12 files changed, 281 insertions, 138 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index eac62ffcc1..067fb5cb86 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -23528,15 +23528,16 @@ The output is in SAM format.")
 (define-public libsbml
   (package
     (name "libsbml")
-    (version "5.18.0")
+    (version "5.20.5")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "mirror://sourceforge/sbml/libsbml/"
-                                  version "/stable/libSBML-"
-                                  version "-core-src.tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/sbmlteam/libsbml")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0slkagrk3nfi2qsksv6b1brj6zhx4bj4bkib2sdycvrcd10ql2lh"))))
+                "1bzsgwblh5l15xxy7kpdwiya5kwm26sj6daqr9i93h04manpqmfw"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9fae9575e8..397ffd1c27 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11060,13 +11060,13 @@ matrix) for the double-truncated multinormal case.")
 (define-public r-rvest
   (package
     (name "r-rvest")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rvest" version))
        (sha256
-        (base32 "19lw0jk8d8x88z247hz761gwbx9f5n3yqnv63mn7pkwl55mpqw3x"))))
+        (base32 "005wadzdhxf6hgr8vl4nl0nfi2crj6467mhwbccqfy26njh38z0y"))))
     (build-system r-build-system)
     (arguments
      (list
diff --git a/gnu/packages/documentation.scm b/gnu/packages/documentation.scm
index b18e62e3db..06dbd4973c 100644
--- a/gnu/packages/documentation.scm
+++ b/gnu/packages/documentation.scm
@@ -410,7 +410,7 @@ the Net to search for documents which are not on the local system.")
 (define-public zeal
   (package
     (name "zeal")
-    (version "0.7.1")
+    (version "0.7.2")
     (source
      (origin
        (method git-fetch)
@@ -419,10 +419,11 @@ the Net to search for documents which are not on the local system.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1yz9zz18rh1d67w40ib4pna70vqkwa9i9nyj423rjysv5rdj2pzp"))))
+        (base32 "1slq3asssszim9y4lvqx08svilmyisk3cl35mmb676fsx7pningn"))))
     (build-system qt-build-system)
     (arguments
       (list
+       #:qtbase qtbase
        #:tests? #f))                    ;no tests
     (native-inputs
      (list extra-cmake-modules pkg-config))
@@ -430,12 +431,10 @@ the Net to search for documents which are not on the local system.")
      (list bash-minimal
            libarchive
            sqlite
-           qtbase-5
-           qtdeclarative-5
-           qtwayland-5
-           qtwebchannel-5
-           qtwebengine-5
-           qtquickcontrols-5
+           qtdeclarative
+           qtwayland
+           qtwebchannel
+           qtwebengine
            qtx11extras
            xcb-util-keysyms))
     (home-page "https://zealdocs.org/")
diff --git a/gnu/packages/electronics.scm b/gnu/packages/electronics.scm
index 56cae54c14..a2c9e3cf09 100644
--- a/gnu/packages/electronics.scm
+++ b/gnu/packages/electronics.scm
@@ -1518,6 +1518,35 @@ verification.")
         #~(modify-phases #$phases
             (delete 'fix-scripts)))))))
 
+(define-public python-pyucis
+  (package
+    (name "python-pyucis")
+    (version "0.1.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/fvutils/pyucis/")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "19bxmhqkdmhbibkbzcjqvzvcni1kzg28nqz9vh6zj73hl26lf2ij"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-pytest
+           python-setuptools))
+    (propagated-inputs
+     (list python-jsonschema-objects
+           python-lxml
+           python-pyyaml))
+    (home-page "https://fvutils.github.io/pyucis//")
+    (synopsis "Python interface to UCIS data")
+    (description
+     "The code{PyUCIS} library provides two APIs for creating and accessing
+coverage data via the @acronym{UCIS, Unified Coverage Interoperability
+Standard} data mode.")
+    (license license:asl2.0)))
+
 (define-public python-cocotb
   (package
     (name "python-cocotb")
diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm
index a45546b62c..b483f620c0 100644
--- a/gnu/packages/gnunet.scm
+++ b/gnu/packages/gnunet.scm
@@ -193,7 +193,7 @@ authentication and support for SSL3 and TLS.")
