Ludovic Courtès <ludo@HIDDEN>
to control <at> debbugs.gnu.org.
Full text available.Received: (at 78443) by debbugs.gnu.org; 7 Jun 2025 15:02:05 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sat Jun 07 11:02:05 2025 Received: from localhost ([127.0.0.1]:49287 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1uNv3d-0000a2-4D for submit <at> debbugs.gnu.org; Sat, 07 Jun 2025 11:02:05 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:60454) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from <andreas@HIDDEN>) id 1uNv3a-0000ZS-28 for 78443 <at> debbugs.gnu.org; Sat, 07 Jun 2025 11:02:02 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id A66A5255; Sat, 7 Jun 2025 17:01:55 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id bLdcznd9Jd49; Sat, 7 Jun 2025 17:01:55 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id E2EB362; Sat, 7 Jun 2025 17:01:54 +0200 (CEST) Date: Sat, 7 Jun 2025 17:01:53 +0200 From: Andreas Enge <andreas@HIDDEN> To: Wiktor =?utf-8?Q?=C5=BBelazny?= <wz@HIDDEN> Subject: Re: [PATCH v2] gnu: python-pulp: Update to 3.1.1. Message-ID: <aERUYYT23eEdceBP@jurong> References: <20250530173428.3882-1-wz@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20250530173428.3882-1-wz@HIDDEN> X-Rspamd-Server: hera X-Rspamd-Queue-Id: A66A5255 X-Spamd-Result: default: False [-5.56 / 15.00]; BAYES_HAM(-3.00)[99.98%]; NEURAL_HAM(-2.96)[-0.986]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; ARC_NA(0.00)[]; TO_DN_SOME(0.00)[]; FREEMAIL_ENVRCPT(0.00)[gmail.com]; RCVD_VIA_SMTP_AUTH(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; FROM_HAS_DN(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; FREEMAIL_CC(0.00)[debbugs.gnu.org,gmail.com] X-Rspamd-Action: no action X-Spamd-Bar: ----- X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 78443 Cc: 78443 <at> debbugs.gnu.org, Sharlatan Hellseher <sharlatanus@HIDDEN> X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) Hello, your v2 patch also modifies snakemake, which needs to be mentioned in the commit message. Also, instead of updating python-pulp, it rather adds a second version. Would it be possible to update snakemake at the same time? (Actually I just see there are lots of different snakemake packages, one for each major version; are all of these really needed? It would be nice if this could be tidied up, possibly by removing outdated dependencies; not necessarily in this patch series, of course.) Andreas
guix-patches@HIDDEN:bug#78443; Package guix-patches.
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From: =?UTF-8?q?Wiktor=20=C5=BBelazny?= <wz@HIDDEN>
To: 78443 <at> debbugs.gnu.org
Subject: [PATCH v2] gnu: python-pulp: Update to 3.1.1.
Date: Fri, 30 May 2025 19:34:28 +0200
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* gnu/packages/python-xyz.scm (python-pulp-2.4): Copy from python-pulp.
* gnu/packages/python-science.scm (snakemake): Use python-pulp-2.4.
* gnu/packages/python-science.scm (snakemake-{5,6,7}): Use python-pulp-2.4.
* gnu/packages/patches/python-pulp-exclude-solver-binaries.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/python-xyz.scm (python-pulp): Update to 3.1.1.
[source]: Update the uri capitalization.
[source]: Add a snippet for skipping a failing test.
[source]: Apply the new patch.
[build-system]: Change to pyproject-build-system.
[native-inputs]: Add cbc, glpk, highs, python-setuptools, and python-wheel.
[propagated-inputs]: Remove python-amply.
[agruments]<#:phases>: Add a phase to remove solver binaries.
[agruments]<#:phases>: Test using pulptest.
[synopsis]: Change according to About in the code repository.
[description]: Extend according to README.rst in the code repository.
