Merge branch 'master' into core-updates

Note: this merge actually changes the 'curl' and 'python-attrs' derivations,
as part of solving caf4a7a2770ef4d05a6e18f40d602e51da749ddc and
12964df69a99de6190422c752fef65ef813f3b6b respectively.

4604d43c0e (gnu: gnutls@3.6.16: Fix cross-compilation.) was ignored because it
cannot currently be tested.

 Conflicts:
	gnu/local.mk
	gnu/packages/aidc.scm
	gnu/packages/boost.scm
	gnu/packages/curl.scm
	gnu/packages/nettle.scm
	gnu/packages/networking.scm
	gnu/packages/python-xyz.scm
	gnu/packages/tls.scm

1 files changed, 93 insertions, 73 deletions

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 56c2732018..bbc51590b6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -29,7 +29,7 @@
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Marius Bakke <marius@gnu.org>
 ;;; 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, 2021 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2016–2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
@@ -1103,9 +1103,6 @@ NetCDF files can also be read and modified.  Python-HDF4 is a fork of
 @url{http://hdfeos.org/software/pyhdf.php,pyhdf}.")
    (license license:expat)))
 
-(define-public python2-hdf4
-  (package-with-python2 python-hdf4))
-
 (define-public python-h5py
   (package
     (name "python-h5py")
@@ -2284,28 +2281,6 @@ information created by most SVG editors.  Optimization options are typically
 lossless but can be tweaked for more aggressive cleaning.")
     (license license:asl2.0)))
 
-(define-public python-mappy
-  (package
-   (name "python-mappy")
-   (version "2.18")
-   (source (origin
-            (method url-fetch)
-            (uri (pypi-uri "mappy" version))
-            (sha256
-             (base32
-              "1a05p7rkmxa6qhm108na8flzj2v45jab06drk59kzk1ip2sgvzqq"))))
-   (build-system python-build-system)
-   (native-inputs
-    `(("python-cython" ,python-cython)))
-   (inputs
-    `(("zlib" ,zlib)))
-   (home-page "https://github.com/lh3/minimap2")
-   (synopsis "Python binding for minimap2")
-   (description "This package provides a convenient interface to minimap2,
-a fast and accurate C program to align genomic and transcribe nucleotide
-sequences.")
-   (license license:expat)))
-
 (define-public python-mechanize
   (package
     (name "python-mechanize")
@@ -2825,14 +2800,14 @@ matching them against a list of media-ranges.")
 (define-public python-miniboa
   (package
     (name "python-miniboa")
-    (version "1.0.7")
+    (version "1.0.8")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "miniboa" version))
        (sha256
         (base32
-         "09jh3pn4rh7kh7jayanf8jzy6gp03791b5a193w6148cf3i6k9m3"))))
+         "002c1aki9hsrwj5plrwdrf3sk8rn95fqylqyjx2arrjfpsih4dgs"))))
     (build-system python-build-system)
     (home-page "https://github.com/shmup/miniboa")
     (synopsis "Simple, single-threaded Telnet server")
@@ -5310,23 +5285,16 @@ color scales, and color space conversion easy.  It has support for:
     (description (package-description python-numpy))
     (license (package-license python-numpy))))
 
-(define-public python2-numpy-documentation
-  (let ((numpy-documentation (package-with-python2 python-numpy-documentation)))
-    (package
-      (inherit numpy-documentation)
-      (native-inputs `(("python2-functools32" ,python2-functools32)
-                       ,@(package-native-inputs numpy-documentation))))))
-
 (define-public python-pygit2
   (package
     (name "python-pygit2")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pygit2" version))
        (sha256
-        (base32 "1j71iskvirkm8jzfmwdm79v69878m9iix8a8cn4xidgr3nmkisyb"))))
+        (base32 "0qjd5aqpmla64da4pb47vdnrmnqdbn7248a4fzs7f5q1ax7fmb3s"))))
     (build-system python-build-system)
     (arguments
      '(#:tests? #f))            ; tests don't run correctly in our environment
@@ -6236,13 +6204,13 @@ the OleFileIO module from PIL, the Python Image Library.")
 (define-public python-pikepdf
   (package
     (name "python-pikepdf")
-    (version "2.12.1")
+    (version "2.12.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pikepdf" version))
        (sha256
-        (base32 "1si1x4dc4i4ghyirjfws1zkgiwk8kypnpp4gf68haascrdy7znqw"))))
+        (base32 "1r68zh8whp8wg4brjf5vha8h1ly8pjqyb37pfw91hyxfn6cm9wsz"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #false))                ;require python-xmp-toolkit
@@ -7054,9 +7022,6 @@ cluster directly from Python.  You can directly map Python functions onto the
 cluster without needing to write any wrapper code yourself.")
     (license license:gpl3+)))
 
