GNU bug report logs - #76150
[PATCH 00/16] More patches towards SageMath.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: guix-patches <at> gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 00/16] More patches towards SageMath.
Date: Sun,  9 Feb 2025 01:50:06 +0000

This series adds some optional packages for SageMath and updates other standard packages.

The version bumps to m4ri, m4rie, python-cvxopt and singular are required for the latest version of sage. The other patches introduce new optional packages.

Vinicius Monego (16):
  gnu: Add normaliz.
  gnu: Add python-pynormaliz.
  gnu: Add python-nibabel.
  gnu: python-cvxopt: Update to 1.3.2.
  gnu: Add msolve.
  gnu: Add python-cylp.
  gnu: singular: Remove package labels.
  gnu: singular: Update to 4.4.0p7.
  gnu: singular: Use G-Expressions.
  gnu: Add python-pysingular.
  gnu: m4ri: Update to 20200125.
  gnu: m4rie: Update to 20200125.
  gnu: Add hpcombi.
  gnu: Add libsemigroups.
  gnu: Add plantri.
  gnu: Add glucose.

 gnu/packages/algebra.scm        | 157 ++++++++++++++++++++++++++++----
 gnu/packages/graph.scm          |  35 ++++++-
 gnu/packages/maths.scm          | 153 ++++++++++++++++++++++++++++++-
 gnu/packages/python-science.scm |  35 ++++++-
 4 files changed, 356 insertions(+), 24 deletions(-)


base-commit: 05516fcb24799d00947751a434dd797f3fbb9d64
-- 
2.48.1

Message #8 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 76150 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 01/16] gnu: Add normaliz.
Date: Sun,  9 Feb 2025 01:52:18 +0000

* gnu/packages/algebra.scm (normaliz): New variable.

Change-Id: I3e0936c598b0a5fdd88af9d22280137d42c45cc5
---
 gnu/packages/algebra.scm | 28 +++++++++++++++++++++++++++-
 1 file changed, 27 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index afca739766..f1d4820dcb 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -12,7 +12,7 @@
 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling <at> bjoernhoefling.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba <at> kadziolka.net>
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll <at> gmail.com>
-;;; Copyright © 2020, 2021, 2023, 2024 Vinicius Monego <monego <at> posteo.net>
+;;; Copyright © 2020, 2021, 2023, 2024, 2025 Vinicius Monego <monego <at> posteo.net>
 ;;; Copyright © 2021 Lars-Dominik Braun <ldb <at> leibniz-psychology.org>
 ;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
 ;;; Copyright © 2023 Mehmet Tekman <mtekman89 <at> gmail.com>
@@ -1017,6 +1017,32 @@ (define-public ginac
 extends it by a set of algebraic capabilities.")
     (license license:gpl2+)))
 
+(define-public normaliz
+  (package
+    (name "normaliz")
+    (version "3.10.4")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/normaliz/Normaliz")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1smla96wjyv5ygg77ps9np6bfzp2qynq8vd1msybabi4621cnrma"))))
+    (build-system gnu-build-system)
+    (native-inputs (list autoconf automake libtool pkg-config))
+    ;; Flint is optional. TODO: Try to build with nauty and cocoalib support.
+    ;; The configure script fails to find nauty.h.
+    (inputs (list flint gmp))
+    (home-page "https://www.normaliz.uni-osnabrueck.de/")
+    (synopsis "Tool for discrete convex geometry")
+    (description "Normaliz is a tool for computations in affine monoids,
+vector configurations, rational polyhedra and rational cones.  Normaliz now
+computes rational and algebraic polyhedra, i.e., polyhedra defined over real
+algebraic extensions of QQ.")
+    (license license:gpl3+)))
+
 (define-public eigen
   (package
     (name "eigen")
-- 
2.48.1

Message #11 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 76150 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 02/16] gnu: Add python-pynormaliz.
Date: Sun,  9 Feb 2025 01:52:19 +0000

* gnu/packages/algebra.scm (python-pynormaliz): New variable.

