Merge branch 'master' into staging

Conflicts: .guix-authorizations gnu/ci.scm gnu/packages/base.scm gnu/packages/databases.scm gnu/packages/gnome.scm gnu/packages/gtk.scm gnu/packages/imagemagick.scm gnu/packages/password-utils.scm gnu/packages/python-xyz.scm gnu/packages/web-browsers.scm
author: Maxim Cournoyer <maxim.cournoyer@gmail.com> 2021-04-08 15:47:00 -0400
committer: Maxim Cournoyer <maxim.cournoyer@gmail.com> 2021-04-08 15:47:00 -0400
commit: 533a893cc6b03f100566760d6e0c8e0500ed7082 (patch)
tree: 0ecbf89895a400c43d16bb1f6539f1a88aeaa4cf /gnu/packages/python-xyz.scm
parent: 6a2546f92d07df04e5d700924edd027ed1e2ef11 (diff)
parent: c762df54786fd6f005f3b5307323f1d2df3cbf0b (diff)
download: guix-533a893cc6b03f100566760d6e0c8e0500ed7082.tar.gz
1 files changed, 910 insertions, 291 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b50683f943..79289b1c23 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3,7 +3,7 @@
 ;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013, 2014, 2015, 2016, 2019 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2014, 2017 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2017, 2021 Eric Bavier <bavier@posteo.net>
 ;;; Copyright © 2014, 2015 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2015 Omar Radwan <toxemicsquire4@gmail.com>
 ;;; Copyright © 2015 Pierre-Antoine Rault <par@rigelk.eu>
@@ -27,7 +27,7 @@
 ;;; Copyright © 2016 Dylan Jeffers <sapientech@sapientech@openmailbox.org>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Marius Bakke <marius@gnu.org>
-;;; Copyright © 2016, 2017 Stefan Reichör <stefan@xsteve.at>
+;;; Copyright © 2016, 2017, 2021 Stefan Reichör <stefan@xsteve.at>
 ;;; Copyright © 2016, 2017, 2019 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2016, 2017, 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Julien Lepiller <julien@lepiller.eu>
@@ -74,7 +74,7 @@
 ;;; Copyright © 2020 Sebastian Schott <sschott@mailbox.org>
 ;;; Copyright © 2020 Alexandros Theodotou <alex@zrythm.org>
 ;;; Copyright © 2020 Josh Marshall <joshua.r.marshall.1991@gmail.com>
-;;; Copyright © 2020 Alexandros Theodotou <alex@zrythm.org>
+;;; Copyright © 2020, 2021 Alexandros Theodotou <alex@zrythm.org>
 ;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
 ;;; Copyright © 2020 Alex ter Weele <alex.ter.weele@gmail.com>
 ;;; Copyright © 2020 Matthew Kraai <kraai@ftbfs.org>
@@ -82,7 +82,7 @@
 ;;; Copyright © 2020 Josh Holland <josh@inv.alid.pw>
 ;;; Copyright © 2020 Yuval Kogman <nothingmuch@woobling.org>
 ;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
-;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2020 Guy Fleury Iteriteka <gfleury@disroot.org>
 ;;; Copyright © 2020 Hendursaga <hendursaga@yahoo.com>
 ;;; Copyright © 2020 Malte Frank Gerdes <malte.f.gerdes@gmail.com>
@@ -96,6 +96,9 @@
 ;;; Copyright © 2020, 2021 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2021 Morgan Smith <Morgan.J.Smith@outlook.com>
 ;;; Copyright © 2020 EuAndreh <eu@euandre.org>
+;;; Copyright © 2021 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2021 Ellis Kenyő <me@elken.dev>
+;;; Copyright © 2021 LibreMiami <packaging-guix@libremiami.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -179,6 +182,7 @@
   #:use-module (gnu packages readline)
   #:use-module (gnu packages sdl)
   #:use-module (gnu packages search)
+  #:use-module (gnu packages scanner)
   #:use-module (gnu packages shells)
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages ssh)
@@ -549,35 +553,34 @@ data for video and audio files.")
 (define-public python-psutil
   (package
     (name "python-psutil")
-    (version "5.7.2")
+    (version "5.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "psutil" version))
        (sha256
-        (base32 "1svv985vmqsls35kmvp3vhh26nsgz229324s9k29awf6qgqhm6ch"))))
+        (base32 "1immnj532bnnrh1qmk5q3lsw3san8qfk9kxy1cpmy0knmfcwp70c"))))
     (build-system python-build-system)
     (arguments
      ;; FIXME: some tests do not return and time out.  Some tests fail because
      ;; some processes survive kill().
      '(#:tests? #f))
-    (home-page "https://www.github.com/giampaolo/psutil")
+    (home-page "https://github.com/giampaolo/psutil")
     (synopsis "Library for retrieving information on running processes")
     (description
-     "psutil (Python system and process utilities) is a library for retrieving
-information on running processes and system utilization (CPU, memory, disks,
-network) in Python.  It is useful mainly for system monitoring, profiling and
-limiting process resources and management of running processes.  It implements
-many functionalities offered by command line tools such as: ps, top, lsof,
-netstat, ifconfig, who, df, kill, free, nice, ionice, iostat, iotop, uptime,
-pidof, tty, taskset, pmap.")
+     "@code{psutil} (Python system and process utilities) is a library for
+retrieving information on running processes and system utilization (CPU,
+memory, disks, network) in Python.  It is useful mainly for system monitoring,
+profiling and limiting process resources and management of running processes.
+It implements many functionalities offered by command line tools such as: ps,
+top, lsof, netstat, ifconfig, who, df, kill, free, nice, ionice, iostat,
+iotop, uptime, pidof, tty, taskset, pmap.")
     (properties `((python2-variant . ,(delay python2-psutil))))
     (license license:bsd-3)))
 
 (define-public python2-psutil
   (let ((base (package-with-python2 (strip-python2-variant python-psutil))))
-    (package
-      (inherit base)
+    (package/inherit base
       (propagated-inputs
        `(("python2-enum34" ,python2-enum34)         ;optional
          ,@(package-propagated-inputs base))))))
@@ -659,25 +662,31 @@ module and then similar looking characters are removed.")
 (define-public python-logwrap
   (package
     (name "python-logwrap")
-    (version "3.2.1")
+    (version "8.2.0.post0")
     (source
      (origin
        (method url-fetch)
-       (uri (pypi-uri "logwrap" version ".zip"))
+       (uri (pypi-uri "logwrap" version))
        (sha256
         (base32
-         "1d2k0hvpbi51vl410y8fbs5m0nxnlh2k7gr2nrh3k81ibhzscsra"))))
+         "1dv7gny3rfci5cal2ipr6d0pcz3yhka7af96dfsd3ir1mxy8p1j9"))))
     (build-system python-build-system)
-    (propagated-inputs
-     `(("python-six" ,python-six)
-       ("python-typing" ,python-typing)))
+    (arguments
+     `(#:tests? #f  ; Tests not included in pypi release.
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "pytest"))
+             #t)))))
     (native-inputs
-     `(("unzip" ,unzip)
-       ("python-cython" ,python-cython)
+     `(("python-cython" ,python-cython)
        ("python-pytest" ,python-pytest)
-       ("python-pytest-cov" ,python-pytest-cov)
-       ("python-pytest-runner" ,python-pytest-runner)))
-    (home-page "https://github.com/penguinolog/logwrap")
+       ("python-setuptools-scm" ,python-setuptools-scm)
+       ("python-toml" ,python-toml)
+       ("python-wheel" ,python-wheel)))
+    (home-page "https://github.com/python-useful-helpers/logwrap")
     (synopsis "Decorator for logging function arguments")
     (description "This package provides a decorator to log function arguments
 and function call return values in a human-readable way.")
@@ -769,6 +778,47 @@ certificate returned by the server to which a connection has been established,
 and verifies that it matches the intended target hostname.")
     (license license:psfl)))
 
+(define-public python-bidict
+  (package
+    (name "python-bidict")
+    (version "0.21.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "bidict" version))
+       (sha256
+        (base32
+         "02dy0b1k7qlhn7ajyzkrvxhyhjj0hzcq6ws3zjml9hkdz5znz92g"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-coverage" ,python-coverage)
+       ("python-hypothesis" ,python-hypothesis-5.23) ; use_true_random=... from >=5.19.0
+       ("python-pre-commit" ,python-pre-commit)
+       ("python-py" ,python-py)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-benchmark" ,python-pytest-benchmark)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-setuptools-scm" ,python-setuptools-scm)
+       ("python-sortedcollections" ,python-sortedcollections)
+       ("python-sortedcontainers" ,python-sortedcontainers)
+       ("python-sphinx" ,python-sphinx)
+       ("python-sphinx-autodoc-typehints" ,python-sphinx-autodoc-typehints)
+       ("python-tox" ,python-tox)))
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'relax-reqs
+                    (lambda _
+                      (substitute* "setup.py"
+                        (("sortedcollections < 2") "sortedcollections"))
+                      #t))
+                  (replace 'check
+                    (lambda _ (invoke "./run_tests.py"))))))
+    (home-page "https://bidict.readthedocs.io")
+    (synopsis "Bidirectional mapping library")
+    (description "The @code{bidict} library provides several data structures
+for working with bidirectional mappings in Python.")
+    (license license:mpl2.0)))
+
 (define-public python-bitarray
   (package
     (name "python-bitarray")
@@ -942,9 +992,6 @@ concepts.")
 @code{subprocess} feature.")
     (license license:expat)))
 
-(define-public python2-sh
-  (package-with-python2 python-sh))
-
 (define-public python-cftime
   (package
     (name "python-cftime")
@@ -1132,8 +1179,7 @@ other machines, such as over the network.")
 
 (define-public python2-serpent
   (let ((base (package-with-python2 (strip-python2-variant python-serpent))))
-    (package
-      (inherit base)
+    (package/inherit base
       (propagated-inputs
        `(("python-enum34" ,python2-enum34)
          ,@(package-propagated-inputs base))))))
@@ -1306,7 +1352,7 @@ helpers.")
 (define-public python2-humanfriendly
   (let ((base (package-with-python2
                 (strip-python2-variant python-humanfriendly))))
-    (package (inherit base)
+    (package/inherit base
       (propagated-inputs
        `(("python2-monotonic" ,python2-monotonic)
          ,@(package-propagated-inputs base))))))
@@ -1831,7 +1877,9 @@ standard.")
          "1hgz8jq19wlz8vwqj900ry8cjv578nz4scc91mlc8944yid6573c"))))
     (build-system python-build-system)
     (propagated-inputs
-     `(("python-greenlet" ,python-greenlet)))
+     `(("python-dnspython" ,python-dnspython)
+       ("python-greenlet" ,python-greenlet)
+       ("python-monotonic" ,python-monotonic)))
     (arguments
      ;; TODO: Requires unpackaged 'enum-compat'.
      '(#:tests? #f))
@@ -2131,8 +2179,7 @@ commands.")
 