 (define-public gnunet
   (package
     (name "gnunet")
-    (version "0.25.1")
+    (version "0.25.2")
     (source
      (origin
        (method url-fetch)
@@ -201,7 +201,7 @@ authentication and support for SSL3 and TLS.")
                            ".tar.gz"))
        (sha256
         (base32
-         "0p4gcv67rh9832vgi5k31pgpq6hmv6198dfmbyfizyaprlb6qcr1"))))
+         "1rn24rm6z5p0vnk5lwq0jihnbh956n24yd5nmmgv2firbp1nzdza"))))
     (build-system meson-build-system)
     (inputs
      (list bluez
diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index 8a8b36e455..54f7ba9f02 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -330,8 +330,8 @@ compatible, and adds new functionality.")
   (sbcl-package->ecl-package sbcl-3d-math))
 
 (define-public sbcl-3d-matrices
-  (let ((commit "b4f5a58299f8437fad2d77f0879c374e3430f4b5")
-        (revision "2"))
+  (let ((commit "bc1ffa08dcf4732523e09adcf9deba4ddeb559ff")
+        (revision "3"))
     (package
       (name "sbcl-3d-matrices")
       (version (git-version "1.0.0" revision commit))
@@ -339,17 +339,17 @@ compatible, and adds new functionality.")
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/Shinmera/3d-matrices")
+               (url "https://codeberg.org/shinmera/3d-matrices")
                (commit commit)))
          (file-name (git-file-name "cl-3d-matrices" version))
          (sha256
-          (base32 "1s8b4zlmqwyplghs73riz1khf0c5sk64w6b12jd599091d5nr6sr"))))
+          (base32 "0jzckgb5lsmh1gn1f4mczjfc5ckkw01a73wrl1shyb9sil93a751"))))
       (build-system asdf-build-system/sbcl)
       (native-inputs
        (list sbcl-parachute))
       (inputs
        (list sbcl-3d-vectors sbcl-documentation-utils))
-      (home-page "https://shinmera.github.io/3d-matrices/")
+      (home-page "https://codeberg.org/shinmera/3d-matrices")
       (synopsis "Utility library implementing 2x2, 3x3, 4x4 and NxM matrices")
       (description
        "@code{3D-MATRICES} is a library implementing common matrix operations,
@@ -492,8 +492,8 @@ alternative 4x4 matrix representation.")
   (sbcl-package->clasp-package sbcl-3d-transforms))
 
 (define-public sbcl-3d-vectors
-  (let ((commit "257969402864ac3859d77b981abf0aa5373c4e78")
-        (revision "2"))
+  (let ((commit "fc751c65b2285e971c348539bfbc3cbb58b253b0")
+        (revision "3"))
     (package
       (name "sbcl-3d-vectors")
       (version (git-version "3.1.0" revision commit))
@@ -501,11 +501,11 @@ alternative 4x4 matrix representation.")
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/Shinmera/3d-vectors")
+               (url "https://codeberg.org/shinmera/3d-vectors")
                (commit commit)))
          (file-name (git-file-name "cl-3d-vectors" version))
          (sha256
-          (base32 "0vmf7nycc49ydcy0dfs25cgs655kwjc6jcjvpwxw61jq4gl2fh7x"))))
+          (base32 "0im0c4yv3bmlipbpfqfcbkdpqknr4468xjvdmrr01pchc8r4m11j"))))
       (build-system asdf-build-system/sbcl)
       (native-inputs
        (list sbcl-parachute))
@@ -4296,20 +4296,20 @@ operating on them.")
