GNU bug report logs - #77541
[PATCH 01/38] gnu: Add clipper2.

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Package: guix-patches; Reported by: Nicolas Graves <ngraves@HIDDEN>; Keywords: patch; Done: Nicolas Graves <ngraves@HIDDEN>; Maintainer for guix-patches is guix-patches@HIDDEN.

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Subject: [PATCH 38/38] gnu: python-itemloaders: Update to 1.3.2.
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* gnu/packages/python-xyz.scm (python-itemloaders): Update to 1.3.2.
[native-inputs]: Add python-packaging.
[propagated-inputs]: Remove python-w3lib.
---
 gnu/packages/python-xyz.scm | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d18e4cfebd..ceebb018d9 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -39158,17 +39158,21 @@ (define-public python-itemadapter
 (define-public python-itemloaders
   (package
     (name "python-itemloaders")
-    (version "1.1.0")
+    (version "1.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "itemloaders" version))
        (sha256
-        (base32 "0j2aw4ipalj208594x80blpgkh1i63gqqa4nb67b823av9hirn11"))))
+        (base32 "0w37g31n06x6v6b4w7cz3nbq4wl6cv7rrzg3fr203gw3pqx5pbsg"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-pytest python-setuptools python-wheel))
+    (native-inputs
+     (list python-packaging
+           python-pytest
+           python-setuptools
+           python-wheel))
     (propagated-inputs
-     (list python-itemadapter python-jmespath python-parsel python-w3lib))
+     (list python-itemadapter python-jmespath python-parsel))
     (home-page "https://github.com/scrapy/itemloaders")
     (synopsis "Base library for scrapy's ItemLoader")
     (description "Itemloaders is a library that helps you collect data
-- 
2.49.0





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bug#77541; Package guix-patches. Full text available.

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* gnu/packages/machine-learning.scm (python-botorch): Update to
0.13.0.
[native-inputs]: Add python-pyre-extensions.
---
 gnu/packages/machine-learning.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 4bf7442e09..e62535d890 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -6161,7 +6161,7 @@ (define-public python-gpytorch
 (define-public python-botorch
   (package
     (name "python-botorch")
-    (version "0.11.3")
+    (version "0.13.0")
     (source (origin
               (method git-fetch) ;no tests in PyPI
               (uri (git-reference
@@ -6170,7 +6170,7 @@ (define-public python-botorch
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0nf9zrg1khvckb8kdpffqc3bnlhc0x03jd1560qmjamwl3j59m02"))))
+                "1sxgxdq892vg5xj30kb86003b9rwsipc95c7p1zdv865y4f38a8y"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:test-flags #~(list "-k" "not test_all_cases_covered")
@@ -6189,7 +6189,8 @@ (define-public python-botorch
                              python-pyro-ppl
                              python-pytorch
                              python-scipy))
-    (native-inputs (list python-pytest
+    (native-inputs (list python-pyre-extensions
+                         python-pytest
                          python-pytest-cov
                          python-setuptools
                          python-setuptools-scm
-- 
2.49.0





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bug#77541; Package guix-patches. Full text available.

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* gnu/packages/iso-codes.scm (python-country-converter)[native-inputs]:
Add python-wheel.
---
 gnu/packages/iso-codes.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/iso-codes.scm b/gnu/packages/iso-codes.scm
index fd04d13a9f..ad9b90a564 100644
--- a/gnu/packages/iso-codes.scm
+++ b/gnu/packages/iso-codes.scm
@@ -122,7 +122,8 @@ (define-public python-country-converter
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
-           python-setuptools))
+           python-setuptools
+           python-wheel))
     (propagated-inputs
      (list python-pandas))
     (home-page "https://github.com/IndEcol/country_converter")
-- 
2.49.0





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* gnu/packages/python-web.scm (python-flask-seasurf): Update to 2.0.0.
---
 gnu/packages/python-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 8bb808b846..a740f9638b 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -5433,13 +5433,13 @@ (define-public python-flask-compress
 (define-public python-flask-seasurf
   (package
     (name "python-flask-seasurf")
-    (version "1.1.1")
+    (version "2.0.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "Flask-SeaSurf" version))
               (sha256
                (base32
-                "1aaib4n27q0f2alp87mhv3f79vg7qckp71rphbd0mb39qw470lsl"))))
+                "0g5dsm2ikv8q4qcrb2446pbs972l5wkxyfmxsriqdsl02nz06h4f"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:tests? #false)) ;there are none
-- 
2.49.0





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* gnu/packages/django.scm (python-django-rq): Update to 3.0.0.
[arguments]{test-flags}: Ignore failing tests.
{phases}: Replace 'check phase replacement by a simpler 'pre-check
configuration phase.
[native-inputs]: Add python-pytest, python-pytest-django.
[propagated-inputs]: Add python-redis, python-pyaml.
---
 gnu/packages/django.scm | 28 +++++++++++++++-------------
 1 file changed, 15 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index cb9df0d2df..44d47b39ab 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -1055,39 +1055,41 @@ (define-public python-django-redis
 (define-public python-django-rq
   (package
     (name "python-django-rq")
-    (version "2.7.0")
+    (version "3.0.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "django-rq" version))
               (sha256
                (base32
-                "0aw0fi0lg80qgdp9fhjbnlhvfh2p09rgy1nj6hxpyhi37kihni2h"))))
+                "1b371w4cdjlz83i2sg4gpx0z3svl3bfrn6zfy661374hv62xpnkv"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      #~(list "-k" "not test_scheduled_jobs and not test_started_jobs")
       #:phases
-      '(modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (invoke "redis-server" "--daemonize" "yes")
-               (invoke "django-admin" "test" "django_rq"
-                       "--settings=django_rq.tests.settings"
-                       "--pythonpath=.")))))))
+      #~(modify-phases %standard-phases
+          (add-before 'check 'pre-check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "redis-server" "--daemonize" "yes")
+                (setenv "DJANGO_SETTINGS_MODULE" "django_rq.tests.settings")
+                (setenv "PYTHONPATH" (getcwd))))))))
     (native-inputs
      (list python-django-redis
-           python-mock
+           python-pytest
+           python-pytest-django
            python-rq-scheduler
            python-setuptools
            python-wheel
            redis
            tzdata-for-tests))
     (propagated-inputs
-     (list python-django python-rq))
+     (list python-django python-redis python-rq python-pyaml))
     (home-page "https://github.com/ui/django-rq")
     (synopsis "Django integration with RQ")
     (description
-      "Django integration with RQ, a Redis based Python queuing library.
+     "Django integration with RQ, a Redis based Python queuing library.
 Django-RQ is a simple app that allows you to configure your queues in django's
 settings.py and easily use them in your project.")
     (license license:expat)))
-- 
2.49.0





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This is a leaf package in python, broken and undevelopped for 10 years.

* gnu/packages/python-web.scm (python-cookies): Delete variable.
---
 gnu/packages/python-web.scm | 22 ----------------------
 1 file changed, 22 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index e82d59037c..8bb808b846 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -5496,28 +5496,6 @@ (define-public python-flask-multistatic
 for overriding static files.")
     (license license:gpl3+)))
 
-(define-public python-cookies
-  (package
-    (name "python-cookies")
-    (version "2.2.1")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "cookies" version))
-              (sha256
-               (base32
-                "13pfndz8vbk4p2a44cfbjsypjarkrall71pgc97glk5fiiw9idnn"))))
-    (build-system python-build-system)
-    (arguments
-     `(;; test are broken: https://gitlab.com/sashahart/cookies/issues/3
-       #:tests? #f))
-    (native-inputs
-     (list python-pytest))
-    (synopsis "HTTP cookie parser and renderer")
-    (description "A RFC 6265-compliant HTTP cookie parser and renderer in
-Python.")
-    (home-page "https://gitlab.com/sashahart/cookies")
-    (license license:expat)))
-
 (define-public python-responses
   (package
     (name "python-responses")
-- 
2.49.0





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bug#77541; Package guix-patches. Full text available.

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* gnu/packages/python-web.scm (python-port-for): Update to 0.7.4.
[build-system]: Switch to pyproject.
[native-inputs]: Remove python-mock.  Add python-setuptools,
python-wheel.
---
 gnu/packages/python-web.scm | 18 +++++-------------
 1 file changed, 5 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 579386e5ab..e82d59037c 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -7701,26 +7701,18 @@ (define-public grip
 (define-public python-port-for
   (package
     (name "python-port-for")
-    (version "0.4")
+    (version "0.7.4")
     (source
      (origin
        (method url-fetch)
-       (uri (pypi-uri "port-for" version))
+       (uri (pypi-uri "port_for" version))
        (sha256
-        (base32
-         "1pncxlj25ggw99r0ijfbkq70gd7cbhqdx5ivsxy4jdp0z14cpda7"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'use-urllib3
-           (lambda _
-             (substitute* "port_for/_download_ranges.py"
-               (("urllib2") "urllib3")))))))
+        (base32 "13826s2d4hzzmv69wws6a7ryhminclv2bqaw6cpl929gnbki6xzw"))))
+    (build-system pyproject-build-system)
     (propagated-inputs
      (list python-urllib3))
     (native-inputs
-     (list python-mock))
+     (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/kmike/port-for/")
     (synopsis "TCP localhost port finder and association manager")
     (description
-- 
2.49.0





Information forwarded to guix-patches@HIDDEN:
bug#77541; Package guix-patches. Full text available.

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* gnu/packages/databases.scm (python-rq-scheduler): Update to 0.14.
[build-system]: Switch to pyproject.
[arguments]{test-flags}: Ignore failing tests.  They fail because of
mcron's requirements to be run with root when -u flag is used.
{phases}: Remove 'check phase replacement.
[native-inputs]: Add python-crontab, python-freezegun, python-pytest,
python-setuptools, python-wheel.  Remove which.
---
 gnu/packages/databases.scm | 37 +++++++++++++++++++++++--------------
 1 file changed, 23 insertions(+), 14 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 4ecf237115..1aebf982ae 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4647,7 +4647,7 @@ (define-public python-rq
 (define-public python-rq-scheduler
   (package
     (name "python-rq-scheduler")
-    (version "0.10.0")
+    (version "0.14")
     (home-page "https://github.com/rq/rq-scheduler")
     (source (origin
               (method git-fetch)
@@ -4657,21 +4657,30 @@ (define-public python-rq-scheduler
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0xg6yazqs5kbr2ayvhvljs1h5vgx5k5dds613fmhswln7gglf9hk"))))
-    (build-system python-build-system)
+                "09fh9m2vcl1jndq35xp1x0j8ih009r71qmhn2pkl93fykrqfavyn"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases (modify-phases %standard-phases
-                  (add-before 'check 'start-redis
-                    (lambda _
-                      (invoke "redis-server" "--daemonize" "yes")))
-                  (replace 'check
-                    (lambda _
-                      (substitute* "run_tests.py"
-                        (("/usr/bin/env")
-                         (which "env")))
-                      (invoke "./run_tests.py"))))))
+     (list
+      #:test-flags
+      #~(list "-k" (string-append "not test_cron"
+                                  " and not test_job_creation_with"
+                                  " and not test_job_with_crontab"))
+      #:phases #~(modify-phases %standard-phases
+                   (add-before 'check 'start-redis
+                     (lambda _
+                       (invoke "redis-server" "--daemonize" "yes")))
+                   (add-after 'unpack 'loosen-requirements
+                     (lambda _
+                       (substitute* "setup.py"
+                         (("crontab>=[0-9.]*")
+                          "python-crontab")))))))
     (native-inputs
-     (list redis which))
+     (list python-crontab
+           python-freezegun
+           python-pytest
+           python-setuptools
+           python-wheel
+           redis))
     (propagated-inputs
      (list python-croniter python-rq))
     (synopsis "Job scheduling capabilities for RQ (Redis Queue)")
-- 
2.49.0





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bug#77541; Package guix-patches. Full text available.

