0\"\n")))))))
+    (propagated-inputs (list python-click
+                             python-databind-core
+                             python-databind-json
+                             python-docspec
+                             python-docspec-python
+                             python-docstring-parser
+                             python-jinja2
+                             python-nr-util
+                             python-pyyaml
+                             python-requests
+                             python-tomli
+                             python-tomli-w
+                             python-watchdog
+                             python-yapf))
+    (native-inputs (list python-poetry-core))
+    (home-page "https://pypi.org/project/pydoc-markdown/")
+    (synopsis "Create Python API documentation in Markdown format")
+    (description "Pydoc-Markdown is a tool to create Python API documentation
+in Markdown format.  Instead of executing your Python code like so many other
+documentation tools, it parses it using docspec instead.")
+    (license license:expat)))
+
 (define-public python-pydocstyle
   (package
     (name "python-pydocstyle")
@@ -7274,6 +7698,20 @@ programming language and the extended Cython programming language.  It makes
 writing C extensions for Python as easy as Python itself.")
     (license license:asl2.0)))
 
+;; Needed for scipy
+(define-public python-cython-0.29.35
+  (package
+    (inherit python-cython)
+    (name "python-cython")
+    (version "0.29.35")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "Cython" version))
+              (sha256
+               (base32
+                "09y5r22nyswqpwc02agla1bnzh2jx2db25pnq9pc5cq8pyh1yf3f"))))
+    (properties '())))
+
 (define-public python-cython-3
   (package
     (inherit python-cython)
@@ -7646,7 +8084,7 @@ color scales, and color space conversion easy.  It has support for:
     (native-inputs
      (list python-pytest python-pytest-mock))
     (propagated-inputs
-     (list python-cryptography python-gssapi python-ruamel.yaml))
+     (list python-cryptography python-gssapi python-krb5 python-ruamel.yaml))
     (home-page "https://github.com/jborean93/pyspnego")
     (synopsis "Python SPNEGO library")
     (description "The @code{pyspnego} Python library handles Negotiate, NTLM,
@@ -8095,16 +8533,25 @@ comparison.
 (define-public python-matplotlib
   (package
     (name "python-matplotlib")
-    (version "3.5.2")
+    (version "3.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "matplotlib" version))
        (sha256
-        (base32 "18h78s5ld1i6mz00w258hy29909nfr3ddq6ry9kq18agw468bks8"))))
-    (build-system python-build-system)
+        (base32 "18amhxyxa6yzy1nwky4ggdgvvxnbl3qz2lki05vfx0dqf6w7ia81"))))
+    (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      '(list "-m" "not network"
+             "-k"
+             (string-append
+              ;; This one fails with a small difference in the upper left.
+              "not test_figure_legend_outside"
+              ;; The 'test_lazy_auto_backend_selection' fails
+              ;; because it would require an X server; skip it.
+              " and not test_lazy_auto_backend_selection"))
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'build 'pretend-version
@@ -8168,49 +8615,30 @@ backend=Agg
 basedirlist = ~a,~a
 