   (sbcl-package->ecl-package sbcl-cl-algebraic-data-type))
 
 (define-public sbcl-cl-all
-  (let ((commit "4ce1ea9d9f33c0dd6212044e7952a0c854757ace")
-        (revision "0"))
+  (let ((commit "8db710a4a92a25ca7c8f09fe1ad91a48ad6bd0c9")
+        (revision "1"))
     (package
       (name "sbcl-cl-all")
-      (version (git-version "1.0.0" revision commit))
+      (version (git-version "2.0.0" revision commit))
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/Shinmera/cl-all")
+               (url "https://codeberg.org/shinmera/cl-all")
                (commit commit)))
          (file-name (git-file-name "cl-all" version))
          (sha256
-          (base32 "0n4sjarj373zpxn78m32rmhxnsnr8qahdslrd9vrkkwjpzar2bwp"))))
+          (base32 "08jsbnkapijn0v4n5h9g6s87i279xmg4fnbw6jajylrg512n38cx"))))
       (build-system asdf-build-system/sbcl)
       (outputs '("out" "bin"))
       (arguments
@@ -4323,7 +4323,7 @@ operating on them.")
                  outputs
                  #:entry-program '((cl-all:toplevel arguments))
                  #:compress? #t))))))
-      (home-page "https://github.com/Shinmera/cl-all")
+      (home-page "https://shinmera.com/docs/cl-all")
       (synopsis "Evaluate Common Lisp expressions in multiple implementations")
       (description "@samp{cl-all} is a library and script for evaluating Common
 Lisp expressions in multiple implementations.")
@@ -14253,11 +14253,11 @@ database files (dbf and db3 files).")
   (sbcl-package->ecl-package sbcl-db3))
 
 (define-public sbcl-dbi
-  (let ((commit "738a74dd69adb2a7c21fa67e140d89c7df25b227")
-        (revision "2"))
+  (let ((commit "be4df4f236391f4e4150a1fe77f8acc92b9f3996")
+        (revision "3"))
     (package
       (name "sbcl-dbi")
-      (version (git-version "0.9.5" revision commit))
+      (version (git-version "0.11.1" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -14266,7 +14266,7 @@ database files (dbf and db3 files).")
                (commit commit)))
          (file-name (git-file-name "cl-dbi" version))
          (sha256
-          (base32 "0f8z7an8ssg8mdf9k781r4ygdppv798v6f08ibgpd8mv8a6491fg"))))
+          (base32 "0n3lh0rng5gbbb9aqcrszvc99f80j5zk1hdrcvz20qg6c31hhjl6"))))
       (build-system asdf-build-system/sbcl)
       (native-inputs
        `(("alexandria" ,sbcl-alexandria)
@@ -22962,11 +22962,11 @@ extensions to Common Lisp.  It contains:
   (sbcl-package->clasp-package sbcl-misc-extensions))
 
 (define-public sbcl-mito
-  (let ((commit "47ba4865ca4bb2894b53703a49a299e973f8eb86")
-        (revision "3"))
+  (let ((commit "10c22b64047053b079beb5168d21222abe4d4b1d")
+        (revision "4"))
     (package
       (name "sbcl-mito")
-      (version (git-version "0.1" revision commit))
+      (version (git-version "0.2.0" revision commit))
       (home-page "https://github.com/fukamachi/mito")
       (source
        (origin
@@ -22976,23 +22976,24 @@ extensions to Common Lisp.  It contains:
                (commit commit)))
          (file-name (git-file-name "mito" version))
          (sha256
-          (base32 "0313nxlj1zqw6zyc23xpf85v0jk32sg0543ql8363jki0pmg7yhs"))))
+          (base32 "0yx1hf22k3wgl0b274i25i6cnshijzy7wppi6clgmhi2y5svgddr"))))
       (build-system asdf-build-system/sbcl)
       (native-inputs
        (list sbcl-prove))
       (inputs
-       `(("alexandria" ,sbcl-alexandria)
-         ("cl-package-locks" ,sbcl-cl-package-locks)
-         ("cl-ppcre" ,sbcl-cl-ppcre)
-         ("cl-reexport" ,sbcl-cl-reexport)
-         ("closer-mop" ,sbcl-closer-mop)
-         ("dbi" ,sbcl-dbi)
-         ("dissect" ,sbcl-dissect)
-         ("esrap" ,sbcl-esrap)
-         ("local-time" ,sbcl-local-time)
-         ("sxql" ,sbcl-sxql)
-         ("trivia" ,sbcl-trivia)
-         ("uuid" ,sbcl-uuid)))
+       (list sbcl-alexandria
+             sbcl-chipz
+             sbcl-cl-package-locks
+             sbcl-cl-ppcre
+             sbcl-cl-reexport
+             sbcl-closer-mop
+             sbcl-dbi
+             sbcl-dissect
+             sbcl-esrap
+             sbcl-local-time
+             sbcl-sxql
+             sbcl-trivia
+             sbcl-uuid))
       (arguments
        '(#:phases
          (modify-phases %standard-phases
diff --git a/gnu/packages/prolog.scm b/gnu/packages/prolog.scm
index cc81f7400d..6a11852bc7 100644
--- a/gnu/packages/prolog.scm
+++ b/gnu/packages/prolog.scm
@@ -189,7 +189,7 @@ it.")