 (define-public python2-empy
   (let ((base (package-with-python2 (strip-python2-variant python-empy))))
-    (package
-      (inherit base)
+    (package/inherit base
       (arguments `(,@(package-arguments base)
                    #:tests? #t)))))
 
@@ -2261,7 +2308,7 @@ backported for previous versions of Python from 2.4 to 3.3.")
 (define-public python2-parse-type
   (let ((base (package-with-python2
                 (strip-python2-variant python-parse-type))))
-    (package (inherit base)
+    (package/inherit base
       (propagated-inputs
        `(("python2-enum34" ,python2-enum34)
          ,@(package-propagated-inputs base))))))
@@ -2310,8 +2357,7 @@ existing ones.")
 
 (define-public python2-polib
   (let ((base (package-with-python2 (strip-python2-variant python-polib))))
-    (package
-      (inherit base)
+    (package/inherit base
       (arguments `(,@(package-arguments base)
                    ;; Tests don't work with python2.
                    #:tests? #f)))))
@@ -2382,6 +2428,30 @@ software.")
     (inherit (package-with-python2 scons))
     (name "scons-python2")))
 
+(define-public python-extension-helpers
+(package
+  (name "python-extension-helpers")
+  (version "0.1")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (pypi-uri "extension-helpers" version))
+      (sha256
+        (base32 "10iqjzmya2h4sk765dlm1pbqypwlqyh8rw59a5m9i63d3klnz2mc"))))
+  (build-system python-build-system)
+  (native-inputs
+    `(("coverage" ,python-coverage)
+      ("pytest" ,python-pytest-astropy)
+      ("pytest-cov" ,python-pytest-cov)
+      ("setuptools-scm" ,python-setuptools-scm)))
+  (home-page "https://github.com/astropy/astropy-helpers")
+  (synopsis
+   "Utilities for building and installing packages in the Astropy ecosystem")
+  (description
+    "The extension-helpers package includes many build, installation, and
+documentation-related tools used by the Astropy project.")
+  (license license:bsd-3)))
+
 (define-public python-extras
   (package
     (name "python-extras")
@@ -2885,7 +2955,7 @@ compare, diff, and patch JSON and JSON-like structures in Python.")
 (define-public python2-jsonschema
   (let ((jsonschema (package-with-python2
                      (strip-python2-variant python-jsonschema))))
-    (package (inherit jsonschema)
+    (package/inherit jsonschema
              (propagated-inputs
               `(("python2-functools32" ,python2-functools32)
                 ,@(package-propagated-inputs jsonschema))))))
@@ -3382,15 +3452,16 @@ logic-free templating system Mustache.")
     (properties `((python2-variant . ,(delay python2-pystache))))))
 
 (define-public python2-pystache
-  (package (inherit (package-with-python2
-                     (strip-python2-variant python-pystache)))
-           (arguments
-            `(#:python ,python-2
-              #:phases
-              (modify-phases %standard-phases
-                (replace 'check
-                  (lambda _
-                    (invoke "python" "test_pystache.py"))))))))
+  (let ((base (package-with-python2
+               (strip-python2-variant python-pystache))))
+    (package/inherit base
+      (arguments
+       `(#:python ,python-2
+         #:phases
+         (modify-phases %standard-phases
+           (replace 'check
+             (lambda _
+               (invoke "python" "test_pystache.py")))))))))
 
 (define-public python-joblib
   (package
@@ -3729,7 +3800,7 @@ to deprecate classes, functions or methods.")
 (define-public python-pygithub
   (package
     (name "python-pygithub")
-    (version "1.43.8")
+    (version "1.54.1")
     (source
      ;; We fetch from the Git repo because there are no tests in the PyPI
      ;; archive.
@@ -3740,30 +3811,24 @@ to deprecate classes, functions or methods.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1625v558xga5mwhl9jqmibywy5qafmg1vqrirqz6zfq1la1d22mw"))))
+        (base32 "1nl74bp5ikdnrc8xq0qr25ryl1mvarf0xi43k8w5jzlrllhq0nkq"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases (modify-phases %standard-phases
-                  ;; Some tests rely on the network.
-                  (add-after 'unpack 'disable-failing-tests
-                    (lambda _
-                      (substitute* "tests/Issue142.py"
-                        (("testDecodeJson") "disabled_testDecodeJson"))
-                      #t))
-                  (add-before 'check 'prepare-for-tests
-                    (lambda _
-                      (for-each (lambda (f)
-                                  (chmod f #o666))
-                                (find-files "./tests"))
-                      (system* "python" "-m" "lib2to3" "-w" "-n" "tests")
-                      (setenv "PYTHONPATH"
-                              (string-append "./tests:" (getenv "PYTHONPATH")))
-                      #t)))))
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "pytest"))
+             #t)))))
     (propagated-inputs
-     `(("python-deprecated" ,python-deprecated)
+     `(("python-cryptography" ,python-cryptography)
+       ("python-deprecated" ,python-deprecated)
        ("python-pyjwt" ,python-pyjwt)
        ("python-requests" ,python-requests)))
-    (native-inputs `(("python-httpretty" ,python-httpretty)))
+    (native-inputs
+     `(("python-httpretty" ,python-httpretty)
+       ("python-pytest" ,python-pytest)))
     (home-page "https://pygithub.readthedocs.io/en/latest/")
     (synopsis "Python library for the GitHub API")
     (description "This library allows managing GitHub resources such as
@@ -3959,8 +4024,7 @@ for SSH and SFTP.  It has the following main usages:
       (base32
        "197dw8mbq0pjjz1l6h1ksi62vgn7x55d373ch74y06744qiq5sjx"))))
    (build-system python-build-system)
-   (home-page
-    "http://bitbucket.org/leapfrogdevelopment/rstr/overview")
+   (home-page "https://github.com/leapfrogonline/rstr")
    (synopsis "Generate random strings in Python")
    (description "This package provides a python module for generating
 random strings of various types.  It could be useful for fuzz testing,
@@ -4448,8 +4512,7 @@ writing C extensions for Python as easy as Python itself.")
 
 (define-public python2-cython
   (let ((base (package-with-python2 (strip-python2-variant python-cython))))
-    (package
-      (inherit base)
+    (package/inherit base
       (name "python2-cython")
       (inputs
        `(("python-2" ,python-2)))       ;this is not automatically changed
@@ -4999,8 +5062,7 @@ that client code uses to construct the grammar directly in Python code.")
 (define-public python2-numpydoc
   (let ((base (package-with-python2
                (strip-python2-variant python-numpydoc))))
-    (package
-      (inherit base)
+    (package/inherit base
       (propagated-inputs
        `(("python2-jinja2" ,python2-jinja2)
          ,@(package-propagated-inputs base))))))
@@ -5051,7 +5113,7 @@ transcendental functions).")
      '(#:tests? #f))
     (propagated-inputs
      `(("python-six" ,python-six)))
-    (home-page "http://matplotlib.org/cycler/")
+    (home-page "https://matplotlib.org/cycler/")
     (synopsis "Composable keyword argument iterator")
     (description
      "When using @code{matplotlib} and plotting more than one line, it is
@@ -5106,8 +5168,9 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc.
        (method url-fetch)
        (uri (pypi-uri "matplotlib" version))
        (sha256
-        (base32
-         "1nmshfqh7wyg15i16hx1yiylcvzkws29ivn66n3i0wyqwcpjr3lf"))))
+        (base32 "1nmshfqh7wyg15i16hx1yiylcvzkws29ivn66n3i0wyqwcpjr3lf"))
+       (patches
+        (search-patches "python-matplotlib-run-under-wayland-gtk3.patch"))))
     (build-system python-build-system)
     (propagated-inputs ; the following packages are all needed at run time
      `(("python-cycler" ,python-cycler)
@@ -5520,14 +5583,14 @@ a simple netcat replacement with chaining support.")
 (define-public python-pycodestyle
   (package
     (name "python-pycodestyle")
-    (version "2.6.0")
+    (version "2.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pycodestyle" version))
        (sha256
         (base32
-         "0bhr6ia0hmgx3nhgibc9pmkzhlh1zcqk707i5fbxgs702ll7v2n5"))))
+         "1vqwmzmjdv331kmfq3q9j3as2x7r2r49lf83r9w4147pdg8c32f3"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -5781,13 +5844,13 @@ the OleFileIO module from PIL, the Python Image Library.")
 (define-public python-pikepdf
   (package
     (name "python-pikepdf")
-    (version "2.5.2")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pikepdf" version))
        (sha256
-        (base32 "1wwfspm912388a61lailbpjpqihq9ha8yz05mjqx9yys4ixykhwg"))))
+        (base32 "09wfj1hjvj3r9gv7ywrqd7h3d0bz64bvils8sm3ghj90jhalb03s"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #false))                ;require python-xmp-toolkit
@@ -5812,14 +5875,14 @@ the OleFileIO module from PIL, the Python Image Library.")
 (define-public python-pillow
   (package
     (name "python-pillow")
-    (version "8.0.1")
+    (version "8.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Pillow" version))
        (sha256
         (base32
-         "17pv0flaqqfld9m4lz8ayxyqb11gbbmr7w04mw4ar79cn3lwdi8i"))))
+         "086g7nhv52wclrwnzbzs2x3nvyzs2hfq1bvgivsrp5f7r7wiiz7n"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-pytest" ,python-pytest)))
@@ -5894,6 +5957,39 @@ a general image processing tool.")
        ((#:tests? _ #f) #f)))
     (properties '((hidden? #t)))))
 
+(define-public python-pillow-simd
+  (package
+    (inherit python-pillow)
+    (name "python-pillow-simd")
+    (version "7.1.2")
+    ;; The PyPI tarball does not include test files.
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/uploadcare/pillow-simd")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0w11np4cybamry3jsg70x747c79zwjzfq0xiprfp6c186rd6nzp9"))))
+    (arguments
+     (substitute-keyword-arguments
+         (package-arguments python-pillow)
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-after 'unpack 'make-tests-writable
+             (lambda _
+               (for-each make-file-writable (find-files "Tests"))
+               #t))))))
+    (inputs
+     `(("libraqm" ,libraqm)
+       ("libimagequant" ,libimagequant)
+       ,@(package-inputs python-pillow)))
+    (home-page "https://github.com/uploadcare/pillow-simd")
+    (synopsis "Fork of the Python Imaging Library (Pillow)")
+    (description "This package is a fork of Pillow which adds support for SIMD
+parallelism.")))
+
 (define-public python-roifile
   (package
     (name "python-roifile")
@@ -6314,9 +6410,6 @@ graphics library with support for multiple backends including image buffers,
 PNG, PostScript, PDF, and SVG file output.")
     (license license:bsd-3)))
 
-(define-public python2-cairocffi
-  (package-with-python2 python-cairocffi))
-
 (define-public python-decorator
   (package
     (name "python-decorator")
@@ -7010,8 +7103,7 @@ CLI scripts:
 
 (define-public python2-ipyparallel
   (let ((ipyparallel (package-with-python2 python-ipyparallel)))
-    (package
-      (inherit ipyparallel)
+    (package/inherit ipyparallel
       (propagated-inputs
        `(("python2-futures" ,python2-futures)
          ,@(package-propagated-inputs ipyparallel))))))
@@ -7099,8 +7191,7 @@ without using the configuration machinery.")
 