Change-Id: I41a7ea4066302d1195913815eb030c45dec9014d
---
gnu/local.mk | 1 +
.../python-pulp-exclude-solver-binaries.patch | 36 ++++++++++++++++
gnu/packages/python-science.scm | 8 ++--
gnu/packages/python-xyz.scm | 42 +++++++++++++++++++
4 files changed, 83 insertions(+), 4 deletions(-)
create mode 100644 gnu/packages/patches/python-pulp-exclude-solver-binaries.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index f534768c2de..424a8d92f1d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -2028,6 +2028,7 @@ dist_patch_DATA = \
%D%/packages/patches/python-matplotlib-fix-legend-loc-best-test.patch \
%D%/packages/patches/python-random2-getrandbits-test.patch \
%D%/packages/patches/python-pillow-use-zlib-1.3.patch \
+ %D%/packages/patches/python-pulp-exclude-solver-binaries.patch \
%D%/packages/patches/python-pydocstyle-add-support-for-pep701.patch \
%D%/packages/patches/python-pyreadstat-link-libiconv.patch \
%D%/packages/patches/python-sip-include-dirs.patch \
diff --git a/gnu/packages/patches/python-pulp-exclude-solver-binaries.patch b/gnu/packages/patches/python-pulp-exclude-solver-binaries.patch
new file mode 100644
index 00000000000..57e9a1421b0
--- /dev/null
+++ b/gnu/packages/patches/python-pulp-exclude-solver-binaries.patch
@@ -0,0 +1,36 @@
+This patch excludes solver binary executables that the project uses for
+testing. In the package definition, solvers are provided as native inputs,
+instead.
+
+This is an original patch. It was not submitted upstream.
+
+diff --git a/pyproject.toml b/pyproject.toml
+index 82f9d48..0925858 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -61,26 +61,11 @@ dev = [
+ [tool.setuptools]
+ packages = [
+ "pulp",
+- "pulp.solverdir",
+- "pulp.solverdir.cbc.linux.i32",
+- "pulp.solverdir.cbc.linux.i64",
+- "pulp.solverdir.cbc.linux.arm64",
+- "pulp.solverdir.cbc.win.i32",
+- "pulp.solverdir.cbc.win.i64",
+- "pulp.solverdir.cbc.osx.i64",
+ "pulp.apis",
+ "pulp.tests"]
+ # This is a workaround for https://github.com/astral-sh/uv/issues/9513
+ license-files = []
+
+-[tool.setuptools.package-data]
+-"pulp.solverdir.cbc.linux.i32"= ["*", "*.*"]
+-"pulp.solverdir.cbc.linux.i64"= ["*", "*.*"]
+-"pulp.solverdir.cbc.linux.arm64"= ["*", "*.*"]
+-"pulp.solverdir.cbc.win.i32"= ["*", "*.*"]
+-"pulp.solverdir.cbc.win.i64"= ["*", "*.*"]
+-"pulp.solverdir.cbc.osx.i64"= ["*", "*.*"]
+-
+ [project.scripts]
+ pulptest = "pulp.tests.run_tests:pulpTestAll"
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 376ae67570c..fdfa88c56c7 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -4976,7 +4976,7 @@ (define-public snakemake
python-nbformat
python-packaging
python-psutil
- python-pulp
+ python-pulp-2.4 ;https://github.com/snakemake/snakemake/issues/2607
python-pyyaml
python-requests
python-reretry
@@ -5068,7 +5068,7 @@ (define-public snakemake-5
python-nbformat
python-networkx
python-psutil
- python-pulp
+ python-pulp-2.4 ;https://github.com/snakemake/snakemake/issues/2607
python-pyyaml
python-ratelimiter
python-requests
@@ -5155,7 +5155,7 @@ (define-public snakemake-6
python-nbformat
python-networkx
python-psutil
- python-pulp
+ python-pulp-2.4 ;https://github.com/snakemake/snakemake/issues/2607