 (define-public trealla
   (package
     (name "trealla")
-    (version "2.83.21")
+    (version "2.83.23")
     (source
      (origin
        (method git-fetch)
@@ -198,7 +198,7 @@ it.")
          (url "https://github.com/trealla-prolog/trealla")
          (commit (string-append "v" version))))
        (sha256
-        (base32 "18qa91g395kqi7a7rrhrfbrx2w5yil3rg8k3fmfng47i8i7522hm"))
+        (base32 "18j824bvypk4z36xd59gafwb3ssl5fh6jlfrrzskpcllbpslcajl"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (native-inputs
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 0beff7d6e0..4aec58282a 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2977,6 +2977,63 @@ other HTTP libraries.")
      "Cheroot is a high-performance, pure-Python HTTP server.")
     (license license:bsd-3)))
 
+(define-public python-cherrypy
+  (package
+    (name "python-cherrypy")
+    (version "18.10.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/cherrypy/cherrypy")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1mhs64z75mj3rk4rgxc3xm1yksaj253rj9czhk4632blz5yi0kbn"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(map
+         (lambda (test)
+           (string-append "--deselect=cherrypy/test/" test))
+         (list
+          ;; XXX: Unraisable exceptions.
+          "test_config_server.py::ServerConfigTests::testMaxRequestSize"
+          "test_core.py::CoreRequestHandlingTest::testRanges"
+          "test_core.py::CoreRequestHandlingTest::testRedirect"
+          "test_encoding.py::EncodingTests::\
+test_multipart_decoding_bigger_maxrambytes"
+          "test_encoding.py::EncodingTests::\
+test_test_http.py::HTTPTests::test_post_filename_with_special_characters"
+          "test_http.py::HTTPTests::test_post_multipart"
+          "test_http.py::HTTPTests::test_post_filename_with_special_characters"
+          "test_mime.py::SafeMultipartHandlingTest::test_Flash_Upload"
+          "test_tutorials.py::TutorialTest::test09Files"))))
+    (propagated-inputs
+     (list python-cheroot
+           python-jaraco-collections
+           python-more-itertools
+           python-portend
+           python-zc-lockfile))
+    (native-inputs
+     (list python-objgraph
+           python-path
+           python-pytest
+           python-pytest-cov
+           python-pytest-forked
+           python-pytest-services
+           python-pytest-sugar
+           python-requests-toolbelt
+           python-setuptools))
+    (home-page "https://www.cherrypy.dev")
+    (synopsis "Object-Oriented HTTP framework")
+    (description
+     "CherryPy is a pythonic, object-oriented web framework.  It helps in
+building web applications in the same way any other object-oriented Python
+program would be built.")
+    (license license:bsd-3)))
+
 (define-public httpie
   (package
     (name "httpie")
@@ -6078,23 +6135,42 @@ HTTP via a UNIX domain socket.")