 [packages]
-tests = True~%" (assoc-ref inputs "tcl") (assoc-ref inputs "tk"))))))
+tests = True~%" #$(this-package-input "tcl") #$(this-package-input "tk"))))))
           (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
+            (lambda* (#:key tests? test-flags #:allow-other-keys)
               (when tests?
                 ;; Step out of the source directory to avoid interference.
                 (with-directory-excursion "/tmp"
                   ;; Run the installed tests, which is what we want since not
                   ;; everything gets built in the source directory.
-                  (invoke "pytest"
-                          "-n" (number->string (parallel-job-count))
-                          "-m" "not network" "--pyargs" "matplotlib"
-                          "-k"
-                          (string-append
-                           ;; The 'test_lazy_auto_backend_selection' fails
-                           ;; because it would require an X server; skip it.
-                           "not test_lazy_auto_backend_selection"
-                           ;; test_getattr fails for the GTK backend because
-                           ;; of an unexpected warning from Python 3.10
-                           ;; (via the gi module):
-                           ;; https://gitlab.gnome.org/GNOME/pygobject/-/issues/494
-                           " and not test_getattr")))))))))
-    (propagated-inputs
-     (list gobject-introspection
-           python-cairocffi
-           python-certifi
+                  (apply invoke "pytest"
+                         "-n" (number->string (parallel-job-count))
+                         "--pyargs" "matplotlib"
+                         test-flags))))))))
+    (propagated-inputs
+     (list python-contourpy
            python-cycler
            python-dateutil
            python-fonttools-minimal
+           python-importlib-resources
            python-kiwisolver
            python-numpy
            python-packaging
            python-pillow
-           ;; ;; 'pycairo'.  However, 'pygobject' makes use of a 'pycairo' 'context'
-           ;; ;; From version 1.4.0 'matplotlib' makes use of 'cairocffi' instead of
-           ;; ;; https://cairocffi.readthedocs.io/en/stable/cffi_api.html#converting-pycairo-wrappers-to-cairocffi
-           ;; ;; object.  For this reason we need to import both libraries.
-           ;; python-pycairo
-           python-pygobject
            python-pyparsing
-           python-pytz
-           python-six
-           `(,python "tk")
-           python-wxpython))
+           `(,python "tk")))
     (inputs
      (list cairo
            freetype
@@ -8221,6 +8649,7 @@ tests = True~%" (assoc-ref inputs "tcl") (assoc-ref inputs "tk"))))))
            tk))
     (native-inputs
      (list pkg-config
+           pybind11
            python-pytest
            python-pytest-timeout
            python-pytest-xdist
@@ -8374,7 +8803,9 @@ three-way Venn diagrams in @code{matplotlib}.")
      (list
       #:test-flags
       ;; This test fails with ValueError: not enough values to unpack.
-      #~(list "--deselect" "tests/test_spy.py::test_cli")))
+      #~(list "--deselect" "tests/test_spy.py::test_cli"
+              ;; XXX: unknown failure
+              "--deselect" "tests/test_spy.py::test_png")))
     (home-page "https://github.com/nschloe/matplotx")
     (synopsis "Minimal matplotlib styles")
     (description
@@ -8407,6 +8838,48 @@ clean plots with a minimalistic style.")
 complex-valued functions.")
     (license license:gpl3+)))
 
+(define-public python-cppheaderparser
+  (package
+    (name "python-cppheaderparser")
+    (version "2.7.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "CppHeaderParser" version))
+       (sha256
+        (base32 "0hncwd9y5ayk8wa6bqhp551mcamcvh84h89ba3labc4mdm0k0arq"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #f))     ; no tests
+    (propagated-inputs (list python-ply))
+    (home-page "http://senexcanis.com/open-source/cppheaderparser/")
+    (synopsis
+     "Parse C++ header files and generate a data structure representing the class")
+    (description
+     "CppHeaderParser is a pure python module that will parse C++ header files
+and generate a data structure representing the class.")
+    (license license:bsd-3)))
+
+(define-public python-cppy
+  (package
+    (name "python-cppy")
+    (version "1.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "cppy" version))
+       (sha256
+        (base32 "06zysv86j7wqb1rl88ab4clbjf7iahhv9gfyqlasr18hggqkpd43"))))
+    (build-system pyproject-build-system)
+    (home-page "https://github.com/nucleic/cppy")
+    (synopsis "C++ header library for Python extension modules")
+    (description "This package is a small C++ header library which makes it
+easier to write Python extension modules.  The primary feature is a
+@code{PyObject} smart pointer which automatically handles reference counting
+and provides convenience methods for performing common object operations.")
+    (license license:bsd-3)))
+
 (define-public python-perfplot
   (package
     (name "python-perfplot")
@@ -8877,6 +9350,39 @@ also add custom data, viewing options, and passwords to PDF files.  It can
 retrieve text and metadata from PDFs as well as merge entire files together.")
     (license license:bsd-3)))
 
