Package: guix-patches;
Reported by: Wiktor Żelazny <wz <at> freeshell.de>
Date: Thu, 15 May 2025 13:48:02 UTC
Severity: normal
Tags: patch
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guix-patches <at> gnu.org:bug#78443; Package guix-patches.
(Thu, 15 May 2025 13:48:02 GMT) Full text and rfc822 format available.Wiktor Żelazny <wz <at> freeshell.de>:guix-patches <at> gnu.org.
(Thu, 15 May 2025 13:48:02 GMT) Full text and rfc822 format available.Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: Wiktor Żelazny <wz <at> freeshell.de> To: guix-patches <at> gnu.org Subject: [PATCH] gnu: python-pulp: Update to 3.1.1. Date: Thu, 15 May 2025 15:45:32 +0200
* 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
guix-patches <at> gnu.org:bug#78443; Package guix-patches.
(Mon, 26 May 2025 16:57:01 GMT) Full text and rfc822 format available.Message #8 received at 78443 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 78443 <at> debbugs.gnu.org Cc: wzelazny <at> vurv.cz Subject: [PATCH] gnu: python-pulp: Update to 3.1.1. Date: Mon, 26 May 2025 17:56:36 +0100
[Message part 1 (text/plain, inline)]
Hi, Thanks for the patch. After appling it snakemake <at> 5.32.2 has failed. Please check with 'guix build -P1 python-pulp' You might also may open a PR on <https://codeberg.org/guix/guix> -- Oleg
[signature.asc (application/pgp-signature, inline)]
guix-patches <at> gnu.org:bug#78443; Package guix-patches.
(Fri, 30 May 2025 17:37:02 GMT) Full text and rfc822 format available.Message #11 received at 78443 <at> debbugs.gnu.org (full text, mbox):
From: Wiktor Żelazny <wz <at> freeshell.de> 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
* 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
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.