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Got stuck with wxpython, but here's a few updates tracked locally from
./pre-inst-env guix build --dependents python-setuptools.
We have a big issue with a number of packages in bioinformatics that
are simply not developped anymore. It's a big part of the failing
packages there, but I don't feel comfortable removing them since
there's quite some and that they are undevelopped for 4 years not 10
years.
Nicolas Graves (18):
gnu: python-biom-format: Update to 2.1.16.
gnu: pairadise: Add missing native-inputs.
gnu: python-cleanlab: Update to 2.7.1.
gnu: python-cesium: Move to (gnu packages astronomy).
gnu: python-bx-python: Update to 0.13.0.
gnu: crossmap: Add missing python-pyparsing native-input.
gnu: python-cell2cell: Update to 0.7.4.
gnu: python-ncls: Update to 0.0.68.
gnu: python-nptyping: Ignore failing test.
gnu: python-pegasusio: Update to 0.9.1.
gnu: Add python-colored-traceback.
gnu: Add python-unix-ar.
gnu: pwntools: Update to 4.4.0.
gnu: python-debtcollector: Update to 3.0.0.
gnu: Standardize python-oslo.* package names.
gnu: python-netaddr: Move to (gnu packages python-web).
gnu: python-netaddr: Update to 1.3.0.
gnu: python-aiosmtpd: Update to 1.4.6.
gnu/packages/astronomy.scm | 40 +++++++++++
gnu/packages/bioinformatics.scm | 30 ++++----
gnu/packages/cybersecurity.scm | 16 ++++-
gnu/packages/machine-learning.scm | 4 +-
gnu/packages/mail.scm | 27 ++++---
gnu/packages/openstack.scm | 100 ++++++++++++++------------
gnu/packages/python-check.scm | 2 +
gnu/packages/python-compression.scm | 28 ++++++++
gnu/packages/python-web.scm | 24 ++++++-
gnu/packages/python-xyz.scm | 105 +++++++++++-----------------
10 files changed, 233 insertions(+), 143 deletions(-)
--
2.49.0
Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) Content-Type: text/plain; charset=utf-8 X-Loop: help-debbugs@HIDDEN From: help-debbugs@HIDDEN (GNU bug Tracking System) To: Nicolas Graves <ngraves@HIDDEN> Subject: bug#77246: Acknowledgement ([PATCH python-team 00/18] One more iteration with a few fixes ) Message-ID: <handler.77246.B.17428874986118.ack <at> debbugs.gnu.org> References: <20250325072424.20360-1-ngraves@HIDDEN> X-Gnu-PR-Message: ack 77246 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 77246 <at> debbugs.gnu.org Date: Tue, 25 Mar 2025 07:25:02 +0000 Thank you for filing a new bug report with debbugs.gnu.org. This is an automatically generated reply to let you know your message has been received. Your message is being forwarded to the package maintainers and other interested parties for their attention; they will reply in due course. Your message has been sent to the package maintainer(s): guix-patches@HIDDEN If you wish to submit further information on this problem, please send it to 77246 <at> debbugs.gnu.org. Please do not send mail to help-debbugs@HIDDEN unless you wish to report a problem with the Bug-tracking system. --=20 77246: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D77246 GNU Bug Tracking System Contact help-debbugs@HIDDEN with problems
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Subject: [bug#77246] [PATCH 01/18] gnu: python-biom-format: Update to 2.1.16.
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* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.16.
---
gnu/packages/bioinformatics.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7e0896fd5b..0b45ae08e0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3885,7 +3885,7 @@ (define-public python-bioframe
(define-public python-biom-format
(package
(name "python-biom-format")
- (version "2.1.12")
+ (version "2.1.16")
(source
(origin
(method git-fetch)
@@ -3897,7 +3897,7 @@ (define-public python-biom-format
(file-name (git-file-name name version))
(sha256
(base32
- "06x2d8fv80jp86kd66fm3ragmxrpa2j0lzsbm337ziqjnpsdwc0f"))
+ "1npxjsi7r0w8diq6s37q21cqgrqifl7f483lfn72bn7qrvkvbpyz"))
(modules '((guix build utils)))
;; Delete generated C files.
(snippet
--
2.49.0
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* gnu/packages/bioinformatics.scm (pairadise)[native-inputs]: Add
python-setuptools and python-wheel.
---
gnu/packages/bioinformatics.scm | 1 +
1 file changed, 1 insertion(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0b45ae08e0..5065e40a8b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14424,6 +14424,7 @@ (define-public pairadise
(lambda _ (chdir "pairadise")))
(add-before 'build '2to3
(lambda _ (invoke "2to3" "--write" "--nobackups" "."))))))