+(define-public python-pdf2image
+  (package
+    (name "python-pdf2image")
+    (version "1.17.0")
+    ;; No tests in the PyPI tarball.
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Belval/pdf2image")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0xd8q939zqa8flfcdhbgyadiwqb8sgnd42cbr6n1l2jl9fnix45v"))))
+    (build-system pyproject-build-system)
+    (arguments
+     ;; The following excluded tests assume hardcoded binary paths to
+     ;; /usr/bin/pdftoppm and /usr/bin/pdftocairo.
+     '(#:test-flags '("--exclude=^test_use_poppler_path$"
+                      "--exclude=^test_use_poppler_path_with_trailing_slash$")))
+    (propagated-inputs (list python-pillow))
+    (inputs (list poppler))
+    (native-inputs (list python-nose which))
+    (home-page "https://github.com/Belval/pdf2image")
+    (synopsis
+     "Python wrapper around @command{pdftoppm} and @command{pdftocairo}")
+    (description
+     "This package provides a Python API wrapping the @command{pdftoppm} and
+@command{pdftocairo} command line tools.  It can convert @file{PDF} files to a
+Python list with elements of type @code{PIL.Image} (from the
+@code{python-pillow} library).")
+    (license license:expat)))
+
 (define-public python-pikepdf
   (package
     (name "python-pikepdf")
@@ -9207,19 +9713,21 @@ regions of interest, geometric shapes, paths, text, etc for image overlays.")
 (define-public python-tifffile
   (package
     (name "python-tifffile")
-    (version "2021.4.8")
+    (version "2023.12.9")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "tifffile" version))
        (sha256
         (base32
-         "16r0hw7shka1bqf28bv198lj2jhf2r9gy3s5zv4nf5cfsfm8pajm"))))
+         "1f6d8qdlq0zlksfdhp1mhj9icpwhw4cz47r4i80m6r0a328xmlcx"))))
     (build-system python-build-system)
     ;; Tests require lfdfiles, which depends on tifffile
     (arguments `(#:tests? #f))
     (propagated-inputs
-     (list python-numpy python-imagecodecs))
+     (list python-numpy))
+    (native-inputs
+     (list python-pytest))
     (home-page "https://www.lfd.uci.edu/~gohlke/")
     (synopsis "Read and write TIFF(r) files")
     (description "This package lets you read image and metadata from many
@@ -9437,14 +9945,14 @@ from FFMPEG, reliably terminating the process when done.")
 (define-public python-imageio
   (package
     (name "python-imageio")
-    (version "2.26.0")
+    (version "2.33.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "imageio" version))
        (sha256
         (base32
-         "0dgddhi5dlpry5j4d3256v09pcziyj3ii47yx0zi68xprm11d7qn"))))
+         "1kn1gj9vc1mkirs39x3nkw2d56paiagi24kkxksrig9pn502swkq"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -9471,9 +9979,10 @@ from FFMPEG, reliably terminating the process when done.")
               (delete-file "tests/test_freeimage.py"))))))
     (inputs (list freeimage))
     (propagated-inputs
-     (list python-imageio-ffmpeg python-numpy python-pillow python-psutil))
+     (list python-imageio-ffmpeg python-numpy python-pillow python-tifffile))
     (native-inputs
-     (list python-pytest))
+     (list python-black python-flake8 python-fsspec python-pytest
+           python-pytest-cov))
     (home-page "https://imageio.github.io/")
     (synopsis "Library for reading and writing a wide range of image data")
     (description
@@ -9735,6 +10244,43 @@ service.  It allows you to invoke commands on target Windows machines from
 any machine that can run Python.")
     (license license:expat)))
 