-(define-public python2-gridmap
-  (package-with-python2 python-gridmap))
-
 (define-public python-honcho
   (package
     (name "python-honcho")
@@ -8844,9 +8809,6 @@ more advanced mathematics.")
 multiprecision arithmetic.")
     (license license:lgpl3+)))
 
-(define-public python2-bigfloat
-  (package-with-python2 python-bigfloat))
-
 (define-public python-sympy
   (package
     (name "python-sympy")
@@ -9100,25 +9062,29 @@ applications.")
 (define-public python-pyzmq
   (package
     (name "python-pyzmq")
-    (version "22.0.3")
+    (version "22.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyzmq" version))
        (sha256
-        (base32 "0bgrn65cxfz1c1sjrgyq5dy1mkhppxxbizd5wvrl03cq4zhkrxpp"))))
+        (base32 "0pa1y97z75xqyca9xfp9zrzksydbgzsxf8yh0hwp0rgahpfxch3h"))))
     (build-system python-build-system)
     (arguments
      `(#:configure-flags
        (list (string-append "--zmq=" (assoc-ref %build-inputs "zeromq")))
-       ;; FIXME: You must build pyzmq with 'python setup.py build_ext
-       ;; --inplace' for 'python setup.py test' to work.
-       #:tests? #f))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'build-extensions
+           (lambda _
+             ;; Cython extensions have to be built before running the tests.
+             (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (inputs
      `(("zeromq" ,zeromq)))
     (native-inputs
      `(("pkg-config" ,pkg-config)
-       ("python-nose" ,python-nose)))
+       ("python-cython" ,python-cython)
+       ("python-pytest" ,python-pytest)))
     (home-page "https://github.com/zeromq/pyzmq")
     (synopsis "Python bindings for 0MQ")
     (description
@@ -13292,7 +13258,7 @@ ISO 8859, etc.).")
        ("python-pytest-cov" ,python-pytest-cov)
        ("python-pytest-xdist" ,python-pytest-xdist)))
     (inputs
-     `(("qtbase" ,qtbase)))
+     `(("qtbase" ,qtbase-5)))
     (propagated-inputs
      `(("python-h5py" ,python-h5py)
        ("python-numpy" ,python-numpy)
@@ -13687,6 +13653,56 @@ is made as zipfile like as possible.")
 (define-public python2-rarfile
   (package-with-python2 python-rarfile))
 
+(define-public python-rich
+  (package
+    (name "python-rich")
+    (version "10.2.2")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "rich" version))
+              (sha256
+               (base32
+                "1z5m5brcdf3vndpavcqj5nl35xby4x5rfj48klhwqycfqf3g9cqp"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs tests? #:allow-other-keys)
+             (when tests?
+               (copy-recursively (string-append
+                                  (assoc-ref inputs "tests") "/tests")
+                                 "tests")
+               (invoke "python" "-m" "pytest" "-vv")))))))
+    (propagated-inputs
+     `(("python-attrs" ,python-attrs)
+       ("python-colorama" ,python-colorama)
+       ("python-commonmark" ,python-commonmark)
+       ("python-ipywidgets" ,python-ipywidgets)
+       ("python-pygments" ,python-pygments)
+       ("python-typing-extensions" ,python-typing-extensions)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("tests"
+        ;; The release on pypi comes without tests.  We can't build from this
+        ;; checkout, though, because installation requires an invocation of
+        ;; poetry.
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/willmcgugan/rich")
+                 (commit (string-append "v" version))))
+           (file-name (git-file-name name version))
+           (sha256
+            (base32
+             "19f4svb363sn5708qkpa6lakmiwzyb25h8kmh7bqrsbbrvi9hr70"))))))
+    (home-page "https://github.com/willmcgugan/rich")
+    (synopsis "Render rich text and more to the terminal")
+    (description
+     "This is a Python package for rendering rich text, tables, progress bars,
+syntax highlighting, markdown and more to the terminal.")
+    (license license:expat)))
+
 (define-public python-magic
   (package
     (name "python-magic")
@@ -14266,9 +14282,6 @@ graphviz.")
 format.")
     (license license:gpl2+)))
 