python-pyyaml
python-py-tes
python-ratelimiter
@@ -5253,7 +5253,7 @@ (define-public snakemake-7
python-nbformat
python-networkx
python-psutil
- python-pulp
+ python-pulp-2.4 ;https://github.com/snakemake/snakemake/issues/2607
python-pyyaml
python-py-tes
python-requests
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 0058c665e3d..090b534b368 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15041,6 +15041,48 @@ (define-public python-amply
(license license:epl1.0)))
(define-public python-pulp
+ (package
+ (name "python-pulp")
+ (version "3.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pulp" version))
+ ;; https://github.com/coin-or/pulp/issues/832
+ (modules '((guix build utils)))
+ (snippet '(substitute* "pulp/tests/test_pulp.py"
+ ((" def test_time_limit_no_solution")
+ " @unittest.skip
+ def test_time_limit_no_solution")))
+ (sha256
+ (base32 "15bdjv0hpzg3lfbz25w16sf4h3gkpd4mhvysgynak73wj47362ih"))
+ (patches (search-patches "python-pulp-exclude-solver-binaries.patch"))))
+ (build-system pyproject-build-system)
+ (native-inputs (list cbc ;a solver for testing
+ glpk ;a solver for testing
+ highs ;a solver for testing
+ python-setuptools
+ python-wheel))
+ (arguments
+ `(#:phases (modify-phases %standard-phases
+ (add-before 'build 'remove-solver-binaries
+ (lambda _
+ (delete-file-recursively "pulp/solverdir/")))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (if tests?
+ (invoke "pulptest")))))))
+ (home-page "https://github.com/coin-or/pulp")
+ (synopsis "Python Linear Programming API")
+ (description
+ "PuLP is an linear and mixed integer programming modeler written in
+Python. With PuLP, it is simple to create MILP optimisation problems and solve
+them with the latest open-source (or proprietary) solvers. PuLP can generate
+MPS or LP files and call solvers such as GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI,
+MOSEK, XPRESS, CHOCO, MIPCL, HiGHS, SCIP/FSCIP.")
+ (license license:expat)))
+
+(define-public python-pulp-2.4
(package
(name "python-pulp")
(version "2.4")
base-commit: b750d54703d849fe58dcacf94f23d34ab85b23a2
--
2.49.0
guix-patches@HIDDEN:bug#78443; Package guix-patches.
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[86.8.111.200]) by smtp.gmail.com with ESMTPSA id 5b1f17b1804b1-447f73d3d6csm249268005e9.19.2025.05.26.09.56.38 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 26 May 2025 09:56:38 -0700 (PDT) From: Sharlatan Hellseher <sharlatanus@HIDDEN> To: 78443 <at> debbugs.gnu.org Subject: [PATCH] gnu: python-pulp: Update to 3.1.1. Date: Mon, 26 May 2025 17:56:36 +0100 Message-ID: <87sekrjoor.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 78443 Cc: wzelazny@HIDDEN X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) --=-=-= Content-Type: text/plain Hi, Thanks for the patch. After appling it snakemake@HIDDEN has failed. Please check with 'guix build -P1 python-pulp' You might also may open a PR on <https://codeberg.org/guix/guix> -- Oleg --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQJKBAEBCgA0FiEEmEeB3micIcJkGAhndtcnv/Ys0rUFAmg0nUQWHHNoYXJsYXRh bnVzQGdtYWlsLmNvbQAKCRB21ye/9izStTdbEACTPVY3KqPdHrNJSXlZkF8Zbwj1 