+(define-public python-manimpango
+  (package
+    (name "python-manimpango")
+    (version "0.5.0")
+    (source
+     (origin
+       (method git-fetch) ; no tests data in PyPi package
+       (uri (git-reference
+             (url "https://github.com/ManimCommunity/ManimPango")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "00mrvswk8yly0m13jq0f432pr19sy3j6w37lrv78ah1j6jz9n50h"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'build-extensions
+            (lambda _
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+    (native-inputs
+      (list pkg-config
+            python-cython
+            python-pytest
+            python-pytest-cov))
+    (inputs
+     (list pango))
+    (home-page "https://manimpango.manim.community/")
+    (synopsis "Bindings for Pango for using with Manim")
+    (description
+     "Python bindings for ManimPango which is a C binding for Pango,
+using Cython.
+
+ManimPango is internally used in Manim to render (non-LaTeX) text.")
+    (license license:expat)))
+
 (define-public python-xcffib
   (package
     (name "python-xcffib")
@@ -12242,17 +12788,32 @@ SVG, EPS, PNG and terminal output.")
 (define-public python-seaborn
   (package
     (name "python-seaborn")
-    (version "0.12.0")
+    (version "0.13.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "seaborn" version))
               (sha256
                (base32
-                "08vvnp4ps86857imxz2l5xi2vir5xdcdp3apq4badb4b5llifgw9"))))
+                "0ycibcs6kvd3xi4zsxna81claqifyb9dn6z6jwc5x7lqqplnbbdz"))))
     (build-system pyproject-build-system)
-    (propagated-inputs (list python-pandas python-matplotlib python-numpy
-                             python-scipy))
-    (native-inputs (list python-flit-core python-pypa-build python-pytest))
+    (propagated-inputs
+     (list python-ipykernel
+           python-matplotlib
+           python-mypy
+           python-nbconvert
+           python-numpy
+           python-numpydoc
+           python-pandas
+           python-pyyaml
+           python-scipy
+           python-statsmodels))
+    (native-inputs
+     (list python-flake8
+           python-flit-core
+           python-pre-commit
+           python-pytest
+           python-pytest-cov
+           python-pytest-xdist))
     (home-page "https://seaborn.pydata.org/")
     (synopsis "Statistical data visualization")
     (description
@@ -12984,6 +13545,22 @@ validate this input and generate a PEP 643-compliant metadata
 file (e.g. @file{PKG-INFO}).")
     (license license:expat)))
 
+(define-public python-pyproject-metadata-0.7
+  (package
+    (inherit python-pyproject-metadata)
+    (name "python-pyproject-metadata")
+    (version "0.7.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/FFY00/python-pyproject-metadata")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0yvs59ymz5gdix34a95wxlxvk9bnvjgrzsnmnc3ws7whpfv3yasm"))))))
+
 ;; pep621 was renamed to pyproject-metadata.
 (define-public python-pep621
   (deprecated-package "python-pep621" python-pyproject-metadata))
@@ -13697,6 +14274,24 @@ almost any existing Python modules, and an easy way for outside developers to
 add functionality and customization to your projects with their own plugins.")
     (license license:expat)))
 
+(define-public python-strenum
+  (package
+    (name "python-strenum")
+    (version "0.4.15")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "StrEnum" version))
+       (sha256
+        (base32 "1zrfr1shin5wyfnfxc7jpk013594wasrp4ni9l70fhjlf2mvb3w7"))))
+    (build-system pyproject-build-system)
+    (arguments (list #:tests? #false)) ;there are none.
+    (home-page "https://github.com/irgeek/StrEnum")
+    (synopsis "Enum that inherits from str")
+    (description "StrEnum is a Python @code{enum.Enum} that inherits from
+@code{str} to complement @code{enum.IntEnum} in the standard library.")
+    (license license:expat)))
+
 (define-public python-pysendfile
   (package
     (name "python-pysendfile")
@@ -14466,6 +15061,27 @@ tasks, sockets, files, locks, and queues.")
 designed to efficiently cope with extremely large amounts of data.")
     (license license:bsd-3)))
 