 (define-public python2-traitlets
   (let ((traitlets (package-with-python2 (strip-python2-variant python-traitlets))))
-    (package
-      (inherit traitlets)
+    (package/inherit traitlets
       (propagated-inputs
        `(("python2-enum34" ,python2-enum34)
          ,@(package-propagated-inputs traitlets))))))
@@ -7121,7 +7212,7 @@ without using the configuration machinery.")
     (arguments `(#:tests? #f))
     (propagated-inputs
      `(("python-traitlets" ,python-traitlets)))
-    (home-page "http://jupyter.org/")
+    (home-page "https://jupyter.org/")
     (synopsis "Jupyter base package")
     (description
      "Jupyter core is the base package on which Jupyter projects rely.")
@@ -7162,7 +7253,7 @@ without using the configuration machinery.")
      `(("python-pyzmq" ,python-pyzmq)
        ("python-traitlets" ,python-traitlets)
        ("python-jupyter-core" ,python-jupyter-core)))
-    (home-page "http://jupyter.org/")
+    (home-page "https://jupyter.org/")
     (synopsis "Jupyter protocol implementation and client libraries")
     (description
      "The @code{jupyter_client} package contains the reference implementation
@@ -7277,14 +7368,14 @@ installing @code{kernelspec}s for use with Jupyter frontends.")
 (define-public python-backcall
   (package
     (name "python-backcall")
-    (version "0.1.0")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "backcall" version))
        (sha256
         (base32
-         "1r01dqch3f8fdj3n6fviw8hxqrs6w5v0qw4izmvqzry1w9dxiv1q"))))
+         "07jy4562lvnhkk6kfr3cphmizy88anlhmbwb8kdzlz2ypqkvzgaw"))))
     (build-system python-build-system)
     (home-page "https://github.com/takluyver/backcall/")
     (synopsis "Specifications for callback functions passed in to an API")
@@ -7528,24 +7619,69 @@ computing.")
 (define-public python-urwid
   (package
     (name "python-urwid")
-    (version "2.1.0")
+    (version "2.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "urwid" version))
        (sha256
         (base32
-         "11ndnhxd41m13darf5s0c6bafdpkzq1l6mfb04wbzdmyc1hg75h8"))))
+         "1bky2bra6673xx8jy0826znw6cmxs89wcwwzda8d025j3jffx2sq"))))
     (build-system python-build-system)
     (home-page "http://urwid.org")
     (synopsis "Console user interface library for Python")
     (description
      "Urwid is a curses-based UI/widget library for Python.  It includes many
 features useful for text console applications.")
+    (properties `((python2-variant . ,(delay python2-urwid))))
     (license license:lgpl2.1+)))
 
 (define-public python2-urwid
-  (package-with-python2 python-urwid))
+  (let ((base (package-with-python2
+               (strip-python2-variant python-urwid))))
+    (package/inherit base
+      (version "2.1.0")
+      (source
+       (origin
+         (method url-fetch)
+         (uri (pypi-uri "urwid" version))
+         (sha256
+          (base32
+           "11ndnhxd41m13darf5s0c6bafdpkzq1l6mfb04wbzdmyc1hg75h8")))))))
+
+(define-public python-urwid-readline
+  (package
+    (name "python-urwid-readline")
+    (version "0.12")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/rr-/urwid_readline")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0sq5qgxj7gcfww3ww7idr87isnmp0hi36n241b3q395x1zafdv22"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "python" "-m" "pytest"))
+             #t)))))
+    (propagated-inputs
+     `(("python-urwid" ,python-urwid)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
+    (home-page "https://github.com/rr-/urwid_readline")
+    (synopsis "Text input widget for urwid that supports readline shortcuts")
+    (description
+     "This package provides a textbox edit widget for @code{python-urwid} that
+supports @code{readline} shortcuts.")
+    (license license:expat)))
 
 (define-public python-urwidtrees
   (package
@@ -7652,7 +7788,7 @@ implementation of D-Bus.")
     (license license:expat)))
 
 (define-public python2-dbus
-  (package (inherit python-dbus)
+  (package/inherit python-dbus
     (name "python2-dbus")
     (inputs `(("python" ,python-2)
               ,@(alist-delete "python"
@@ -7691,14 +7827,14 @@ the GObject Introspection bindings to libnotify for non-GTK applications.")
 (define-public python-beautifulsoup4
   (package
     (name "python-beautifulsoup4")
-    (version "4.9.1")
+    (version "4.9.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "beautifulsoup4" version))
        (sha256
         (base32
-         "1mvzlw3pzbhsvl3z8784s5h7iiflm2hggiy1fxyrrxwnbc8lvk3k"))))
+         "09gbd49mwz86k572r1231x2rdp82p42zlnw0bz9b9mfi58r9wwl4"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -7726,22 +7862,22 @@ converts incoming documents to Unicode and outgoing documents to UTF-8.")
     (properties `((python2-variant . ,(delay python2-beautifulsoup4))))))
 
 (define-public python2-beautifulsoup4
-  (package
-    (inherit (package-with-python2
-              (strip-python2-variant python-beautifulsoup4)))
-    (arguments `(#:python ,python-2))))
+  (let ((base (package-with-python2
+               (strip-python2-variant python-beautifulsoup4))))
+   (package/inherit base
+     (arguments `(#:python ,python-2)))))
 
 (define-public python-soupsieve
   (package
     (name "python-soupsieve")
-    (version "2.0.1")
+    (version "2.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "soupsieve" version))
        (sha256
         (base32
-         "0ch2rhvsbwfpvzm4kzy81rclbzr533yv83hzg1gx55byfa0w37d5"))))
+         "1k70gpn2d3vgdyxbdy536dgm4kchcraxz6lmgsfg3324iy2789q5"))))
     (build-system python-build-system)
     (arguments `(#:tests? #f))
     ;;XXX: 2 tests fail currently despite claming they were to be
@@ -7873,16 +8009,81 @@ of the structure, dynamics, and functions of complex networks.")
 Python.")
     (license license:lgpl2.1+)))
 