 (define-public python-requests-unixsocket
   (deprecated-package "python-requests-unixsocket" python-requests-unixsocket2))
 
-(define-public python-requests_ntlm
+(define-public python-requests-ntlm
   (package
-    (name "python-requests_ntlm")
-    (version "1.2.0")
+    (name "python-requests-ntlm")
+    (version "1.3.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "requests_ntlm" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/requests/requests-ntlm")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32
-         "1a0np7lk8ma1plv1s4aw5q9h2z3aljprkl9qsfypqcaf0zsqbhik"))))
-    (build-system python-build-system)
+        (base32 "0snsk66zdihdlyfjz2zgpyfgdyjg814m3cc4g3my09hdnb5xvagv"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; XXX: Connection refused.
+      #~(list "-k" (string-join
+                    (list "not test_ntlm_http_with_cbt"
+                          "test_ntlm_http_without_cbt"
+                          "test_ntlm_https_with_cbt"
+                          "test_ntlm_https_without_cbt")
+                    " and not "))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'spawn-test-server
+            (lambda _
+              ;; Taken from .github/workflows/ci.yml.
+              (spawn "python"
+                     (list "python" "-m" "tests.test_server")))))))
     (propagated-inputs
      (list python-cryptography python-pyspnego python-requests))
+    (native-inputs (list python-flask python-pytest python-setuptools))
     (home-page "https://github.com/requests/requests-ntlm")
-    (synopsis
-     "NTLM authentication support for Requests")
+    (synopsis "NTLM authentication support for Requests")
     (description
      "This package allows for HTTP NTLM authentication using the requests
 library.")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b5aa148e14..37108fa59e 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7746,6 +7746,35 @@ you traverse a schema like paths and access a schema on demand with separate
 dereferencing accessor layer.")
     (license license:asl2.0)))
 
+(define-public python-jsonschema-objects
+  (package
+    (name "python-jsonschema-objects")
+    (version "0.5.7")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/cwacek/python-jsonschema-objects/")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0p3m0fbj25brhfma4bl47xjq6x4ay14yx284qwrki96dwd6v46xd"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-pytest
+           python-pytest-mock
+           python-setuptools))
+    (propagated-inputs
+     (list python-inflection
+           python-jsonschema
+           python-markdown))
+    (home-page "http://python-jsonschema-objects.readthedocs.org/")
+    (synopsis "Automatic Python binding generation from JSON schemas")
+    (description
+     "This package provides an automatic class-based binding to JSON
+Schemas for use in python.")
+    (license license:expat)))
+
 (define-public python-jsonschema-specifications
   (package
     (name "python-jsonschema-specifications")
@@ -12965,50 +12994,52 @@ that requires its specific capabilities.")
 
 (define-public python-ffmpeg-python
   ;; The latest release (0.2.0) is old and its test suite crashs on Python 3.10.
-  (let ((commit "df129c7ba30aaa9ffffb81a48f53aa7253b0b4e6") (revision "0"))
-    (package
-      (name "python-ffmpeg-python")
-      (version (git-version "0.2.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/kkroening/ffmpeg-python.git")
-                      (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "1zj4ac37n4igfj21zy405mdlvbpv6jyb12wfpszf8zkhhj2qby4c"))))
-      (build-system python-build-system)
-      (arguments
-       (list
-        #:phases
-        #~(modify-phases %standard-phases
-            (add-after 'unpack 'hardcode-ffmpeg
-              (lambda* (#:key inputs #:allow-other-keys)
-                (define ffmpeg (search-input-file inputs "bin/ffmpeg"))
+  (package
+    (name "python-ffmpeg-python")
+    (properties '((commit . "df129c7ba30aaa9ffffb81a48f53aa7253b0b4e6")
+                  (revision . "0")))
+    (version (git-version "0.2.0"
+                          (assoc-ref properties 'revision)
+                          (assoc-ref properties 'commit)))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/kkroening/ffmpeg-python.git")
+              (commit (assoc-ref properties 'commit))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1zj4ac37n4igfj21zy405mdlvbpv6jyb12wfpszf8zkhhj2qby4c"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "-k" "not test_pipe and not test__probe")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'hardcode-ffmpeg
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((ffmpeg (search-input-file inputs "bin/ffmpeg")))
                 (substitute* "ffmpeg/_run.py"
                   (("cmd='ffmpeg'")
                    (string-append "cmd='" ffmpeg "'")))
                 (substitute* "ffmpeg/tests/test_ffmpeg.py"
                   (("out_file.compile\\(\\) == \\['ffmpeg'")
-                   (string-append "out_file.compile() == ['" ffmpeg "'")))))
-            ;; Some tests fail with ffmpeg 5+
-            (replace 'check
-              (lambda* (#:key tests? #:allow-other-keys)
-                (when tests?