+ (native-inputs (list python-setuptools python-wheel))
(inputs (list star))
(propagated-inputs (list python-pysam))
(home-page "https://github.com/Xinglab/PAIRADISE")
--
2.49.0
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* gnu/packages/machine-learning.scm (python-cleanlab): Update to 2.7.1.
---
gnu/packages/machine-learning.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index f762e0dc3c..490827b038 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -2315,7 +2315,7 @@ (define-public python-scikit-rebate
(define-public python-cleanlab
(package
(name "python-cleanlab")
- (version "2.7.0")
+ (version "2.7.1")
;; The version on pypi does not come with tests.
(source (origin
(method git-fetch)
@@ -2325,7 +2325,7 @@ (define-public python-cleanlab
(file-name (git-file-name name version))
(sha256
(base32
- "0f8v5246nzy22r7zswv9vbpxc7wxaqjwry9iq0fqjp2ffch88h6j"))))
+ "073w45azq496x4bhrh8mdywcrg3gk33n13w1pqh1kiykw826ld9b"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.49.0
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Subject: [bug#77246] [PATCH 04/18] gnu: python-cesium: Move to (gnu packages astronomy).
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The dependencies of this package are already in (gnu packages astronomy).
* gnu/packages/python-xyz.scm (python-cesium): Move from here…
* gnu/packages/astronomy.scm (python-cesium): …to here.
---
gnu/packages/astronomy.scm | 40 ++++++++++++++++++++++++++++++++++++
gnu/packages/python-xyz.scm | 41 -------------------------------------
2 files changed, 40 insertions(+), 41 deletions(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 621cabe3d8..2552aaa42a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2449,6 +2449,46 @@ (define-public python-ci-watson
"This package contains a helper functionality to test ROMAN and JWST.")
(license license:bsd-3)))
+(define-public python-cesium
+ (package
+ (name "python-cesium")
+ (version "0.12.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "cesium" version))
+ (sha256
+ (base32
+ "0jr0ycqz9ns6mcskm4sxx92k40fj3v0x9knjaw5ac9f3mpqxsfbv"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; The installed test files contain the /gnu/store location, not the
+ ;; location of the discovered test files from the build directory.
+ ;; The test framework doesn't like this. The easiest way around
+ ;; this mismatch is to jump to the output directory.
+ (add-before 'check 'check-chdir
+ (lambda _ (chdir #$output))))))
+ (propagated-inputs
+ (list python-click ;XXX required by python-dask
+ python-cloudpickle
+ python-dask
+ python-gatspy
+ python-joblib
+ python-numpy
+ python-pandas
+ python-scikit-learn
+ python-scipy
+ python-toolz))
+ (native-inputs (list python-cython python-pytest python-setuptools-scm
+ python-setuptools python-wheel))
+ (home-page "https://pypi.org/project/cesium/")
+ (synopsis "Library for time-series feature extraction and processing")
+ (description
+ "Cesium is a library for time-series feature extraction and processing.")
+ (license license:bsd-3)))
+
(define-public python-cmyt
(package
(name "python-cmyt")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 8a6453e592..1acc381d9f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -185,7 +185,6 @@ (define-module (gnu packages python-xyz)
#:use-module (gnu packages adns)
#:use-module (gnu packages aidc)
#:use-module (gnu packages algebra)
- #:use-module (gnu packages astronomy)
#:use-module (gnu packages attr)
#:use-module (gnu packages audio)
#:use-module (gnu packages autotools)
@@ -21407,46 +21406,6 @@ (define-public python-celery
synchronously (wait until ready).")
(license license:bsd-3)))
-(define-public python-cesium
- (package
- (name "python-cesium")
- (version "0.12.1")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "cesium" version))
- (sha256
- (base32
- "0jr0ycqz9ns6mcskm4sxx92k40fj3v0x9knjaw5ac9f3mpqxsfbv"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:phases
- #~(modify-phases %standard-phases
- ;; The installed test files contain the /gnu/store location, not the
- ;; location of the discovered test files from the build directory.
- ;; The test framework doesn't like this. The easiest way around
- ;; this mismatch is to jump to the output directory.