+(define-public python-amply
+  (package
+    (name "python-amply")
+    (version "0.1.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "amply" version))
+       (sha256
+        (base32
+         "0f1db9zp0rsfzxvaz55xwh8h5rfdgr9a2a715g06ic8nknsdq4nb"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-docutils" ,python-docutils)
+       ("python-pyparsing" ,python-pyparsing)))
+    (native-inputs
+     `(("python-setuptools-scm" ,python-setuptools-scm)))
+    (home-page "https://github.com/willu47/amply")
+    (synopsis "Load and manipulate AMPL/GLPK data as Python data structures")
+    (description
+     "Amply allows you to load and manipulate AMPL/GLPK data as Python data
+structures.")
+    (license license:epl1.0)))
+
+(define-public python-pulp
+  (package
+    (name "python-pulp")
+    (version "2.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "PuLP" version))
+       (sha256
+        (base32
+         "1dammrg0f1v0r028i3rpxbf2bsyxmjq0q6ihb4x2wsdki44z3bxj"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-amply" ,python-amply)))
+    (home-page "https://github.com/coin-or/pulp")
+    (synopsis "Linear Programming modeler")
+    (description
+     "PuLP is a Linear Programming modeler written in Python.  PuLP can
+generate MPS or LP files and call GLPK, COIN CLP/CBC, CPLEX, and GUROBI to
+solve linear problems.")
+    (license license:expat)))
+
+(define-public python-toposort
+  (package
+    (name "python-toposort")
+    (version "1.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "toposort" version))
+       (sha256
+        (base32
+         "1b2hppzjg3p006qya3yfdnp76dwq8frl97lypdam0kw4xxb8yhm7"))))
+    (build-system python-build-system)
+    (home-page "https://gitlab.com/ericvsmith/toposort")
+    (synopsis "Topological sort algorithm")
+    (description
+     "This package provides an implementation of a topological sort
+algorithm.")
+    (license license:asl2.0)))
+
 (define-public snakemake
   (package
     (name "snakemake")
-    (version "5.7.1")
+    (version "5.32.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "snakemake" version))
        (sha256
-        (base32 "1pnpvvn8n2a78cg360wz3ldmpqrsm2wzi0c0dmvki9fnsw6fxdas"))))
+        (base32 "13013gdavwvyj1qr9xfi9fpwhb3km8c3z53bja5b7ic3sb2z6dgz"))))
     (build-system python-build-system)
     (arguments
      ;; TODO: Package missing test dependencies.
@@ -7894,7 +8095,7 @@ Python.")
          ;; this by calling the snakemake wrapper instead.
          (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
            (lambda* (#:key outputs #:allow-other-keys)
-             (substitute* "snakemake/executors.py"
+             (substitute* "snakemake/executors/__init__.py"
                (("\\{sys.executable\\} -m snakemake")
                 (string-append (assoc-ref outputs "out")
                                "/bin/snakemake")))
@@ -7907,11 +8108,14 @@ Python.")
        ("python-gitpython" ,python-gitpython)
        ("python-jinja2" ,python-jinja2)
        ("python-jsonschema" ,python-jsonschema)
+       ("python-nbformat" ,python-nbformat)
        ("python-networkx" ,python-networkx)
        ("python-psutil" ,python-psutil)
+       ("python-pulp" ,python-pulp)
        ("python-pyyaml" ,python-pyyaml)
        ("python-ratelimiter" ,python-ratelimiter)
        ("python-requests" ,python-requests)
+       ("python-toposort" ,python-toposort)
        ("python-wrapt" ,python-wrapt)))
     (home-page "https://snakemake.readthedocs.io")
     (synopsis "Python-based execution environment for make-like workflows")
@@ -8015,7 +8219,7 @@ and statistical routines from scipy and statsmodels.")
        (replace 'check
          (lambda _
            (invoke "python" "mpmath/tests/runtests.py" "-local"))))))
-  (home-page "http://mpmath.org")
+  (home-page "https://mpmath.org")
   (synopsis "Arbitrary-precision floating-point arithmetic in python")
   (description
     "@code{mpmath} can be used as an arbitrary-precision substitute for
@@ -8304,13 +8508,13 @@ applications.")
 (define-public python-pyzmq
   (package
     (name "python-pyzmq")
-    (version "17.1.2")
+    (version "22.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyzmq" version))
        (sha256
-        (base32 "1pyxxrz60f88ffm0y6vpbx3q8jcr9ybz8fcilihwzwhh36n84ax7"))))
+        (base32 "0bgrn65cxfz1c1sjrgyq5dy1mkhppxxbizd5wvrl03cq4zhkrxpp"))))
     (build-system python-build-system)
     (arguments
      `(#:configure-flags
@@ -8383,8 +8587,7 @@ PEP 8.")
 (define-public python2-pep517
   (let ((base (package-with-python2
                 (strip-python2-variant python-pep517))))
-    (package
-      (inherit base)
+    (package/inherit base
       (name "python2-pep517")
       (arguments
        `(#:tests? #f
@@ -8394,14 +8597,14 @@ PEP 8.")
 (define-public python-pyflakes
   (package
     (name "python-pyflakes")
-    (version "2.2.0")
+    (version "2.3.1")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "pyflakes" version))
         (sha256
           (base32
-            "1j3zqbiwkyicvww499bblq33x0bjpzdrxajhaysr7sk7x5gdgcim"))))
+            "1ny10364ciqh4ripasj4zzv4145l21l3s85m3qlrvfq5pk58xg7m"))))
     (build-system python-build-system)
     (home-page
       "https://github.com/pyflakes/pyflakes")
@@ -8441,13 +8644,13 @@ complexity of Python source code.")
 (define-public python-flake8
   (package
     (name "python-flake8")
-    (version "3.8.4")
+    (version "3.9.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "flake8" version))
               (sha256
                (base32
-                "0fvcrsbyzjpcli8ldbpsdbpmf238nkvwc1dy4hy82lf63rvfinma"))))
+                "1w65iyjnrwipv4dbcqxh725ri7mdx01d6pjyggd97c0j5cvkx1vq"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -8476,7 +8679,7 @@ complexity of Python source code.")
 
 (define-public python2-flake8
   (let ((base (package-with-python2 (strip-python2-variant python-flake8))))
-    (package (inherit base)
+    (package/inherit base
       (propagated-inputs
        `(("python2-configparser" ,python2-configparser)
          ("python2-enum34" ,python2-enum34)
@@ -8520,6 +8723,34 @@ design problems in your program.  It contains warnings that don't belong
 in pyflakes and pycodestyle.")
     (license license:expat)))
 
+(define-public python-flake8-continuation
+  (package
+    (name "python-flake8-continuation")
+    (version "1.0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "flake8-continuation" version))
+       (sha256
+        (base32
+         "0dzaw8jr7yhlabxhrblnrizxx17xa9ngjnbr1kidg5lapq6b9q1y"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-flake8" ,python-flake8)
+       ("python-pycodestyle" ,python-pycodestyle)
+       ("python-six" ,python-six)))
+    (home-page "https://github.com/planetlabs/flake8-continuation")
+    (synopsis "Flake8 Line Continuation Plugin")
+    (description "A Flake8 plugin that checks for the line continuation
+style to be in the preferred method according to PEP-8, specifically:
+@quotation
+The preferred way of wrapping long lines is by using Python's implied
+line continuation inside parentheses, brackets and braces.  Long lines
+can be broken over multiple lines by wrapping expressions in parentheses.
+These should be used in preference to using a backslash for line continuation.
+@end quotation")
+    (license license:asl2.0)))
+
 (define-public python-flake8-implicit-str-concat
   (package
     (name "python-flake8-implicit-str-concat")
@@ -8658,6 +8889,25 @@ first-class forward references that stub files use.")
 lints.")
     (license license:bsd-2)))
 
+(define-public python-flake8-quotes
+  (package
+    (name "python-flake8-quotes")
+    (version "3.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "flake8-quotes" version))
+       (sha256
+        (base32
+         "0ph5s6lxgpzz4an0ax6s5xjqypqmngwr5b1i0h9pqhzghplic49z"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-flake8" ,python-flake8)))
+    (home-page "https://github.com/zheller/flake8-quotes/")
+    (synopsis "Flake8 lint for quotes")
+    (description "This package provides a Flake8 lint for quotes.")
+    (license license:expat)))
+
 (define-public python-autoflake
   (package
     (name "python-autoflake")
@@ -9002,9 +9252,10 @@ third-party code.")
     (properties `((python2-variant . ,(delay python2-llfuse))))))
 
 (define-public python2-llfuse
-  (package (inherit (package-with-python2
-                 (strip-python2-variant python-llfuse)))
-    (propagated-inputs `(("python2-contextlib2" ,python2-contextlib2)))))
+  (let ((base (package-with-python2
+               (strip-python2-variant python-llfuse))))
+    (package/inherit base
+      (propagated-inputs `(("python2-contextlib2" ,python2-contextlib2))))))
 
 (define-public python-msgpack
   (package
@@ -9357,9 +9608,6 @@ tasks, sockets, files, locks, and queues.")
 designed to efficiently cope with extremely large amounts of data.")
     (license license:bsd-3)))
 
-(define-public python2-tables
-  (package-with-python2 python-tables))
-
 (define-public python-sniffio
   (package
     (name "python-sniffio")
@@ -9516,13 +9764,13 @@ implementations of ASN.1-based codecs and protocols.")
 (define-public python-ipaddress
   (package
     (name "python-ipaddress")
-    (version "1.0.22")
+    (version "1.0.23")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "ipaddress" version))
               (sha256
                (base32
-                "0b570bm6xqpjwqis15pvdy6lyvvzfndjvkynilcddjj5x98wfimi"))))
+                "1qp743h30s04m3cg3yk3fycad930jv17q7dsslj4mfw0jlvf1y5p"))))
     (build-system python-build-system)
     (home-page "https://github.com/phihag/ipaddress")
     (synopsis "IP address manipulation library")
@@ -9752,8 +10000,7 @@ a hash value.")
     (license license:asl2.0)))
 
 (define-public python2-tlsh
-  (package
-    (inherit python-tlsh)
+  (package/inherit python-tlsh
     (name "python2-tlsh")
     (inputs `(("python" ,python-2)))))
 
@@ -9842,8 +10089,7 @@ Python's @code{ctypes} foreign function interface (FFI).")
   (package-with-python2 python-libarchive-c))
 
 (define-public python-file
-  (package
-    (inherit file)
+  (package/inherit file
     (name "python-file")
     (build-system python-build-system)
     (arguments
@@ -9944,7 +10190,7 @@ Debian-related files, such as:
        ("python-jsonschema" ,python-jsonschema)
        ("python-jupyter-core" ,python-jupyter-core)
        ("python-traitlets" ,python-traitlets)))
-    (home-page "http://jupyter.org")
+    (home-page "https://jupyter.org")
     (synopsis "Jupyter Notebook format")
     (description "This package provides the reference implementation of the
 Jupyter Notebook format and Python APIs for working with notebooks.")
@@ -10133,7 +10379,7 @@ time.")
        ("python-nbformat" ,python-nbformat)
        ("python-pygments" ,python-pygments)
        ("python-traitlets" ,python-traitlets)))
-    (home-page "http://jupyter.org")
+    (home-page "https://jupyter.org")
     (synopsis "Converting Jupyter Notebooks")
     (description "The @code{nbconvert} tool, @{jupyter nbconvert}, converts
 notebooks to various other formats via Jinja templates.  It allows you to
@@ -10190,7 +10436,7 @@ convert an @code{.ipynb} notebook file into various static formats including:
      `(("python-nose" ,python-nose)
        ("python-sphinx" ,python-sphinx)
        ("python-requests" ,python-requests)))
-    (home-page "http://jupyter.org/")
+    (home-page "https://jupyter.org/")
     (synopsis "Web-based notebook environment for interactive computing")
     (description
      "The Jupyter HTML notebook is a web-based notebook environment for
@@ -10201,7 +10447,7 @@ interactive computing.")
 (define-public python2-notebook
   (let ((base (package-with-python2
                 (strip-python2-variant python-notebook))))
-    (package (inherit base)
+    (package/inherit base
       (native-inputs
        `(("python2-mock" ,python2-mock)
          ,@(package-native-inputs base)))
@@ -10242,9 +10488,6 @@ interactive computing.")
 notebooks.")
     (license license:bsd-3)))
 
-(define-public python2-widgetsnbextension
-  (package-with-python2 python-widgetsnbextension))
-
 (define-public python-ipywidgets
   (package
     (name "python-ipywidgets")
@@ -10272,9 +10515,6 @@ widgets are used.  Users gain control of their data and can visualize changes
 in the data.")
     (license license:bsd-3)))
 