-(define-public python2-fastimport
-  (package-with-python2 python-fastimport))
-
 (define-public python-twisted
   (package
     (name "python-twisted")
@@ -15147,13 +15160,13 @@ collections of data.")
 (define-public python-prompt-toolkit
   (package
     (name "python-prompt-toolkit")
-    (version "3.0.9")
+    (version "3.0.18")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "prompt_toolkit" version))
        (sha256
-        (base32 "0bvjp62cs6aj9lrh7njzxdjgg8pjfw3qgmr551243d9ivmcapvn5"))))
+        (base32 "1g1kq1aimhm23k2dmlmnznfzc83l6ly65g0h32hqz8injcdz3d71"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -15257,18 +15270,19 @@ well.")
 (define-public ptpython
   (package
     (name "ptpython")
-    (version "3.0.5")
+    (version "3.0.17")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "ptpython" version))
               (sha256
                (base32
-                "0c2ry5gwi2v99slna62j8r2bwq0hpzmvgdryqg9m6x57vbjfg52h"))))
+                "1phk1grcvn456igjg8gwjjg8bf4kszddq5nd5sdlz3hslg62a7ci"))))
     (build-system python-build-system)
     (arguments
-     '(#:tests? #f)) ; FIXME: No tests in pypi tarball.
+     `(#:tests? #f)) ;there are no tests
     (propagated-inputs
      `(("python-appdirs" ,python-appdirs)
+       ("python-black" ,python-black)
        ("python-jedi" ,python-jedi)
        ("python-prompt-toolkit" ,python-prompt-toolkit)
        ("python-pygments" ,python-pygments)))
@@ -16867,8 +16881,9 @@ and bit flag values.")
     (arguments
      `(#:phases (modify-phases %standard-phases
                   (replace 'check
-                    (lambda _
-                      (invoke "pytest"))))))
+                    (lambda* (#:key tests? #:allow-other-keys)
+                      (when tests?
+                        (invoke "pytest")))))))
     (native-inputs
      `(("python-coverage" ,python-coverage)
        ("python-hypothesis" ,python-hypothesis)
@@ -21160,18 +21175,26 @@ library's @code{threading} module.")
 (define-public python-toolz
   (package
     (name "python-toolz")
-    (version "0.9.0")
+    (version "0.11.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "toolz" version))
        (sha256
         (base32
-         "1j9i7fdjnx9dz35fdj5gvgxx6585ja9sxgaiv65if77nlxz0m7wj"))))
+         "1grz3zvw5ixwqqlbv0n7j11mlcxb66cirh5i9x9zw8kqy0hpk967"))))
     (build-system python-build-system)
-    ;; FIXME: tests cannot be computed: "Can't perform this operation for
-    ;; unregistered loader type"
-    (arguments '(#:tests? #f))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "python" "-m" "pytest" "--doctest-modules"
+                       "--pyargs" "toolz")))))))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
     (home-page "https://github.com/pytoolz/toolz/")
     (synopsis "List processing tools and functional utilities")
     (description
@@ -21386,9 +21409,6 @@ This Python package wraps the Blosc library.")
 append on old values.  Partd excels at shuffling operations.")
     (license license:bsd-3)))
 
-(define-public python2-partd
-  (package-with-python2 python-partd))
-
 (define-public python-fsspec
   (package
     (name "python-fsspec")
@@ -25204,14 +25224,14 @@ disk files in asyncio applications.")
 (define-public python-dataclasses
   (package
     (name "python-dataclasses")
-    (version "0.7")
+    (version "0.8")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "dataclasses" version))
         (sha256
           (base32
-            "1rh8111fbws2vxyf2qy2zw3x6p6cq1jfz8pf904gig5qwg56sjj9"))))
+            "15sc12nrc7gxwb30vfa6frzdnpmbap9ibi1fr1yrbkra6izhcyc4"))))
     (build-system python-build-system)
     (home-page
       "https://github.com/ericvsmith/dataclasses")
@@ -25499,7 +25519,7 @@ implementations.")
         ("swig" ,swig)))
     (inputs
       `(("python-wrapper" ,python-wrapper)
-        ("qtbase" ,qtbase)
+        ("qtbase" ,qtbase-5)
         ("libxi" ,libxi)
         ("libice" ,libice)
         ("soqt" ,soqt)