- (add-before 'check 'check-chdir
- (lambda _ (chdir #$output))))))
- (propagated-inputs
- (list python-click ;XXX required by python-dask
- python-cloudpickle
- python-dask
- python-gatspy
- python-joblib
- python-numpy
- python-pandas
- python-scikit-learn
- python-scipy
- python-toolz))
- (native-inputs (list python-cython python-pytest python-setuptools-scm
- python-setuptools python-wheel))
- (home-page "https://pypi.org/project/cesium/")
- (synopsis "Library for time-series feature extraction and processing")
- (description
- "Cesium is a library for time-series feature extraction and processing.")
- (license license:bsd-3)))
-
(define-public python-translitcodec
(package
(name "python-translitcodec")
--
2.49.0
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* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.13.0.
---
gnu/packages/bioinformatics.scm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5065e40a8b..d19c40cf40 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5337,16 +5337,16 @@ (define-public bwa-meth
(define-public python-bx-python
(package
(name "python-bx-python")
- (version "0.9.0")
+ (version "0.13.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/bxlab/bx-python")
- (commit "4f4a48d3f227ae390c1b22072867ba86e347bdef")))
+ (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "1c914rw8phiw7zwzngz9i9hdciz5lq53drwdbpl2bd2sf5bj2biy"))))
+ "13318a3lydyg8fxawdb7anrny9a1j1sc1q4nd6pjg8ki5zr9r713"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.49.0
X-Loop: help-debbugs@HIDDEN
Subject: [bug#77246] [PATCH 06/18] gnu: crossmap: Add missing python-pyparsing native-input.
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* gnu/packages/bioinformatics.scm (python-pyparsing)[native-inputs]:
Add python-pyparsing.
---
gnu/packages/bioinformatics.scm | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d19c40cf40..c6fc760ec0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5994,7 +5994,7 @@ (define-public crossmap
(list python-bx-python python-numpy python-pybigwig python-pysam
zlib))
(native-inputs
- (list python-cython python-nose))
+ (list python-cython python-nose python-pyparsing))
(home-page "https://crossmap.sourceforge.net/")
(synopsis "Convert genome coordinates between assemblies")
(description
--
2.49.0
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Subject: [bug#77246] [PATCH 07/18] gnu: python-cell2cell: Update to 0.7.4.
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* gnu/packages/bioinformatics.scm (python-cell2cell): Update to 0.7.4.
[source]{origin}: Relax requirements in snippet.
---
gnu/packages/bioinformatics.scm | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c6fc760ec0..172902541a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2406,7 +2406,7 @@ (define-public python-bulkvis
(define-public python-cell2cell
(package
(name "python-cell2cell")
- (version "0.6.8")
+ (version "0.7.4")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -2415,7 +2415,7 @@ (define-public python-cell2cell
(file-name (git-file-name name version))
(sha256
(base32
- "1hwww0rcv8sc4k312n4d0jhbyix1jjqgv5djg25bw8127q5iym3s"))
+ "02cqc5rm0qkm0np1k7bim1w7f5qjnwf1jcm5albd9cpvfs4bwgdr"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -2431,6 +2431,8 @@ (define-public python-cell2cell
(("'statannotations',") "")
;; We provide version 1.0.4, which should be fine.
(("'gseapy == 1.0.3'") "'gseapy'")
+ ;; We provide version 0.9.0, which should be fine.
+ (("'tensorly == 0.8.1'") "'tensorly'")
;; Using matplotlib 3.5.2 leads to this bug:
;; https://github.com/earmingol/cell2cell/issues/19 but we
;; can't package a different minor version of matplotlib
--
2.49.0
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* gnu/packages/python-xyz.scm (python-ncls): Update to 0.0.68.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-cython, python-pandas, python-pytest,
python-setuptools, python-wheel.
---
gnu/packages/python-xyz.scm | 16 +++++++++++++---
1 file changed, 13 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1acc381d9f..26b4a76670 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3895,14 +3895,24 @@ (define-public python-ncclient
(define-public python-ncls
(package
(name "python-ncls")
- (version "0.0.65")
+ (version "0.0.68")
(source (origin
(method url-fetch)
(uri (pypi-uri "ncls" version))
(sha256
(base32
- "1wx06xqknd2r98w8z93f47g5dpxzn92kamhj8vkq0nj569hf7cg1"))))
- (build-system python-build-system)
+ "14xsnzr34xa4rwfcdjry9aqjs8i03s9fzy6jgrwj3fr3n6msbal1"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; Those tests fail with warnings (not errors) for the Numpy update.
+ ;; Remove it at next python-team iteration.