7TeY4jzH9Ytc3mJPNi6BZV84k1SoZMjk+/smPnsREdaUQOlb+zLhO/Ox1lw3oSpd FcGN47/lx/giS11aCcKnwIo3PgTkPgsUZcG0t9jBHtYL2ssiOSIyHvj+Q6Tn7+TD HG+73ikzYiiegiqx4yfSFL+Qcc3YhiPWymhcJ/NZ6lYfTy8cC/QY0QlEgkcrspkY zM4qebHcKK+1Q4r9QP33cmx1kNIK4FgWWDALKOzIUr4GvWgJqeWqUsEJFiWd1FHe r6QApsQ4qMY26gPQUJ8VvbdsEb5RYgwH+ym38W4OHaevd4tYwpbZvQvEV6G0ta9M UJ7xdjm2BFeizpnI1+/w+fGSUgDs9YMtYByhbZP9nXkgyMIVvydQibWSTCUVe/vC FxSmce7Kkwmlb0fdH2pjO/Rw8Eeic7B6yqHpBShPy3SibW24yDxDus99q4nDA3/8 3aa24cg8bsW6UrGNiGT5+0L2htB7l2JUeOVaR1k5C+1u0QQqwHUuzTnXbTRZbS/H fjb/3HBwlSmpwDngBgZyOBmobKWJnUhc5fDuVIMfU0N8nivzrVeOhLGgjH0Vp98X 2uWeMq5h/EGdxtAVO2piUMfwrMI+IGxap3YtTP4PX1Jqo9hROSIxiGZ+boyXLg8P GhqfL3HS5uMJhQlEWA== =2e/S -----END PGP SIGNATURE----- --=-=-=--
guix-patches@HIDDEN:bug#78443; Package guix-patches.
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To: guix-patches@HIDDEN
Subject: [PATCH] gnu: python-pulp: Update to 3.1.1.
Date: Thu, 15 May 2025 15:45:32 +0200
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* gnu/packages/patches/python-pulp-exclude-solver-binaries.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/python-xyz.scm (python-pulp): Update to 3.1.1.
[source]: Update the uri capitalization.
[source]: Add a snippet for skipping a failing test.
[source]: Apply the new patch.
[build-system]: Change to pyproject-build-system.
[native-inputs]: Add cbc, glpk, highs, python-setuptools, and python-wheel.
[propagated-inputs]: Remove python-amply.
[agruments]<#:phases>: Add a phase to remove solver binaries.
[agruments]<#:phases>: Test using pulptest.
[synopsis]: Change according to About in the code repository.
[description]: Extend according to README.rst in the code repository.
Change-Id: I1a0644da575da997f9d31cf9099d738e95d5f3a0
---
gnu/local.mk | 1 +
.../python-pulp-exclude-solver-binaries.patch | 36 ++++++++++++++++
gnu/packages/python-xyz.scm | 42 ++++++++++++++-----
3 files changed, 68 insertions(+), 11 deletions(-)
create mode 100644 gnu/packages/patches/python-pulp-exclude-solver-binaries.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index dfafe8b8953..0074805dd40 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -2021,6 +2021,7 @@ dist_patch_DATA = \
%D%/packages/patches/python-matplotlib-fix-legend-loc-best-test.patch \
%D%/packages/patches/python-random2-getrandbits-test.patch \
%D%/packages/patches/python-pillow-use-zlib-1.3.patch \
+ %D%/packages/patches/python-pulp-exclude-solver-binaries.patch \
%D%/packages/patches/python-pydocstyle-add-support-for-pep701.patch \
%D%/packages/patches/python-pyreadstat-link-libiconv.patch \
%D%/packages/patches/python-sip-include-dirs.patch \
diff --git a/gnu/packages/patches/python-pulp-exclude-solver-binaries.patch b/gnu/packages/patches/python-pulp-exclude-solver-binaries.patch
new file mode 100644
index 00000000000..57e9a1421b0
--- /dev/null
+++ b/gnu/packages/patches/python-pulp-exclude-solver-binaries.patch
@@ -0,0 +1,36 @@
+This patch excludes solver binary executables that the project uses for
+testing. In the package definition, solvers are provided as native inputs,
+instead.
+
+This is an original patch. It was not submitted upstream.