+(define-public python-tasklogger
+  (package
+    (name "python-tasklogger")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "tasklogger" version))
+       (sha256
+        (base32 "1901mibcp6aiyjy8afnybrxnb0dkbdxlbvjqbr3gginlw7dr18xh"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-deprecated))
+    (native-inputs (list python-coverage python-coveralls python-nose2
+                         python-numpy))
+    (home-page "https://github.com/scottgigante/tasklogger")
+    (synopsis "Extension to the core Python logging library")
+    (description "This package provides an extension to the core Python
+logging library for logging the beginning and completion of tasks and
+subtasks.")
+    (license license:gpl2)))
+
 (define-public python-sniffio
   (package
     (name "python-sniffio")
@@ -16658,18 +17274,19 @@ applications.")
 (define-public python-click-default-group
   (package
     (name "python-click-default-group")
-    (version "1.2.2")
+    (version "1.2.4")
     (source (origin
               (method url-fetch)
-              (uri (pypi-uri "click-default-group" version))
+              (uri (pypi-uri "click_default_group" version))
               (sha256
                (base32
-                "015r78jk8gznfw0dphpwaqcx5mhg5822b55w5xbb6i7sin70wmnr"))))
-    (build-system python-build-system)
-    (arguments
-      `(#:tests? #f)) ; no target
+                "07i5w47lbihcb3cvs08vynz725z9skvhhzrarnk6qi8dxjckqgzb"))))
+    (build-system pyproject-build-system)
+    (arguments (list #:tests? #false)) ;there are none
     (propagated-inputs
      (list python-click))
+    (native-inputs
+     (list python-flit-core python-pytest))
     (synopsis "Extends click.Group")
     (description "This package extends click.Group to invoke a command without
 explicit subcommand name.")
@@ -17255,13 +17872,13 @@ document.")
 (define-public python-symengine
   (package
     (name "python-symengine")
-    (version "0.10.0")
+    (version "0.11.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "symengine" version))
        (sha256
-        (base32 "0i97lb6h8jk0k98805mkw6id5r537469zbh2d95320azq9nfj824"))))
+        (base32 "0n54rdpmz3bmxrbjqflmlrgc27rvik1jkv6x3cjvgsq4p0lhvlqd"))))
     (build-system python-build-system)
     (arguments
      (list
@@ -17275,7 +17892,7 @@ document.")
                     (invoke "nosetests" "-v" "symengine.tests"))
                   (format #t "test suite not run~%")))))))
     (native-inputs
-     (list cmake python-cython python-nose))
+     (list cmake python-cython-3 python-nose))
     (inputs
      (list symengine))
     (home-page "https://github.com/symengine/symengine.py")
@@ -19521,6 +20138,25 @@ and pluralizes English words, and transforms strings from CamelCase to
 underscored string.")
     (license license:expat)))
 
+(define-public python-krb5
+  (package
+    (name "python-krb5")
+    (version "0.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "krb5" version))
+       (sha256
+        (base32 "1jivws8dsscsmyqngbc71r4qw8qmn98pqmhylz01r5dd1ljfw9bi"))))
+    (build-system pyproject-build-system)
+    (inputs (list mit-krb5))
+    (native-inputs (list python-cython python-k5test python-pytest))
+    (home-page "https://github.com/jborean93/pykrb5")
+    (synopsis "Kerberos API bindings for Python")
+    (description "This library provides Python functions that wraps the
+Kerberos 5 C API.")
+    (license license:expat)))
+
 (define-public python-pylev
   (package
     (name "python-pylev")
@@ -19942,6 +20578,36 @@ feels like an AST.")
      (arguments '(#:tests? #f))
      (native-inputs '()))))
 
+(define-public python-typeapi
+  (package
+    (name "python-typeapi")
+    (version "2.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "typeapi" version))
+       (sha256
+        (base32 "1652fc04gn6nkw8izim0g7v586f64fla6clinp5xq9rf739w3cs9"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #false                   ;there are none
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'patch-build-system
+           (lambda _
+             (substitute* "pyproject.toml"
+               (("^docs =.*") "docs = []\n")))))))
+    (propagated-inputs (list python-typing-extensions))
+    (native-inputs (list python-poetry-core))
+    (home-page "https://pypi.org/project/typeapi/")
+    (synopsis "Type hints")
+    (description "The typeapi package provides an object-oriented interface
+for introspecting PEP484 type hints at runtime, including forward references
+that make use of the more recent PEP585 and PEP604 type hint features in
+Python versions that don't natively support them.")
+    (license license:expat)))
+
 (define-public python-typing-inspect
   (package
     (name "python-typing-inspect")
@@ -19966,16 +20632,18 @@ inspection of types defined in the Python standard typing module.")
 (define-public python-lazy-loader
   (package
     (name "python-lazy-loader")
-    (version "0.2")
+    (version "0.3")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "lazy_loader" version))
               (sha256
                (base32
-                "12piaj94m5wbx33cxb80xgnsvzgya6cp90zj12qsq064fm8pmp0f"))))
+                "0dwghffnsjjf4pi4gwbl43rx04jmap375hdamafs5cpm6j78js1v"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pytest python-pytest-cov))
+     (list python-pre-commit
+           python-pytest
+           python-pytest-cov))
     (propagated-inputs
      (list python-flit-core))
     (home-page "https://scientific-python.org/specs/spec-0001/")
@@ -20801,6 +21469,26 @@ multitouch applications.")
 Design spec without sacrificing ease of use or application performance.")
     (license license:expat)))
 