+ (list #:test-flags ''("--ignore=examples/test_all_overlaps_both.py"
+ "--ignore=examples/test_find_overlap_list.py")))
+ (native-inputs (list python-cython
+ python-pandas
+ python-pytest
+ python-setuptools
+ python-wheel))
(propagated-inputs (list python-numpy))
(home-page "https://github.com/endrebak/ncls")
(synopsis "Nested containment list data structure")
--
2.49.0
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* gnu/packages/python-check.scm (python-nptyping)[arguments]
{test-flags}: Ignore failing test.
---
gnu/packages/python-check.scm | 2 ++
1 file changed, 2 insertions(+)
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 55dd88ada3..265581a17f 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -2636,6 +2636,8 @@ (define-public python-nptyping
(list
#:test-flags
#~(list
+ ;; This one started failing with the last update of Numpy.
+ "--ignore=tests/test_beartype.py"
;; Multiple failures due to undefined names (typing package must be
;; too outdated, or perhaps they use a newer pandas).
"--ignore=tests/test_mypy.py"
--
2.49.0
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* gnu/packages/python-xyz.scm (python-colored-traceback): New variable.
---
gnu/packages/python-xyz.scm | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 26b4a76670..5c849ca6a2 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1595,6 +1595,34 @@ (define-public python-colored
names for 256 color terminal setups.")
(license license:expat)))
+(define-public python-colored-traceback
+ ;; No tags in upstream repository.
+ (let ((commit "98e6dea7111f7681db823c518f18026374a832b9")
+ (revision "0"))
+ (package
+ (name "python-colored-traceback")
+ (version (git-version "0.4.2" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/staticshock/colored-traceback.py")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "19d5mpwk7398b8fjh6abnr96wz70vf5vb4p207r8sny748rwx451"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; Tests are incompatible with current python version.
+ (list #:tests? #f))
+ (propagated-inputs (list python-colorama python-pygments))
+ (native-inputs (list python-setuptools python-wheel))
+ (home-page "https://github.com/staticshock/colored-traceback.py")
+ (synopsis "Automatically color uncaught exception tracebacks")
+ (description "This package provides python utilities to automatically
+color uncaught exception tracebacks.")
+ (license license:isc))))
+
(define-public python-colorful
(package
(name "python-colorful")
--
2.49.0
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* gnu/packages/python-compression.scm (python-unix-ar): New variable.
---
gnu/packages/python-compression.scm | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)
diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
index 5b994d408f..6892b9253c 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -11,6 +11,7 @@
;;; Copyright © 2024 TakeV <takev@HIDDEN>
;;; Copyright © 2023 Ivan Vilata i Balaguer <ivan@HIDDEN>
;;; Copyright © 2024 Maxim Cournoyer <maxim.cournoyer@HIDDEN>
+;;; Copyright © 2025 Nicolas Graves <ngraves@HIDDEN>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -764,6 +765,33 @@ (define-public bitshuffle-for-snappy
(inputs '())
(native-inputs '())))
+(define-public python-unix-ar
+ (package
+ (name "python-unix-ar")
+ (version "0.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "unix_ar" version))
+ (sha256
+ (base32 "0kicwxsh28x8r34a7cgzv2i65gsd4qjw2vf29pwq4fpsf3n2i4xz"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; These tests have timestamp-related issues.
+ (list #:test-flags
+ #~(list "-m" "unittest" "-k" "not test_add and not test_addfile")
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (apply invoke "python" test-flags))))))
+ (native-inputs (list python-pytest python-setuptools python-wheel))
+ (home-page "https://github.com/getninjas/unix_ar")
+ (synopsis "AR file handling in Python")
+ (description "This package provides utilities to handle AR files in
+Python.")
+ (license license:bsd-3)))
+
(define-public python-zipp
(package
(name "python-zipp")
--
2.49.0
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* gnu/packages/cybersecurity.scm (pwntools): Update to 4.4.0.