+
+diff --git a/pyproject.toml b/pyproject.toml
+index 82f9d48..0925858 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -61,26 +61,11 @@ dev = [
+ [tool.setuptools]
+ packages = [
+ "pulp",
+- "pulp.solverdir",
+- "pulp.solverdir.cbc.linux.i32",
+- "pulp.solverdir.cbc.linux.i64",
+- "pulp.solverdir.cbc.linux.arm64",
+- "pulp.solverdir.cbc.win.i32",
+- "pulp.solverdir.cbc.win.i64",
+- "pulp.solverdir.cbc.osx.i64",
+ "pulp.apis",
+ "pulp.tests"]
+ # This is a workaround for https://github.com/astral-sh/uv/issues/9513
+ license-files = []
+
+-[tool.setuptools.package-data]
+-"pulp.solverdir.cbc.linux.i32"= ["*", "*.*"]
+-"pulp.solverdir.cbc.linux.i64"= ["*", "*.*"]
+-"pulp.solverdir.cbc.linux.arm64"= ["*", "*.*"]
+-"pulp.solverdir.cbc.win.i32"= ["*", "*.*"]
+-"pulp.solverdir.cbc.win.i64"= ["*", "*.*"]
+-"pulp.solverdir.cbc.osx.i64"= ["*", "*.*"]
+-
+ [project.scripts]
+ pulptest = "pulp.tests.run_tests:pulpTestAll"
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 5d0ac818398..923da91821d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15037,23 +15037,43 @@ (define-public python-amply
(define-public python-pulp
(package
(name "python-pulp")
- (version "2.4")
+ (version "3.1.1")
(source
(origin
(method url-fetch)
- (uri (pypi-uri "PuLP" version))
+ (uri (pypi-uri "pulp" version))
+ ;; https://github.com/coin-or/pulp/issues/832
+ (modules '((guix build utils)))
+ (snippet '(substitute* "pulp/tests/test_pulp.py"
+ ((" def test_time_limit_no_solution")
+ " @unittest.skip
+ def test_time_limit_no_solution")))
(sha256
- (base32
- "1dammrg0f1v0r028i3rpxbf2bsyxmjq0q6ihb4x2wsdki44z3bxj"))))
- (build-system python-build-system)
- (propagated-inputs
- (list python-amply))
+ (base32 "15bdjv0hpzg3lfbz25w16sf4h3gkpd4mhvysgynak73wj47362ih"))
+ (patches (search-patches "python-pulp-exclude-solver-binaries.patch"))))
+ (build-system pyproject-build-system)
+ (native-inputs (list cbc ;a solver for testing
+ glpk ;a solver for testing
+ highs ;a solver for testing
+ python-setuptools
+ python-wheel))
+ (arguments
+ `(#:phases (modify-phases %standard-phases
+ (add-before 'build 'remove-solver-binaries
+ (lambda _
+ (delete-file-recursively "pulp/solverdir/")))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (if tests?
+ (invoke "pulptest")))))))
(home-page "https://github.com/coin-or/pulp")
- (synopsis "Linear Programming modeler")
+ (synopsis "Python Linear Programming API")
(description
- "PuLP is a Linear Programming modeler written in Python. PuLP can
-generate MPS or LP files and call GLPK, COIN CLP/CBC, CPLEX, and GUROBI to
-solve linear problems.")
+ "PuLP is an linear and mixed integer programming modeler written in
+Python. With PuLP, it is simple to create MILP optimisation problems and solve
+them with the latest open-source (or proprietary) solvers. PuLP can generate
+MPS or LP files and call solvers such as GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI,
+MOSEK, XPRESS, CHOCO, MIPCL, HiGHS, SCIP/FSCIP.")
(license license:expat)))
(define-public python-py-partiql-parser
base-commit: ff50f88935f6d04664ad3c907a9bff62714668c6
--
2.49.0
Wiktor Żelazny <wz@HIDDEN>:guix-patches@HIDDEN.
Full text available.guix-patches@HIDDEN:bug#78443; Package guix-patches.
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