+(define-public python-asyncinject
+  (package
+    (name "python-asyncinject")
+    (version "0.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "asyncinject" version))
+       (sha256
+        (base32 "0x57idiy19lzyn32klgm06r223z8gr2aqqk91gysbshq7jg8g3pf"))))
+    (build-system pyproject-build-system)
+    (native-inputs (list python-pytest python-pytest-asyncio))
+    (home-page "https://github.com/simonw/asyncinject")
+    (synopsis
+     "Run async workflows using pytest-fixtures-style dependency injection")
+    (description
+     "This package lets you run asynchronous workflows using
+pytest-fixtures-style dependency injection.")
+    (license license:asl2.0)))
+
 (define-public python-asynckivy
   (package
     (name "python-asynckivy")
@@ -21106,6 +21794,26 @@ JSON) codec.")
      ;; number of files with other licenses.
      (list license:gpl2+ license:asl2.0 license:lgpl2.1+ license:cc-by-sa3.0))))
 
+(define-public python-namex
+  (package
+    (name "python-namex")
+    (version "0.0.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "namex" version))
+       (sha256
+        (base32 "16ynrq245c3nywv476izrc4bcacm9gxjzgr67ng91g929ny6bfl4"))))
+    (build-system pyproject-build-system)
+    (arguments (list #:tests? #false))  ;there are none
+    (home-page "https://github.com/fchollet/namex")
+    (synopsis
+     "Separate implementation and public API surface of Python packages")
+    (description
+     "This package provides a simple utility to separate the
+implementation of your Python package and its public API surface.")
+    (license license:asl2.0)))
+
 (define-public python-natsort
   (package
     (name "python-natsort")
@@ -24156,58 +24864,6 @@ profiling, and getting datetime-aware @acronym{UTC, Coordinated Universal
 Time} values as well as an event scheduler.")
     (license license:expat)))
 
-(define-public python-activepapers
-  (package
-    (name "python-activepapers")
-    (version "0.2.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "ActivePapers.Py" version))
-       (sha256
-        (base32
-         "12wkhjh90ffipjzv10swndp2xv9hd7xrxvg6v0n4n3i411pj4xb8"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:modules ((ice-9 ftw)
-                  (srfi srfi-1)
-                  (guix build utils)
-                  (guix build python-build-system))
-
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'delete-python2-code
-           (lambda _
-             (for-each delete-file
-                       '("lib/activepapers/builtins2.py"
-                         "lib/activepapers/standardlib2.py"
-                         "lib/activepapers/utility2.py"))))
-         (replace 'check
-           (lambda _
-             ;; Deactivate the test cases that download files
-             (setenv "NO_NETWORK_ACCESS" "1")
-             ;; For some strange reason, some tests fail if nosetests runs all
-             ;; test modules in a single execution. They pass if each test
-             ;; module is run individually.
-             (for-each (lambda (filename)
-                         (invoke "nosetests"
-                                 (string-append "tests/" filename)))
-                       (scandir "tests"
-                                (lambda (filename)
-                                  (string-suffix? ".py" filename)))))))))
-    (native-inputs
-     (list python-tempdir python-nose))
-    (propagated-inputs
-     (list python-h5py))
-    (home-page "https://www.activepapers.org/")
-    (synopsis "Executable papers for scientific computing")
-    (description
-     "ActivePapers is a tool for working with executable papers, which
-combine data, code, and documentation in single-file packages,
-suitable for publication as supplementary material or on repositories
-such as figshare or Zenodo.")
-    (license license:bsd-3)))
-
 (define-public python-semver
   (package
     (name "python-semver")
@@ -24410,15 +25066,19 @@ such as lines length, trailing spaces, indentation, etc.")
 (define-public python-yapf
   (package
     (name "python-yapf")
-    (version "0.29.0")
+    (version "0.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "yapf" version))
        (sha256
         (base32
-         "1pj3xzblmbssshi889b6n9hwqbjpabw6j0fimlng2sshd3226bki"))))
-    (build-system python-build-system)
+         "06vxqski7qss2h2iy4fd04czym0cwjrzkaab9h03wzpg6xfhixd3"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     (list python-importlib-metadata python-platformdirs python-tomli))
+    (native-inputs
+     (list python-pytest))
     (home-page "https://github.com/google/yapf")
     (synopsis "Formatter for Python code")
     (description "YAPF is a formatter for Python code.  It's based off of
@@ -24825,6 +25485,24 @@ based on the CPython 2.7 and 3.7 parsers.")
 with PEP 484 argument (and return) type annotations.")
     (license license:expat)))
 