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* gnu/packages/python-xyz.scm (python-stone): Update to 3.3.9.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject.
[arguments]: Remove field.
[propagated-inputs]: Add python-jinja2, python-packaging.
[native-inputs]: Add python-setuptools, python-wheel. Remove
python-coverage, python-mock.
---
 gnu/packages/python-xyz.scm | 41 +++++++++++--------------------------
 1 file changed, 12 insertions(+), 29 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e63e41ba18..d18e4cfebd 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -29754,38 +29754,21 @@ (define-public python-userspacefs
 (define-public python-stone
   (package
     (name "python-stone")
-    (version "3.2.1")
+    (version "3.3.9")
     (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "stone" version))
-        (sha256
-         (base32
-          "0xby5mpsms7b2rv8j6mvxzmzz5i9ii01brb9ylxz6kiv2i08piwv"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'change-version-requirements
-           (lambda _
-             ;; Match the requirement in test/requirements.txt
-             (substitute* "setup.py"
-               (("pytest < 5") "pytest < 7"))
-             ;; We don't care about a coverage report.
-             (substitute* "test/requirements.txt"
-               (("coverage.*") "coverage\n"))))
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               ;; These tests don't import correctly.
-               (delete-file "test/test_js_client.py")
-               (delete-file "test/test_tsd_types.py")
-               (delete-file "test/test_python_gen.py")
-               (invoke "pytest")))))))
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/dropbox/stone")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1x0kj4jygssjn66lbkln95chhf85vzy1wnpziy9jvpf4kbc1bmfy"))))
+    (build-system pyproject-build-system)
     (propagated-inputs
-     (list python-ply python-six))
+     (list python-jinja2 python-packaging python-ply python-six))
     (native-inputs
-     (list python-coverage python-mock python-pytest python-pytest-runner))
+     (list python-pytest python-pytest-runner python-setuptools python-wheel))
     (home-page "https://github.com/dropbox/stone")
     (synopsis "Official Api Spec Language for Dropbox")
     (description
-- 
2.49.0





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bug#77541; Package guix-patches. Full text available.

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* gnu/packages/python-xyz.scm (python-crontab): Update to 3.2.0.
[build-system]: Switch to pyproject.
[arguments]{test-flags}: Ignore test.
{phases}: Remove phase 'disable-failing-tests. Add phase
default-to-mcron.
[inputs]: Add mcron.
[native-inputs]: Add python-pytest, python-setuptools, python-wheel.
---
 gnu/packages/python-xyz.scm | 36 +++++++++++++++++-------------------
 1 file changed, 17 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b526c6161a..e63e41ba18 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -231,6 +231,7 @@ (define-module (gnu packages python-xyz)
   #:use-module (gnu packages gsasl)
   #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages gtk)
+  #:use-module (gnu packages guile-xyz)
   #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages image)
@@ -31789,32 +31790,29 @@ (define-public python-croniter
 (define-public python-crontab
   (package
     (name "python-crontab")
-    (version "3.0.0")
+    (version "3.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri name version))
        (sha256
-        (base32 "0yd3vdhl7z8lxa30czsry65srha51ppdcwnhjgxx9pwx0djp9yvr"))))
-    (build-system python-build-system)
+        (base32 "0sy3qlki43n6qmhzzzyya4wcs50mcp3mg1ddn9h39plsscfps1j0"))))
+    (build-system pyproject-build-system)
     (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'check 'disable-failing-tests
-            (lambda _
-              (substitute* '("tests/test_compatibility.py"
-                             "tests/test_frequency.py")
-                (("test_07_non_posix_shell")
-                 "__off_test_07_non_posix_shell")
-                ;; Fails on leap years
-                (("test_19_frequency_at_month")
-                 "__off_test_19_frequency_at_month")
-                ;; AssertionError: 48 != 24
-                (("test_20_frequency_at_year")
-                 "__off_test_20_frequency_at_year")))))))
+     (list #:test-flags
+           ;; This test is made for Windows.
+           #~(list "-k" "not test_07_non_posix_shell")
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'defaults-to-mcron
+                 (lambda* (#:key inputs #:allow-other-keys)
+                   (substitute* "crontab.py"
+                     (("/usr/bin/crontab")
+                      (search-input-file inputs "bin/crontab"))))))))
     (inputs
-     (list python-dateutil))
+     (list mcron python-dateutil))
+    (native-inputs
+     (list python-pytest python-setuptools python-wheel))
     (home-page "https://gitlab.com/doctormo/python-crontab/")
     (synopsis "Module for reading and writing crontab files")
     (description "This Python module can read, write crontab files, and
-- 
2.49.0





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bug#77541; Package guix-patches. Full text available.

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Subject: [PATCH 23/38] gnu: python-bed-reader: Fix build and enable tests.
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* gnu/packages/bioinformatics.scm (python-bed-reader): Fix build and enable tests.
[source]{snippet}: Delete bundled website-related javascript.
{patches}: Use the store-cached instead of pooch-cached samples.
[arguments]{tests?}: Enable them.
{cargo-test-flags}: Skip doc tests. Skip failing tests.
{cargo-inputs}: Improve style.
{cargo-development-inputs}: Improve style.
{phases}: Add phases 'set-data-path, 'patch-data-path to use
store-cached samples for library and tests.  Rewrite phase
'prepare-python-module to rely more on the existing info in
pyproject.toml.  Rewrite phase 'check-python entirely, and
marginaly rewrite phase 'install-python-library to match 'check-python
phase style.
{modules}: Adapt accordingly.
{propagated-inputs}: Remove python-pooch. Add python-scipy.

(bed-sample-files): Add origin, used in python-bed-reader.

* gnu/packages/patches/python-bed-reader-use-store-samples.patch: Add
patch.
* gnu/local.mk: Record patch.
---
 gnu/local.mk                                  |   1 +
 gnu/packages/bioinformatics.scm               | 195 ++++++++++++------
 .../python-bed-reader-use-store-samples.patch | 147 +++++++++++++
 3 files changed, 284 insertions(+), 59 deletions(-)
 create mode 100644 gnu/packages/patches/python-bed-reader-use-store-samples.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 1bf8f8deba..6c2466114d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -2008,6 +2008,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-3.12-fix-tests.patch		\
   %D%/packages/patches/python-accupy-use-matplotx.patch		\
   %D%/packages/patches/python-accupy-fix-use-of-perfplot.patch	\
+  %D%/packages/patches/python-bed-reader-use-store-samples.patch	\
   %D%/packages/patches/python-chai-drop-python2.patch		\
   %D%/packages/patches/python-clarabel-blas.patch		\
   %D%/packages/patches/python-docrepr-fix-tests.patch		\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4dbedc09f9..c5fe295f6c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2167,6 +2167,20 @@ (define-public python-bcbio-gff/biopython-1.73
       (modify-inputs (package-propagated-inputs python-bcbio-gff)
         (replace "python-biopython" python-biopython-1.73))))))
 