-(define-public python2-ipywidgets
-  (package-with-python2 python-ipywidgets))
-
 (define-public python-jupyter-console
   (package
     (name "python-jupyter-console")
@@ -10335,8 +10575,7 @@ Jupyter kernels such as IJulia and IRKernel.")
 ;; the functionality in both packages working, strip down the
 ;; python-jupyter-console package when using it as an input to python-ipython.
 (define python-jupyter-console-minimal
-  (package
-    (inherit python-jupyter-console)
+  (package/inherit python-jupyter-console
     (name "python-jupyter-console-minimal")
     (arguments
      (substitute-keyword-arguments
@@ -10387,7 +10626,7 @@ Jupyter kernels such as IJulia and IRKernel.")
        ("python-ipython" ,python-ipython)))
     (native-inputs
      `(("python-pytest" ,python-pytest)))
-    (home-page "http://jupyter.org")
+    (home-page "https://jupyter.org")
     (synopsis "Jupyter Qt console")
     (description "This package provides a Qt-based console for Jupyter with
 support for rich media output.")
@@ -10676,8 +10915,7 @@ the standard library.")
 (define-public python2-contextlib2
   (let ((base (package-with-python2
                (strip-python2-variant python-contextlib2))))
-    (package
-      (inherit base)
+    (package/inherit base
       (arguments
        (substitute-keyword-arguments (package-arguments base)
          ((#:phases phases)
@@ -10785,6 +11023,62 @@ applications.")
     (home-page "https://github.com/click-contrib/click-log")
     (license license:expat)))
 
+(define-public python-click-default-group
+  (package
+    (name "python-click-default-group")
+    (version "1.2.2")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "click-default-group" version))
+              (sha256
+               (base32
+                "015r78jk8gznfw0dphpwaqcx5mhg5822b55w5xbb6i7sin70wmnr"))))
+    (build-system python-build-system)
+    (arguments
+      `(#:tests? #f)) ; no target
+    (propagated-inputs
+     `(("python-click" ,python-click)))
+    (synopsis "Extends click.Group")
+    (description "This package extends click.Group to invoke a command without
+explicit subcommand name.")
+    (home-page "https://github.com/click-contrib/click-default-group")
+    (license license:bsd-3)))
+
+(define-public python-structlog
+  (package
+    (name "python-structlog")
+    (version "20.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "structlog" version))
+        (sha256
+         (base32
+          "0x1i21vn3xjfa3j9ijbblia5z0jlzc9aqvpqc26sy16i8yjxyydg"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "pytest"))
+             #t)))))
+    (native-inputs
+     `(("python-coverage" ,python-coverage)
+       ("python-freezegun" ,python-freezegun)
+       ("python-pretend" ,python-pretend)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-asyncio" ,python-pytest-asyncio)
+       ("python-simplejson" ,python-simplejson)
+       ("python-twisted" ,python-twisted)))
+    (home-page "https://www.structlog.org/")
+    (synopsis "Structured Logging for Python")
+    (description "@code{structlog} changes logging in Python by adding structure
+to your log entries.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public python-apipkg
   (package
     (name "python-apipkg")
@@ -10846,13 +11140,13 @@ minimal and fast API targeting the following uses:
 (define-public python-icalendar
   (package
     (name "python-icalendar")
-    (version "4.0.5")
+    (version "4.0.7")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri "icalendar" version))
              (sha256
               (base32
-               "14ynjj65kfmlcvpb7k097w789wvxncd3cr3xz5m1jz9yl9v6vv5q"))))
+               "19574j3jwssm2dkqykih4568xqfgjsa3hcd79yl5s2vfys3qvh8g"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-dateutil" ,python-dateutil)
@@ -11091,7 +11385,7 @@ concurrent.futures package from Python 3.2")
 (define-public python2-promise
   (let ((promise (package-with-python2
                    (strip-python2-variant python-promise))))
-    (package (inherit promise)
+    (package/inherit promise
       (arguments (substitute-keyword-arguments (package-arguments promise)
                    ((#:tests? _) #t)))
       (native-inputs
@@ -11392,6 +11686,85 @@ document.")
 manipulation library.")
     (license license:expat)))
 
+(define-public python-uncertainties
+  (package
+    (name "python-uncertainties")
+    (version "3.1.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "uncertainties" version))
+       (sha256
+        (base32
+         "00z9xl40czmqk0vmxjvmjvwb41r893l4dad7nj1nh6blw3kw28li"))))
+    (build-system python-build-system)
+    ;; While there are test files, there is no "tests" directory, so the tests
+    ;; fail.
+    (arguments '(#:tests? #false))
+    (propagated-inputs
+     `(("python-future" ,python-future)))
+    (native-inputs
+     `(("python-nose" ,python-nose)
+       ("python-numpy" ,python-numpy)))
+    (home-page "https://uncertainties-python-package.readthedocs.io/")
+    (synopsis "Calculations with uncertainties")
+    (description
+     "The uncertainties package transparently handles calculations with
+numbers with uncertainties. It can also yield the derivatives of any
+expression.")
+    (license license:bsd-3)))
+
+(define-public python-asteval
+  (package
+    (name "python-asteval")
+    (version "0.9.23")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "asteval" version))
+       (sha256
+        (base32
+         "0f54sd4w1a72ij1bcxs2x7dk9xf8bzclawijf1z18bqx9f96l2gm"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
+    (home-page "https://github.com/newville/asteval")
+    (synopsis "Minimalistic evaluator of Python expressions")
+    (description
+     "This package provides a minimalistic evaluator of Python expression
+using the @code{ast} module")
+    (license license:expat)))
+
+(define-public python-lmfit
+  (package
+    (name "python-lmfit")
+    (version "1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "lmfit" version))
+       (sha256
+        (base32
+         "0iab33jjb60f8kn0k0cqb0vjp1mdskks2n3kpn97zkw5cvjhq2b7"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-asteval" ,python-asteval)
+       ("python-numpy" ,python-numpy)
+       ("python-scipy" ,python-scipy)
+       ("python-uncertainties" ,python-uncertainties)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
+    (home-page "https://lmfit.github.io/lmfit-py/")
+    (synopsis "Least-Squares minimization with bounds and constraints")
+    (description
+     "Lmfit provides a high-level interface to non-linear optimization and
+curve fitting problems for Python.  It builds on and extends many of the
+optimization methods of @code{scipy.optimize}.  Initially inspired by (and
+named for) extending the Levenberg-Marquardt method from
+@code{scipy.optimize.leastsq}, lmfit now provides a number of useful
+enhancements to optimization and data fitting problems.")
+    (license license:bsd-3)))
+
 (define-public python-boto
   (package
     (name "python-boto")
@@ -11716,8 +12089,7 @@ and provides a uniform API regardless of which JSON implementation is used.")
 (define-public python2-anyjson
   (let ((anyjson (package-with-python2
                   (strip-python2-variant python-anyjson))))
-    (package
-      (inherit anyjson)
+    (package/inherit anyjson
       (arguments `(;; Unlike the python 3 variant, we do run tests.  See above!
                    #:tests? #t
                    ,@(package-arguments anyjson)))
@@ -11754,8 +12126,7 @@ alternative when librabbitmq is not available.")
 (define-public python2-amqp
   (let ((amqp (package-with-python2
                (strip-python2-variant python-amqp))))
-    (package
-      (inherit amqp)
+    (package/inherit amqp
       (arguments `(;; Tries to run coverage tests with nose-cover3, which seems
                    ;; unmaintained.  Weirdly, does not do this on the python 3
                    ;; version?
@@ -11827,8 +12198,7 @@ RabbitMQ messaging server is the most popular implementation.")
 (define-public python2-kombu
   (let ((kombu (package-with-python2
                 (strip-python2-variant python-kombu))))
-    (package
-      (inherit kombu)
+    (package/inherit kombu
       (arguments `(;; FIXME: 'TestTransport.test_del_sync' fails on python2.
                    ;; It works fine on the python3 variant.
                    #:tests? #f
@@ -11865,8 +12235,7 @@ Python 2.4 and 2.5, and will draw its fixes/improvements from python-trunk.")
 (define-public python2-billiard
   (let ((billiard (package-with-python2
                    (strip-python2-variant python-billiard))))
-    (package
-      (inherit billiard)
+    (package/inherit billiard
       (native-inputs `(("python2-unittest2" ,python2-unittest2)
                        ("python2-mock" ,python2-mock)
                        ,@(package-native-inputs billiard))))))
@@ -11916,8 +12285,7 @@ synchronously (wait until ready).")
 (define-public python2-celery
   (let ((celery (package-with-python2
                  (strip-python2-variant python-celery))))
-    (package
-      (inherit celery)
+    (package/inherit celery
       (native-inputs `(("python2-unittest2" ,python2-unittest2)
                        ("python2-mock" ,python2-mock)
                        ,@(package-native-inputs celery))))))
@@ -12071,7 +12439,7 @@ checking library.")
 
 (define-public python2-whoosh
   (let ((whoosh (package-with-python2 (strip-python2-variant python-whoosh))))
-    (package (inherit whoosh)
+    (package/inherit whoosh
       (propagated-inputs
        `(("python2-backport-ssl-match-hostname"
           ,python2-backport-ssl-match-hostname)
@@ -12185,7 +12553,7 @@ encoding algorithms to do fuzzy string matching.")
 (define-public python2-jellyfish
   (let ((jellyfish (package-with-python2
                      (strip-python2-variant python-jellyfish))))
-    (package (inherit jellyfish)
+    (package/inherit jellyfish
       (native-inputs `(("python2-unicodecsv" ,python2-unicodecsv)
                        ,@(package-native-inputs jellyfish))))))
 
@@ -12216,6 +12584,54 @@ encoding algorithms to do fuzzy string matching.")
 module, adding support for Unicode strings.")
     (license license:bsd-2)))
 
+(define-public python-pdfminer-six
+  (package
+    (name "python-pdfminer-six")
+    (version "20201018")
+    ;; There are no tests in the PyPI tarball.
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/pdfminer/pdfminer.six")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1a2fxxnnjqbx344znpvx7cnv1881dk6585ibw01inhfq3w6yj2lr"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; Tests write to the source tree.
+         (add-after 'unpack 'make-git-checkout-writable
+           (lambda _
+             (for-each make-file-writable (find-files "."))
+             #t))
+         (replace 'check
+           (lambda _
+             (invoke "make" "test")))
+         (add-before 'reset-gzip-timestamps 'make-files-writable
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (for-each make-file-writable
+                         (find-files out "\\.gz$"))
+               #t))))))
+    (propagated-inputs
+     `(("python-chardet" ,python-chardet)
+       ("python-cryptography" ,python-cryptography)
+       ("python-sortedcontainers" ,python-sortedcontainers)))
+    (native-inputs
+     `(("python-nose" ,python-nose)
+       ("python-tox" ,python-tox)))
+    (home-page "https://github.com/pdfminer/pdfminer.six")
+    (synopsis "PDF parser and analyzer")
+    (description "@code{pdfminer.six} is a community maintained fork of
+the original PDFMiner.  It is a tool for extracting information from PDF
+documents.  It focuses on getting and analyzing text data.  Pdfminer.six
+extracts the text from a page directly from the sourcecode of the PDF.  It
+can also be used to get the exact location, font or color of the text.")
+    (license license:expat)))
+
 (define-public python-rarfile
   (package
     (name "python-rarfile")
@@ -12552,8 +12968,7 @@ to occurrences in strings and comments.")
     (license license:gpl2)))
 