-                  (invoke "pytest" "-vv"
-                          "-k" "not test_pipe and not test__probe")))))))
-      (inputs (list ffmpeg))
-      (propagated-inputs (list python-future))
-      (native-inputs (list python-future python-numpy python-pytest
-                           python-pytest-mock python-pytest-runner))
-      (home-page "https://github.com/kkroening/ffmpeg-python")
-      (synopsis "Python bindings for FFmpeg with complex filtering support")
-      (description
-       "ffmpeg-python allows you to write FFmpeg filtergraphs in familiar
+                   (format #f "out_file.compile() == [~s" ffmpeg)))))))))
+    (inputs (list ffmpeg))
+    (propagated-inputs (list python-future))
+    (native-inputs (list python-future
+                         python-numpy
+                         python-pytest
+                         python-pytest-mock
+                         python-setuptools))
+    (home-page "https://github.com/kkroening/ffmpeg-python")
+    (synopsis "Python bindings for FFmpeg with complex filtering support")
+    (description
+     "ffmpeg-python allows you to write FFmpeg filtergraphs in familiar
 Python terms, taking care of running ffmpeg with the correct command-line
 arguments.  It handles arbitrarily large (directed-acyclic) signal graphs.")
-      (license license:asl2.0))))
+    (license license:asl2.0)))
 
 (define-public python-imageio-ffmpeg
   (package
@@ -13358,23 +13389,23 @@ all of your favorite programs.")
 (define-public python-pywinrm
   (package
     (name "python-pywinrm")
-    (version "0.4.1")
+    (version "0.5.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "pywinrm" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/diyan/pywinrm/")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32
-         "10gabhhg3rgacd5ahmi2r128z99fzbrbx6mz1nnq0dxmhmn5rpjf"))))
-    (build-system python-build-system)
+        (base32 "0jp7rps6zg5b6n98lfkwbhv72982sxxnqc4v4i6hjlq1ycjmmb8r"))))
+    (build-system pyproject-build-system)
     (propagated-inputs
-     (list python-six python-requests_ntlm python-xmltodict
-           python-kerberos))
+     (list python-requests python-requests-ntlm python-xmltodict))
     (native-inputs
-     (list python-mock python-pytest))
+     (list python-mock python-pytest python-setuptools))
     (home-page "https://github.com/diyan/pywinrm/")
-    (synopsis
-     "Python library for Windows Remote Management (WinRM)")
+    (synopsis "Python library for Windows Remote Management (WinRM)")
     (description
      "pywinrm is a Python client for the Windows Remote Management (WinRM)
 service.  It allows you to invoke commands on target Windows machines from
@@ -13533,16 +13564,19 @@ etc.  The core of this module is a decorator factory.")
        (uri (pypi-uri "drmaa" version))
        (sha256
         (base32 "0xzqriqyvk5b8hszbavsyxd29wm3sxirm8zvvdm73rs2iq7w4hkx"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     ;; The test suite requires libdrmaa which is provided by the cluster
     ;; environment.  At runtime the environment variable DRMAA_LIBRARY_PATH
     ;; should be set to the path of the libdrmaa library.
     (arguments
-     '(#:tests? #f
-       #:phases (modify-phases %standard-phases
-                  ;; Loading the library fails because DRMAA_LIBRARY_PATH
-                  ;; is not configured.
-                  (delete 'sanity-check))))
+     (list
+      #:tests? #f
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; Loading the library fails because DRMAA_LIBRARY_PATH
+          ;; is not configured.
+          (delete 'sanity-check))))
+    (native-inputs (list python-setuptools))
     (home-page "https://pypi.org/project/drmaa/")
     (synopsis "Python bindings for the DRMAA library")
     (description
@@ -13570,11 +13604,11 @@ Python language binding specification.")