+(define bed-sample-files
+  (let* ((name "bed-sample-files")
+         (commit "a06dc0450e484090f15656ffd5d317813a5e1e01")
+         (revision "0")
+         (version (git-version "0.0.0" revision commit)))
+    (origin
+      (method git-fetch)
+      (uri (git-reference
+            (url "https://github.com/fastlmm/bed-sample-files")
+            (commit commit)))
+      (file-name (git-file-name name version))
+      (sha256
+       (base32 "1ldr2lvgbcykxa9i2s2298mhfh0sz96aaxs5dx217aipa9vsrjwk")))))
+
 (define-public python-bed-reader
   (package
     (name "python-bed-reader")
@@ -2176,80 +2190,124 @@ (define-public python-bed-reader
        (method url-fetch)
        (uri (pypi-uri "bed_reader" version))
        (sha256
-        (base32 "1c8ibwvz3b069w7ffh9aasz16lfkmx4z0249c2v909a21mrkkd6n"))))
+        (base32 "1c8ibwvz3b069w7ffh9aasz16lfkmx4z0249c2v909a21mrkkd6n"))
+       (modules '((guix build utils)))
+       ;; Bundled unused javascript & co.
+       (snippet #~(delete-file-recursively "_static"))
+       (patches
+        (search-patches "python-bed-reader-use-store-samples.patch"))))
     (build-system cargo-build-system)
     (arguments
      (list
-      ;; Many of the tests (both the Rust tests and the Python tests) require
-      ;; Internet access to fetch samples.
-      #:tests? #false
       #:install-source? #false
       #:features '(list "extension-module")
-      #:cargo-test-flags '(list "--features=extension-module")
+      #:cargo-test-flags
+      '(list "--features=extension-module"
+             ;; Skip doc tests.
+             "--lib" "--bins" "--tests" "--"
+             ;; This test is the only one not matched by our regexp.
+             "--skip=http_one"
+             ;; These test require a 84 GB file.
+             "--skip=http_two"
+             "--skip=http_cloud_urls_md_3")
       #:cargo-inputs
-      `(("rust-anyinput" ,rust-anyinput-0.1)
-        ("rust-bytecount" ,rust-bytecount-0.6)
-        ("rust-byteorder" ,rust-byteorder-1)
-        ("rust-bytes" ,rust-bytes-1)
-        ("rust-cloud-file" ,rust-cloud-file-0.2)
-        ("rust-derive-builder" ,rust-derive-builder-0.20)
-        ("rust-dpc-pariter" ,rust-dpc-pariter-0.4)
-        ("rust-fetch-data" ,rust-fetch-data-0.2)
-        ("rust-futures-util" ,rust-futures-util-0.3)
-        ("rust-itertools" ,rust-itertools-0.13)
-        ("rust-ndarray" ,rust-ndarray-0.16)
-        ("rust-ndarray-npy" ,rust-ndarray-npy-0.9)
-        ("rust-num-traits" ,rust-num-traits-0.2)
-        ("rust-numpy" ,rust-numpy-0.22)
-        ("rust-pyo3" ,rust-pyo3-0.22)
-        ("rust-pyo3-build-config" ,rust-pyo3-build-config-0.22)
-        ("rust-rayon" ,rust-rayon-1)
-        ("rust-statrs" ,rust-statrs-0.17)
-        ("rust-thiserror" ,rust-thiserror-1)
-        ("rust-tokio" ,rust-tokio-1))
+      (list rust-anyinput-0.1
+            rust-bytecount-0.6
+            rust-byteorder-1
+            rust-bytes-1
+            rust-cloud-file-0.2
+            rust-derive-builder-0.20
+            rust-dpc-pariter-0.4
+            rust-fetch-data-0.2
+            rust-futures-util-0.3
+            rust-itertools-0.13
+            rust-ndarray-0.16
+            rust-ndarray-npy-0.9
+            rust-num-traits-0.2
+            rust-numpy-0.22
+            rust-pyo3-0.22
+            rust-pyo3-build-config-0.22
+            rust-rayon-1
+            rust-statrs-0.17
+            rust-thiserror-1
+            rust-tokio-1)
       #:cargo-development-inputs
-      `(("rust-anyhow" ,rust-anyhow-1)
-        ("rust-ndarray-rand" ,rust-ndarray-rand-0.15)
-        ("rust-rusoto-credential" ,rust-rusoto-credential-0.48)
-        ("rust-temp-testdir" ,rust-temp-testdir-0.2)
-        ("rust-thousands" ,rust-thousands-0.2))
+      (list rust-anyhow-1
+            rust-ndarray-rand-0.15
+            rust-rusoto-credential-0.48
+            rust-temp-testdir-0.2
+            rust-thousands-0.2)
       #:imported-modules
       (append %cargo-build-system-modules
               %pyproject-build-system-modules)
       #:modules
       '((guix build cargo-build-system)
         ((guix build pyproject-build-system) #:prefix py:)
-        (guix build utils))
+        (guix build utils)
+        (ice-9 match)
+        (ice-9 rdelim))
       #:phases
       #~(modify-phases %standard-phases
+          (add-after 'configure 'set-data-path
+            (lambda _
+              ;; This var is still necessary despite the patch-data-path phase.
+              ;; Otherwise more tests fail with a read-only filesystem error.
+              (setenv "BED_READER_DATA_DIR" #+bed-sample-files)))
+          (add-after 'unpack 'patch-data-path
+            (lambda _
+              ;; If BED_READER_DATA_DIR is unset, default to bed-sample-files.
+              (substitute* "bed_reader/_sample_data.py"
+                (("os\\.environ\\.get\\(\"BED_READER_DATA_DIR\"" all)
+                 (format #f "~a, ~s" all #+bed-sample-files)))
+              ;; XXX: More work is necessary to use another
+              ;; version of sample files with BED_READER_DATA_DIR
+              ;; Currently, only the hardcoded Guix version is working.
+              (substitute* '("bed_reader/tests/test_open_bed_cloud.py"
+                             "src/bed_cloud.rs"
+                             "src/lib.rs"
+                             "src/supplemental_documents/cloud_urls_etc.md"
+                             "tests/tests_api_cloud.rs")
+                (("\
+https://raw\\.githubusercontent\\.com/fastlmm/bed-sample-files/main")
+                 (string-append "file://" #+bed-sample-files)))
+              (substitute* "src/tests.rs"
+                (("bed_reader/tests/data")
+                 #+bed-sample-files))))
           (add-after 'install 'prepare-python-module
             (lambda _
-              ;; We don't use maturin.
-              (delete-file "pyproject.toml")
-              (call-with-output-file "pyproject.toml"
-                (lambda (port)
-                  (format port "\
+              ;; We don't use maturin. Conveniently, what we want to drop
+              ;; from pyproject.toml is at the end of the file.
+              (rename-file "pyproject.toml" "pyproject.toml.bak")
+              (call-with-input-file "pyproject.toml.bak"
+                (lambda (in)
+                  (call-with-output-file "pyproject.toml"
+                    (lambda (out)
+                      (let loop ()
+                        (match (read-line in)
+                          ((? eof-object? eof)
+                           eof)
+                          ("[build-system]"
+                           (and (format out "\
 [build-system]
 build-backend = 'setuptools.build_meta'
 requires = ['setuptools']
+
+[tool.setuptools.packages.find]
+where = [\".\"]
+exclude = [\"src\", \"docs\", \"tests\", \"Cargo.toml\"]
 ")))
-              (call-with-output-file "setup.cfg"
-                (lambda (port)
-                  (format port "\
-[metadata]
-name = bed-reader
-version = ~a
-
-[options]
-packages = find:
-
-[options.packages.find]
-exclude =
-  src
-  docs
-  tests
-  Cargo.toml
-" #$version)))))
+                          ("samples = [\"pooch>=1.5.0\"]"
+                           (and (format out "samples = []~%")
+                                (loop)))
+                          ("[project]"
+                           (and (format out "\
+[project]
+version = ~s
+" #$version)
+                                (loop)))
+                          (line
+                           (and (format out "~a~%" line)
+                                (loop)))))))))))
           (add-after 'prepare-python-module 'enable-bytecode-determinism
             (assoc-ref py:%standard-phases 'enable-bytecode-determinism))
           (add-after 'enable-bytecode-determinism 'build-python-module
@@ -2261,16 +2319,35 @@ (define-public python-bed-reader
               (let ((site (string-append #$output "/lib/python"
                                          #$(version-major+minor
                                             (package-version python))
-                                         "/site-packages")))
-                (mkdir-p site)
+                                         "/site-packages/")))
+                (mkdir-p (string-append site "bed_reader"))
                 (copy-file "target/release/libbed_reader.so"
-                           (string-append site "/bed_reader/bed_reader.so")))))
+                           (string-append site "bed_reader/bed_reader.so")))))
           (add-after 'install-python-library 'add-install-to-pythonpath
             (assoc-ref py:%standard-phases 'add-install-to-pythonpath))
           (add-after 'add-install-to-pythonpath 'check-python
-            (lambda* (#:key tests? test-flags #:allow-other-keys)
+            (lambda* (#:key tests? #:allow-other-keys)
               (when tests?
-                (apply invoke "pytest" "-v" #$output test-flags)))))))
+                (let ((site (string-append #$output "/lib/python"
+                                           #$(version-major+minor
+                                              (package-version python))
+                                           "/site-packages/"))
+                      (data-dir "bed_reader/tests/data"))
+                  (symlink (canonicalize-path data-dir)
+                           (string-append site data-dir))
+                  (invoke "pytest" "-v" #$output
+                          ;; These test require a 84 GB file.
+                          "-k" (string-join
+                                (list "not test_http_two"
+                                      "test_http_cloud_urls_rst_3"
+                                      "test_http_cloud_urls_rst_4"
+                                      ;; XXX: python-pooch dependency removed
+                                      "test_optional_dependencies")
+                                " and not "))
+                  (delete-file-recursively
+                   (string-append site "bed_reader/tests"))
+                  (delete-file-recursively
+                   (string-append #$output "/.pytest_cache")))))))))
     (native-inputs (list python-pytest
                          python-pytest-cov
                          python-pytest-datadir
@@ -2278,7 +2355,7 @@ (define-public python-bed-reader
                          python-recommonmark
                          python-sphinx))
     (inputs (list python-wrapper))
-    (propagated-inputs (list python-numpy python-pandas python-pooch))
+    (propagated-inputs (list python-numpy python-pandas python-scipy))
     (home-page "https://fastlmm.github.io/")
     (synopsis "Read and write the PLINK BED format, simply and efficiently")
     (description
diff --git a/gnu/packages/patches/python-bed-reader-use-store-samples.patch b/gnu/packages/patches/python-bed-reader-use-store-samples.patch
new file mode 100644
index 0000000000..813f155225
--- /dev/null
+++ b/gnu/packages/patches/python-bed-reader-use-store-samples.patch
@@ -0,0 +1,147 @@
+From 7e6bcdfeed54500ca533d2f0eb12078248c43c77 Mon Sep 17 00:00:00 2001
+Message-ID: <7e6bcdfeed54500ca533d2f0eb12078248c43c77.1743682382.git.ngraves@HIDDEN>
+From: Nicolas Graves <ngraves@HIDDEN>
+Date: Thu, 3 Apr 2025 11:33:58 +0200
+Subject: [PATCH] samples: Use deterministic samples in Guix.
+
+---
+ bed_reader/_sample_data.py | 86 +++++++++-----------------------------
+ 1 file changed, 19 insertions(+), 67 deletions(-)
+
+diff --git a/bed_reader/_sample_data.py b/bed_reader/_sample_data.py
+index 6ca4cc0..6a1146e 100644
+--- a/bed_reader/_sample_data.py
++++ b/bed_reader/_sample_data.py
+@@ -1,33 +1,8 @@
++import os
+ import tempfile
+ from pathlib import Path, PurePath
+ from typing import Union
+ 
+-try:
+-    import pooch
+-
+-    """
+-    Load sample data.
+-    """
+-
+-    POOCH = pooch.create(
+-        # Use the default cache folder for the OS
+-        path=pooch.os_cache("bed_reader"),
+-        # The remote data is on Github
+-        base_url="https://raw.githubusercontent.com/"
+-        + "fastlmm/bed-sample-files/main/",
+-        # If this is a development version, get the data from the master branch
+-        version_dev="main",
+-        # The registry specifies the files that can be fetched
+-        env="BED_READER_DATA_DIR",
+-    )
+-
+-    # Get registry file from package_data
+-    registry_file = Path(__file__).parent / "tests/registry.txt"
+-    # Load this registry file
+-    POOCH.load_registry(registry_file)
+-except ImportError:
+-    pooch = None
+-
+ 
+ def sample_file(filepath: Union[str, Path]) -> str:
+     """Retrieve a sample .bed file. (Also retrieves associated .fam and .bim files).
+@@ -40,50 +15,41 @@ def sample_file(filepath: Union[str, Path]) -> str:
+     Returns
+     -------
+     str
+-        Local name of sample .bed file.
+-
+-
+-    .. note::
+-        This function requires the :mod:`pooch` package. Install `pooch` with:
+-
+-        .. code-block:: bash
+-
+-            pip install --upgrade bed-reader[samples]
+-
+-
+-    By default this function puts files under the user's cache directory.
+-    Override this by setting
+-    the `BED_READER_DATA_DIR` environment variable.
++        Local path of sample .bed file.
+ 
+     Example
+     --------
+ 
+     .. doctest::
+ 
+-        >>> # pip install bed-reader[samples]  # if needed
+         >>> from bed_reader import sample_file
+         >>>
+         >>> file_name = sample_file("small.bed")
+         >>> print(f"The local file name is '{file_name}'")
+         The local file name is '...small.bed'
+-
+     """
+-    if pooch is None:
+-        raise ImportError(
+-            "The function sample_file() requires pooch. "
+-            + "Install it with 'pip install --upgrade bed-reader[samples]'.",
++    filepath = Path(filepath)
++    sample_dir = os.environ.get("BED_READER_DATA_DIR")
++    if sample_dir is None:
++        raise EnvironmentError(
++            "BED_READER_DATA_DIR environment variable is not set. "
++            "This should point to the directory containing the sample files."
+         )
+ 
+-    filepath = Path(filepath)
+-    file_string = str(filepath)
+-    if file_string.lower().endswith(".bed"):
+-        POOCH.fetch(file_string[:-4] + ".fam")
+-        POOCH.fetch(file_string[:-4] + ".bim")
+-    return POOCH.fetch(file_string)
++    file_path = Path(sample_dir) / filepath
++
++    # Check if file exists
++    if not file_path.exists():
++        raise FileNotFoundError(
++            f"Sample file '{filepath}' not found in {sample_dir}. "
++            f"Make sure you're using the latest samples in BED_READER_DATA_DIR."
++        )
++
++    return str(file_path)
+ 
+ 
+ def sample_url(filepath: Union[str, Path]) -> str:
+-    """Retrieve a URL to a sample .bed file. (Also makes ready associated .fam and .bim files).
++    """Retrieve a URL to a sample .bed file.
+ 
+     Parameters
+     ----------
+@@ -95,25 +61,11 @@ def sample_url(filepath: Union[str, Path]) -> str:
+     str
+         URL to sample .bed file.
+ 
+-
+-    .. note::
+-        This function requires the :mod:`pooch` package. Install `pooch` with:
+-
+-        .. code-block:: bash
+-
+-            pip install --upgrade bed-reader[samples]
+-
+-
+-    By default this function puts files under the user's cache directory.
+-    Override this by setting
+-    the `BED_READER_DATA_DIR` environment variable.
+-
+     Example
+     --------
+ 
+     .. doctest::
+ 
+-        >>> # pip install bed-reader[samples]  # if needed
+         >>> from bed_reader import sample_url
+         >>>
+         >>> url = sample_url("small.bed")
+-- 
+2.49.0
+
-- 
2.49.0





Information forwarded to guix-patches@HIDDEN:
bug#77541; Package guix-patches. Full text available.

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* gnu/packages/databases.scm (python-rq): Update to 2.3.1.
[build-system]: Switch to pyproject.
[arguments]{phases}: Delete 'check phase replacement. Improve style.
[native-inputs]: Add python-hatchling.
---
 gnu/packages/databases.scm | 30 +++++++++++++-----------------
 1 file changed, 13 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 097617e094..4ecf237115 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4611,7 +4611,7 @@ (define-public python-aioredis
 (define-public python-rq
   (package
     (name "python-rq")
-    (version "1.11.1")
+    (version "2.3.1")
     (source
      (origin
        (method git-fetch)
@@ -4620,24 +4620,20 @@ (define-public python-rq
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0dnjm2s036l4j4ypq0h903vh132dp2wiwjrn8jicz1nw829dqpzf"))))
-    (build-system python-build-system)
+        (base32 "1w9aqvbvh1mfpgng0mdcskxl5y3ybcqqai5dnwgvg18am0xxhya6"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases (modify-phases %standard-phases
-                  (add-before 'check 'start-redis
-                    (lambda _
-                      (invoke "redis-server" "--daemonize" "yes")))
-                  (replace 'check
-                    (lambda* (#:key outputs #:allow-other-keys)
-                      (let ((out (assoc-ref outputs "out")))
-                        ;; Drop test that needs the SDK for Sentry.io.
-                        (delete-file "tests/test_sentry.py")
-                        ;; Ensure 'rq' and 'rqworker' ends up on PATH.
-                        (setenv "PATH" (string-append out "/bin:"
-                                                      (getenv "PATH")))
-                        (invoke "pytest" "-vv")))))))
+     (list
+      #:phases #~(modify-phases %standard-phases
+                   (add-before 'check 'start-redis
+                     (lambda _
+                       (invoke "redis-server" "--daemonize" "yes"))))))
     (native-inputs
-     (list python-mock python-psutil python-pytest redis))
+     (list python-hatchling
+           python-mock
+           python-psutil
+           python-pytest
+           redis))
     (propagated-inputs
      (list python-click python-redis))
     (home-page "https://python-rq.org/")
-- 
2.49.0





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* gnu/packages/python-web.scm (python-furl): Update to 2.1.4.
[build-system]: Swtich to pyproject.
[arguments]{test-flags}: Ignore failing tests.
[propagated-inputs]: Sort.
[native-inputs]: Add python-pytest, python-setuptools, python-wheel.
---
 gnu/packages/python-web.scm | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index bf379c3699..579386e5ab 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1941,19 +1941,23 @@ (define-public python-falcon-cors
 (define-public python-furl
   (package
     (name "python-furl")
-    (version "2.1.3")
+    (version "2.1.4")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "furl" version))
         (sha256
-          (base32
-            "0knc76pm8pzigs3bpx9fccfsfxqrgblqphar46hq9i364vz8hqas"))))
-    (build-system python-build-system)
+          (base32 "05b058xisv8kghvcpaxvssml2jjkh1cmzyrrjwk2kjb62985fxl7"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:test-flags
+           #~(list "-k" (string-append "not test_hosts"
+                                       " and not test_netloc"
+                                       " and not test_odd_urls"))))
     (propagated-inputs
-     (list python-six python-orderedmultidict))
+     (list python-orderedmultidict python-six))
     (native-inputs
-     (list python-flake8))
+     (list python-flake8 python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/gruns/furl")
     (synopsis "URL manipulation in Python")
     (description "Furl provides an easy-to-use alternative to the
-- 
2.49.0





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bug#77541; Package guix-patches. Full text available.

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* gnu/packages/python-crypto.scm (python-pgpy): Fix tests.
[build-system]: Switch to pyproject.
[arguments]{phases}: Remove argument.
{test-flags}: Ignore failing tests.
[native-inputs]: Add python-setuptools.
---
 gnu/packages/python-crypto.scm | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index 13ad37bca8..fc57afb862 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -1634,17 +1634,14 @@ (define-public python-pgpy
         (uri (pypi-uri "PGPy" version))
         (sha256
          (base32 "10w3h934fi1ijx72ppn67a50yhkf8n1db6xx02gk2fjc7wsjx717"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (invoke "pytest")))))))
+     (list #:test-flags
+           ;; All broken tests are in this file.
+           ;; They fail with ValueError: key_size must be at least 1024-bits.
+           #~(list "--ignore" "tests/test_10_exceptions.py")))
     (native-inputs
-     (list python-pytest
-           python-wheel))
+     (list python-pytest python-setuptools python-wheel))
     (propagated-inputs (list python-cryptography python-pyasn1))
     (home-page "https://github.com/SecurityInnovation/PGPy")
     (synopsis "Python implementation of OpenPGP")
-- 
2.49.0





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* gnu/packages/finance.scm (python-duniterpy): Update to 1.2.1.
[source]: Switch to git-fetch to get tests.
[arguments]: Remove field.
[native-inputs]: Replace python-poetry-core by
python-poetry-core-next.  Add python-pytest.
[propagated-inputs]: Remove python-attrs.
---
 gnu/packages/finance.scm | 40 ++++++++++------------------------------
 1 file changed, 10 insertions(+), 30 deletions(-)

diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 69cee44386..680ebe467c 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -1412,42 +1412,22 @@ (define-public python-stdnum
 (define-public python-duniterpy
   (package
     (name "python-duniterpy")
-    (version "1.1.1")
+    (version "1.2.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "duniterpy" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://git.duniter.org/clients/python/duniterpy")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0h0fsawsrjd50lb1bkysb21ph39qlhmiymd3r5vs695qxvbwaqaa"))))
+        (base32 "1ysh9b5lzg053hv4iw3zbn7hid05qssiwmrl8sir8qlk958r8x60"))))
     (build-system pyproject-build-system)
-    (arguments
-     ;; FIXME: Tests fail with: "TypeError: block_uid() missing 1 required
-     ;; positional argument: 'value'".
-     `(#:tests? #f
-       #:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'loosen-requirements
-                    (lambda _
-                      (substitute* "pyproject.toml"
-                        (("mnemonic = \"\\^0\\.19")
-                         "mnemonic = \">=0.19")
-                        (("jsonschema = \"\\^3\\.2")
-                         "jsonschema = \">=3.2"))))
-                  (add-after 'unpack 'adjust-for-new-libnacl
-                    (lambda _
-                      ;; Mimic upstream commit ad8f6a26e9e7067; remove
-                      ;; for newer versions of duniterpy.
-                      (substitute* "pyproject.toml"
-                        (("libnacl = \"1\\.8")
-                         "libnacl = \">=1.9"))
-                      (substitute* "duniterpy/key/ascii_armor.py"
-                        (("from libnacl\\.version import version as libnacl_version")
-                         "import importlib.metadata
-libnacl_version = importlib.metadata.version('libnacl')")))))))
     (native-inputs
-     (list python-poetry-core))
+     (list python-poetry-core-next
+           python-pytest))
     (propagated-inputs
-     (list python-attrs
-           python-base58
+     (list python-base58
            python-graphql-core
            python-jsonschema
            python-libnacl
-- 
2.49.0





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* gnu/packages/python-xyz.scm (python-qasync)[arguments]{test-flags}:
Ignore failing tests.
---
 gnu/packages/python-xyz.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f262ccefcb..b526c6161a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21749,7 +21749,10 @@ (define-public python-qasync
         (base32 "0j6ksfnq9qfjdfppbkdz7jh6w0gnslwnckhafmlgim29b25g0z51"))))
     (build-system pyproject-build-system)
     (arguments
-     (list #:phases
+     (list #:test-flags
+           ;; XXX: Added with python@HIDDEN, not fixed upstream.
+           #~(list "-k" "not test_regression_bug13")
+           #:phases
            #~(modify-phases %standard-phases
                (add-before 'check 'set-qpa
                  (lambda _
-- 
2.49.0





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bug#77541; Package guix-patches. Full text available.

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* gnu/packages/python-build.scm (python-poetry-core-next): New variable.
---
 gnu/packages/python-build.scm | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/gnu/packages/python-build.scm b/gnu/packages/python-build.scm
index 6bea44fee6..9ac325094d 100644
--- a/gnu/packages/python-build.scm
+++ b/gnu/packages/python-build.scm
@@ -571,6 +571,16 @@ (define-public python-poetry-core
 compatible build front-ends to build Poetry managed projects.")
     (license license:expat)))
 
+(define-public python-poetry-core-next
+  (package/inherit python-poetry-core
+    (version "2.1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "poetry_core" version))
+       (sha256
+        (base32 "015a0802radb2x5wsbywm4fggv4s1srh8zyml5v58xgrxg8bpnzr"))))))
+
 ;;; This package exists to bootstrap python-tomli.
 (define-public python-flit-core-bootstrap
   (package
-- 
2.49.0





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To: 77541 <at> debbugs.gnu.org
Subject: [PATCH 24/38] gnu: python-pysnptools: Fix build and enable tests.
Date: Fri,  4 Apr 2025 21:16:56 +0200
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* gnu/packages/bioinformatics.scm (python-pysnptools): Fix build and enable
tests.
[arguments]{test-flags}: Ignore failing tests.
{phases}: Add 'patch-data-path and 'loosen-requirements phases.

(pysnptools-examples-files): Add origin.
(bgen-sample-files): Add origin.
---
 gnu/packages/bioinformatics.scm | 80 ++++++++++++++++++++++++++++++---
 1 file changed, 75 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c5fe295f6c..3f612fd701 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3715,6 +3715,49 @@ (define-public python-pygam
 familiar to anyone with experience of scikit-learn or scipy.")
     (license license:asl2.0)))
 
+(define bgen-sample-files
+  (let* ((name "bgen-sample-files")
+         (commit "7b1bc74f58b326ca19606fa5f3c6093d48367993")
+         (revision "0")
+         (version (git-version "0.0.0" revision commit)))
+    (origin
+      (method git-fetch)
+      (uri (git-reference
+            (url "https://github.com/fastlmm/bgen-sample-files")
+            (commit commit)))
+      (file-name (git-file-name name version))
+      (sha256
+       (base32 "1b8jkscccyspfr3y1b66xvwnljcha08r2i24v9d6hcm5zii0l54w")))))
+
+(define pynsptools-examples-files
+  (let* ((name "pysnptools-examples-files")
+         ;; taken from pysnptools/util/pysnptools.hashdown.json
+         (commit "ed14e050b2b75e7f4ddb73d512fbe928bbdb2b85")
+         (revision "0")
+         (version (git-version "0.0.0" revision commit)))
+    (origin
+      (method git-fetch)
+      (uri (git-reference
+            (url "https://github.com/fastlmm/PySnpTools")
+            (commit commit)))
+      (file-name (git-file-name name version))
+      (sha256
+       (base32 "0hznpj15kx2sla16wlmcqz21n2vi2qb1493v30vz75hnm1m4iwm1"))
+      (modules '((guix build utils)
+                 (ice-9 ftw)))
+      (snippet
+       #~(begin
+           ;; Delete everything except for examples directory:
+           (define (delete-except exceptions)
+             (lambda (file)
+               (unless (member file `("." ".." ,@exceptions))
+                 (delete-file-recursively file))))
+           (for-each (delete-except '("pysnptools" "tests")) (scandir "."))
+           (with-directory-excursion "pysnptools"
+             (for-each (delete-except '("examples")) (scandir ".")))
+           (with-directory-excursion "tests"
+             (for-each (delete-except '("datasets")) (scandir "."))))))))
+
 (define-public python-pysnptools
   (package
     (name "python-pysnptools")
@@ -3724,12 +3767,39 @@ (define-public python-pysnptools
        (method url-fetch)
        (uri (pypi-uri "pysnptools" version))
        (sha256
-        (base32
-         "1babnyky5fk93as1ybdvpz9x3x5099gkgscxflngzfswin23mspk"))))
+        (base32 "1babnyky5fk93as1ybdvpz9x3x5099gkgscxflngzfswin23mspk"))))
     (build-system pyproject-build-system)
-    ;; Tests require test data from python-bed-reader, which fetches data with
-    ;; python-pooch.
-    (arguments (list #:tests? #f))
+    (arguments
+     (list
+      #:test-flags
+      #~(list
+         ;; These tests require the bgen feature and an additional input.
+         "--ignore" "pysnptools/distreader/bgen.py"
+         "--ignore" "pysnptools/distreader/test_bgen2.py"
+         "--ignore" "pysnptools/distreader/distreader.py"
+         "-k" "not pysnptools.distreader.distdata.DistData.val \
+and not pysnptools.distreader.disthdf5.DistHdf5.write \
+and not pysnptools.distreader.distmemmap.DistMemMap.write"
+         ;; These tests require network connection.
+         "--ignore" "pysnptools/util/_example_file.py"
+         "--ignore" "pysnptools/util/filecache/hashdown.py")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-data-path
+            (lambda _
+              (substitute* "pysnptools/util/pysnptools.hashdown.json"
+                (("https://github\\.com/fastlmm/PySnpTools/\
+raw/ed14e050b2b75e7f4ddb73d512fbe928bbdb2b85")
+                 (string-append "file://" #+pynsptools-examples-files)))
+              (substitute* "pysnptools/util/bgen.hashdown.json"
+                (("https://raw\\.githubusercontent\\.com\
+/fastlmm/bgen-sample-files/7b1bc74f58b326ca19606fa5f3c6093d48367993")
+                 (string-append "file://" #+bgen-sample-files)))))
+          (add-after 'unpack 'loosen-requirements
+            (lambda _
+              (substitute* "pyproject.toml"
+                (("(h5py|psutil|wheel)>=[0-9.]*" all target)
+                 target)))))))
     (propagated-inputs
      (list python-bed-reader
            python-cloudpickle
-- 
2.49.0





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bug#77541; Package guix-patches. Full text available.

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* gnu/packages/machine-learning.scm (gpytorch): Remove uneeded inputs.
[arguments]{test-flags}: Ignore costly examples tests.
[native-inputs]: Remove python-coverage, python-flake8,
python-flake8-print, python-twine.
---
 gnu/packages/machine-learning.scm | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 615768c492..dcebf89376 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -6135,18 +6135,16 @@ (define-public python-gpytorch
     (arguments
      (list #:test-flags
            ;; test_deprecated_methods fails with an AssertionError.
-           #~(list "-k" (string-append "not test_deprecated_methods"))))
+           #~(list "-k" (string-append "not test_deprecated_methods")
+                   ;; Ignore lenghty tests of little relevance.
+                   "--ignore=test/examples/")))
     (propagated-inputs (list python-linear-operator
                              python-mpmath
                              python-scikit-learn
                              python-scipy))
-    (native-inputs (list python-coverage
-                         python-flake8
-                         python-flake8-print
-                         python-nbval
+    (native-inputs (list python-nbval
                          python-pytest
-                         python-setuptools
-                         python-twine))
+                         python-setuptools))
     (home-page "https://gpytorch.ai")
     (synopsis "Implementation of Gaussian Processes in PyTorch")
     (description
-- 
2.49.0





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* gnu/packages/statistics.scm (python-pgmpy): Update to 1.0.0.
[arguments]{test-flags}: Ignore failing tests.
[native-inputs]: Add python-pyro-ppl, python-setuptools, python-wheel,
python-xgboost.
---
 gnu/packages/statistics.scm | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 40991caab5..f883786f81 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -8312,7 +8312,7 @@ (define-public ruby-enumerable-statistics
 (define-public python-pgmpy
   (package
     (name "python-pgmpy")
-    (version "0.1.24")
+    (version "1.0.0")
     (source
      (origin
        (method git-fetch)  ;pypi package does not include test data
@@ -8322,8 +8322,14 @@ (define-public python-pgmpy
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0fvzh6v0yhgdryczamvzhfy2ymywkh0ssx4rl47xnfvi43hnij90"))))
+         "1hg6wrg3jcac71zn4gknni1wrn38wa86ka3sgp2bndz59mx6sr2s"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:test-flags
+           #~(list "-k" (string-append
+                         "not test_pillai"
+                         " and not test_estimate_with_cache_no_llm_calls"
+                         " and not test_estimate_with_orientations"))))
     (propagated-inputs (list python-daft
                              python-joblib
                              python-networkx
@@ -8337,7 +8343,11 @@ (define-public python-pgmpy
                              python-statsmodels
                              python-tqdm))
     (native-inputs (list python-mock
-                         python-pytest))
+                         python-pyro-ppl
+                         python-pytest
+                         python-setuptools
+                         python-wheel
+                         python-xgboost))
     (home-page "https://github.com/pgmpy/pgmpy")
     (synopsis "Probabilistic Graphical Models library")
     (description "This package provides a library for Probabilistic
-- 
2.49.0





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* gnu/packages/machine-learning.scm (python-gpytorch): Update to 1.14.
[arguments]{test-flags}: Ignore additional failing test.
[propagated-inputs]: Add python-jaxtyping.
[native-inputs]: Add python-setuptools, python-wheel.
---
 gnu/packages/machine-learning.scm | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index e5dd247c7d..4bf7442e09 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -6124,27 +6124,34 @@ (define-public python-linear-operator
 (define-public python-gpytorch
   (package
     (name "python-gpytorch")
-    (version "1.12")
+    (version "1.14")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "gpytorch" version))
               (sha256
                (base32
-                "1pwsccll1hrgkifdmlxzcn6cvnwvyq2cimqzbfgihr13yw51cb6w"))))
+                "13cs6dx8qa5j4ygji9w5xbmaqc68ihqyzz33fyyf9qa6d8gc2b03"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:test-flags
-           ;; test_deprecated_methods fails with an AssertionError.
-           #~(list "-k" (string-append "not test_deprecated_methods")
+           #~(list "-k" (string-append
+                         ;; test_deprecated_methods fails with an AssertionError.
+                         "not test_deprecated_methods"
+                         ;; This test is flaky: Expects gradients of 0 exactly,
+                         ;; can get negligible ones (e-10 to e-16).
+                         " and not test_optimization_optimal_error")
                    ;; Ignore lenghty tests of little relevance.
                    "--ignore=test/examples/")))
-    (propagated-inputs (list python-linear-operator
+    (propagated-inputs (list python-jaxtyping
+                             python-linear-operator
                              python-mpmath
                              python-scikit-learn
                              python-scipy))
     (native-inputs (list python-nbval
                          python-pytest
-                         python-setuptools))
+                         python-setuptools
+                         python-setuptools-scm
+                         python-wheel))
     (home-page "https://gpytorch.ai")
     (synopsis "Implementation of Gaussian Processes in PyTorch")
     (description
-- 
2.49.0





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bug#77541; Package guix-patches. Full text available.

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* gnu/packages/machine-learning.scm (python-botorch)[native-inputs]:
Add python-setuptools, python-wheel.
---
 gnu/packages/machine-learning.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index dcebf89376..e5dd247c7d 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -6184,7 +6184,9 @@ (define-public python-botorch
                              python-scipy))
     (native-inputs (list python-pytest
                          python-pytest-cov
-                         python-setuptools-scm))
+                         python-setuptools
+                         python-setuptools-scm
+                         python-wheel))
     (home-page "https://botorch.org")
     (synopsis "Bayesian Optimization in PyTorch")
     (description
-- 
2.49.0





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* gnu/packages/machine-learning.scm (python-linear-operator): Update
to 0.6.
[propagated-inputs]: Remove python-typeguard. Add python-mpmath.
[native-inputs]: Remove python-flake8, python-flake8-print,
python-twine. Add python-typeguard, python-wheel.
---
 gnu/packages/machine-learning.scm | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index fb1d5d2eed..615768c492 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -6098,24 +6098,23 @@ (define-public python-pyro-ppl
 (define-public python-linear-operator
   (package
     (name "python-linear-operator")
-    (version "0.5.2")
+    (version "0.6")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "linear_operator" version))
               (sha256
                (base32
-                "03drb4hn9nn8jrqd9vbalihhahgpdm956hbs05bix7svradhknaw"))))
+                "0m56f3zrm8xh1bpwh4g7jfc79rf4j94g6zmz663b58pig4w6dqm9"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-jaxtyping
+                             python-mpmath
                              python-pytorch
-                             python-scipy
-                             python-typeguard))
-    (native-inputs (list python-flake8
-                         python-flake8-print
-                         python-pytest
+                             python-scipy))
+    (native-inputs (list python-pytest
                          python-setuptools
                          python-setuptools-scm
-                         python-twine))
+                         python-typeguard
+                         python-wheel))
     (home-page "https://github.com/cornellius-gp/linear_operator/")
     (synopsis "Linear operator implementation")
     (description "LinearOperator is a PyTorch package for abstracting away the
-- 
2.49.0





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* gnu/packages/engineering.scm (python-lcapy)[native-inputs]: Add
python-setuptools, python-wheel.
---
 gnu/packages/engineering.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index ff268a1e08..e4aa046d3d 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -3138,7 +3138,9 @@ (define-public python-lcapy
                              python-scipy
                              python-sympy
                              python-wheel))
-    (native-inputs (list python-pytest))
+    (native-inputs (list python-pytest
+                         python-setuptools
+                         python-wheel))
     (home-page "https://github.com/mph-/lcapy")
     (synopsis "Symbolic linear circuit analysis")
     (description "Lcapy is a Python package for linear circuit analysis.  It
-- 
2.49.0





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bug#77541; Package guix-patches. Full text available.

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* gnu/packages/python-xyz.scm (python-pyro4): Update to 4.82.
[build-system]: Switch to pyproject-build-system.
[arguments]{tests?}: Remove to enable tests.
{test-flags}: Skip missing tests.
{phases}: Add 'check phase replacement.
[native-inputs]: Add python-setuptools, python-wheel.
---
 gnu/packages/python-xyz.scm | 45 ++++++++++++++++++++++++++++++++-----
 1 file changed, 40 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f36e5a3141..f262ccefcb 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -28438,18 +28438,53 @@ (define-public python-semver
 (define-public python-pyro4
   (package
     (name "python-pyro4")
-    (version "4.77")
+    (version "4.82")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Pyro4" version))
        (sha256
-        (base32 "0gsjg869y4gpy265s1gj1f2qy6jn5iz8r2bwwnq78r1r5yi15zib"))))
-    (build-system python-build-system)
+        (base32 "1yr1rv2afmq55wb14sx9qplzkqw7fya9rprsqdyxfbg90h45n7si"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:tests? #f)) ;FIXME: Some tests require network access.
+     (list #:test-flags
+           #~(list "-k"
+                   (string-join
+                    ;; Those tests require network.
+                    (list "testBCstart"
+                          "testAutoClean"
+                          "testDaemonPyroObj"
+                          "testLookupAndRegister"
+                          "testLookupInvalidHmac"
+                          "testLookupUnixsockParsing"
+                          "testMulti"
+                          "testRefuseDottedNames"
+                          "testResolve"
+                          "testBCLookup0000"
+                          "testPyroname"
+                          "testResolveAsymmetricHmacUsage"
+                          "testResolveWrongHmac"
+                          "testStartNSfunc"
+                          "testCustomDictClass"
+                          "testDictClassFail"
+                          "testBroadcast"
+                          "testGetIP"
+                          ;; XXX: Unclear why this test fails.
+                          "testCustomClassFail")
+                    " and not "))
+           #:phases
+           #~(modify-phases %standard-phases
+               (replace 'check
+                 (lambda* (#:key tests? test-flags #:allow-other-keys)
+                   (if tests?
+                       (apply invoke "python" "-m" "unittest" test-flags)
+                       (format #t "test suite not run.~%")))))))
     (native-inputs
-     (list python-cloudpickle python-dill python-msgpack))
+     (list python-cloudpickle
+           python-dill
+           python-msgpack
+           python-setuptools
+           python-wheel))
     (propagated-inputs
      (list python-serpent))
     (home-page "https://pyro4.readthedocs.io")
-- 
2.49.0





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* gnu/packages/python-xyz.scm (python-attr): Update to 0.3.2.
---
 gnu/packages/python-xyz.scm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 01dfc0799f..8100b030c5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -31373,15 +31373,16 @@ (define-public python-doctest-ignore-unicode
 (define-public python-attr
   (package
     (name "python-attr")
-    (version "0.3.1")
+    (version "0.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "attr" version))
        (sha256
-        (base32
-         "0pbpskvxp5hzdvcaf766ljwpckshir8sf7z6jqji6zyib20594ch"))))
-    (build-system python-build-system)
+        (base32 "1x2627x0n2rxx8wib4cksbjjnncff8finq97k37dq70qd2kvrvhw"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-setuptools python-wheel))
     (home-page "https://github.com/denis-ryzhkov/attr")
     (synopsis "Decorator for attributes of target function or class")
     (description "Simple decorator to set attributes of target function or
-- 
2.49.0





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* gnu/packages/python-xyz.scm (python-serpent): Update to 1.41.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools, python-wheel.
---
 gnu/packages/python-xyz.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 8100b030c5..f36e5a3141 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4368,16 +4368,16 @@ (define-public python-semantic-version
 (define-public python-serpent
   (package
     (name "python-serpent")
-    (version "1.28")
+    (version "1.41")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "serpent" version))
        (sha256
-        (base32 "1arnckykpkvv2qrp49l1k7q5mr5pisswl0rvdx98x8wsl1n361pk"))))
-    (build-system python-build-system)
+        (base32 "15bhxpihxvbphsvp4wyh2kwfz7xasmki9zwcsj3l6r66wdgh61q4"))))
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-attrs python-pytz))
+     (list python-attrs python-pytz python-setuptools python-wheel))
     (home-page "https://github.com/irmen/Serpent")
     (synopsis "Serializer for literal Python expressions")
     (description
-- 
2.49.0





Information forwarded to guix-patches@HIDDEN:
bug#77541; Package guix-patches. Full text available.

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* gnu/packages/python-xyz.scm (python-property-cached): Fix build.
* gnu/packages/patches/python-property-cached-asyncio-3_11.patch: Add
patch.
* gnu/local.mk: Record patch.
---
 gnu/local.mk                                  |   1 +
 .../python-property-cached-asyncio-3_11.patch | 201 ++++++++++++++++++
 gnu/packages/python-xyz.scm                   |   4 +-
 3 files changed, 205 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/python-property-cached-asyncio-3_11.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 93f346481d..1bf8f8deba 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -2129,6 +2129,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-memcached-syntax-warnings.patch	\
   %D%/packages/patches/python-mox3-python3.6-compat.patch	\
   %D%/packages/patches/python-packaging-test-arch.patch		\
+  %D%/packages/patches/python-property-cached-asyncio-3_11.patch	\
   %D%/packages/patches/python-pyan3-fix-absolute-path-bug.patch \
   %D%/packages/patches/python-pyan3-fix-positional-arguments.patch \
   %D%/packages/patches/python-pytorch-fix-codegen.patch		\
diff --git a/gnu/packages/patches/python-property-cached-asyncio-3_11.patch b/gnu/packages/patches/python-property-cached-asyncio-3_11.patch
new file mode 100644
index 0000000000..21c176947e
--- /dev/null
+++ b/gnu/packages/patches/python-property-cached-asyncio-3_11.patch
@@ -0,0 +1,201 @@
+From d89186b47dc25c5ef5907c146edf3f792d50774b Mon Sep 17 00:00:00 2001
+Message-ID: <d89186b47dc25c5ef5907c146edf3f792d50774b.1743608515.git.ngraves@HIDDEN>
+From: Nicolas Graves <ngraves@HIDDEN>
+Date: Wed, 2 Apr 2025 17:29:45 +0200
+Subject: [PATCH] Update to python 3.11
+
+---
+ property_cached/__init__.py             | 21 +++-------
+ tests/test_async_cached_property.py     |  3 +-
+ tests/test_coroutine_cached_property.py | 51 ++++++++++---------------
+ 3 files changed, 27 insertions(+), 48 deletions(-)
+
+diff --git a/property_cached/__init__.py b/property_cached/__init__.py
+index 3353048..c033542 100644
+--- a/property_cached/__init__.py
++++ b/property_cached/__init__.py
+@@ -3,6 +3,7 @@ import functools
+ import pkg_resources
+ import threading
+ import weakref
++from inspect import iscoroutinefunction
+ from time import time
+ 
+ 
+@@ -31,12 +32,12 @@ class cached_property(property):
+         if obj is None:
+             return self
+ 
+-        if asyncio and asyncio.iscoroutinefunction(self.func):
+-            return self._wrap_in_coroutine(obj)
+-
+         value = self.cache.get(obj, self._sentinel)
+         if value is self._sentinel:
+-            value = self.cache[obj] = self.func(obj)
++            if iscoroutinefunction(self.func):
++                self.cache[obj] = value = asyncio.ensure_future(self.func(obj))
++            else:
++                self.cache[obj] = value = self.func(obj)
+ 
+         return value
+ 
+@@ -49,18 +50,6 @@ class cached_property(property):
+     def __delete__(self, obj):
+         del self.cache[obj]
+ 
+-    def _wrap_in_coroutine(self, obj):
+-
+-        @functools.wraps(obj)
+-        @asyncio.coroutine
+-        def wrapper():
+-            value = self.cache.get(obj, self._sentinel)
+-            if value is self._sentinel:
+-                self.cache[obj] = value = asyncio.ensure_future(self.func(obj))
+-            return value
+-
+-        return wrapper()
+-
+ 
+ class threaded_cached_property(cached_property):
+     """
+diff --git a/tests/test_async_cached_property.py b/tests/test_async_cached_property.py
+index 1af139d..32b3410 100644
+--- a/tests/test_async_cached_property.py
++++ b/tests/test_async_cached_property.py
+@@ -9,8 +9,7 @@ import property_cached as cached_property
+ 
+ def unittest_run_loop(f):
+     def wrapper(*args, **kwargs):
+-        coro = asyncio.coroutine(f)
+-        future = coro(*args, **kwargs)
++        future = f(*args, **kwargs)
+         loop = asyncio.get_event_loop()
+         loop.run_until_complete(future)
+ 
+diff --git a/tests/test_coroutine_cached_property.py b/tests/test_coroutine_cached_property.py
+index 40e443b..5864301 100644
+--- a/tests/test_coroutine_cached_property.py
++++ b/tests/test_coroutine_cached_property.py
+@@ -14,8 +14,7 @@ import property_cached as cached_property
+ 
+ def unittest_run_loop(f):
+     def wrapper(*args, **kwargs):
+-        coro = asyncio.coroutine(f)
+-        future = coro(*args, **kwargs)
++        future = f(*args, **kwargs)
+         loop = asyncio.get_event_loop()
+         loop.run_until_complete(future)
+ 
+@@ -33,14 +32,12 @@ def CheckFactory(cached_property_decorator):
+             self.control_total = 0
+             self.cached_total = 0
+ 
+-        @asyncio.coroutine
+-        def add_control(self):
++        async def add_control(self):
+             self.control_total += 1
+             return self.control_total
+ 
+         @cached_property_decorator
+-        @asyncio.coroutine
+-        def add_cached(self):
++        async def add_cached(self):
+             self.cached_total += 1
+             return self.cached_total
+ 
+@@ -52,74 +49,68 @@ class TestCachedProperty(unittest.TestCase):
+ 
+     cached_property_factory = cached_property.cached_property
+ 
+-    @asyncio.coroutine
+-    def assert_control(self, check, expected):
++    async def assert_control(self, check, expected):
+         """
+         Assert that both `add_control` and 'control_total` equal `expected`
+         """
+-        value = yield from check.add_control()
++        value = await check.add_control()
+         self.assertEqual(value, expected)
+         self.assertEqual(check.control_total, expected)
+ 
+-    @asyncio.coroutine
+-    def assert_cached(self, check, expected):
++    async def assert_cached(self, check, expected):
+         """
+         Assert that both `add_cached` and 'cached_total` equal `expected`
+         """
+         print("assert_cached", check.add_cached)
+-        value = yield from check.add_cached
++        value = await check.add_cached
+         self.assertEqual(value, expected)
+         self.assertEqual(check.cached_total, expected)
+ 
+     @unittest_run_loop
+-    @asyncio.coroutine
+-    def test_cached_property(self):
++    async def test_cached_property(self):
+         Check = CheckFactory(self.cached_property_factory)
+         check = Check()
+ 
+         # The control shows that we can continue to add 1
+-        yield from self.assert_control(check, 1)
+-        yield from self.assert_control(check, 2)
++        await self.assert_control(check, 1)
++        await self.assert_control(check, 2)
+ 
+         # The cached version demonstrates how nothing is added after the first
+-        yield from self.assert_cached(check, 1)
+-        yield from self.assert_cached(check, 1)
++        await self.assert_cached(check, 1)
++        await self.assert_cached(check, 1)
+ 
+         # The cache does not expire
+         with freeze_time("9999-01-01"):
+-            yield from self.assert_cached(check, 1)
++            await self.assert_cached(check, 1)
+ 
+         # Typically descriptors return themselves if accessed though the class
+         # rather than through an instance.
+         self.assertTrue(isinstance(Check.add_cached, self.cached_property_factory))
+ 
+     @unittest_run_loop
+-    @asyncio.coroutine
+-    def test_reset_cached_property(self):
++    async def test_reset_cached_property(self):
+         Check = CheckFactory(self.cached_property_factory)
+         check = Check()
+ 
+         # Run standard cache assertion
+-        yield from self.assert_cached(check, 1)
+-        yield from self.assert_cached(check, 1)
++        await self.assert_cached(check, 1)
++        await self.assert_cached(check, 1)
+ 
+         # Clear the cache
+         del check.add_cached
+ 
+         # Value is cached again after the next access
+-        yield from self.assert_cached(check, 2)
+-        yield from self.assert_cached(check, 2)
++        await self.assert_cached(check, 2)
++        await self.assert_cached(check, 2)
+ 
+     @unittest_run_loop
+-    @asyncio.coroutine
+-    def test_none_cached_property(self):
++    async def test_none_cached_property(self):
+         class Check(object):
+             def __init__(self):
+                 self.cached_total = None
+ 
+             @self.cached_property_factory
+-            @asyncio.coroutine
+-            def add_cached(self):
++            async def add_cached(self):
+                 return self.cached_total
+ 
+-        yield from self.assert_cached(Check(), None)
++        await self.assert_cached(Check(), None)
+-- 
+2.49.0
+
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 46efd10292..01dfc0799f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -11700,7 +11700,9 @@ (define-public python-property-cached
        (method url-fetch)
        (uri (pypi-uri "property-cached" version ".zip"))
        (sha256
-        (base32 "0wxv5sdx1p7ils36j6j6hfscz8v2vzbq212i8y8r0lrnxpqlx71y"))))
+        (base32 "0wxv5sdx1p7ils36j6j6hfscz8v2vzbq212i8y8r0lrnxpqlx71y"))
+       (patches
+        (search-patches "python-property-cached-asyncio-3_11.patch"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.49.0





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This package is now a leaf package that fails to build.

* gnu/packages/python-xyz.scm (pybind11-2.3): Delete variable.
---
 gnu/packages/python-xyz.scm | 20 --------------------
 1 file changed, 20 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 4abe04007d..46efd10292 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -29832,26 +29832,6 @@ (define-public pybind11-2.10
                 "0rbcfvl7y472sykzdq3vrkw83kar0lpzhk3wq9yj9cdydl8cpfcz"))
               (file-name (git-file-name name version))))))
 
-;; This is needed for python-vaex-core.
-(define-public pybind11-2.3
-  (package
-    (inherit pybind11)
-    (name "pybind11")
-    (version "2.3.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/pybind/pybind11")
-                    (commit (string-append "v" version))))
-              (sha256
-               (base32
-                "11b6dniri8m05spfd2a19irz82shf4sdca73566bniggrf3zclnf"))
-              (file-name (git-file-name name version))))
-    (arguments
-     (substitute-keyword-arguments (package-arguments pybind11)
-       ((#:tests? tests? #false)
-        #false)))))
-
 (define-public python-pooch
   (package
     (name "python-pooch")
-- 
2.49.0





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bug#77541; Package guix-patches. Full text available.

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* gnu/packages/python-science.scm (python-vaex-core): Update to 4.17.1.
* gnu/packages/patches/python-vaex-core-fix-tsl-use.patch: Add patch.
* gnu/local.mk: Record patch.
---
 gnu/local.mk                                  |  1 +
 .../python-vaex-core-fix-tsl-use.patch        | 67 +++++++++++++++++++
 gnu/packages/python-science.scm               | 44 ++++++++----
 3 files changed, 100 insertions(+), 12 deletions(-)
 create mode 100644 gnu/packages/patches/python-vaex-core-fix-tsl-use.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 18ba0073fc..93f346481d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -2142,6 +2142,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-robotframework-sshlibrary-rf5-compat.patch \
   %D%/packages/patches/python-unittest2-python3-compat.patch	\
   %D%/packages/patches/python-unittest2-remove-argparse.patch	\
+  %D%/packages/patches/python-vaex-core-fix-tsl-use.patch	\
   %D%/packages/patches/python-vega-datasets-remove-la-riots-code.patch	\
   %D%/packages/patches/python-versioneer-guix-support.patch	\
   %D%/packages/patches/python-werkzeug-tests.patch		\
diff --git a/gnu/packages/patches/python-vaex-core-fix-tsl-use.patch b/gnu/packages/patches/python-vaex-core-fix-tsl-use.patch
new file mode 100644
index 0000000000..f4f6fc1c48
--- /dev/null
+++ b/gnu/packages/patches/python-vaex-core-fix-tsl-use.patch
@@ -0,0 +1,67 @@
+From 8cb8808b3ceccf4ab3ac542739ef490abe7e76b3 Mon Sep 17 00:00:00 2001
+Message-ID: <8cb8808b3ceccf4ab3ac542739ef490abe7e76b3.1743597010.git.ngraves@HIDDEN>
+From: Nicolas Graves <ngraves@HIDDEN>
+Date: Wed, 2 Apr 2025 14:29:40 +0200
+Subject: [PATCH] Fix tsl map use
+
+---
+ packages/vaex-core/src/hash_string.hpp | 25 ++++++++++++++++---------
+ 1 file changed, 16 insertions(+), 9 deletions(-)
+
+diff --git a/packages/vaex-core/src/hash_string.hpp b/packages/vaex-core/src/hash_string.hpp
+index d3b60199..0ed69d1c 100644
+--- a/packages/vaex-core/src/hash_string.hpp
++++ b/packages/vaex-core/src/hash_string.hpp
+@@ -39,13 +39,15 @@ class hash_base : public hash_common<Derived, T, hashmap<T, int64_t>> {
+         for (int i = 0; i < nmaps; i++) {
+             string_arrays.emplace_back(std::make_shared<StringList64>());
+             StringList64 *strings = string_arrays[i].get();
+-            // equal_to<string_ref>& eq = this->maps[i].key_eq();
+-            this->maps[i].m_ht.strings_equals = strings;
+-            this->maps[i].m_ht.strings_hash = strings;
++            equal_to<key_type> eq;
++            eq.strings_equals = strings;
++            hash<key_type> h;
++            h.strings_hash = strings;
++            this->maps[i] = hashmap_type(8, h, eq);
+         }
+     };
+ 
+-    virtual std::string _get(hashmap_type &map, typename hashmap_type::key_type key) override { return map.m_ht.strings_equals->get(key.index); };
++    virtual std::string _get(hashmap_type &map, typename hashmap_type::key_type key) override { return string_arrays[0]->get(key.index); };
+ 
+     size_t bytes_used() const {
+         int64_t buffer_size = 0; // collect buffer size
+@@ -391,9 +393,12 @@ class ordered_set : public hash_base<ordered_set<T>, T, T, V> {
+     template <class SL>
+     static ordered_set *create(std::shared_ptr<SL> keys, int64_t null_value, int64_t nan_count, int64_t null_count, std::string *fingerprint) {
+         ordered_set *set = new ordered_set(1);
+-        set->maps[0].m_ht.strings_equals = keys.get();
+-        set->maps[0].m_ht.strings_hash = keys.get();
+         set->string_arrays[0] = keys;
++        equal_to<key_type> eq;
++        eq.strings_equals = keys.get();
++        hash<key_type> h;
++        h.strings_hash = keys.get();
++        set->maps[0] = hashmap_type(keys->length, h, eq);
+         {
+             size_t size = keys->length;
+             set->maps[0].reserve(size);
+@@ -701,9 +706,11 @@ class index_hash : public hash_base<index_hash<T>, T, T, V> {
+             // string_arrays_overflow.emplace_back(std::make_shared<StringList64>());
+             // for each key in overflow, it should be present in the main string array
+             StringList64 *strings = this->string_arrays[i].get();
+-            // equal_to<string_ref>& eq = this->maps[i].key_eq();
+-            overflows[i].m_ht.strings_equals = strings;
+-            overflows[i].m_ht.strings_hash = strings;
++            equal_to<key_type> eq;
++            eq.strings_equals = strings;
++            hash<key_type> h;
++            h.strings_hash = strings;
++            overflows[i] = overflow_type(8, h, eq);
+         }
+     }
+ 
+-- 
+2.49.0
+
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 3bf266582d..73e08fccbe 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -4097,24 +4097,44 @@ (define-public python-opt-einsum
 (define-public python-vaex-core
   (package
     (name "python-vaex-core")
-    (version "4.17.1")
+    (version "4.18.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "vaex-core" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://www.github.com/maartenbreddels/vaex")
+             (commit (string-append "core-v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1rzx5px3fwi5mh1z8y91brvffk7dkhj287lnmqp8zp6836kkqhya"))
-       (modules '((guix build utils)))
+        (base32 "1sp096msbzgjlwi8c1ink2bp4pjff9pvikqz1y1li8d3in4gpgdr"))
+       (patches
+        (search-patches "python-vaex-core-fix-tsl-use.patch"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)))
        (snippet
-        ;; Remove bundled libraries
-        '(for-each delete-file-recursively
-                   (list "vendor/boost"
-                         "vendor/pcre"
-                         "vendor/pybind11")))))
+        #~(begin
+            ;; Delete everything except for vaex-core itself:
+            (define (delete-except exception)
+              (lambda (file)
+                (unless (member file `("." ".." ,exception))
+                  (delete-file-recursively file))))
+            (for-each (delete-except "packages") (scandir "."))
+            (with-directory-excursion "packages"
+              (for-each (delete-except "vaex-core") (scandir ".")))
+            (for-each (lambda (file)
+                        (unless (member file '("." ".."))
+                          (rename-file
+                           (string-append "packages/vaex-core/" file)
+                           file)))
+                      (scandir "packages/vaex-core"))
+            (delete-file-recursively "packages")
+            (delete-file-recursively "vendor")))))
     (build-system pyproject-build-system)
-    (arguments (list #:tests? #false)) ;require vaex.server and others, which require vaex-core.
+    (arguments
+     ;; require vaex.server and others, which require vaex-core.
+     (list #:tests? #false))
     (inputs
-     (list boost pcre pybind11-2.3))
+     (list boost pcre pybind11 string-view-lite tsl-hopscotch-map))
     (propagated-inputs
      (list python-aplus
            python-blake3
-- 
2.49.0





Information forwarded to guix-patches@HIDDEN:
bug#77541; Package guix-patches. Full text available.

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* gnu/packages/python-science.scm (python-pytensor): Update to 2.30.1.
[arguments]{test-flags}: Use field.
{phases}: Remove 'check phase replacement. Add phase 'pre-check.
---
 gnu/packages/python-science.scm | 43 +++++++++++++++++----------------
 1 file changed, 22 insertions(+), 21 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 49e46f7ff3..3bf266582d 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -2465,7 +2465,7 @@ (define-public python-xarray-schema
 (define-public python-pytensor
   (package
     (name "python-pytensor")
-    (version "2.18.1")
+    (version "2.30.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2474,10 +2474,28 @@ (define-public python-pytensor
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0qa0y13xfm6w7ry7gp0lv84c8blyg34a9ns7ynwqyhf9majq08s5"))))
+                "008ivcrab9j256mcrfrcd1xlkq5qicsx97wqaxaxwk1ynnmxdqbn"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      #~(list ;; test_tensor_basic.py file requires JAX.
+         "--ignore" "tests/link/jax/test_tensor_basic.py"
+         ;; No module named 'pytensor.scan.scan_perform'
+         "--ignore" "pytensor/scan/scan_perform_ext.py"
+         ;; Skip benchmark tests.
+         "-k" (string-append
+               "not test_elemwise_speed"
+               " and not test_logsumexp_benchmark"
+               " and not test_fused_elemwise_benchmark"
+               " and not test_scan_multiple_output"
+               " and not test_vector_taps_benchmark"
+               " and not test_cython_performance")
+         ;; Skip computationally intensive tests.
+         "--ignore" "tests/scan/"
+         "--ignore" "tests/tensor/"
+         "--ignore" "tests/sandbox/"
+         "--ignore" "tests/sparse/sandbox/")
       #:phases
       #~(modify-phases %standard-phases
           ;; Replace version manually because pytensor uses
@@ -2499,27 +2517,10 @@ (define-public python-pytensor
               (substitute* "setup.py"
                 (("versioneer.get_version\\(\\)")
                  (string-append "\"" #$version "\"")))))
-          (replace 'check
+          (add-before 'check 'pre-check
             (lambda* (#:key tests? #:allow-other-keys)
               (when tests?
-                (setenv "HOME" "/tmp") ; required for most tests
-                ;; Test discovery fails, have to call pytest by hand.
-                ;; test_tensor_basic.py file requires JAX.
-                (invoke "python" "-m" "pytest" "-vv"
-                        "--ignore" "tests/link/jax/test_tensor_basic.py"
-                        ;; Skip benchmark tests.
-                        "-k" (string-append
-                              "not test_elemwise_speed"
-                              " and not test_logsumexp_benchmark"
-                              " and not test_fused_elemwise_benchmark"
-                              " and not test_scan_multiple_output"
-                              " and not test_vector_taps_benchmark"
-                              " and not test_cython_performance")
-                        ;; Skip computationally intensive tests.
-                        "--ignore" "tests/scan/"
-                        "--ignore" "tests/tensor/"
-                        "--ignore" "tests/sandbox/"
-                        "--ignore" "tests/sparse/sandbox/")))))))
+                (setenv "HOME" "/tmp"))))))) ; required for most tests
     (native-inputs (list python-cython
                          python-pytest
                          python-pytest-mock
-- 
2.49.0





Information forwarded to guix-patches@HIDDEN:
bug#77541; Package guix-patches. Full text available.

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* gnu/packages/cpp.scm (string-view-lite): New variable.
---
 gnu/packages/cpp.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index 4c645f0f9d..7d0135044a 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -3795,6 +3795,26 @@ (define-public nativefiledialog-extended
 \"source files\" or \"image files\") where supported.")
     (license license:zlib)))
 
+(define-public string-view-lite
+  (package
+    (name "string-view-lite")
+    (version "1.8.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/martinmoene/string-view-lite")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1mfp3lmqx7ac0545akxd2v05rrapa3byz8q4gb9rqy94pcqbfyc5"))))
+    (build-system cmake-build-system)
+    (home-page "https://github.com/martinmoene/string-view-lite")
+    (synopsis "C++17 string-view for older C++")
+    (description "This package provides a compatibility header-only library
+for C++17 string-view.")
+    (license license:boost1.0)))
+
 (define-public tsl-hopscotch-map
   (package
     (name "tsl-hopscotch-map")
-- 
2.49.0





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* gnu/packages/machine-learning.scm (python-pytroch-geometric):
[arguments]{test-flags}: Skip test_type_repr failing test.
---
 gnu/packages/machine-learning.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index e7923bd503..fb1d5d2eed 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -5399,7 +5399,10 @@ (define-public python-pytorch-geometric
                    ;; These refuse to be run on CPU and really want a GPU
                    " and not test_add_random_walk_pe"
                    " and not test_asap"
-                   " and not test_two_hop"))
+                   " and not test_two_hop"
+                   ;; Failed when switched to python@HIDDEN
+                   ;; typing module internals
+                   " and not test_type_repr"))
       #:phases
       '(modify-phases %standard-phases
          (add-after 'unpack 'delete-top-level-directories
-- 
2.49.0





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* gnu/packages/bioinformatics.scm (mageck)[native-inputs]: Add
python-wheel.
---
 gnu/packages/bioinformatics.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 804cf057e2..4dbedc09f9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9975,6 +9975,8 @@ (define-public mageck
                                (with-directory-excursion (string-append "demo/" dir)
                                  (invoke "bash" script))))
                             tests))))))))
+    (native-inputs
+     (list python-wheel))
     (inputs
      (list python-numpy
            python-scipy
-- 
2.49.0





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* gnu/packages/python-xyz.scm (autokey)[native-inputs]: Add
python-wheel.
---
 gnu/packages/python-xyz.scm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 12d6800a1c..4abe04007d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7938,7 +7938,11 @@ (define-public autokey
               (setenv "LANG" "")
               ;; required for tests/test_configmanager.py
               (setenv "HOME" "/tmp"))))))
-    (native-inputs (list python-pytest python-pytest-cov python-pyhamcrest))
+    (native-inputs
+     (list python-pytest
+           python-pytest-cov
+           python-pyhamcrest
+           python-wheel))
     (inputs
      (list bash-minimal ; for wrap-program
            gtksourceview-3
-- 
2.49.0





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* gnu/packages/bioinformatics.scm (scregseg)[native-inputs]: Add
python-wheel.
---
 gnu/packages/bioinformatics.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e7685faf02..804cf057e2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -24241,7 +24241,8 @@ (define-public scregseg
              (substitute* "setup.py"
                (("'sklearn',") "")))))))
     (native-inputs
-     (list python-cython))
+     (list python-cython
+           python-wheel))
     (propagated-inputs
      (list python-scikit-learn
            python-scipy
-- 
2.49.0





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bug#77541; Package guix-patches. Full text available.

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* gnu/packages/image-processing.scm (labelme)[native-inputs]: Add
python-wheel.
---
 gnu/packages/image-processing.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
index 296dec738a..5a3e6f69ef 100644
--- a/gnu/packages/image-processing.scm
+++ b/gnu/packages/image-processing.scm
@@ -1845,7 +1845,8 @@ (define-public labelme
     (native-inputs
      (list python-pytest
            python-pytest-qt
-           xorg-server-for-tests))
+           xorg-server-for-tests
+           python-wheel))
     (propagated-inputs
      (list python-imgviz
            python-matplotlib
-- 
2.49.0





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bug#77541; Package guix-patches. Full text available.

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Subject: [PATCH 01/38] gnu: Add clipper2.
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* gnu/packages/cpp.scm (clipper2): New variable.
---
 gnu/packages/cpp.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index a102a5d468..4c645f0f9d 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -44,6 +44,7 @@
 ;;; Copyright © 2024 Jakob Kirsch <jakob.kirsch@HIDDEN>
 ;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus@HIDDEN>
 ;;; Copyright © 2025 Sergio Pastor Pérez <sergio.pastorperez@HIDDEN>
+;;; Copyright © 2025 Nicolas Graves <ngraves@HIDDEN>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2620,6 +2621,40 @@ (define-public clipper
 The library is based on Vatti's clipping algorithm.")
     (license license:boost1.0)))
 
+(define-public clipper2
+  (package
+    (inherit clipper)
+    (name "clipper2")
+    (version "1.5.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/AngusJohnson/Clipper2")
+             (commit (string-append "Clipper2_" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1w8cmx712k45cb8gh9dakmbmybiwdx8c0b45mwpcldywx2lwxi2j"))
+       (modules '((guix build utils)))
+       (snippet #~(for-each
+                   delete-file-recursively
+                   '("CSharp" "DLL" "Delphi")))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "-DUSE_EXTERNAL_GTEST=ON"
+              "-DCLIPPER2_EXAMPLES=OFF")
+      #:phases #~(modify-phases %standard-phases
+                   (add-after 'unpack 'chdir
+                     (lambda _
+                       (chdir "CPP"))))))
+    (native-inputs (list googletest))
+    (home-page "https://github.com/AngusJohnson/Clipper2")
+    (description
+     (string-append (package-description clipper) "\
+Note: This package is a major update of the original clipper library."))))
+
 (define-public pcg-cpp
   (let ((commit "ffd522e7188bef30a00c74dc7eb9de5faff90092")
         (revision "2"))
-- 
2.49.0





Information forwarded to guix-patches@HIDDEN:
bug#77541; Package guix-patches. Full text available.
bug closed, send any further explanations to 77541 <at> debbugs.gnu.org and Nicolas Graves <ngraves@HIDDEN> Request was from Nicolas Graves <ngraves@HIDDEN> to control <at> debbugs.gnu.org. Full text available.

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Subject: [PATCH 01/38] gnu: Add clipper2.
Date: Fri,  4 Apr 2025 21:06:57 +0200
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* gnu/packages/cpp.scm (clipper2): New variable.
---
 gnu/packages/cpp.scm | 36 +++++++++++++++++++++++++++++++++++-
 1 file changed, 35 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index a102a5d468..946484d325 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -44,7 +44,7 @@
 ;;; Copyright © 2024 Jakob Kirsch <jakob.kirsch@HIDDEN>
 ;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus@HIDDEN>
 ;;; Copyright © 2025 Sergio Pastor Pérez <sergio.pastorperez@HIDDEN>
-;;;
+;;; Copyright © 2025 Nicolas Graves <ngraves@HIDDEN>
 ;;; This file is part of GNU Guix.
 ;;;
 ;;; GNU Guix is free software; you can redistribute it and/or modify it
@@ -2620,6 +2620,40 @@ (define-public clipper
 The library is based on Vatti's clipping algorithm.")
     (license license:boost1.0)))
 
+(define-public clipper2
+  (package
+    (inherit clipper)
+    (name "clipper2")
+    (version "1.5.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/AngusJohnson/Clipper2")
+             (commit (string-append "Clipper2_" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1w8cmx712k45cb8gh9dakmbmybiwdx8c0b45mwpcldywx2lwxi2j"))
+       (modules '((guix build utils)))
+       (snippet #~(for-each
+                   delete-file-recursively
+                   '("CSharp" "DLL" "Delphi")))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "-DUSE_EXTERNAL_GTEST=ON"
+              "-DCLIPPER2_EXAMPLES=OFF")
+      #:phases #~(modify-phases %standard-phases
+                   (add-after 'unpack 'chdir
+                     (lambda _
+                       (chdir "CPP"))))))
+    (native-inputs (list googletest))
+    (home-page "https://github.com/AngusJohnson/Clipper2")
+    (description
+     (string-append (package-description clipper) "\
+Note: This package is a major update of the original clipper library."))))
+
 (define-public pcg-cpp
   (let ((commit "ffd522e7188bef30a00c74dc7eb9de5faff90092")
         (revision "2"))
-- 
2.49.0





Acknowledgement sent to Nicolas Graves <ngraves@HIDDEN>:
New bug report received and forwarded. Copy sent to guix-patches@HIDDEN. Full text available.
Report forwarded to guix-patches@HIDDEN:
bug#77541; Package guix-patches. Full text available.
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