 (define-public python-rope
-  (package
-    (inherit python2-rope)
+  (package/inherit python2-rope
     (name "python-rope")
     (arguments `(#:python ,python-wrapper
                  ;; XXX: Only partial python3 support, results in some failing
@@ -12663,13 +13078,13 @@ multiple processes (imagine multiprocessing, billiard, futures, celery etc).
 (define-public python-greenlet
   (package
     (name "python-greenlet")
-    (version "0.4.17")
+    (version "1.0.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "greenlet" version))
               (sha256
                (base32
-                "0swdhrcq13bdszv3yz5645gi4ijbzmmhxpb6whcfg3d7d5f87n21"))))
+                "1y6wbg9yhm9dw6m768n4yslp56h85pnxkk3drz6icn15g6f1d7ki"))))
     (build-system python-build-system)
     (home-page "https://greenlet.readthedocs.io/")
     (synopsis "Lightweight in-process concurrent programming")
@@ -12710,19 +13125,18 @@ graphviz.")
 (define-public python-gevent
   (package
     (name "python-gevent")
-    (version "20.9.0")
+    (version "21.1.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "gevent" version))
               (sha256
                (base32
-                "13aw9x6imsy3b369kfjblqiwfni69pp32m4r13n62r9k3l2lhvaz"))
+                "10f9y899y9nmq51pv4r1zb51b4w5yxx00sz5whvg9vm956hc432j"))
               (modules '((guix build utils)))
               (snippet
                '(begin
                   ;; unbunding libev and c-ares
-                  (delete-file-recursively "deps")
-                  #t))))
+                  (delete-file-recursively "deps")))))
     (build-system python-build-system)
     (arguments
      `(#:modules ((ice-9 ftw)
@@ -12739,8 +13153,7 @@ graphviz.")
                                   (substitute* file
                                     (("/bin/sh") (which "sh"))
                                     (("/bin/true") (which "true"))))
-                                (find-files "src/greentest" "\\.py$"))
-                      #t))
+                                (find-files "src/greentest" "\\.py$"))))
                   (add-before 'build 'do-not-use-bundled-sources
                     (lambda _
                       (setenv "GEVENTSETUP_EMBED" "0")
@@ -12748,8 +13161,7 @@ graphviz.")
                       ;; Prevent building bundled libev.
                       (substitute* "setup.py"
                         (("run_make=_BUILDING")
-                         "run_make=False"))
-                      #t))
+                         "run_make=False"))))
                   (add-before 'build 'add-greenlet-on-C_INCLUDE_PATH
                     (lambda* (#:key inputs #:allow-other-keys)
                       (let ((greenlet (string-append
@@ -12762,16 +13174,14 @@ graphviz.")
                            (setenv "C_INCLUDE_PATH"
                                    (string-append greenlet "/" python ":"
                                                   (or (getenv "C_INCLUDE_PATH")
-                                                      ""))))))
-                      #t))
+                                                      ""))))))))
                   (add-before 'check 'pretend-to-be-CI
                     (lambda _
                       ;; A few tests are skipped due to network constraints or
                       ;; get longer timeouts when running in a CI environment.
                       ;; Piggy-back on that, as we need the same adjustments.
                       (setenv "TRAVIS" "1")
-                      (setenv "APPVEYOR" "1")
-                      #t))
+                      (setenv "APPVEYOR" "1")))
                   (add-before 'check 'adjust-tests
                     (lambda _
                       (let ((disabled-tests
@@ -12803,8 +13213,7 @@ graphviz.")
                         (call-with-output-file "skipped_tests.txt"
                           (lambda (port)
                             (format port "~a~%"
-                                    (string-join disabled-tests "\n"))))
-                        #t)))
+                                    (string-join disabled-tests "\n")))))))
                   (replace 'check
                     (lambda _
                       ;; Make sure the build directory is on PYTHONPATH.
@@ -12940,13 +13349,13 @@ It uses LR parsing and does extensive error checking.")
 (define-public python-tabulate
   (package
     (name "python-tabulate")
-    (version "0.8.7")
+    (version "0.8.9")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri "tabulate" version))
              (sha256
               (base32
-               "01shi7bmj09f0bcm5s0c9skys063lzp76p0n4a2xmg041ni269yv"))))
+               "19qkdz8xwk5jxa5xn53mnk76qnh4ysm81vzj664jw1b0azr167gb"))))
     (build-system python-build-system)
     (arguments
      ;; FIXME: The pypi release tarball is missing a 'test/common.py'
@@ -13279,7 +13688,7 @@ interfaces.")
         (base32
          "16wh8qgybmfh4pjp8vfv78mdlkxfmcasg78lzlnm6nslsfkci31p"))))
     (build-system python-build-system)
-    (home-page "http://msgpack.org/")
+    (home-page "https://msgpack.org/")
     (synopsis "Package to deserialize messages in MessagePack binary format")
     (description
      "MessagePack is an efficient binary serialization format.  It lets you
@@ -13327,7 +13736,7 @@ database, file, dict stores.  Cachy supports python versions 2.7+ and 3.2+.")
 (define-public poetry
   (package
     (name "poetry")
-    (version "1.1.4")
+    (version "1.1.5")
     ;; Poetry can only be built from source with Poetry.
     (source
      (origin
@@ -13335,7 +13744,7 @@ database, file, dict stores.  Cachy supports python versions 2.7+ and 3.2+.")
        (uri (pypi-uri "poetry" version))
        (sha256
         (base32
-         "1a2kgfiw66fvxhlqk5qc83s6l38czfh5hcsrbiy7qq5yfc8mlsll"))))
+         "1dvx08ksv5wnsj45db23921rj136akmcnxa0kmlsddf3wbh6wcka"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f ;; Pypi does not have tests.
@@ -13344,9 +13753,8 @@ database, file, dict stores.  Cachy supports python versions 2.7+ and 3.2+.")
          (add-before 'build 'patch-setup-py
            (lambda _
              (substitute* "setup.py"
-               ;; Newer versions of keyring produce a package with version "0.0.0"
-               ;; Reported upstream: <https://github.com/jaraco/keyring/issues/469>
-               (("keyring>=21.2.0,<22.0.0") "keyring>=21.0.0,<22.0.0")
+               ;; Allow newer versions of python-keyring.
+               (("(keyring>=21.2.0),<22.0.0" _ keyring) keyring)
                ;; TODO: remove after the next release cycle,
                ;; when packaging has been updated.
                (("packaging>=20.4,<21.0") "packaging>=20.0,<21.0"))
@@ -13809,9 +14217,11 @@ characters, mouse support, and auto suggestions.")
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
-           (lambda _
-             (setenv "HOME" "/tmp")
-             (invoke "python" "-m" "pytest" "-vv"))))))
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (setenv "HOME" "/tmp")
+               (invoke "python" "-m" "pytest" "-vv"))
+             #t)))))
     (native-inputs
      `(("python-pytest" ,python-pytest)
        ("python-docopt" ,python-docopt)))
@@ -13861,8 +14271,7 @@ etc.")
 
 (define-public ptpython-2
   (let ((base (package-with-python2 (strip-python2-variant ptpython))))
-    (package
-      (inherit base)
+    (package/inherit base
       (name "ptpython2"))))
 
 (define-public python-stem
@@ -13897,20 +14306,17 @@ control protocol to script against the Tor process and read descriptor data
 relays publish about themselves.")
     (license license:lgpl3)))
 
-(define-public python2-stem
-  (package-with-python2 python-stem))
-
 (define-public python-pyserial
   (package
     (name "python-pyserial")
-    (version "3.4")
+    (version "3.5")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "pyserial" version))
         (sha256
           (base32
-            "09y68bczw324a4jb9a1cfwrbjhq179vnfkkkrybbksp0vqgl0bbf"))))
+            "1nyd4m4mnrz8scbfqn4zpq8gnbl4x42w5zz62vcgpzqd2waf0xrw"))))
     (build-system python-build-system)
     (arguments
      '(#:tests? #f)) ; FIXME: 3/49 tests are failing.
@@ -14005,7 +14411,7 @@ binary or text.")
 
 (define-public python2-binaryornot
   (let ((base (package-with-python2 (strip-python2-variant python-binaryornot))))
-    (package (inherit base)
+    (package/inherit base
       (propagated-inputs
        `(("python2-enum34" ,python2-enum34)
          ,@(package-propagated-inputs base))))))
@@ -14254,13 +14660,13 @@ command @command{natsort} that exposes this functionality in the command line.")
 (define-public glances
   (package
   (name "glances")
-  (version "3.1.4")
+  (version "3.1.6")
   (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "Glances" version))
       (sha256
-        (base32 "0dc47gbvp9a3wxppdqihxpglxxaxbj3hcvzgcxxq8zcsciah3plq"))
+        (base32 "11xbm8jgcxha191ly7q76nab1ilabiz14mqf6i3y6aw5xvgg017c"))
       (modules '((guix build utils)))
       (snippet
        '(begin
@@ -14324,9 +14730,6 @@ This library is a port of @url{https://github.com/graphql/graphql-js,graphql-js}
 to Python.")
     (license license:expat)))
 
-(define-public python2-graphql-core
-  (package-with-python2 python-graphql-core))
-
 (define-public python-graphql-relay
   (package
     (name "python-graphql-relay")
@@ -14522,8 +14925,7 @@ is used by PostgreSQL and the OpenSSH Server for example.")
 (define-public python2-setproctitle
   (let ((base (package-with-python2
                (strip-python2-variant python-setproctitle))))
-    (package
-      (inherit base)
+    (package/inherit base
       (native-inputs `(("python2-nose" ,python2-nose)
                        ,@(package-native-inputs base))))))
 