+(define-public python-typeguard-4
+  (package
+    (inherit python-typeguard)
+    (name "python-typeguard")
+    ;; This is the latest version we can use, because python-typeguard >=
+    ;; 4.0.1 requires python-typing-extensions >= 4.7.0.
+    (version "4.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "typeguard" version))
+       (sha256
+        (base32 "11yrc7pv2fajmicwiyc92sb5gphlw3zbxww8f2prrsh6rgdv6kqr"))))
+    (build-system pyproject-build-system)
+    (arguments
+     '())
+    (propagated-inputs (list python-typing-extensions))))
+
 (define-public bpython
   (package
     (name "bpython")
@@ -25521,6 +26199,22 @@ library: to minimize boilerplate code in traditional extension modules by
 inferring type information using compile-time introspection.")
     (license license:bsd-3)))
 
+;; Needed for scipy
+(define-public pybind11-2.10
+  (package
+    (inherit pybind11)
+    (name "pybind11")
+    (version "2.10.4")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/pybind/pybind11")
+                    (commit (string-append "v" version))))
+              (sha256
+               (base32
+                "0rbcfvl7y472sykzdq3vrkw83kar0lpzhk3wq9yj9cdydl8cpfcz"))
+              (file-name (git-file-name name version))))))
+
 ;; This is needed for python-vaex-core.
 (define-public pybind11-2.3
   (package
@@ -26627,7 +27321,8 @@ parentdir_prefix = dask-
           (add-before 'check 'pre-check
             (lambda _ (chdir "/tmp"))))))
     (propagated-inputs
-     (list python-cloudpickle
+     (list python-click ;needed at runtime
+           python-cloudpickle
            python-fsspec
            python-importlib-metadata ;needed at runtime for dask/_compatibility.py
            python-numpy
@@ -26637,8 +27332,7 @@ parentdir_prefix = dask-
            python-toolz
            python-pyyaml))
     (native-inputs
-     (list python-click
-           python-importlib-metadata
+     (list python-importlib-metadata
            python-pytest python-pytest-runner python-pytest-rerunfailures
            python-versioneer))
     (home-page "https://github.com/dask/dask/")
@@ -28665,14 +29359,24 @@ lowercase.")
 (define-public python-pypng
   (package
     (name "python-pypng")
-    (version "0.0.20")
+    (version "0.20220715.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pypng" version))
        (sha256
-        (base32 "02qpa22ls41vwsrzw9r9qhj1nhq05p03hb5473pay6y980s86chh"))))
-    (build-system python-build-system)
+        (base32 "1hg24zja235bkbny82hx7sy7qlzfbabxph2lvqaq61vgm4xl773k"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         (add-before 'check 'pre-check
+           (lambda _
+             (setenv "PYTHONPATH"
+                     (string-append (getcwd) "/code:"
+                                    (getenv "GUIX_PYTHONPATH"))))))))
+    (native-inputs (list python-pytest))
     (home-page "https://github.com/drj11/pypng")
     (synopsis "Pure Python PNG image encoder/decoder")
     (description
@@ -32547,30 +33251,40 @@ Python @code{set} interface.")
 (define-public dynaconf
   (package
     (name "dynaconf")
-    (version "3.1.7")
+    (version "3.2.4")
     (source
      (origin
        (method git-fetch)
        (uri
         (git-reference
-         (url "https://github.com/rochacbruno/dynaconf")
+         (url "https://github.com/dynaconf/dynaconf")
          (commit version)))
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0pjyjsdzairpn5vq8nzddhxwxmr18grn272nj31wcy2ipwdl3c3h"))
+         "0fj2ffvzfvjf4d7f672h5x5fzq26f8hax9j3dfsix158fwm0212w"))
        (patches (search-patches "dynaconf-unvendor-deps.patch"))
        (modules '((guix build utils)))
        (snippet '(begin
                    ;; Remove vendored dependencies
                    (let ((unvendor '("click" "dotenv" "ruamel" "toml")))
                      (with-directory-excursion "dynaconf/vendor"
-                       (for-each delete-file-recursively unvendor))
-                     (with-directory-excursion "dynaconf/vendor_src"
-                       (for-each delete-file-recursively unvendor)))))))
-    (build-system python-build-system)
+                       (for-each delete-file-recursively unvendor)))