---
gnu/packages/cybersecurity.scm | 16 +++++++++++++---
1 file changed, 13 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/cybersecurity.scm b/gnu/packages/cybersecurity.scm
index cb03cbd5aa..c66740b744 100644
--- a/gnu/packages/cybersecurity.scm
+++ b/gnu/packages/cybersecurity.scm
@@ -3,6 +3,7 @@
;;; Copyright © 2020, 2021 Tobias Geerinckx-Rice <me@HIDDEN>
;;; Copyright © 2021 c4droid <c4droid@HIDDEN>
;;; Copyright © 2021 Raghav Gururajan <rg@HIDDEN>
+;;; Copyright © 2025 Nicolas Graves <ngraves@HIDDEN>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -30,9 +31,11 @@ (define-module (gnu packages cybersecurity)
#:use-module (gnu packages engineering)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
- #:use-module (gnu packages python-xyz)
+ #:use-module (gnu packages python-build)
+ #:use-module (gnu packages python-compression)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
+ #:use-module (gnu packages python-xyz)
#:use-module (gnu packages time)
#:use-module (gnu packages bioinformatics) ;python-intervaltree
#:use-module (gnu packages emulators))
@@ -123,24 +126,26 @@ (define-public ropgadget
(define-public pwntools
(package
(name "pwntools")
- (version "4.4.0")
+ (version "4.15.0b1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pwntools" version))
(sha256
(base32
- "1qw7j0wwm1878aia08gyw5xljjr26qsbp45w65n4qff672sha5n5"))))
+ "091fsk9rvbjkcsp8mmww0ka26dvznmj4pbqwaiygcw90g3v94zgd"))))
(build-system python-build-system)
(arguments
'(#:tests? #f)) ;XXX: needs a specific version of unicorn
(propagated-inputs
(list capstone
+ python-colored-traceback
python-dateutil
python-intervaltree
python-mako
python-packaging
python-paramiko
+ python-pathlib2
python-psutil
python-pyelftools
python-pygments
@@ -148,9 +153,14 @@ (define-public pwntools
python-pysocks
python-requests
ropgadget
+ python-rpyc
python-six
python-sortedcontainers
+ python-unix-ar
+ python-zstandard
unicorn))
+ (native-inputs
+ (list python-setuptools python-toml python-wheel))
(home-page "https://github.com/Gallopsled/pwntools")
(synopsis
"Capture-the-flag (CTF) framework and exploit development library")
--
2.49.0
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* gnu/packages/openstack.scm (python-debtcollector): Update to 3.0.0.
[source]: Patch {origin} to remove unwanted native-inputs.
[build-system]: Switch to pyproject-build-system.
[propagated-inputs]: Remove python-six.
[native-inputs]: Add python-doc8, python-fixtures,
python-openstackdocstheme, python-reno, python-setuptools,
python-stestr and python-wheel. Remove python-subunit and
python-testrepository.
---
gnu/packages/openstack.scm | 24 +++++++++++++++++-------
1 file changed, 17 insertions(+), 7 deletions(-)
diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index ac283bd019..80fad32068 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -115,20 +115,30 @@ (define-public python-cliff
(define-public python-debtcollector
(package
(name "python-debtcollector")
- (version "1.19.0")
+ (version "3.0.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "debtcollector" version))
(sha256
- (base32
- "06c7vyn184y9f0lsrwaz13aq63hdz5fjrd191b8nifx6acsni42f"))))
- (build-system python-build-system)
+ (base32 "0vzarkvjclci98d8lvkix6qj59f7rxp1qg2x6q6is7qfbg91g29a"))
+ (modules '((guix build utils)))
+ (snippet #~(begin
+ (substitute* "test-requirements.txt"
+ (("^(coverage|hacking|pre-commit).*")
+ ""))))))
+ (build-system pyproject-build-system)
(propagated-inputs
- (list python-pbr python-six python-wrapt))
+ (list python-pbr python-wrapt))
(native-inputs
- (list ;; Tests.
- python-subunit python-testrepository python-testtools))
+ (list python-doc8
+ python-fixtures
+ python-openstackdocstheme
+ python-reno
+ python-setuptools
+ python-stestr
+ python-testtools
+ python-wheel))
(home-page "https://www.openstack.org/")
(synopsis
"Find deprecated patterns and strategies in Python code")
--
2.49.0
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* gnu/packages/openstack.scm (python-oslo.concurrency,
python-oslo.config, python-oslo.context, python-oslo.i18n,
python-oslo.log, python-oslo.serialization, python-oslo.utils): Rename
packages.