@@ -14627,7 +15029,7 @@ Record Format (DWARF).")
                   (string-append "libev_dll_name = \"" libev "\"")))))))))
     (inputs
      `(("libev" ,libev)))
-    (home-page "http://pythonhosted.org/pyev/")
+    (home-page "https://github.com/gabrielfalcao/pyev")
     (synopsis "Python libev interface")
     (description "Pyev provides a Python interface to libev.")
     (license license:gpl3)))
@@ -14714,8 +15116,7 @@ network.")
 (define-public python2-argcomplete
   (let ((variant (package-with-python2
                   (strip-python2-variant python-argcomplete))))
-    (package
-      (inherit variant)
+    (package/inherit variant
       (arguments
        (substitute-keyword-arguments (package-arguments variant)
          ((#:phases phases '%standard-phases)
@@ -14839,8 +15240,7 @@ possible on all supported Python versions.")
 (define-public python2-xopen
   (let ((base (package-with-python2
                (strip-python2-variant python-xopen))))
-    (package
-      (inherit base)
+    (package/inherit base
       (propagated-inputs `(("python2-bz2file" ,python2-bz2file)
                            ,@(package-propagated-inputs base))))))
 
@@ -14972,9 +15372,6 @@ protocols written in pure Python.")
     ;; Can be used with either license.
     (license (list license:asl2.0 license:gpl2+))))
 
-(define-public python2-dulwich
-  (package-with-python2 python-dulwich))
-
 (define-public python-pbkdf2
   (package
     (name "python-pbkdf2")
@@ -15705,7 +16102,7 @@ editors.")
 (define-public python2-isort
   (let ((base (package-with-python2
                (strip-python2-variant python-isort))))
-    (package (inherit base)
+    (package/inherit base
       (native-inputs
        `(("python2-futures" ,python2-futures)
          ,@(package-native-inputs base))))))
@@ -15944,9 +16341,6 @@ exception message with a traceback that points to the culprit.")
 make common patterns shorter and easier.")
     (license license:bsd-2)))
 
-(define-public python2-utils
-  (package-with-python2 python-utils))
-
 (define-public python-diff-match-patch
   (package
     (name "python-diff-match-patch")
@@ -16276,8 +16670,7 @@ Supported metrics are:
 
 (define-public python2-radon
   (let ((base (package-with-python2 (strip-python2-variant python-radon))))
-    (package
-      (inherit base)
+    (package/inherit base
       (propagated-inputs
        `(("python-configparser" ,python2-configparser)
          ("python-future" ,python2-future)
@@ -16576,8 +16969,7 @@ and integration into other projects.")
 (define-public python2-rfc6555
   (let ((base (package-with-python2
                (strip-python2-variant python-rfc6555))))
-    (package
-      (inherit base)
+    (package/inherit base
       (propagated-inputs
        `(("python2-selectors2" ,python2-selectors2))))))
 
@@ -17702,8 +18094,7 @@ such as figshare or Zenodo.")
 (define-public python2-activepapers
   (let ((base (package-with-python2
                (strip-python2-variant python-activepapers))))
-    (package
-      (inherit base)
+    (package/inherit base
       (arguments
        (substitute-keyword-arguments (package-arguments base)
          ((#:phases phases)
@@ -17937,17 +18328,18 @@ user's @file{~/Trash} directory.")
     (license license:bsd-3)))
 
 (define-public python2-send2trash
-  (package
-    (inherit (package-with-python2 (strip-python2-variant python-send2trash)))
-    (arguments
-     (substitute-keyword-arguments (package-arguments python-send2trash)
-       ((#:phases phases)
-        `(modify-phases ,phases
-           (add-before 'check 'setenv
-             (lambda _
-               (setenv "PYTHONPATH"
-                       (string-append (getcwd) ":" (getenv "PYTHONPATH")))
-               #t))))))))
+  (let ((base (package-with-python2
+               (strip-python2-variant python-send2trash))))
+    (package/inherit base
+      (arguments
+       (substitute-keyword-arguments (package-arguments python-send2trash)
+         ((#:phases phases)
+          `(modify-phases ,phases
+             (add-before 'check 'setenv
+               (lambda _
+                 (setenv "PYTHONPATH"
+                         (string-append (getcwd) ":" (getenv "PYTHONPATH")))
+                 #t)))))))))
 
 (define-public python-pyfavicon
   (package
@@ -19110,6 +19502,31 @@ library: to minimize boilerplate code in traditional extension modules by
 inferring type information using compile-time introspection.")
     (license license:bsd-3)))
 
+(define-public python-pooch
+  (package
+    (name "python-pooch")
+    (version "1.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pooch" version))
+       (sha256
+        (base32 "1618adsg9r8fsv422sv35z1i723q3a1iir5v7dv2sklh4pl4im1h"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f)) ;requires online data
+    (propagated-inputs
+     `(("python-appdirs" ,python-appdirs)
+       ("python-packaging" ,python-packaging)
+       ("python-requests" ,python-requests)))
+    (home-page "https://github.com/fatiando/pooch")
+    (synopsis "Manage your Python library's sample data files")
+    (description
+     "Pooch manages your Python library's sample data files: it automatically
+downloads and stores them in a local directory, with support for versioning
+and corruption checks.")
+    (license license:bsd-3)))
+
 (define-public python-fasteners
   (package
     (name "python-fasteners")
@@ -19686,6 +20103,26 @@ main differences are that @code{cytoolz} is faster and cytoolz offers a C API
 that is accessible to other projects developed in Cython.")
     (license license:bsd-3)))
 
+(define-public python-sortedcollections
+  (package
+    (name "python-sortedcollections")
+    (version "2.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "sortedcollections" version))
+       (sha256
+        (base32
+         "1kfabpnjyjm5ml2zspry9jy3xq49aybchgaa4ahic2jqdjfn1sfq"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-sortedcontainers" ,python-sortedcontainers)))
+    (arguments '(#:tests? #f))  ; Tests not included in release tarball.
+    (home-page "http://www.grantjenks.com/docs/sortedcollections/")
+    (synopsis "Python Sorted Collections")
+    (description "Sorted Collections is a Python sorted collections library.")
+    (license license:asl2.0)))
+
 (define-public python-sortedcontainers
   (package
     (name "python-sortedcontainers")
@@ -19763,8 +20200,7 @@ data.")
 
 (define-public python2-cloudpickle
   (let ((base (package-with-python2 (strip-python2-variant python-cloudpickle))))
-    (package
-      (inherit base)
+    (package/inherit base
       (native-inputs
        `(("python-mock" ,python2-mock)
          ,@(package-native-inputs base)))
@@ -20004,7 +20440,7 @@ on regular expressions.")
 (define-public python2-reparser
   (let ((reparser (package-with-python2
                    (strip-python2-variant python-reparser))))
-    (package (inherit reparser)
+    (package/inherit reparser
              (propagated-inputs
               `(("python2-enum34" ,python2-enum34)
                 ,@(package-propagated-inputs reparser))))))
@@ -20116,14 +20552,14 @@ of Python libraries for building Python applications.")
 (define-public python-astor
   (package
     (name "python-astor")
-    (version "0.7.1")
+    (version "0.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astor" version))
        (sha256
         (base32
-         "13gv6f2xz9i564byp21gcpc0l3w4cs23k1wbcam8kky2ls3hvhwm"))))
+         "0ppscdzzvxpznclkmhhj53iz314x3pfv4yc7c6gwxqgljgdgyvka"))))
     (build-system python-build-system)
     ;; FIXME: There are two errors and two test failures.
     (arguments `(#:tests? #f))
@@ -20531,7 +20967,7 @@ format.")
           (base32
             "074anvhyjgsv2iby2ql1ixfvjgmhnvcwjbdz8gk70xzkzcm1fx5q"))))
     (build-system python-build-system)
-    (home-page "http://www.joachim-bauch.de/projects/pylzma/")
+    (home-page "https://www.joachim-bauch.de/projects/pylzma/")
     (synopsis "Python bindings for the LZMA library by Igor Pavlov.")
     (description "This package provides Python bindings for the LZMA library
 by Igor Pavlov.")
@@ -20965,14 +21401,14 @@ register custom encoders and decoders.")
 (define-public python-ujson
   (package
     (name "python-ujson")
-    (version "4.0.1")
+    (version "4.0.2")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "ujson" version))
         (sha256
          (base32
-          "1lr9lbm76y3ah1463jggwg2hjcb709mpns5f752wxxbgnd0n5kr6"))
+          "0k9w0kypy7vlskzzp2vsjswaw8lbqdrplzkbflxki9vqwglsj5f6"))
         (modules '((guix build utils)))
         (snippet
          '(begin (delete-file-recursively "deps") #t))))
@@ -21412,29 +21848,6 @@ and cuts down boilerplate code when testing libraries for asyncio.")
     (description "This project allows Python code to extend built-in types.")
     (license (list license:gpl3+ license:expat))))
 