+                   ;; Lower coverage quality gate for unit tests
+                   (substitute* ".coveragerc"
+                     (("fail_under = 95") "fail_under = 50"))))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     `(#:test-flags
+       '("-k"
+         ,(let ((click-tests '("test_negative_get"
+                               "test_inspect_invalid_format")))
+            ;; Disable integration tests
+            (string-append "not integration and not "
+                           ;; These tests fail because we use Click 8.* instead of
+                           ;; Click 7
+                           (string-join click-tests " and not "))))
+       #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-for-click-8
            (lambda _
@@ -32578,14 +33292,19 @@ Python @code{set} interface.")
                (("click.get_os_args\\()") ;deprecated from Click 8.1+
                 "sys.argv[1:]"))))
          (replace 'check
-           (lambda* (#:key tests? outputs #:allow-other-keys)
+           (lambda* (#:key tests? test-flags #:allow-other-keys)
              (when tests?
                ;; These tests depend on hvac and a live Vault process.
                (delete-file "tests/test_vault.py")
-               (invoke "make" "test_only")))))))
+               (apply invoke
+                      `("py.test" ,@test-flags "-v"
+                        "--cov-config" ".coveragerc"
+                        "--cov=dynaconf"
+                        "-l" "--tb=short"
+                        "--maxfail=1" "tests/"))))))))
     (propagated-inputs
      (list python-click python-configobj python-dotenv-0.13.0
-           python-ruamel.yaml python-toml))
+           python-ruamel.yaml python-toml python-tomli))
     (native-inputs
      (list python-django python-flask python-pytest python-pytest-cov
            python-pytest-mock))
@@ -32752,18 +33471,20 @@ of several plugins.")
 (define-public python-doit
   (package
     (name "python-doit")
-    (version "0.34.0")
+    (version "0.36.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "doit" version))
         (sha256
-          (base32 "0bf0m9n0hyjvjpv051zd26725j8jr23gyvc37v3kkadwbh8dxwcf"))))
-    (build-system python-build-system)
+          (base32 "1g1lwaxb9q3a6c24sr3gw5bspsk5frbrk2frb7z25jqljp67rl3i"))))
+    (build-system pyproject-build-system)
+    ;; This is not a serious test failure.  It's probably due to the load path
+    ;; at test time.
+    (arguments (list #:test-flags '(list "-k" "not test_execute")))
     (propagated-inputs
-      (list python-cloudpickle python-pyinotify))
-    (native-inputs
-      (list python-pytest))
+     (list python-cloudpickle python-importlib-metadata))
+    (native-inputs (list python-pytest))
     (home-page "https://pydoit.org")
     (synopsis "Automation tool to execute any kind of task in a build-tools
 fashion")
@@ -32772,7 +33493,7 @@ build-tools to execute any kind of task.
 
 A task describes some computation to be done (actions), and contains some
 extra meta-data.  The actions can be external programs or Python functions.  A
-single task may define more than one action.doit uses the task’s meta-data
+single task may define more than one action.  doit uses the task’s meta-data
 to:
 
 @itemize
@@ -32804,6 +33525,26 @@ to:
      "This package provides a port of the serialize and unserialize functions of PHP for Python")
     (license license:bsd-3)))
 
+(define-public python-pydevtool
+  (package
+    (name "python-pydevtool")
+    (version "0.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pydevtool" version))
+       (sha256
+        (base32 "12pwhvvm4pgvfxj18ylb66drxm28b2cpb5rbxqrsrk1k7m7vmqr5"))))
+    (build-system pyproject-build-system)
+    (arguments (list #:tests? #false)) ;no tests
+    (propagated-inputs (list python-doit python-rich-click))
+    (home-page "https://github.com/pydoit/pydevtool")
+    (synopsis "CLI dev tools powered by pydoit")
+    (description "This package provides command line tools, powered by pydoit.
+It offers integration with @code{click} and @code{rich} for custom CLI and
+these linters: @code{pycodestlye}, @code{pyflakes}")
+    (license license:expat)))
+
 (define-public nikola
   (package
     (name "nikola")