---
gnu/packages/openstack.scm | 76 +++++++++++++++++++-------------------
1 file changed, 38 insertions(+), 38 deletions(-)
diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index 80fad32068..e78a1f614f 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -396,11 +396,11 @@ (define-public python-tempest
python-fixtures
python-jsonschema
python-netaddr
- python-oslo.concurrency
- python-oslo.config
- python-oslo.log
- python-oslo.serialization
- python-oslo.utils
+ python-oslo-concurrency
+ python-oslo-config
+ python-oslo-log
+ python-oslo-serialization
+ python-oslo-utils
python-paramiko
python-prettytable
python-pyyaml
@@ -447,7 +447,7 @@ (define-public python-tempest-lib
python-httplib2
python-iso8601
python-jsonschema
- python-oslo.log
+ python-oslo-log
python-paramiko
python-six))
(native-inputs
@@ -465,9 +465,9 @@ (define-public python-tempest-lib
;;; Packages from the Oslo library
;;;
-(define-public python-oslo.concurrency
+(define-public python-oslo-concurrency
(package
- (name "python-oslo.concurrency")
+ (name "python-oslo-concurrency")
(version "5.0.0")
(source (origin
(method url-fetch)
@@ -500,8 +500,8 @@ (define-public python-oslo.concurrency
python-fixtures
python-stestr
python-eventlet))
- (propagated-inputs (list python-fasteners python-oslo.config
- python-oslo.i18n python-oslo.utils))
+ (propagated-inputs (list python-fasteners python-oslo-config
+ python-oslo-i18n python-oslo-utils))
(home-page "https://docs.openstack.org/oslo.concurrency/latest/")
(synopsis "Oslo Concurrency library")
(description "The Oslo Concurrency Library provides utilities for safely
@@ -509,9 +509,9 @@ (define-public python-oslo.concurrency
for running external processes.")
(license asl2.0)))
-(define-public python-oslo.config
+(define-public python-oslo-config
(package
- (name "python-oslo.config")
+ (name "python-oslo-config")
(version "8.7.1")
(source
(origin
@@ -525,7 +525,7 @@ (define-public python-oslo.config
(propagated-inputs
(list python-debtcollector
python-netaddr
- python-oslo.i18n
+ python-oslo-i18n
python-rfc3986
python-requests
python-stevedore
@@ -537,9 +537,9 @@ (define-public python-oslo.config
.ini style configuration files.")
(license asl2.0)))
-(define-public python-oslo.context
+(define-public python-oslo-context
(package
- (name "python-oslo.context")
+ (name "python-oslo-context")
(version "5.0.0")
(source
(origin
@@ -576,9 +576,9 @@ (define-public python-oslo.context
pipeline and used by various modules such as logging.")
(license asl2.0)))
-(define-public python-oslo.i18n
+(define-public python-oslo-i18n
(package
- (name "python-oslo.i18n")
+ (name "python-oslo-i18n")
(version "3.20.0")
(source
(origin
@@ -602,9 +602,9 @@ (define-public python-oslo.i18n
in an application or library.")
(license asl2.0)))
-(define-public python-oslo.log
+(define-public python-oslo-log
(package
- (name "python-oslo.log")
+ (name "python-oslo-log")
(version "5.0.0")
(source
(origin
@@ -622,11 +622,11 @@ (define-public python-oslo.log
(propagated-inputs
(list python-dateutil
python-debtcollector
- python-oslo.config
- python-oslo.context
- python-oslo.i18n
- python-oslo.utils
- python-oslo.serialization
+ python-oslo-config
+ python-oslo-context
+ python-oslo-i18n
+ python-oslo-utils
+ python-oslo-serialization
python-pyinotify))
(native-inputs
(list python-fixtures python-oslotest python-stestr python-testtools
@@ -639,9 +639,9 @@ (define-public python-oslo.log
handlers and support for context specific logging (like resource id’s etc).")
(license asl2.0)))
-(define-public python-oslo.serialization
+(define-public python-oslo-serialization
(package
- (name "python-oslo.serialization")
+ (name "python-oslo-serialization")
(version "4.2.0")
(source
(origin
@@ -657,10 +657,10 @@ (define-public python-oslo.serialization
(lambda* (#:key tests? #:allow-other-keys)
(when tests? (invoke "stestr" "run")))))))
(propagated-inputs
- (list python-msgpack python-oslo.utils python-pbr python-pytz))
+ (list python-msgpack python-oslo-utils python-pbr python-pytz))
(native-inputs
;; For tests.
- (list python-netaddr python-oslo.i18n python-oslotest python-stestr))
+ (list python-netaddr python-oslo-i18n python-oslotest python-stestr))
(home-page "https://launchpad.net/oslo")
(synopsis "Oslo serialization library")
(description
@@ -767,9 +767,9 @@ (define-public python-oslotest
for debugging, and better support for mocking results.")