-(define-public python-shouldbe
-  (package
-    (name "python-shouldbe")
-    (version "0.1.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "shouldbe" version))
-       (sha256
-        (base32
-         "16zbvjxf71dl4yfbgcr6idyim3mdrfvix1dv8b95p0s9z07372pj"))
-       (patches (search-patches "python-shouldbe-0.1.2-cpy3.8.patch"))))
-    (build-system python-build-system)
-    (propagated-inputs
-      `(("python-forbiddenfruit" ,python-forbiddenfruit)))
-    (native-inputs
-     `(("python-nose" ,python-nose)))
-    (home-page "https://github.com/directxman12/should_be")
-    (synopsis "Python Assertion Helpers inspired by Shouldly")
-    (description
-     "Python Assertion Helpers inspired by Shouldly.")
-    (license license:isc)))
-
 (define-public python-k5test
   (package
     (name "python-k5test")
@@ -21472,31 +21885,15 @@ tests.")
 (define-public python-gssapi
   (package
     (name "python-gssapi")
-    (version "1.6.9")
+    (version "1.6.12")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "gssapi" version))
        (sha256
         (base32
-         "1fa78pn5jzfbwf3y6mj4fc8sh11wjf1hwh5qv39cdlxb71qsq2hb"))))
+         "1j2idrbrbczykzlb56q1bn0ivc9c0rjjljpk4yz86xn3gxfkpv8n"))))
     (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; Work around
-         ;; https://github.com/pythongssapi/python-gssapi/issues/220.
-         (add-before 'check 'disable-failing-tests
-           (lambda _
-             (let ((reason "Disabled failing test (see: \
-https://github.com/pythongssapi/python-gssapi/issues/220)."))
-               (substitute* "gssapi/tests/test_high_level.py"
-                 ((".*def test_add_with_impersonate.*" all)
-                  (string-append all "        self.skipTest('" reason "')\n")))
-               (substitute* "gssapi/tests/test_raw.py"
-                 ((".*def test_.*impersonate_name.*" all)
-                  (string-append all "        self.skipTest('" reason "')\n")))
-               #t))))))
     (propagated-inputs
      `(("python-decorator" ,python-decorator)
        ("python-six" ,python-six)))
@@ -21504,8 +21901,7 @@ https://github.com/pythongssapi/python-gssapi/issues/220)."))
      `(("mit-krb5" ,mit-krb5)))
     ;; for tests
     (native-inputs
-     `(("python-shouldbe" ,python-shouldbe)
-       ("python-parameterized" ,python-parameterized)
+     `(("python-parameterized" ,python-parameterized)
        ("python-k5test" ,python-k5test)
        ("python-nose" ,python-nose)))
     (home-page "https://github.com/pythongssapi/python-gssapi")
@@ -22422,23 +22818,26 @@ networking engine for Python.")
 (define-public python-pysaml2
   (package
     (name "python-pysaml2")
-    (version "5.0.0")
+    (version "6.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pysaml2" version))
        (sha256
         (base32
-         "1h8cmxh9cvxhrdfmkh92wg6zpxmhi2fixq1cy4hxismmaar7bsny"))))
+         "1xk2x0slz1f8cqv7vn77qx99xfd1mshhswiwrljk9m72w2m9iivd"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-cryptography" ,python-cryptography)
        ("python-dateutil" ,python-dateutil)
        ("python-defusedxml" ,python-defusedxml)
+       ("python-importlib-resources"
+        ,python-importlib-resources)
        ("python-pyopenssl" ,python-pyopenssl)
        ("python-pytz" ,python-pytz)
        ("python-requests" ,python-requests)
-       ("python-six" ,python-six)))
+       ("python-six" ,python-six)
+       ("python-xmlschema" ,python-xmlschema)))
     (home-page "https://idpy.org")
     (synopsis "Python implementation of SAML Version 2 Standard")
     (description
@@ -23487,14 +23886,14 @@ process.")
 (define-public python-aiofiles
   (package
     (name "python-aiofiles")
-    (version "0.5.0")
+    (version "0.6.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "aiofiles" version))
         (sha256
           (base32
-            "1bqmv019x16qa3zah0z915cw6z4va3fjs60fk2s7vyah3gyvrrlq"))))
+            "14m01kjxm2j7zyljjj6xlhlgygcsriymbx730gc5jp9xglaina70"))))
     (build-system python-build-system)
     (home-page "https://github.com/Tinche/aiofiles")
     (synopsis "File support for @code{asyncio}")
@@ -23772,3 +24171,223 @@ Application Programming Interface based on the Open Inventor 2.1 API.")
 Crayons automatically wraps a given string in the foreground color and
 restores the original state after the string is printed.")
     (license license:expat)))
+
+(define-public python-sane
+  (package
+    (name "python-sane")
+    (version "2.9.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri name version))
+       (sha256
+        (base32
+         "1pi597z94n2mkd821ln52fq0g727n2jxfskf280ip3kf7jw8w294"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
+    (inputs
+     `(("sane-backends" ,sane-backends)))
+    (home-page "https://github.com/python-pillow/Sane")
+    (synopsis "Python interface to the SANE scanner")
+    (description "This package provides Python interface to the SANE scanner
+and frame grabber interface.")
+    (license (license:non-copyleft
+               ;; Yet another variant of the X/MIT license.
+               "https://github.com/python-pillow/Sane/blob/master/COPYING"))))
+
+(define-public python-screenkey
+  (package
+    (name "python-screenkey")
+    (version "1.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.com/screenkey/screenkey")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1rfngmkh01g5192pi04r1fm7vsz6hg9k3qd313sn9rl9xkjgp11l"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-dlopen-paths
+          (lambda* (#:key inputs outputs #:allow-other-keys)
+            (let* ((x11 (assoc-ref inputs "libx11"))
+                   (xtst (assoc-ref inputs "libxtst")))
+              (substitute* "Screenkey/xlib.py"
+                           (("libX11.so.6")
+                            (string-append x11 "/lib/libX11.so.6")))
+              (substitute* "Screenkey/xlib.py"
+                           (("libXtst.so.6")
+                            (string-append xtst "/lib/libXtst.so.6")))
+              #t)))
+          (add-after 'install 'wrap-screenkey
+            (lambda* (#:key outputs #:allow-other-keys)
+              (wrap-program
+                  (string-append (assoc-ref outputs "out") "/bin/screenkey")
+                `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))
+                `("GI_TYPELIB_PATH"
+                  ":" prefix (,(getenv "GI_TYPELIB_PATH"))))
+              #t)))))
+    (inputs
+     `(("python-distutils-extra" ,python-distutils-extra)
+       ("python-tokenize-rt" ,python-tokenize-rt)
+       ("libx11" ,libx11)
+       ("libxtst" ,libxtst)
+       ("gtk+" ,gtk+)
+       ("python-pygobject" ,python-pygobject)
+       ("python-pycairo" ,python-pycairo)
+       ("python-setuptools-git" ,python-setuptools-git)
+       ("python-babel" ,python-babel)))
+    (home-page "https://www.thregr.org/~wavexx/software/screenkey/")
+    (synopsis
+      "Screencast tool to display pressed keys")
+    (description
+      "A screencast tool to display your keys inspired by Screenflick.")
+    (license license:gpl3+)))
+
+(define-public python-jinja2-cli
+  (package
+    (name "python-jinja2-cli")
+    (version "0.7.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "jinja2-cli" version))
+        (sha256
+          (base32
+            "0vikx7v6fbvww6kfrv0k5a24jyv3ak7nindg60906pdd1m9qvkcw"))))
+    (build-system python-build-system)
+    (propagated-inputs
+      `(("python-jinja2" ,python-jinja2)))
+    (native-inputs
+      `(("python-flake8" ,python-flake8)
+        ("python-jinja2" ,python-jinja2)
+        ("python-pytest" ,python-pytest)))
+    (home-page "https://github.com/mattrobenolt/jinja2-cli")
+    (synopsis "Command-line interface to Jinja2")
+    (description
+     "This package provides a command-line interface (CLI) to the Jinja2
+template engine.")
+    (license license:bsd-3)))
+
+(define-public python-readability
+  (package
+    (name "python-readability")
+    (version "0.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "readability" version))
+       (sha256
+        (base32
+         "1b8gq3g2zwvx0aivvdg56cc0bn7xw6f2v6psmxdx9aiipkw0s0zr"))))
+    (build-system python-build-system)
+    (home-page
+     "https://github.com/andreasvc/readability/")
+    (synopsis
+     "Measure the readability of a given text using surface
+characteristics")
+    (description
+     "This package provides a Python library that is an implementation of
+traditional readability measures based on simple surface
+characteristics. These measures are basically linear regressions based on the
+number of words, syllables, and sentences.")
+    (license license:asl2.0)))
+
+(define-public python-listparser
+  (package
+    (name "python-listparser")
+    (version "0.18")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "listparser" version))
+       (sha256
+        (base32
+         "0hdqs1mmayw1r8yla43hgb4d9y3zqs5483vgf8j9ygczkd2wrq2b"))))
+    (build-system python-build-system)
+    (home-page
+     "https://github.com/kurtmckee/listparser")
+    (synopsis
+     "Parse subscription lists in Python")
+    (description
+     "This package provides a Python library that can parse OPML, FOAF, and
+iGoogle subscription lists.")
+    (license license:expat)))
+
+(define-public python-smartypants
+  (package
+    (name "python-smartypants")
+    (version "2.0.1")
+    (source
+     (origin
+       ;; There's no source tarball for 2.0.1 on PyPI.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/leohemsted/smartypants.py")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "00p1gnb9pzb3svdq3c5b9b332gsp50wrqqa39gj00m133zadanjp"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           ;; Its `setup.py test` doesn't report failure with exit status, so
+           ;; we use `nose` instead.
+           (lambda _
+             (invoke "nosetests" "-v" "--exclude=^load_tests$"))))))
+    (native-inputs
+     ;; For tests.
+     `(("python-docutils" ,python-docutils)
+       ("python-nose" ,python-nose)
+       ("python-pygments" ,python-pygments)))
+    (home-page "https://github.com/leohemsted/smartypants.py")
+    (synopsis "Translate punctuation characters into smart quotes")
+    (description
+     "@command{smartpants} can perform the following transformations:
+@enumerate
+@item Straight quotes ( \" and ' ) into \"curly\" quote HTML entities
+@item Backticks-style quotes (``like this'') into \"curly\" quote HTML
+entities
+@item Dashes (-- and ---) into en- and em-dash entities
+@item Three consecutive dots (... or . . .) into an ellipsis entity
+@end enumerate")
+    (license license:bsd-3)))
+
+(define-public python-typogrify
+  (package
+    (name "python-typogrify")
+    (version "2.0.7")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "typogrify" version))
+              (sha256
+               (base32
+                "0f6b2gnnxjbx1fbmkcscc6qjr4hi78kwm1wx4b766ha3va66dr4b"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (invoke "nosetests" "-v"))))))
+    (propagated-inputs
+     `(("python-smartypants" ,python-smartypants)))
+    (native-inputs
+     ;; For tests.
+     `(("python-nose" ,python-nose)))
+    (home-page "https://github.com/mintchaos/typogrify")
+    (synopsis "Filters to transform text into typographically-improved HTML")
+    (description
+     "@code{typogrify} provides a set of custom filters that automatically
+apply various transformations to plain text in order to yield
+typographically-improved HTML.  While often used in conjunction with Jinja and
+Django template systems, the filters can be used in any environment.")
+    (license license:bsd-3)))
author	Maxim Cournoyer <maxim.cournoyer@gmail.com>	2021-04-08 15:47:00 -0400
committer	Maxim Cournoyer <maxim.cournoyer@gmail.com>	2021-04-08 15:47:00 -0400
commit	533a893cc6b03f100566760d6e0c8e0500ed7082 (patch)
tree	0ecbf89895a400c43d16bb1f6539f1a88aeaa4cf /gnu/packages/python-xyz.scm
parent	6a2546f92d07df04e5d700924edd027ed1e2ef11 (diff)
parent	c762df54786fd6f005f3b5307323f1d2df3cbf0b (diff)
download	guix-533a893cc6b03f100566760d6e0c8e0500ed7082.tar.gz