                  (substitute* '("grako/util.py"
                                 "grako/walkers.py")
                    (("collections\\.Mapping") "collections.abc.Mapping"))))))
-    (build-system python-build-system)
-    (arguments '(#:tests? #f)) ; Test file 'grako.ebnf' is missing from archive.
-    (native-inputs
-     (list unzip python-pytest python-pytest-runner))
-    (home-page "https://bitbucket.org/neogeny/grako")
+    (build-system pyproject-build-system)
+     ;; XXX: Test file 'grako.ebnf' is missing from archive.
+    (arguments (list #:tests? #f))
+    (native-inputs (list unzip python-pytest python-setuptools))
+    (home-page "https://pypi.org/project/grako")
     (synopsis "EBNF parser generator")
     (description
      "Grako takes a grammar in a variation of EBNF as input, and outputs a
@@ -13639,7 +13673,7 @@ you to actually draw things with your favorite toolkit.")
 (define-public python-gridmap
   (package
     (name "python-gridmap")
-    (version "0.14.0")
+    (version "0.15.0")
     (source
      (origin
        (method git-fetch)
@@ -13648,15 +13682,20 @@ you to actually draw things with your favorite toolkit.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0v0sgpg6pz8h61f9aqjf5xk0ipr512bbz8dxzjjylksj135qr19l"))))
-    (build-system python-build-system)
+        (base32 "0w1sxvhv5ldbzkx70q7036yvny0zsylc4zj7nzmp3nhjdl8whlrm"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:tests? #f    ;FIXME: Requires python-cherrypy.
-       #:phases (modify-phases %standard-phases
-                  ;; Importing the web server module requires cherrypy, too.
-                  (delete 'sanity-check))))
+     (list #:tests? #f ;XXX: freezes or timeout
+           #:test-backend #~'nose))
+    (native-inputs
+     (list ;; python-pynose
+           python-setuptools))
     (propagated-inputs
-     (list python-psutil python-drmaa python-pyzmq))
+     (list python-cherrypy
+           python-cloudpickle
+           python-psutil
+           python-drmaa
+           python-pyzmq))
     (home-page "https://github.com/pygridtools/gridmap")
     (synopsis "Create jobs on a cluster directly from Python")
     (description
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 82512f80e6..efd307aea1 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -414,9 +414,6 @@ problems for efficient solution on parallel systems.")
     (license license:gpl3+)
     (home-page "https://openfoam.org")))
 
-(define-public openfoam
-  (deprecated-package "openfoam" openfoam-org))
-
 (define-public openfoam-com
   ;; This is a fork of 'openfoam-org', maintained separately.
   (package
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 688db00783..87e40e1177 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -244,12 +244,13 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
            pango
            readline
            gtk+
-           gtksourceview-3
+           gtksourceview-4
            spread-sheet-widget
            zlib))
     (native-inputs
      (list autoconf ;for tests
            `(,glib "bin") ;for glib-genmarshal
+           glibc-locales ;for test 1597: tex non-ascii
            perl
            pkg-config
            python-3 ;for tests
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 2ef3e4ea3e..09917f2880 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -3134,7 +3134,7 @@ video streaming services of the Finnish national broadcasting company Yle.")
 (define-public yt-dlp
   (package
     (name "yt-dlp")
-    (version "2025.10.14")
+    (version "2025.10.22")
     (source
      (origin
        (method git-fetch)
@@ -3146,7 +3146,7 @@ video streaming services of the Finnish national broadcasting company Yle.")
        (snippet #~(substitute* "pyproject.toml"
                     (("^.*Programming Language :: Python :: 3\\.13.*$") "")))
        (sha256
-        (base32 "187rwpdh881m922h6m32pikqah1wlxjqww73ijw511i2fnwykfy7"))))
+        (base32 "19viqfk3gnl6yk9p17kp0a21w18yr32qii4grm3mys758ws881ld"))))
     (build-system pyproject-build-system)
     (arguments
      (list