GNU bug report logs - #78443
[PATCH] gnu: python-pulp: Update to 3.1.1.

Previous Next

To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 78443 in the body.
You can then email your comments to 78443 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

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

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)]

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

Message #14 received at 78443 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Wiktor Żelazny <wz <at> freeshell.de>
Cc: 78443 <at> debbugs.gnu.org, Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: Re: [PATCH v2] gnu: python-pulp: Update to 3.1.1.
Date: Sat, 7 Jun 2025 17:01:53 +0200

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

Message #21 received at 78443-done <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Wiktor Żelazny <wz <at> freeshell.de>
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>, 78443-done <at> debbugs.gnu.org
Subject: Re: [PATCH v2] gnu: python-pulp: Update to 3.1.1.
Date: Mon, 7 Jul 2025 13:19:11 +0200

Closing for lack of feedback. If you would still like to propose a
patch, please take my comments into account and submit a new pull
request on codeberg.

Andreas

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.