(license asl2.0)))
-(define-public python-oslo.utils
+(define-public python-oslo-utils
(package
- (name "python-oslo.utils")
+ (name "python-oslo-utils")
(version "4.12.0")
(source
(origin
@@ -786,7 +786,7 @@ (define-public python-oslo.utils
(when tests? (invoke "stestr" "run")))))))
(propagated-inputs
(list python-debtcollector
- python-oslo.i18n
+ python-oslo-i18n
python-iso8601
python-netaddr
python-netifaces
@@ -853,8 +853,8 @@ (define-public python-keystoneauth1
python-hacking
python-lxml
python-oauthlib
- python-oslo.config
- python-oslo.utils
+ python-oslo-config
+ python-oslo-utils
python-oslotest
python-pbr
python-pyyaml
@@ -917,10 +917,10 @@ (define-public python-keystoneclient
python-iso8601
python-keystoneauth1
python-netaddr
- python-oslo.config
- python-oslo.i18n
- python-oslo.serialization
- python-oslo.utils
+ python-oslo-config
+ python-oslo-i18n
+ python-oslo-serialization
+ python-oslo-utils
python-prettytable
python-requests
python-six
@@ -1081,7 +1081,7 @@ (define-public python-openstacksdk
python-statsd
python-stestr
python-testscenarios
- python-oslo.config
+ python-oslo-config
python-oslotest))
(propagated-inputs (list python-appdirs
python-cryptography
--
2.49.0
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* gnu/packages/python-xyz.scm (python-netaddr): Move from here…
* gnu/packages/python-web.scm (python-netaddr): …to here.
---
gnu/packages/python-web.scm | 20 ++++++++++++++++++++
gnu/packages/python-xyz.scm | 20 --------------------
2 files changed, 20 insertions(+), 20 deletions(-)
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index af37cb5bef..4d4a6d9422 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -4362,6 +4362,26 @@ (define-public python-ndg-httpsclient
(home-page "https://github.com/cedadev/ndg_httpsclient/")
(license license:bsd-3)))
+(define-public python-netaddr
+ (package
+ (name "python-netaddr")
+ (version "0.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "netaddr" version))
+ (sha256
+ (base32
+ "0hx2npi0wnhwlcybilgwlddw6qffx1mb7a3sj4p9s7bvl33mgk6n"))))
+ (build-system python-build-system)
+ (arguments `(#:tests? #f)) ;; No tests.
+ (home-page "https://github.com/drkjam/netaddr/")
+ (synopsis "Pythonic manipulation of network addresses")
+ (description
+ "A Python library for representing and manipulating IPv4, IPv6, CIDR, EUI
+and MAC network addresses.")
+ (license license:bsd-3)))
+
(define-public python-nh3
(package
(name "python-nh3")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 5c849ca6a2..4ff34b0551 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -17221,26 +17221,6 @@ (define-public python-msgpack-transitional
((".fromstring\\(") ".frombytes("))
#t))))))))
-(define-public python-netaddr
- (package
- (name "python-netaddr")
- (version "0.8.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "netaddr" version))
- (sha256
- (base32
- "0hx2npi0wnhwlcybilgwlddw6qffx1mb7a3sj4p9s7bvl33mgk6n"))))
- (build-system python-build-system)
- (arguments `(#:tests? #f)) ;; No tests.
- (home-page "https://github.com/drkjam/netaddr/")
- (synopsis "Pythonic manipulation of network addresses")
- (description
- "A Python library for representing and manipulating IPv4, IPv6, CIDR, EUI
-and MAC network addresses.")
- (license license:bsd-3)))
-
(define-public python-openstep-plist
(package
(name "python-openstep-plist")
--
2.49.0
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* gnu/packages/python-web.scm (python-netaddr): Update to 1.3.0.
[build-system]: Switch to pyproject.
[native-inputs]: Add python-poetry-core, python-pytest,
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 4d4a6d9422..1638ea0a45 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -54,7 +54,7 @@
;;; Copyright © 2022 Peter Polidoro <peter@HIDDEN>
;;; Copyright © 2022 Antero Mejr <antero@HIDDEN>
;;; Copyright © 2022 Luis Henrique Gomes Higino <luishenriquegh2701@HIDDEN>
-;;; Copyright © 2022 Nicolas Graves <ngraves@HIDDEN>
+;;; Copyright © 2022, 2025 Nicolas Graves <ngraves@HIDDEN>
;;; Copyright © 2022 Tomasz Jeneralczyk <tj@HIDDEN>
;;; Copyright © 2022 msimonin <matthieu.simonin@HIDDEN>
;;; Copyright © 2022 Michael Rohleder <mike@HIDDEN>
@@ -4365,18 +4365,20 @@ (define-public python-ndg-httpsclient
(define-public python-netaddr
(package
(name "python-netaddr")
- (version "0.8.0")
+ (version "1.3.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "netaddr" version))
(sha256
- (base32
- "0hx2npi0wnhwlcybilgwlddw6qffx1mb7a3sj4p9s7bvl33mgk6n"))))
- (build-system python-build-system)
- (arguments `(#:tests? #f)) ;; No tests.
- (home-page "https://github.com/drkjam/netaddr/")
- (synopsis "Pythonic manipulation of network addresses")
+ (base32 "12p4ysgawhgkka0sz1dkwgwc2za80dxdp9wvfxivfldmjnc3sg2w"))))
+ (build-system pyproject-build-system)
+ (native-inputs (list python-poetry-core
+ python-pytest
+ python-setuptools
+ python-wheel))
+ (home-page "https://netaddr.readthedocs.io")
+ (synopsis "Pythonic manipulation of network addresses")
(description
"A Python library for representing and manipulating IPv4, IPv6, CIDR, EUI
and MAC network addresses.")
--
2.49.0
X-Loop: help-debbugs@HIDDEN
Subject: [bug#77246] [PATCH 18/18] gnu: python-aiosmtpd: Update to 1.4.6.
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* gnu/packages/mail.scm (python-aiosmtpd): Update to 1.4.6.
[build-system]: Switch to pyproject.
[arguments]{phases}: Delete it.
{test-flags}: Switch a QA test.
[native-inputs]: Remove python-flufl-testing, python-node. Add
python-pytest, python-pytest-asyncio, python-pytest-cov,
python-pytest-mock, python-setuptools, python-wheel.
---
gnu/packages/mail.scm | 27 ++++++++++++---------------
1 file changed, 12 insertions(+), 15 deletions(-)
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 8668cda211..23ecf8660b 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -4706,30 +4706,27 @@ (define-public python-authheaders
(define-public python-aiosmtpd
(package
(name "python-aiosmtpd")
- (version "1.2.2")
+ (version "1.4.6")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/aio-libs/aiosmtpd")
- (commit version)))
+ (commit (string-append "v" version))))
(sha256
- (base32 "0083d6nf75xv8nq1il6jabz36v6c452svy4p402csxwwih5pw6sk"))
+ (base32 "0b5y94zc8pq75sjwsifblzgjnliyclkwypi68b2zffrxcdnz27r2"))
(file-name (git-file-name name version))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
- '(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'delete-failing-tests
- (lambda _
- ;; This test uses an expired certificate.
- (delete-file "aiosmtpd/tests/test_smtps.py")
- #t))
- (replace 'check
- (lambda _
- (invoke "python" "-m" "nose2" "-v"))))))
+ ;; This QA test requires git.
+ (list #:test-flags ''("-k" "not test_ge_master")))
(native-inputs
- (list python-flufl-testing python-nose2))
+ (list python-pytest
+ python-pytest-asyncio
+ python-pytest-cov
+ python-pytest-mock
+ python-setuptools
+ python-wheel))
(propagated-inputs
(list python-atpublic))
(home-page "https://aiosmtpd.readthedocs.io/")
--
2.49.0
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Subject: [bug#77246] [PATCH 10/18] gnu: python-pegasusio: Update to 0.9.1.
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* gnu/packages/bioinformatics.scm (python-pegasusio): Update to 0.9.1.
[propagated-inputs]: Add python-cython, python-setuptools. Remove
python-importlib-metadata.
[native-inputs]: Styling from guix style.
---
gnu/packages/bioinformatics.scm | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 172902541a..0eac49a2a1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3323,30 +3323,31 @@ (define-public python-peaks2utr
(define-public python-pegasusio
(package
(name "python-pegasusio")
- (version "0.7.1")
+ (version "0.9.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "pegasusio" version))
(sha256
(base32
- "0gqygspdy398vjymdy6756jmk99s7fhwav9rivdx59kpqjcdxaz9"))))
+ "1vxi6z7jlznp7sgzlbjsl1dzf1h7ypinllnls0lb2773a8vavg5x"))))
(build-system pyproject-build-system)
;; There are no tests.
(arguments (list #:tests? #false))
(propagated-inputs
(list python-anndata
+ python-cython
python-docopt
python-h5py
- python-importlib-metadata
python-loompy
python-natsort
python-numpy
python-pandas
python-pillow
python-scipy
+ python-setuptools
python-zarr))
- (native-inputs (list python-cython python-setuptools-scm
- python-setuptools python-wheel))
+ (native-inputs (list python-cython python-setuptools python-setuptools-scm
+ python-wheel))
(home-page "https://github.com/lilab-bcb/pegasusio")
(synopsis "Read or write single-cell genomics data")
(description
--
2.49.0
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997 nCipher Corporation Ltd,
1994-97 Ian Jackson.