Merge branch 'master' into gnome-team

1 files changed, 96 insertions, 18 deletions

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d3d91480ac..94e8db934f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -143,6 +143,7 @@
 ;;; Copyright © 2023 Foundation Devices, Inc. <hello@foundationdevices.com>
 ;;; Copyright © c4droid <c4droid@foxmail.com>
 ;;; Copyright © 2023 Janneke Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2023 Attila Lendvai <attila@lendvai.name>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -834,6 +835,31 @@ names for 256 color terminal setups.")
 as functions or string constants to form colored terminal output.")
     (license license:expat)))
 
+(define-public python-construct-classes
+  (package
+    (name "python-construct-classes")
+    (version "0.1.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/matejcik/construct-classes")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0fmr8nfg543lyqk4164a52jb6lwpq98radicbkhhdfckq9lib2wp"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     (list python-construct))
+    (native-inputs
+     (list python-poetry-core
+           python-pytest))
+    (home-page "https://github.com/matejcik/construct-classes")
+    (synopsis "Parse binary structs into dataclasses")
+    (description "This package provides a parser to parse binary structs
+into dataclasses.")
+    (license license:expat)))
+
 (define-public python-yaspin
   (package
     (name "python-yaspin")
@@ -1524,7 +1550,7 @@ of a loop structure or other iterative computation.")
 (define-public python-glymur
   (package
     (name "python-glymur")
-    (version "0.12.0")
+    (version "0.12.8")
     (source
      (origin
        (method git-fetch)   ; no tests data in PyPi package
@@ -1533,7 +1559,7 @@ of a loop structure or other iterative computation.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "03nny8k42yxdyw7sjv43szmg23x3rqplbaf7m0a0lpvwla1dl78i"))))
+        (base32 "0mfyn9j7h13242d41vg12acw55yl2mv6lmgi265hfp11k7g52b6n"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -1562,7 +1588,7 @@ of a loop structure or other iterative computation.")
               ;; which is patched above.
               (delete-file "tests/test_config.py"))))))
     (native-inputs
-     (list python-pytest))
+     (list python-pytest python-scikit-image))
     (inputs
      (list openjpeg  ; glymur/lib/openjp2.py
            libtiff)) ; glymur/lib/tiff.py
@@ -11493,6 +11519,26 @@ GA4GH Task Execution API.")
 algorithm.")
     (license license:asl2.0)))
 
+(define-public python-altgraph
+  (package
+    (name "python-altgraph")
+    (version "0.17.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "altgraph" version))
+       (sha256
+        (base32 "01j48np3g50g6insjkszsz0vifwlm6gspria5vdwlkbciywznnhv"))))
+    (build-system pyproject-build-system)
+    (native-inputs (list python-pytest))
+    (home-page "https://altgraph.readthedocs.io")
+    (synopsis "Python graph network package")
+    (description
+"This package provides tools for constructing graphs, BFS and DFS
+traversals, topological sort, shortest paths, and more with graphviz
+output.")
+    (license license:expat)))
+
 (define-public python-three-merge
   (package
     (name "python-three-merge")
@@ -13493,6 +13539,37 @@ reading and writing MessagePack data.")
                (base32
                 "1109s2yynrahwi64ikax68hx0mbclz8p35afmpphw5dwynb49q7s"))))))
 
+;; This msgpack library's name changed from "python-msgpack" to "msgpack" with
+;; release 0.5. Some packages like borg still call it by the old name for now.
+;; <https://bugs.gnu.org/30662>
+(define-public python-msgpack-transitional
+  (package
+    (inherit python-msgpack)
+    (name "python-msgpack-transitional")
+    (version "0.5.6")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "msgpack" version))
+              (sha256
+               (base32
+                "1hz2dba1nvvn52afg34liijsm7kn65cmn06dl0xbwld6bb4cis0f"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments python-msgpack)
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-after 'unpack 'configure-transitional
+             (lambda _
+               ;; Keep using the old name.
+               (substitute* "setup.py"
+                 (("TRANSITIONAL = False")
+                   "TRANSITIONAL = 1"))
+               ;; This old version is not compatible with Python 3.9
+               (substitute* '("test/test_buffer.py" "test/test_extension.py")
+                 ((".tostring\\(") ".tobytes("))
+               (substitute* '("test/test_buffer.py" "test/test_extension.py")
+                 ((".fromstring\\(") ".frombytes("))
+               #t))))))))
+
 (define-public python-netaddr
   (package
     (name "python-netaddr")
@@ -19251,26 +19328,25 @@ database, file, dict stores.  Cachy supports python versions 2.7+ and 3.2+.")
 (define-public poetry
   (package
     (name "poetry")
-    (version "1.4.2")
+    (version "1.1.12")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "poetry" version))
        (sha256
         (base32
-         "0g0vczn6qa4b2bdkq4k7fm1g739vyxp2iiblwwsrcmw24jj81m8b"))))
+         "0rr54mvcfcv9cv6vw2122y28xvd2pwqpv2x8c8j5ayz3gwsy4rjw"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f                      ;PyPI does not have tests
-       ;; #:phases
-       ;; (modify-phases %standard-phases
-       ;;   (add-before 'build 'patch-setup-py
-       ;;     (lambda _
-       ;;       (substitute* "setup.py"
-       ;;         ;; Relax some of the requirements.
-       ;;         (("(keyring>=21.2.0),<22.0.0" _ keyring) keyring)
-       ;;         (("(packaging>=20.4),<21.0" _ packaging) packaging)))))
-       ))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'patch-setup-py
+           (lambda _
+             (substitute* "setup.py"
+               ;; Relax some of the requirements.
+               (("(keyring>=21.2.0),<22.0.0" _ keyring) keyring)
+               (("(packaging>=20.4),<21.0" _ packaging) packaging)))))))
     (propagated-inputs
      (list python-cachecontrol
            python-cachy
@@ -19279,12 +19355,14 @@ database, file, dict stores.  Cachy supports python versions 2.7+ and 3.2+.")
            python-entrypoints
            python-html5lib
            python-keyring
-           python-msgpack
+           ; Use of deprecated version of msgpack reported upstream:
+           ; https://github.com/python-poetry/poetry/issues/3607
+           python-msgpack-transitional
            python-packaging
            python-pexpect
            python-pip
            python-pkginfo
-           python-poetry-core
+           python-poetry-core-1.0
            python-requests
            python-requests-toolbelt
            python-shellingham
@@ -31817,13 +31895,13 @@ development, testing, production]};
 (define-public python-pudb
   (package
     (name "python-pudb")
-    (version "2022.1.3")
+    (version "2023.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "pudb" version))
               (sha256
                (base32
-                "0jk61qgacvwy6zkz1f55jawax4ggb1aawy6w3wnfkzqrkvd3ms2q"))))
+                "00rgx80inpvsbcydp29mrhw44xizyqdqxvv6lqcak1xs79h3rpqm"))))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases