Package: guix-patches;
Reported by: Nicolas Graves <ngraves <at> ngraves.fr>
Date: Mon, 31 Mar 2025 06:17:01 UTC
Severity: normal
Tags: patch
Done: Sharlatan Hellseher <sharlatanus <at> gmail.com>
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guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:17:02 GMT) Full text and rfc822 format available.Nicolas Graves <ngraves <at> ngraves.fr>:guix-patches <at> gnu.org.
(Mon, 31 Mar 2025 06:17:02 GMT) Full text and rfc822 format available.Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: guix-patches <at> gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH python-team 00/26] Some further updates Date: Mon, 31 Mar 2025 08:13:39 +0200
Some new updates I managed to get to build this wkend. Nicolas Graves (26): gnu: python-zeroc-ice: Update to 3.7.10.1. gnu: python-cchardet: Update to 2.2.0a2. gnu: python-databricks-cli: Update to 0.18.0. gnu: python-jsonargparse: Update to 4.37.0. gnu: python-pyvcf: Use the fork python-pyvcf3. gnu: Remove python-parameterizedtestcase. gnu: Remove python-anyjson. gnu: python-pyquery: Update to 2.0.1. gnu: python-locust: Update to 2.33.2. gnu: rseqc: Switch to pyproject-build-system. gnu: seqmagick: Update to 0.8.6-0.dee6ab9. gnu: Remove python-pyfasta. gnu: taxtastic: Update to 0.11.1. gnu: python-rstr: Update to 3.2.2. Enable tests. gnu: reprotest: Update to 0.7.29. gnu: python-sip: Update to 6.10.0. gnu: Add python-pybktree. gnu: umi-tools: Update to 1.1.6. gnu: cpplint: Update to 2.0.0. gnu: python-patch-ng: Update to 1.18.1. gnu: veusz: Update to 3.6.2. gnu: conan: Update to 2.7.1. gnu: python-cu2qu: Fix tests. gnu: libei: Update to 1.4.0. gnu: openmolar: Fix build. gnu: python-mechanize: Update to 0.4.10. gnu/packages/backup.scm | 4 +- gnu/packages/benchmark.scm | 33 ++- gnu/packages/bioinformatics.scm | 262 +++++++----------- gnu/packages/cpp.scm | 11 +- gnu/packages/diffoscope.scm | 4 +- gnu/packages/fontutils.scm | 7 +- gnu/packages/freedesktop.scm | 19 +- gnu/packages/maths.scm | 73 ++--- gnu/packages/medical.scm | 32 ++- gnu/packages/package-management.scm | 139 +++++----- .../patches/python-sip-include-dirs.patch | 17 +- gnu/packages/python-check.scm | 19 -- gnu/packages/python-web.scm | 18 +- gnu/packages/python-xyz.scm | 159 ++++++----- gnu/packages/qt.scm | 16 +- 15 files changed, 407 insertions(+), 406 deletions(-) -- 2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:20:05 GMT) Full text and rfc822 format available.Message #8 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 01/26] gnu: python-zeroc-ice: Update to 3.7.10.1. Date: Mon, 31 Mar 2025 08:18:29 +0200
* gnu/packages/python-xyz.scm (python-zeroc-ice): Update to 3.7.10.1.
---
gnu/packages/python-xyz.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e93ee1469c..1139f0eaf9 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -40225,13 +40225,13 @@ (define-public python-zbarlight
(define-public python-zeroc-ice
(package
(name "python-zeroc-ice")
- (version "3.7.9")
+ (version "3.7.10.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "zeroc-ice" version))
(sha256
(base32
- "0bqkrjxp2fbz34x3wxkxji39kxinypzg8q2994sibiay29mpipxb"))))
+ "0r46q4hd7xbpvnidbra1prkg4xhmajxjjmclfqgp3pv0lgyslqxh"))))
(build-system pyproject-build-system)
(inputs (list openssl))
(native-inputs (list python-setuptools python-wheel))
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:20:09 GMT) Full text and rfc822 format available.Message #11 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 02/26] gnu: python-cchardet: Update to 2.2.0a2. Date: Mon, 31 Mar 2025 08:18:30 +0200
* gnu/packages/freedesktop.scm (python-cchardet): Update to 2.2.0a2.
---
gnu/packages/freedesktop.scm | 10 +++++++---
1 file changed, 7 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm
index 34dfe20229..0618fdc6f4 100644
--- a/gnu/packages/freedesktop.scm
+++ b/gnu/packages/freedesktop.scm
@@ -68,6 +68,7 @@ (define-module (gnu packages freedesktop)
#:use-module (guix build-system gnu)
#:use-module (guix build-system meson)
#:use-module (guix build-system perl)
+ #:use-module (guix build-system pyproject)
#:use-module (guix build-system python)
#:use-module (guix build-system glib-or-gtk)
#:use-module (guix build-system qt)
@@ -128,6 +129,7 @@ (define-module (gnu packages freedesktop)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages polkit)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-build)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages qt)
@@ -2842,17 +2844,19 @@ (define-public uchardet
(define-public python-cchardet
(package
(name "python-cchardet")
- (version "2.1.7")
+ (version "2.2.0a2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cchardet" version))
(sha256
(base32
- "1bqfz85cd51sw0bvhvdq9ikccxi2ld7g5jpni4jkq1a5clrvca64"))))
- (build-system python-build-system)
+ "08wq5yfaafbjipabfc6kpyvivkk2394w7isv0mwx5agcf8cbnwnx"))))
+ (build-system pyproject-build-system)
(inputs
(list uchardet))
+ (native-inputs
+ (list python-setuptools python-wheel))
(home-page "https://github.com/PyYoshi/cChardet")
(synopsis "High-performance character encoding detection for Python")
(description "cChardet is a character encoding detector, written in
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:20:12 GMT) Full text and rfc822 format available.Message #14 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 03/26] gnu: python-databricks-cli: Update to 0.18.0. Date: Mon, 31 Mar 2025 08:18:31 +0200
* gnu/packages/python-web.scm (python-databricks-cli): Update to
0.18.0.
[build-system]: Switch to pyproject-build-system.
[arguments]: Improve style, use gexps.
[native-inputs]: Add python-setuptools, python-wheel.
---
gnu/packages/python-web.scm | 18 ++++++++++--------
1 file changed, 10 insertions(+), 8 deletions(-)
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 95dd7a126c..5ef6f2ce38 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -3328,7 +3328,7 @@ (define-public python-cssselect
(define-public python-databricks-cli
(package
(name "python-databricks-cli")
- (version "0.17.0")
+ (version "0.18.0")
(home-page "https://github.com/databricks/databricks-cli")
(source (origin
(method git-fetch)
@@ -3336,19 +3336,21 @@ (define-public python-databricks-cli
(file-name (git-file-name name version))
(sha256
(base32
- "1qwbxnx64kw7lrzlyx3hfbnjxpc19cqvvj0gcrkqpyjsgd08vja0"))))
- (build-system python-build-system)
+ "1avag4kwqk2f24r5i0vcmhm6s1gsw6maykhlyj2ixz0qc05pjzvl"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:phases (modify-phases %standard-phases
- (replace 'check
- (lambda _
- (invoke "pytest" "tests" "-vv"))))))
+ (list #:phases #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (invoke "pytest" "tests" "-vv"))))))
(native-inputs
;; For tests.
(list python-decorator
python-mock
python-pytest
- python-requests-mock))
+ python-requests-mock
+ python-setuptools
+ python-wheel))
(propagated-inputs
(list python-click
python-oauthlib
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:20:14 GMT) Full text and rfc822 format available.Message #17 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 05/26] gnu: python-pyvcf: Use the fork python-pyvcf3. Date: Mon, 31 Mar 2025 08:18:33 +0200
* gnu/packages/bioinformatics.scm (python-pyvcf): Define in terms of
'deprecated-package'.
(python-pyvcf3): New variable.
(python-nanosv): Replace python-pyvcf by python-pyvcf3.
---
gnu/packages/bioinformatics.scm | 46 ++++++++++-----------------------
1 file changed, 14 insertions(+), 32 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6274b2d868..659e7cfea0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -23917,51 +23917,33 @@ (define-public tombo
;; Some parts may be BSD-3-licensed.
(license license:mpl2.0)))
-(define-public python-pyvcf
- (let ((commit "476169cd457ba0caa6b998b301a4d91e975251d9")
+;; This is a fork of the original unmaintained python-pyvcf.
+(define-public python-pyvcf3
+ (let ((commit "1fb3789153d1d8e28e2cedf121399f276b5f312a")
(revision "0"))
(package
- (name "python-pyvcf")
- (version (git-version "0.6.8" revision commit))
- ;; Use git, because the PyPI tarballs lack test data.
+ (name "python-pyvcf3")
+ (version (git-version "1.0.3" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/jamescasbon/PyVCF.git")
- ;; Latest release is not tagged.
+ (url "https://github.com/dridk/PyVCF3")
(commit commit)))
(file-name (git-file-name name version))
(sha256
- (base32
- "0qf9lwj7r2hjjp4bd4vc7nayrhblfm4qcqs4dbd43a6p4bj2jv5p"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'patch-sample-script
- (lambda _
- ;; Add Python 3 compatibility to this sample script.
- (substitute* "scripts/vcf_sample_filter.py"
- (("print (.*)\n" _ arg)
- (string-append "print(" arg ")\n")))))
- (add-after 'install 'remove-installed-tests
- ;; Do not install test files.
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (delete-file-recursively (string-append
- (site-packages inputs outputs)
- "/vcf/test")))))))
- (native-inputs
- ;; Older setuptools is needed for use_2to3.
- (list python-cython python-setuptools-57))
- (propagated-inputs
- (list python-pysam python-rpy2))
- (home-page "https://github.com/jamescasbon/PyVCF")
+ (base32 "0i4j5bq5q32q216ja7yvg0mpww5j0b9p8ky5bya4d31wqmygal8z"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs (list python-setuptools))
+ (native-inputs (list python-setuptools python-wheel))
+ (home-page "https://github.com/dridk/PyVCF3")
(synopsis "Variant Call Format parser for Python")
(description "This package provides a @acronym{VCF,Variant Call Format}
parser for Python.")
(license license:expat))))
+(define-deprecated/public-alias python-pyvcf python-pyvcf3)
+
(define-public nanosv
(package
(name "nanosv")
@@ -23974,7 +23956,7 @@ (define-public nanosv
"1wl2daj0bwrl8fx5xi8j8hfs3mp3vg3qycy66538n032v1qkc6xg"))))
(build-system python-build-system)
(inputs
- (list python-configparser python-pysam python-pyvcf))
+ (list python-configparser python-pysam python-pyvcf3))
(home-page "https://github.com/mroosmalen/nanosv")
(synopsis "Structural variation detection tool for Oxford Nanopore data")
(description "NanoSV is a software package that can be used to identify
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:20:15 GMT) Full text and rfc822 format available.Message #20 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 07/26] gnu: Remove python-anyjson. Date: Mon, 31 Mar 2025 08:18:35 +0200
This package is a leaf package in Guix, is stale for 13 years, and its
upstream repository is not even up anymore.
* gnu/packages/python-xyz.scm (python-anyjson): Delete variable.
---
gnu/packages/python-xyz.scm | 28 ----------------------------
1 file changed, 28 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 573aa026c6..545a867de3 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21160,34 +21160,6 @@ (define-public python-pyquery
fast xml and html manipulation.")
(license license:bsd-3)))
-(define-public python-anyjson
- (package
- (name "python-anyjson")
- (version "0.3.3")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "anyjson" version))
- (sha256
- (base32
- "1fjph4alvcscsl5d4b6qpv1yh31jy05jxi1l0xff7lws7j32v09p"))))
- (build-system python-build-system)
- (arguments
- `(;; We could possibly get tests working, but on Python 3 it's not so easy.
- ;; Very strangely, 2to3 is run *during setup.py install* (or bdist, or
- ;; whatever) so this transformation needs to be done before the tests
- ;; can be run. Maybe we could add a build step to transform beforehand
- ;; but it could be annoying/difficult.
- #:tests? #f))
- (native-inputs (list python-setuptools-57)) ;for use_2to3 support
- (home-page "https://bitbucket.org/runeh/anyjson/")
- (synopsis
- "Wraps best available JSON implementation in a common interface")
- (description
- "Anyjson loads whichever is the fastest JSON module installed
-and provides a uniform API regardless of which JSON implementation is used.")
- (license license:bsd-3)))
-
(define-public python-amqp
(package
(name "python-amqp")
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:03 GMT) Full text and rfc822 format available.Message #23 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 04/26] gnu: python-jsonargparse: Update to 4.37.0. Date: Mon, 31 Mar 2025 08:18:32 +0200
* gnu/packages/python-xyz.scm (python-jsonargparse): Update to 4.37.0.
[arguments]{test-flags}: Remove uneeded test-flags.
[propagated-inputs]: Remove python-contextvars,
python-docstring-parser, python-pyyaml, python-typeshed-client.
[native-inputs]: Add python-pypa-build. Remove python-coverage,
python-pycodestyle, python-tox, python-types-requests.
---
gnu/packages/python-xyz.scm | 26 ++++++--------------------
1 file changed, 6 insertions(+), 20 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1139f0eaf9..573aa026c6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5300,40 +5300,26 @@ (define-public python-jsonalias
(define-public python-jsonargparse
(package
(name "python-jsonargparse")
- (version "4.21.1")
+ (version "4.37.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "jsonargparse" version))
(sha256
(base32
- "1k3b60x0zf86fh50y2jyby30gksqriyvvpfnf5mqq0qn7jih01y7"))))
+ "1b9w9j27phj5j00pmhp11lzf53yc4dnwknhxacv2bfyiiaq0af2s"))))
(build-system pyproject-build-system)
(arguments
- (list
- #:test-flags
- '(list "-k" (string-append "not test_env_prefix"
- " and not test_basemodel"
- " and not test_field_default_factory"
- " and not test_field_description"
- " and not test_get_param_relative_import_from_init"
- ;; Strangely, the arguments are interpreted
- ;; as arguments to pytest.
- " and not test_pydantic_types"))))
+ (list #:test-flags
+ '(list "-k" "not test_env_prefix")))
(propagated-inputs
- (list python-contextvars
- python-docstring-parser
- python-pyyaml
- python-typeshed-client))
+ (list python-pyyaml))
(native-inputs
(list python-attrs
- python-coverage
- python-pycodestyle
+ python-pypa-build
python-pydantic
python-pytest
python-pytest-subtests
python-responses
- python-tox
- python-types-requests
python-setuptools
python-wheel))
(home-page "https://github.com/omni-us/jsonargparse/")
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:04 GMT) Full text and rfc822 format available.Message #26 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 09/26] gnu: python-locust: Update to 2.33.2. Date: Mon, 31 Mar 2025 08:18:37 +0200
* gnu/packages/benchmark.scm (python-locust): Update to 2.33.2.
[arguments]{test-flags}: Add additional missing test.
{phases}: Add phase 'pretend-version. Adapt phase fix-version.
[native-inputs]: Remove python-poetry-core,
python-poetry-dynamic-versioning. Add python-hatchling,
python-hatch-vcs.
---
gnu/packages/benchmark.scm | 33 +++++++++++++++++++++++++--------
1 file changed, 25 insertions(+), 8 deletions(-)
diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm
index 8743dc66aa..bc630bf723 100644
--- a/gnu/packages/benchmark.scm
+++ b/gnu/packages/benchmark.scm
@@ -402,7 +402,7 @@ (define (mark-as-non-free directory)
(define-public python-locust
(package
(name "python-locust")
- (version "2.32.5")
+ (version "2.33.2")
;; The archive on Pypi has no tests.
(source (origin
(method git-fetch)
@@ -412,7 +412,7 @@ (define-public python-locust
(file-name (git-file-name name version))
(sha256
(base32
- "0nmhk2k0mbza9slqgms42s6hsfwwmyr275l90an02qaypx066l1n"))))
+ "055is6plxjajzp7v5q108n90j5mvdaylpna98kw9zsqn7mvfq7ms"))))
(build-system pyproject-build-system)
(arguments
(list
@@ -484,10 +484,21 @@ (define-public python-locust
"not test_ramp_up_from_0_to_100_000_users_with_50_user_classes_and_1000_workers_and_5000_spawn_rate"
;; This test fails with "AssertionError:
;; 'stopped' != 'stopping'".
- "not test_distributed_shape") " and "))
+ "not test_distributed_shape"
+ ;; This test fails with AssertionError:
+ ;; "locust [...] != .locust-real"
+ "not test_invalid_stop_timeout_string"
+ ) " and "))
#:phases
#~(modify-phases %standard-phases
;; The build system attempts to detect the version by spawning git.
+ (add-after 'unpack 'pretend-version
+ (lambda _
+ (substitute* "pyproject.toml"
+ (("^dynamic = \\[\"version\"\\].*$")
+ (format #f "version = ~s~%" #$version))
+ (("^source = \"vcs\".*$")
+ "source = \"static\"\n"))))
(add-after 'unpack 'fix-version
(lambda _
(let ((tuple (list
@@ -518,9 +529,15 @@ (define-public python-locust
")))))
(substitute* "pyproject.toml"
- (("setuptools = \">=70.0.0\"") "setuptools = \">=67.0.0\"")
- (("^version =.*") (string-append "version = \"" #$version "\"\n"))
- (("enable = true") "enable = false"))))
+ (("\"setuptools>=.*\",")
+ (string-append "\"setuptools>="
+ #$(package-version
+ (this-package-input "python-setuptools"))
+ "\","))
+ (("^version =.*")
+ (string-append "version = \"" #$version "\"\n"))
+ (("enable = true")
+ "enable = false"))))
(add-before 'check 'increase-resource-limits
(lambda _
;; XXX: Copied from ungoogled-chromium.
@@ -552,8 +569,8 @@ (define-public python-locust
python-werkzeug))
(native-inputs
(list nss-certs-for-test
- python-poetry-core
- python-poetry-dynamic-versioning
+ python-hatchling
+ python-hatch-vcs
python-pyquery
python-pytest
python-retry))
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:05 GMT) Full text and rfc822 format available.Message #29 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 11/26] gnu: seqmagick: Update to 0.8.6-0.dee6ab9. Date: Mon, 31 Mar 2025 08:18:39 +0200
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.6-0.dee6ab9.
---
gnu/packages/bioinformatics.scm | 44 ++++++++++++++++++---------------
1 file changed, 24 insertions(+), 20 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1351a15529..00f0e10475 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12061,30 +12061,34 @@ (define-public seqan-1
("bzip2" ,bzip2)))))
(define-public seqmagick
- (package
- (name "seqmagick")
- (version "0.8.4")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "seqmagick" version))
- (sha256
- (base32
- "0c6skyig8fyylnbj4597pjj9h0dn36rkxrhwd34yrsc6k6f7r8a0"))))
- (build-system pyproject-build-system)
- (inputs
- (list python-biopython python-pygtrie))
- (native-inputs
- (list python-pytest python-setuptools python-wheel))
- (home-page "https://github.com/fhcrc/seqmagick")
- (synopsis "Tools for converting and modifying sequence files")
- (description
- "Bioinformaticians often have to convert sequence files between formats
+ (let ((commit "dee6ab9839cff317142e55678bb12c4c9ab2150f")
+ (revision "0"))
+ (package
+ (name "seqmagick")
+ (version (git-version "0.8.6" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/fhcrc/seqmagick")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0syipb7m44s5bqrhs17bwr28svy2s83j8d93kbazav92jzszzsw4"))))
+ (build-system pyproject-build-system)
+ (inputs
+ (list python-biopython python-pygtrie))
+ (native-inputs
+ (list python-nose python-setuptools python-wheel))
+ (home-page "https://github.com/fhcrc/seqmagick")
+ (synopsis "Tools for converting and modifying sequence files")
+ (description
+ "Bioinformaticians often have to convert sequence files between formats
and do little manipulations on them, and it's not worth writing scripts for
that. Seqmagick is a utility to expose the file format conversion in
BioPython in a convenient way. Instead of having a big mess of scripts, there
is one that takes arguments.")
- (license license:gpl3)))
+ (license license:gpl3))))
(define-public seqtk
(package
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:05 GMT) Full text and rfc822 format available.Message #32 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 14/26] gnu: python-rstr: Update to 3.2.2. Enable tests. Date: Mon, 31 Mar 2025 08:18:42 +0200
* gnu/packages/python-xyz.scm (python-rstr): Update to 3.2.2.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]{phases}: Add phase 'pretend-version.
[native-inputs]: Add python-pytest, python-setuptools,
python-setuptools-scm, python-wheel.
---
gnu/packages/python-xyz.scm | 30 +++++++++++++++++++++++-------
1 file changed, 23 insertions(+), 7 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 57a62c5233..2487ef88a9 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -8719,15 +8719,31 @@ (define-public python-robotframework-seleniumscreenshots
(define-public python-rstr
(package
(name "python-rstr")
- (version "2.2.6")
+ (version "3.2.2")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "rstr" version))
- (sha256
- (base32
- "197dw8mbq0pjjz1l6h1ksi62vgn7x55d373ch74y06744qiq5sjx"))))
- (build-system python-build-system)
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/leapfrogonline/rstr")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1z9d660jnv72jn8qzpa9hddpv5f953js8i75hfhkcw68vmdfndnr"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'build 'pretend-version
+ ;; The version string is usually derived via setuptools-scm, but
+ ;; without the git metadata available, the version string is set to
+ ;; '0.0.0'.
+ (lambda _
+ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))))))
+ (native-inputs (list python-pytest
+ python-setuptools
+ python-setuptools-scm
+ python-wheel))
(home-page "https://github.com/leapfrogonline/rstr")
(synopsis "Generate random strings in Python")
(description "This package provides a python module for generating
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:06 GMT) Full text and rfc822 format available.Message #35 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 13/26] gnu: taxtastic: Update to 0.11.1. Date: Mon, 31 Mar 2025 08:18:41 +0200
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.11.1.
[build-system]: Switch to pyproject-build-system.
[arguments]{test-flags}: Ignore failing test.
{phases}: Improve style with gexp. Update phase
'prepare-directory. Improve phase 'check with test-flags inclusion.
[native-inputs]: Add python-setuptools, python-wheel.
[propagated-inputs]: Sort inputs. Replace python-psycopg2 by both
python-psycopg and python-psycopg2-binary. Add python-sqlparse.
---
gnu/packages/bioinformatics.scm | 69 ++++++++++++++++++---------------
1 file changed, 37 insertions(+), 32 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0f59f73448..1215e67117 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12414,7 +12414,7 @@ (define-public stringtie
(define-public taxtastic
(package
(name "taxtastic")
- (version "0.9.2")
+ (version "0.11.1")
(source (origin
;; The Pypi version does not include tests.
(method git-fetch)
@@ -12424,42 +12424,47 @@ (define-public taxtastic
(file-name (git-file-name name version))
(sha256
(base32
- "1k6wg9ych1j3srnhdny1y4470qlhfg730rb3rm3pq7l7gw62vmgb"))))
- (build-system python-build-system)
+ "18h3vlyx9qp7xymd8ra6jn5h0vzlpzgcd75kslqyv2qcg1a7scc4"))))
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'prepare-directory
- (lambda _
- ;; This test fails, but the error is not caught by the test
- ;; framework, so the tests fail...
- (substitute* "tests/test_taxit.py"
- (("self.cmd_fails\\(''\\)")
- "self.cmd_fails('nothing')"))
- ;; This version file is expected to be created with git describe.
- (mkdir-p "taxtastic/data")
- (with-output-to-file "taxtastic/data/ver"
- (lambda () (display ,version)))))
- (replace 'check
- ;; Note, this fails to run with "-v" as it tries to write to a
- ;; closed output stream.
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "python" "-m" "unittest"))))
- ;; This fails because it cannot find psycopg2 even though it is
- ;; available.
- (delete 'sanity-check))))
+ (list
+ #:test-flags #~(list "-k" "not test_new_nodes02")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'prepare-directory
+ (lambda _
+ ;; This package is unknown to pypi.
+ (substitute* '("requirements.txt" "setup.py")
+ ((".*psycopg-binary.*") ""))
+ ;; This test fails, but the error is not caught by the test
+ ;; framework, so the tests fail...
+ (substitute* "tests/test_taxit.py"
+ (("self.cmd_fails\\(''\\)")
+ "self.cmd_fails('nothing')"))
+ ;; This version file is expected to be created with git describe.
+ (mkdir-p "taxtastic/data")
+ (with-output-to-file "taxtastic/data/ver"
+ (lambda () (display #$version)))))
+ (replace 'check
+ ;; Note, this fails to run with "-v" as it tries to write to a
+ ;; closed output stream.
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (when tests?
+ (apply invoke "python" "-m" "unittest" test-flags)))))))
+ (native-inputs
+ (list python-setuptools python-wheel))
(propagated-inputs
- (list python-sqlalchemy
+ (list python-biopython
python-decorator
- python-biopython
- python-pandas
- python-psycopg2
+ python-dendropy
python-fastalite
- python-pyyaml
- python-six
python-jinja2
- python-dendropy))
+ python-pandas
+ python-psycopg
+ python-psycopg2-binary
+ python-pyyaml
+ python-sqlalchemy-2
+ python-sqlparse))
(home-page "https://github.com/fhcrc/taxtastic")
(synopsis "Tools for taxonomic naming and annotation")
(description
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:07 GMT) Full text and rfc822 format available.Message #38 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 15/26] gnu: reprotest: Update to 0.7.29. Date: Mon, 31 Mar 2025 08:18:43 +0200
* gnu/packages/diffoscope.scm (reprotest): Update to 0.7.29.
---
gnu/packages/diffoscope.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm
index cd5284754d..85eb8937f6 100644
--- a/gnu/packages/diffoscope.scm
+++ b/gnu/packages/diffoscope.scm
@@ -255,7 +255,7 @@ (define (bin command)
(define-public reprotest
(package
(name "reprotest")
- (version "0.7.28")
+ (version "0.7.29")
(source
(origin
(method git-fetch)
@@ -264,7 +264,7 @@ (define-public reprotest
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "06jm82w05qsx3wskch3fm5mpkpj5jmq7r4yram4ixprxc5j8flg8"))))
+ (base32 "17n7pdqil3jmpwcshr6dm5qsbpim3847smgxa82wy33kl2bz1ai8"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:08 GMT) Full text and rfc822 format available.Message #41 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 12/26] gnu: Remove python-pyfasta. Date: Mon, 31 Mar 2025 08:18:40 +0200
This package is archived and deprecated in favor or python-pyfaidx for
7 years.
* gnu/packages/bioinformatics.scm (python-pyfasta): Delete variable.
---
gnu/packages/bioinformatics.scm | 72 ---------------------------------
1 file changed, 72 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 00f0e10475..0f59f73448 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6396,78 +6396,6 @@ (define-public python-pybigwig
accessing bigWig files.")
(license license:expat)))
-(define-public python-pyfasta
- ;; The release on pypi does not contain the test data files.
- (let ((commit "c2f0611c5311f1b1466f2d56560447898b4a8b03")
- (revision "1"))
- (package
- (name "python-pyfasta")
- (version (git-version "0.5.2" revision commit))
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/brentp/pyfasta")
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0a189id3fbv88gssyk6adbmz2ll1mqpmyw8vxmx3fi955gvaq9j7"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:phases
- '(modify-phases %standard-phases
- (add-after 'unpack 'python3.10-compat
- (lambda _
- (substitute* "pyfasta/__init__.py"
- (("from fasta import")
- "from pyfasta.fasta import")
- (("from records import")
- "from pyfasta.records import")
- (("from split_fasta import")
- "from pyfasta.split_fasta import")
- (("in f.iteritems")
- "in f.items"))
- (substitute* "pyfasta/fasta.py"
- (("from collections import Mapping")
- "from collections.abc import Mapping")
- (("from records import")
- "from pyfasta.records import"))
- (substitute* "pyfasta/records.py"
- (("cPickle") "pickle")
- (("\\(int, long\\)")
- "(int, int)")
- ;; XXX: it's not clear if this is really correct.
- (("buffer\\(self\\)")
- "memoryview(bytes(str(self), encoding='utf-8'))")
- (("sys.maxint") "sys.maxsize"))
- (substitute* "pyfasta/split_fasta.py"
- (("from cStringIO import")
- "from io import")
- (("in lens.iteritems") "in lens.items"))
- (substitute* "tests/test_all.py"
- (("f.keys\\(\\)\\) == \\['a-extra'")
- "list(f.keys())) == ['a-extra'")
- (("f.iterkeys\\(\\)") "iter(f.keys())")
- (("tests/data/" m)
- (string-append (getcwd) "/" m))))))))
- (propagated-inputs (list python-numpy))
- (native-inputs (list python-nose python-setuptools python-wheel))
- (home-page "https://github.com/brentp/pyfasta/")
- (synopsis "Pythonic access to fasta sequence files")
- (description
- "This library provides fast, memory-efficient, pythonic (and
-command-line) access to fasta sequence files. It stores a flattened version
-of a fasta sequence file without spaces or headers and uses either a
-@code{mmap} in numpy binary format or @code{fseek}/@code{fread} so the
-sequence data is never read into memory. It saves a pickle (@code{.gdx}) of
-the start and stop (for @code{fseek}/@code{mmap}) locations of each header in
-the fasta file for internal use.
-
-Note that this package has been deprecated in favor of @code{pyfaidx}.")
- (license license:expat))))
-
(define-public python-schema-salad
(package
(name "python-schema-salad")
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:09 GMT) Full text and rfc822 format available.Message #44 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 16/26] gnu: python-sip: Update to 6.10.0. Date: Mon, 31 Mar 2025 08:18:44 +0200
* gnu/packages/qt.scm (python-sip): Update to 6.10.0.
[source]: Add snippet to relax python-setuptools requirement.
[native-inputs]: Remove python-wrapper. Add python-wheel. Sort inputs.
[propagated-inputs]: Remove python-tomli, python-wheel. Sort inputs.
* gnu/packages/backup.scm (vorta)[native-inputs]: Add
python-setuptools, python-wheel.
* gnu/packages/python-xyz.scm (python-echo)[native-inputs]: Add
python-setuptools, python-wheel.
* gnu/packages/patches/python-sip-include-dirs.patch: Refresh patch.
---
gnu/packages/backup.scm | 4 +++-
.../patches/python-sip-include-dirs.patch | 17 ++++++++---------
gnu/packages/python-xyz.scm | 2 ++
gnu/packages/qt.scm | 16 +++++++++-------
4 files changed, 22 insertions(+), 17 deletions(-)
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 13c5590f55..cf06f7c1e6 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -1443,7 +1443,9 @@ (define-public vorta
python-pytest-mock
python-pytest-qt
python-pytest-runner
- python-setuptools-git))
+ python-setuptools
+ python-setuptools-git
+ python-wheel))
(inputs
(list borg
python-appdirs
diff --git a/gnu/packages/patches/python-sip-include-dirs.patch b/gnu/packages/patches/python-sip-include-dirs.patch
index f2ef8fc1b2..e5626030b6 100644
--- a/gnu/packages/patches/python-sip-include-dirs.patch
+++ b/gnu/packages/patches/python-sip-include-dirs.patch
@@ -5,16 +5,15 @@ It seems that we cannot easily change the destination folder of these
files though, so this variable must be set on a per-package basis (and
non through search-path).
---- sip/sipbuild/builder.py 2023-03-22 09:06:37.588792878 +0100
-+++ sip/sipbuild/builder.py 2023-03-22 09:10:35.830181134 +0100
-@@ -254,6 +254,10 @@
+--- sip/sipbuild/builder.py
++++ sip/sipbuild/builder.py
+@@ -227,5 +227,9 @@
os.path.join(project.target_dir,
project.get_bindings_dir()))
-+ # Add extra bindings from environment for GNU Guix.
-+ if 'SIP_INCLUDE_DIRS' in os.environ:
-+ sip_include_dirs.extend(os.environ['SIP_INCLUDE_DIRS'].split(os.pathsep))
++ # Add extra bindings from environment for GNU Guix
++ if 'SIP_INCLUDE_DIRS' in os.environ:
++ sip_include_dirs.extend(os.environ['SIP_INCLUDE_DIRS'].split(os.pathsep))
+
- # Generate the sip.h file for the shared sip module.
- copy_sip_h(abi_major_version, project.build_dir,
- project.sip_module, version_info=project.version_info)
+ # Generate the code for each set of bindings.
+ api_files = []
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 2487ef88a9..e57c834ddb 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3001,7 +3001,9 @@ (define-public python-echo
(native-inputs
(list python-pytest
python-pytest-cov
+ python-setuptools
python-setuptools-scm
+ python-wheel
xorg-server-for-tests))
(home-page "https://github.com/glue-viz/echo")
(synopsis "Callback Properties in Python")
diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm
index 13893d2951..5a69c4baf7 100644
--- a/gnu/packages/qt.scm
+++ b/gnu/packages/qt.scm
@@ -4028,7 +4028,7 @@ (define-public pyotherside-for-qt5
(define-public python-sip
(package
(name "python-sip")
- (version "6.8.6")
+ (version "6.10.0")
(source
(origin
(method url-fetch)
@@ -4038,18 +4038,20 @@ (define-public python-sip
"/sip-" version ".tar.gz")))
(sha256
(base32
- "0ykxq0607f2sdwbl5cxbp0y8pl14bsgzc9nhifpxbibfivj5kjbz"))
+ "176jylhzs2ci2r9f3l75k9dpwhp1dn0qv2cy9phdp62cgmlia1gs"))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Relax setuptools dependency
+ #~(substitute* "pyproject.toml"
+ (("\"setuptools>=.*\",") "\"setuptools\",")))
(patches (search-patches "python-sip-include-dirs.patch"))))
(build-system pyproject-build-system)
(arguments
(list #:tests? #f)) ; No test system found.
(native-inputs
- (list python-wrapper python-setuptools python-setuptools-scm-next))
+ (list python-setuptools python-setuptools-scm-next python-wheel))
(propagated-inputs
- (list python-tomli
- python-packaging
- python-setuptools
- python-wheel))
+ (list python-packaging python-setuptools))
(home-page "https://www.riverbankcomputing.com/software/sip/intro")
(synopsis "Python binding creator for C and C++ libraries")
(description
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:09 GMT) Full text and rfc822 format available.Message #47 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 17/26] gnu: Add python-pybktree. Date: Mon, 31 Mar 2025 08:18:45 +0200
* gnu/packages/backup.scm (python-pybktree): New variable.
---
gnu/packages/python-xyz.scm | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e57c834ddb..ba6a96f714 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -28939,6 +28939,25 @@ (define-public python-pybloom-live
Python.")
(license license:expat)))
+(define-public python-pybktree
+ (package
+ (name "python-pybktree")
+ (version "1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pybktree" version))
+ (sha256
+ (base32 "0asd2lw9c5l5wi4z24k7gkhlprpdkcvs8d94szk56x9xvmy07h7f"))))
+ (build-system pyproject-build-system)
+ (native-inputs (list python-setuptools python-wheel))
+ (home-page "https://github.com/Jetsetter/pybktree")
+ (synopsis "Pythonic BK-tree data structure")
+ (description
+ "This package provides a BK-tree data structure to allow fast querying of
+close matches in Python.")
+ (license license:expat)))
+
(define-public python-pybtex
(package
(name "python-pybtex")
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:11 GMT) Full text and rfc822 format available.Message #50 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 18/26] gnu: umi-tools: Update to 1.1.6. Date: Mon, 31 Mar 2025 08:18:46 +0200
* gnu/packages/bioinformatics.scm (umi-tools): Update to 1.1.6.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[inputs]: Add python-pybktree, python-scipy.
[native-inputs]: Add python-setuptools, python-wheel.
---
gnu/packages/bioinformatics.scm | 18 +++++++++++-------
1 file changed, 11 insertions(+), 7 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1215e67117..91ea4a5b7a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -21424,24 +21424,28 @@ (define-public checkm
(define-public umi-tools
(package
(name "umi-tools")
- (version "1.0.0")
+ (version "1.1.6")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "umi_tools" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/CGATOxford/UMI-tools")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32
- "08y3vz1vcx09whmbsn722lcs6jl9wyrh9i4p3k8j4cb1i32bij4a"))))
- (build-system python-build-system)
+ (base32 "1liykfj4msvcgk8an5qq802jcxwlijqxrvijipqj1pwpxqzl9qnh"))))
+ (build-system pyproject-build-system)
(inputs
(list python-pandas
python-future
python-scipy
python-matplotlib
python-regex
+ python-pybktree
+ python-scipy
python-pysam))
(native-inputs
- (list python-cython))
+ (list python-setuptools python-wheel))
(home-page "https://github.com/CGATOxford/UMI-tools")
(synopsis "Tools for analyzing unique modular identifiers")
(description "This package provides tools for dealing with @dfn{Unique
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:13 GMT) Full text and rfc822 format available.Message #53 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 19/26] gnu: cpplint: Update to 2.0.0. Date: Mon, 31 Mar 2025 08:18:47 +0200
* gnu/packages/cpp.scm (cpplint): Update to 2.0.0.
[arguments]{phases}: Add phase 'patch-build-system.
[native-inputs]: Add python-parameterized, python-pytest-timeout.
---
gnu/packages/cpp.scm | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index d6f24b8fe0..a68c27347a 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -1404,7 +1404,7 @@ (define-public cpp-httplib
(define-public cpplint
(package
(name "cpplint")
- (version "1.5.5")
+ (version "2.0.0")
(source
(origin
(method git-fetch)
@@ -1414,7 +1414,7 @@ (define-public cpplint
(url "https://github.com/cpplint/cpplint")
(commit version)))
(sha256
- (base32 "13l86aq0h1jga949k79k9x3hw2xqchjc162sclg2f99vz98zcz15"))
+ (base32 "06km4wh4944az1hk61g5w8pjhbvbccpgarz1dy7vhwkhfvmvggnk"))
(file-name (git-file-name name version))))
(build-system pyproject-build-system)
(arguments
@@ -1423,6 +1423,11 @@ (define-public cpplint
,@%pyproject-build-system-modules)
#:phases
#~(modify-phases (@ (guix build pyproject-build-system) %standard-phases)
+ (add-after 'unpack 'patch-build-system
+ (lambda _
+ (substitute* "pyproject.toml"
+ (("setuptools\\.build_meta:__legacy__")
+ "setuptools.build_meta"))))
(add-before 'wrap 'reduce-GUIX_PYTHONPATH
(lambda _
;; Hide the transitive native inputs from GUIX_PYTHONPATH
@@ -1449,9 +1454,11 @@ (define-public cpplint
(getenv "TMP_PYTHONPATH")))))))
(native-inputs
(list python-coverage
+ python-parameterized
python-pytest
python-pytest-cov
python-pytest-runner
+ python-pytest-timeout
python-setuptools
python-testfixtures
python-wheel))
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:15 GMT) Full text and rfc822 format available.Message #56 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 20/26] gnu: python-patch-ng: Update to 1.18.1. Date: Mon, 31 Mar 2025 08:18:48 +0200
* gnu/packages/python-xyz.scm (python-patch-ng): Update to 1.18.1.
---
gnu/packages/python-xyz.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index ba6a96f714..61a63e64dc 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -10366,7 +10366,7 @@ (define-public python-norns
(define-public python-patch-ng
(package
(name "python-patch-ng")
- (version "1.17.4")
+ (version "1.18.1")
(source
(origin
(method git-fetch) ;no tests in PyPI archive
@@ -10376,7 +10376,7 @@ (define-public python-patch-ng
(file-name (git-file-name name version))
(sha256
(base32
- "0qxn4ss2s54qy87xrpcybz26kp2fwlaq41x4k9jcmp6d7p0w569m"))))
+ "1kr3h0bkcr02zyfsmwmxfv5b4b9vf3bhsvrlwp6cwrfy3q3qnyq8"))))
(build-system python-build-system)
(arguments
`(#:phases (modify-phases %standard-phases
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:16 GMT) Full text and rfc822 format available.Message #59 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 21/26] gnu: veusz: Update to 3.6.2. Date: Mon, 31 Mar 2025 08:18:49 +0200
* gnu/packages/maths.scm (veusz): Update to 3.6.2.
[build-system]: Switch to pyproject-build-system.
[arguments]: Improve style, use gexps.
{phases}: Remove phase 'fix-sip-dir. Add phase
'fix-pyqt5-include-dir. Refresh phase 'wrap-executable.
[native-inputs]: Add python-astropy, python-setuptools,
python-wheel. Remove python-sip-4.
[inputs]: Add qtwayland-5.
---
gnu/packages/maths.scm | 73 +++++++++++++++++++++++-------------------
1 file changed, 40 insertions(+), 33 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 6826139580..ec8554520b 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -107,6 +107,7 @@ (define-module (gnu packages maths)
#:use-module (guix build-system python)
#:use-module (guix build-system ruby)
#:use-module (gnu packages algebra)
+ #:use-module (gnu packages astronomy)
#:use-module (gnu packages audio)
#:use-module (gnu packages autotools)
#:use-module (gnu packages backup)
@@ -3511,46 +3512,51 @@ (define-public gmsh
(define-public veusz
(package
(name "veusz")
- (version "3.3.1")
+ (version "3.6.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "veusz" version))
(sha256
- (base32 "1q7hi1qwwg4pgiz62isvv1pia85m13bspdpp1q3mrnwl11in0ag0"))))
- (build-system python-build-system)
+ (base32 "1lcmcfr0dcam8g1fp5qip8jnxglxx7i62ln3ix6l4c2bbv21l5y2"))))
+ (build-system pyproject-build-system)
(arguments
- `(;; Tests will fail because they depend on optional packages like
- ;; python-astropy, which is not packaged.
- #:tests? #f
- #:phases
- (modify-phases %standard-phases
- ;; Veusz will append 'PyQt5' to sip_dir by default. That is not how
- ;; the path is defined in Guix, therefore we have to change it.
- (add-after 'unpack 'fix-sip-dir
- (lambda _
- (substitute* "pyqtdistutils.py"
- (("os.path.join\\(sip_dir, 'PyQt5'\\)") "sip_dir"))))
- ;; Now we have to pass the correct sip_dir to setup.py.
- (replace 'build
- (lambda* (#:key inputs #:allow-other-keys)
- ;; We need to tell setup.py where to locate QtCoremod.sip
- ((@@ (guix build python-build-system) call-setuppy)
- "build_ext"
- (list (string-append "--sip-dir="
- (search-input-directory inputs "share/sip"))))))
- ;; Ensure that icons are found at runtime.
- (add-after 'install 'wrap-executable
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (wrap-program (string-append out "/bin/veusz")
- `("QT_PLUGIN_PATH" prefix
- ,(list (string-append (assoc-ref inputs "qtsvg")
- "/lib/qt5/plugins/"))))))))))
+ (list
+ ;; Tests currently fail with exception TypeError:
+ ;; calling <function version ...> returned 3.6.2, not a test
+ #:tests? #f
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; Veusz uses python's site-packages to look for pyqt5_include_dir.
+ (add-after 'unpack 'fix-pyqt5-include-dir
+ (lambda _
+ (substitute* "pyqt_setuptools.py"
+ (("get_path\\('platlib'\\)")
+ (format #f "~s"
+ (string-append
+ #$(this-package-input "python-pyqt")
+ "/lib/python"
+ #$(version-major+minor
+ (package-version python-wrapper))
+ "/site-packages"))))))
+ ;; Ensure that icons are found at runtime.
+ (add-after 'wrap 'wrap-executable
+ (lambda* (#:key inputs #:allow-other-keys)
+ (wrap-program (string-append #$output "/bin/veusz")
+ `("QT_PLUGIN_PATH" prefix
+ ,(list (string-append
+ (string-join
+ (list #$(this-package-input "qtbase")
+ #$(this-package-input "qtsvg")
+ #$(this-package-input "qtwayland"))
+ "/lib/qt5/plugins:")
+ "/lib/qt5/plugins")))))))))
(native-inputs
(list pkg-config
- ;;("python-astropy" ,python-astropy) ;; FIXME: Package this.
- qttools-5 python-sip-4))
+ python-astropy
+ python-setuptools
+ python-wheel
+ qttools-5))
(inputs
(list bash-minimal
ghostscript ;optional, for EPS/PS output
@@ -3558,7 +3564,8 @@ (define-public veusz
python-h5py ;optional, for HDF5 data
python-pyqt
qtbase-5
- qtsvg-5))
+ qtsvg-5
+ qtwayland-5))
(propagated-inputs
(list python-numpy))
(home-page "https://veusz.github.io/")
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:16 GMT) Full text and rfc822 format available.Message #62 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 23/26] gnu: python-cu2qu: Fix tests. Date: Mon, 31 Mar 2025 08:18:51 +0200
* gnu/packages/fontutils.scm (python-cu2qu): Fix tests.
[build-system]: Switch to pyproject-build-system.
[arguments]{test-flags}: Ignore failing test (most likely due to
lagging behing python-fonttools package).
[native-inputs]: Add python-setuptools, python-wheel.
* gnu/packages/python-xyz.scm (python-fonttools-minimal): Add comment.
---
gnu/packages/fontutils.scm | 7 ++++++-
gnu/packages/python-xyz.scm | 1 +
2 files changed, 7 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm
index d2d3b1a260..3ec255b0fa 100644
--- a/gnu/packages/fontutils.scm
+++ b/gnu/packages/fontutils.scm
@@ -504,14 +504,19 @@ (define-public python-cu2qu
(uri (pypi-uri "cu2qu" version ".zip"))
(sha256
(base32 "1x762r7bf39g6aivfvrmq00h6f07abvs9x1xm0fz8l81vq8jz64c"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
+ (arguments
+ ;; XXX: Try to remove it when updating python-fonttools.
+ (list #:test-flags #~(list "-k" "not test_ignore_single_points")))
(propagated-inputs (list python-fonttools))
(native-inputs
(list python-cython
python-defcon
python-pytest
python-pytest-runner
+ python-setuptools
python-setuptools-scm
+ python-wheel
unzip))
(home-page "https://github.com/googlefonts/cu2qu")
(synopsis "Cubic-to-quadratic bezier curve conversion")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 61a63e64dc..015872902a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -16993,6 +16993,7 @@ (define-public python-fs
(license license:expat)))
;;; Tests are left out in the main package to avoid cycles.
+;; XXX: When updating, solve comment in python-cu2qu.
(define-public python-fonttools-minimal
(hidden-package
(package
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:17 GMT) Full text and rfc822 format available.Message #65 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 22/26] gnu: conan: Update to 2.7.1. Date: Mon, 31 Mar 2025 08:18:50 +0200
* gnu/packages/package-management.scm (conan): Update to 2.7.1.
[build-system]: Switch to pyproject-build-system.
[arguments]{test-flags}: Use field. Ignore failing tests (old versions
of cmake, performance tests, docker/premake/scons requirements.
{phases}: Refresh phases. Replace 'check phase by a 'configure-tests
phase and the native 'check phase.
[propagated-inputs]: Replace python-urllib3 by python-urllib3-next.
[native-inputs]: Add python-setuptools, python-wheel.
---
gnu/packages/package-management.scm | 139 +++++++++++++++-------------
1 file changed, 77 insertions(+), 62 deletions(-)
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index a4a96878f7..b5a5adae6e 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -1315,7 +1315,7 @@ (define-public conda
(define-public conan
(package
(name "conan")
- (version "2.0.9")
+ (version "2.7.1")
(source
(origin
(method git-fetch) ; no tests in PyPI archive
@@ -1324,13 +1324,74 @@ (define-public conan
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "1ykfj7c3i0b57s7ql3p2lawxdzd2cn36f3k8p64lyzla8rwv4xdx"))))
- (build-system python-build-system)
+ (base32 "00mrx1ighvf6r6fy2iqxr286w3jfd0gwlzcqsw15cm9axblx5av9"))))
+ (build-system pyproject-build-system)
(arguments
(list
- #:modules '((guix build python-build-system)
+ #:modules '((guix build pyproject-build-system)
(guix build utils)
(ice-9 format))
+ #:test-flags
+ (let ((system (or (%current-target-system)
+ (%current-system))))
+ #~(list "-n" (number->string (parallel-job-count))
+ "-m" "not slow"
+ "--ignore=test/performance/"
+ ;; E ModuleNotFoundError: No module named 'docker'
+ "--ignore=test/functional/command/runner_test.py"
+ ;; Disable problematic tests.
+ "-k"
+ (string-append
+ ;; These tests rely on networking.
+ "not download_retries_errors "
+ "and not ftp "
+ ;; These tests are for old versions of cmake.
+ "and not test_custom_cmake_3_16 "
+ "and not test_custom_cmake_3_17 "
+ "and not test_custom_cmake_3_19 "
+ ;; Guix sets PKG_CONFIG_PATH itself, which is not
+ ;; expected by the following test.
+ "and not pkg_config_path "
+ "and not compare " ;caused by newer node-semver?
+ ;; This test hard-codes a compiler version.
+ "and not test_toolchain "
+ ;; The 'test_list' tests may fail
+ ;; non-deterministically (see:
+ ;; https://github.com/conan-io/conan/issues/13583).
+ "and not test_list "
+ ;; These tests fail when Autoconf attempt to load a
+ ;; shared library in the same directory (see:
+ ;; https://github.com/conan-io/conan/issues/13577).
+ "and not test_other_client_can_link_autotools "
+ "and not test_autotools_lib_template "
+ ;; Sometimes fail: https://github.com/conan-io/conan/issues/15936
+ "and not test_basic_parallel_install "
+ ;; These tests require additional build tools
+ "and not test_premake "
+ "and not test_sconsdeps "
+ ;; Unclear why libc is not found properly
+ "and not test_profile_detect_libc "
+ #$(if (not (string-prefix? "x86_64" system))
+ ;; These tests either assume the machine is
+ ;; x86_64, or require a cross-compiler to target
+ ;; it.
+ (string-append
+ "and not cpp_package "
+ "and not exclude_code_analysis "
+ "and not cmakedeps_multi "
+ "and not locally_build_linux "
+ "and not custom_configuration "
+ "and not package_from_system "
+ "and not cross_build_command "
+ "and not test_package "
+ "and not test_same ")
+ "")
+ #$(if (not (or (string-prefix? "x86_64" system)
+ (string-prefix? "i686" system)))
+ ;; This test only works with default arch "x86",
+ ;; "x86_64", "sparc" or "sparcv9".
+ "and not settings_as_a_dict_conanfile "
+ ""))))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'patch-paths
@@ -1345,21 +1406,22 @@ (define-public conan
;; The test suite expects GCC 9 to be used (see:
;; https://github.com/conan-io/conan/issues/13575). Render the
;; check version agnostic.
- (substitute* "conans/test/functional/toolchains/meson/_base.py"
+ (substitute* "test/functional/toolchains/meson/_base.py"
(("__GNUC__9")
"__GNUC__"))))
(add-after 'unpack 'use-current-cmake-for-tests
(lambda _
- (substitute* (find-files "conans/test" "\\.py$")
- (("@pytest.mark.tool\\(\"cmake\", \"3.23\")")
+ (substitute* (find-files "test" "\\.py$")
+ (("@pytest.mark.tool\\(\"cmake\", \".*\")")
"@pytest.mark.tool(\"cmake\")"))))
(add-before 'check 'configure-tests
(lambda _
(let* ((cmake-version #$(version-major+minor
- (package-version cmake)))
+ (package-version
+ (this-package-native-input "cmake"))))
(pkg-config-version #$(version-major+minor
(package-version pkg-config))))
- (call-with-output-file "conans/test/conftest_user.py"
+ (call-with-output-file "test/conftest_user.py"
(lambda (port)
(format port "\
tools_locations = {
@@ -1378,61 +1440,12 @@ (define-public conan
(add-before 'check 'set-home
(lambda _
(setenv "HOME" "/tmp")))
- (replace 'check
- (lambda* (#:key tests? outputs #:allow-other-keys)
- (define system #$(or (%current-target-system)
- (%current-system)))
+ (add-before 'check 'configure-tests
+ (lambda* (#:key tests? #:allow-other-keys)
(when tests?
(setenv "CONFIG_SHELL" (which "sh"))
(setenv "PATH" (string-append (getenv "PATH") ":"
- #$output "/bin"))
- (invoke "python" "-m" "pytest" "-vv"
- "-n" (number->string (parallel-job-count))
- "-m" "not slow"
- ;; Disable problematic tests.
- "-k"
- (string-append
- ;; These tests rely on networking.
- "not download_retries_errors "
- "and not ftp "
- ;; Guix sets PKG_CONFIG_PATH itself, which is not
- ;; expected by the following test.
- "and not pkg_config_path "
- "and not compare " ;caused by newer node-semver?
- ;; This test hard-codes a compiler version.
- "and not test_toolchain "
- ;; The 'test_list' tests may fail
- ;; non-deterministically (see:
- ;; https://github.com/conan-io/conan/issues/13583).
- "and not test_list "
- ;; These tests fail when Autoconf attempt to load a
- ;; shared library in the same directory (see:
- ;; https://github.com/conan-io/conan/issues/13577).
- "and not test_other_client_can_link_autotools "
- "and not test_autotools_lib_template "
- ;; Sometimes fail: https://github.com/conan-io/conan/issues/15936
- "and not test_basic_parallel_install "
- (if (not (string-prefix? "x86_64" system))
- ;; These tests either assume the machine is
- ;; x86_64, or require a cross-compiler to target
- ;; it.
- (string-append
- "and not cpp_package "
- "and not exclude_code_analysis "
- "and not cmakedeps_multi "
- "and not locally_build_linux "
- "and not custom_configuration "
- "and not package_from_system "
- "and not cross_build_command "
- "and not test_package "
- "and not test_same ")
- "")
- (if (not (or (string-prefix? "x86_64" system)
- (string-prefix? "i686" system)))
- ;; This test only works with default arch "x86",
- ;; "x86_64", "sparc" or "sparcv9".
- "and not settings_as_a_dict_conanfile "
- "")))))))))
+ #$output "/bin"))))))))
(propagated-inputs
(list python-bottle
python-colorama
@@ -1450,7 +1463,7 @@ (define system #$(or (%current-target-system)
python-requests
python-six
python-tqdm
- python-urllib3))
+ python-urllib3-next))
(inputs
(list coreutils)) ;for printenv
(native-inputs
@@ -1467,7 +1480,9 @@ (define system #$(or (%current-target-system)
python-parameterized
python-pytest
python-pytest-xdist
+ python-setuptools
python-webtest
+ python-wheel
which))
(home-page "https://conan.io")
(synopsis "Decentralized C/C++ package manager")
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:17 GMT) Full text and rfc822 format available.Message #68 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 24/26] gnu: libei: Update to 1.4.0. Date: Mon, 31 Mar 2025 08:18:52 +0200
* gnu/packages/freedesktop.scm (libei): Update to 1.4.0.
[native-inputs]: Add dbus, python-pyaml. Remove python-black.
---
gnu/packages/freedesktop.scm | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm
index 0618fdc6f4..95063c1c2b 100644
--- a/gnu/packages/freedesktop.scm
+++ b/gnu/packages/freedesktop.scm
@@ -791,7 +791,7 @@ (define-public libinput-minimal
(define-public libei
(package
(name "libei")
- (version "1.3.0")
+ (version "1.4.0")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -799,7 +799,7 @@ (define-public libei
(commit version)))
(sha256
(base32
- "0idbl20ax060s7m435rszfv7c0bvpinjvq45qbqwvcvp0hg8r9y8"))
+ "04ll43616pyfm7c835azdggx9x3vfykpcg3pzmsfz4f2vl5whalm"))
(snippet
#~(begin
(use-modules (guix build utils))
@@ -821,17 +821,18 @@ (define-public libei
;; liboeffis-1.0.pc requires.private libelogind
(list elogind))
(native-inputs
- (list doxygen
+ (list dbus
+ doxygen
libxml2
munit
pkg-config
python
python-attrs
- python-black
python-dbusmock
python-jinja2
python-pytest
python-structlog
+ python-pyaml
valgrind/interactive))
(home-page "https://libinput.pages.freedesktop.org/libei/")
(synopsis "Emulated Input protocol implementation")
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:18 GMT) Full text and rfc822 format available.Message #71 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 25/26] gnu: openmolar: Fix build. Date: Mon, 31 Mar 2025 08:18:53 +0200
* gnu/packages/medical.scm (openmolar): Fix build.
[build-system]: Switch to pyproject-build-system.
[arguments]{use-setuptools?}: Drop it.
{phases}: Add phase 'set-acceptable-version.
[native-inputs]: Add python-setuptools, python-wheel.
---
gnu/packages/medical.scm | 32 +++++++++++++++++++++-----------
1 file changed, 21 insertions(+), 11 deletions(-)
diff --git a/gnu/packages/medical.scm b/gnu/packages/medical.scm
index c755508db9..25e769c576 100644
--- a/gnu/packages/medical.scm
+++ b/gnu/packages/medical.scm
@@ -19,6 +19,7 @@
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages medical)
+ #:use-module (guix build-system pyproject)
#:use-module (guix build-system python)
#:use-module (guix build-system qt)
#:use-module (guix download)
@@ -29,6 +30,7 @@ (define-module (gnu packages medical)
#:use-module (gnu packages databases)
#:use-module (gnu packages kde-frameworks) ; kirigami
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-build)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
@@ -93,18 +95,26 @@ (define-public openmolar-1
".tar.gz"))
(sha256
(base32 "09vrfqn511vswnj2q9m7srlwdgz066qvqpmja6sg1yl1ibh3cbpr"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
- `(#:use-setuptools? #f
- #:phases (modify-phases %standard-phases
- (add-after 'unpack 'patch-/usr
- (lambda* (#:key outputs #:allow-other-keys)
- (substitute* '("setup.py"
- "src/openmolar/settings/localsettings.py")
- (("/usr")
- (assoc-ref outputs "out"))) #t)))))
- (inputs (list python-pyqtwebengine python-pyqt+qscintilla
- python-mysqlclient qscintilla))
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'patch-/usr
+ (lambda* (#:key outputs #:allow-other-keys)
+ (substitute* '("setup.py"
+ "src/openmolar/settings/localsettings.py")
+ (("/usr") #$output))))
+ (add-after 'unpack 'set-acceptable-version
+ (lambda _
+ (substitute* "src/openmolar/settings/version.py"
+ ((#$version) "1.1.6")))))))
+ (native-inputs
+ (list python-setuptools python-wheel))
+ (inputs (list python-pyqtwebengine
+ python-pyqt+qscintilla
+ python-mysqlclient
+ qscintilla))
(propagated-inputs (list qtwebengine-5))
(home-page "https://openmolar.com/om1")
(synopsis "Dental practice management software")
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:18 GMT) Full text and rfc822 format available.Message #74 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 26/26] gnu: python-mechanize: Update to 0.4.10. Date: Mon, 31 Mar 2025 08:18:54 +0200
* gnu/packages/python-xyz.scm (python-mechanize): Update to 0.4.10.
[build-system]: Switch to pyproject-build-system.
[arguments]{tests?}: Disable them.
{phases}: Add 'configure-tests phase to setup GUIX_PYTHONPATH.
[native-inputs]: Add python-html5-parser, python-html5lib,
python-lxml, python-service-identity, python-setuptools, python-six,
python-twisted, python-wheel.
---
gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++----
1 file changed, 22 insertions(+), 4 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 015872902a..3d2bade3fc 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5167,15 +5167,33 @@ (define-public python-scour
(define-public python-mechanize
(package
(name "python-mechanize")
- (version "0.4.7")
+ (version "0.4.10")
(source
(origin
(method url-fetch)
(uri (pypi-uri "mechanize" version))
(sha256
- (base32
- "02b845y85ka5sl2cj93lll3v326d8bww07bq1q0y1643h7sshwqp"))))
- (build-system python-build-system)
+ (base32 "1pvxjnhqi6iq7nnjksnfvyzxcibbwfjc9fzp22v0msp7kdzr9shx"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; XXX: Unclear why tests are failing.
+ (list #:tests? #f
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'check 'configure-tests
+ (lambda _
+ (setenv "GUIX_PYTHONPATH"
+ (string-append (getcwd) "/test-tools:"
+ (getenv "GUIX_PYTHONPATH"))))))))
+ (native-inputs
+ (list python-html5-parser
+ python-html5lib
+ python-lxml
+ python-service-identity
+ python-setuptools
+ python-six
+ python-twisted
+ python-wheel))
(propagated-inputs
(list python-html5lib))
(home-page "https://github.com/python-mechanize/mechanize")
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:18 GMT) Full text and rfc822 format available.Message #77 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 08/26] gnu: python-pyquery: Update to 2.0.1. Date: Mon, 31 Mar 2025 08:18:36 +0200
* gnu/packages/python-xyz.scm (python-pyquery): Update to 2.0.1.
[build-system]: Switch to pyproject-build-system.
[arguments]{test-flags}: Ignore a test that requires network access.
[native-inputs]: Add python-pytest, python-pytest-cov,
python-requests, python-setuptools, python-webob, python-webtest,
python-wheel.
[propagated-inputs]: Sort inputs.
---
gnu/packages/python-xyz.scm | 19 ++++++++++++++-----
1 file changed, 14 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 545a867de3..57a62c5233 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21140,19 +21140,28 @@ (define-public python-cookiecutter
(define-public python-pyquery
(package
(name "python-pyquery")
- (version "1.2.17")
+ (version "2.0.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyquery" version))
(sha256
(base32
- "1xia20wm0vx5dk85kcwgh13bylz8qh47ffjxssd2586r60xi783a"))))
- (build-system python-build-system)
+ "1brg6aawb9m5mdfmc6g7v5r6pczbx67r4l9cn5yh6bdi0qkvp501"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; This test requires network access.
+ (list #:test-flags #~(list "-k" "not test_get")))
(native-inputs
- (list python-webob python-webtest))
+ (list python-pytest
+ python-pytest-cov
+ python-requests
+ python-setuptools
+ python-webob
+ python-webtest
+ python-wheel))
(propagated-inputs
- (list python-lxml python-cssselect))
+ (list python-cssselect python-lxml))
(home-page "https://github.com/gawel/pyquery")
(synopsis "Make jQuery-like queries on xml documents")
(description "pyquery allows you to make jQuery queries on xml documents.
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:19 GMT) Full text and rfc822 format available.Message #80 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 06/26] gnu: Remove python-parameterizedtestcase. Date: Mon, 31 Mar 2025 08:18:34 +0200
This package is a leaf package in Guix, has been abandonned for 11
years (aside from a License change).
* gnu/packages/python-check.scm (python-parameterizedtestcase): Delete variable.
---
gnu/packages/python-check.scm | 19 -------------------
1 file changed, 19 deletions(-)
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 265581a17f..c3a787f6b8 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -2960,25 +2960,6 @@ (define-public python-pandas-vet
in an opinionated way.")
(license license:expat)))
-(define-public python-parameterizedtestcase
- (package
- (name "python-parameterizedtestcase")
- (version "0.1.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "parameterizedtestcase" version))
- (sha256
- (base32 "0zhjmsd16xacg4vd7zb75kw8q9khn52wvad634v1bvz7swaivk2c"))))
- (build-system python-build-system)
- (native-inputs (list python-setuptools-57)) ;for use_2to3
- (home-page
- "https://github.com/msabramo/python_unittest_parameterized_test_case")
- (synopsis "Parameterized tests for Python's unittest module")
- (description "This package provides parameterized tests for Python's
-@code{unittest} module taking inspiration from pytest.")
- (license license:expat)))
-
(define-public python-pytest-rerunfailures
(package
(name "python-pytest-rerunfailures")
--
2.49.0
guix-patches <at> gnu.org:bug#77400; Package guix-patches.
(Mon, 31 Mar 2025 06:21:19 GMT) Full text and rfc822 format available.Message #83 received at 77400 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77400 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 10/26] gnu: rseqc: Switch to pyproject-build-system. Date: Mon, 31 Mar 2025 08:18:38 +0200
* gnu/packages/bioinformatics.scm (rseqc):
[build-system]: Switch to pyproject-build-system.
[inputs]: Sort inputs. Add python-pyparsing, python-setuptools,
python-wheel.
---
gnu/packages/bioinformatics.scm | 13 ++++++++-----
1 file changed, 8 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 659e7cfea0..1351a15529 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10828,13 +10828,16 @@ (define-public rseqc
(sha256
(base32
"0gbb9iyb7swiv5455fm5rg98r7l6qn27v564yllqjd574hncpx6m"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(inputs
- (list python-cython
- python-bx-python
- python-pybigwig
- python-pysam
+ (list python-bx-python
+ python-cython
python-numpy
+ python-pybigwig
+ python-pyparsing
+ python-pysam
+ python-setuptools
+ python-wheel
zlib))
(native-inputs
(list python-nose))
--
2.49.0
Sharlatan Hellseher <sharlatanus <at> gmail.com>:Nicolas Graves <ngraves <at> ngraves.fr>:Message #88 received at 77400-done <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 77400-done <at> debbugs.gnu.org Subject: [PATCH python-team 00/26] Some further updates Date: Mon, 31 Mar 2025 22:58:31 +0100
[Message part 1 (text/plain, inline)]
Hi Nicoals, Thank you for your contribution. I could build the whole patch series on my local checkout just fine: --8<---------------cut here---------------start------------->8--- /gnu/store/s8akwvrglgifr593la3v4fwib8gf1pax-conan-2.7.1 /gnu/store/3m0va0fb1xp11xrmwjfc1j7jakmbzz7y-cpplint-2.0.0 /gnu/store/g5drhqvl2rw59s0hrkskjhjxyl5g6mi0-libei-1.4.0 /gnu/store/jlhlqpq99zf2as3c4p7750fkrzqzah0z-openmolar-1.1.6-g81838c85 /gnu/store/hd1km0h9lcbm7mbcb1r93rlnafklmgxn-python-cchardet-2.2.0a2 /gnu/store/nph80sm8kdzy32nhbsamb7k41kvy8msi-python-cu2qu-1.6.7.post1 /gnu/store/1xp14gihifzw7wrl9nj5sy36gsj7v8w9-python-databricks-cli-0.18.0 /gnu/store/m66j1y0zf4nw6ii1vpqykl72a3xly64f-python-jsonargparse-4.37.0 /gnu/store/0wh2v4fk2mcg6lx23ys5ij1pwdzzdhhq-python-locust-2.33.2 /gnu/store/qdpzy0rwk28gf6csn8hb71114mb34ig5-python-mechanize-0.4.10 /gnu/store/yg5h4q7ldf7gr2952mjypxv5yfdlvask-python-patch-ng-1.18.1 /gnu/store/d7wg669vaajf12pxajgi68c7xh2iflxj-python-pybktree-1.1 /gnu/store/sgrqv9kb36af2g6c6bcp7z68f46j6jk4-python-pyquery-2.0.1 /gnu/store/7irx8vkb06fw8fck8awyg9izm5ad2i02-python-pyvcf3-1.0.3-0.1fb3789 /gnu/store/xalx3n9r7f3kxwvb9k3538r6hi05361i-python-rstr-3.2.2 /gnu/store/0j9mbcka0l2sa3z6yyx0jn15rsdzkg9j-python-sip-6.10.0 /gnu/store/kzzk57rd01lymp5vdabjdla965pw8yah-python-zeroc-ice-3.7.10.1 /gnu/store/9q0835kwxz1x4fk558ra6zlr3q9xscvj-reprotest-0.7.29 /gnu/store/8l42zb10sksjyr057rqzwc2acghz6v2w-rseqc-3.0.1 /gnu/store/1spa3r6j28dis33y8c5g1iwhjl010s9r-seqmagick-0.8.6-0.dee6ab9 /gnu/store/ff5v4ncfjbbixlaywawh93q1723p2gj1-taxtastic-0.11.1 /gnu/store/pngvj2k03w1c5aj67gzrvh7whhdhnb4a-umi-tools-1.1.6 /gnu/store/gsxb8b5fl101jpsqgac0hwvl5ymnk5mh-veusz-3.6.2 --8<---------------cut here---------------end--------------->8--- Pushed to python-team branch. -- Oleg
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