Change-Id: I94379cfeed2a67bb4ffbda34823e4e000f4f961e
---
 gnu/packages/algebra.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index f1d4820dcb..4e111a542a 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1043,6 +1043,35 @@ (define-public normaliz
 algebraic extensions of QQ.")
     (license license:gpl3+)))
 
+(define-public python-pynormaliz
+  (package
+    (name "python-pynormaliz")
+    (version "2.21")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pynormaliz" version))
+       (sha256
+        (base32 "0hsyxml71i2b9pa375ipbfpackj3y67jlg2rxgc433sfy3895wvf"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #f ; tests need normaliz to be built with nauty support
+      #:phases #~(modify-phases %standard-phases
+                   (replace 'check
+                     (lambda* (#:key tests? #:allow-other-keys)
+                       (if tests?
+                           (invoke "python" "tests/runtests.py")))))))
+    (native-inputs (list python-setuptools python-wheel))
+    (inputs (list flint gmp normaliz))
+    (home-page "https://github.com/Normaliz/PyNormaliz")
+    (synopsis "Python interface to Normaliz")
+    (description
+     "PyNormaliz provides an interface to Normaliz via libNormaliz.  It offers
+the complete functionality of Normaliz, and can be used interactively from
+Python.")
+    (license license:gpl2+)))
+
 (define-public eigen
   (package
     (name "eigen")
-- 
2.48.1

Message #14 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 76150 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 03/16] gnu: Add python-nibabel.
Date: Sun,  9 Feb 2025 01:52:20 +0000

* gnu/packages/python-science.scm (python-nibabel): New variable.

Change-Id: I27d3841def6f360ae3996aacb787142bcfa92291
---
 gnu/packages/python-science.scm | 35 ++++++++++++++++++++++++++++++++-
 1 file changed, 34 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 7772dce248..bd7ea99c60 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -9,7 +9,7 @@
 ;;; Copyright © 2019, 2021, 2022, 2023, 2024 Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
 ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul <at> autistici.org>
 ;;; Copyright © 2020 Pierre Langlois <pierre.langlois <at> gmx.com>
-;;; Copyright © 2020, 2021, 2022, 2023, 2024 Vinicius Monego <monego <at> posteo.net>
+;;; Copyright © 2020-2025 Vinicius Monego <monego <at> posteo.net>
 ;;; Copyright © 2021 Greg Hogan <code <at> greghogan.com>
 ;;; Copyright © 2021 Roel Janssen <roel <at> gnu.org>
 ;;; Copyright © 2021 Paul Garlick <pgarlick <at> tourbillion-technology.com>
@@ -1128,6 +1128,39 @@ (define-public python-pyet
 Evapotranspiration using various standard methods.")
     (license license:expat)))
 
+(define-public python-nibabel
+  (package
+    (name "python-nibabel")
+    (version "5.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "nibabel" version))
+       (sha256
+        (base32 "16snprwgp7qzp51j3mx0zdn7brvx6r14ankldi24ny0w7d8adp0b"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; AttributeError: 'dict' object has no attribute 'add'.
+      #:test-flags #~(list "-k" "not test_first and not test_second")))
+    (propagated-inputs (list python-importlib-resources python-numpy
+                             python-packaging python-typing-extensions))
+    (native-inputs (list python-hatch-vcs
+                         python-hatchling
+                         python-pytest
+                         python-pytest-httpserver
+                         python-pytest-xdist))
+    (home-page "https://nipy.org/nibabel/")
+    (synopsis "Read and write access to common neuroimaging file formats")
+    (description
+     "@code{nibabel} is a library that provides read and write access to
+common neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2
+and later), GIFTI, NIfTI1, NIfTI2, CIFTI-2, MINC1, MINC2, AFNI BRIK/HEAD,
+ECAT and Philips PAR/REC.  In addition, NiBabel also supports FreeSurfer’s
+MGH, geometry, annotation and morphometry files, and provides some limited
+support for DICOM.")
+    (license license:expat)))
+
 (define-public python-tspex
   (package
     (name "python-tspex")
-- 
2.48.1

Message #17 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 76150 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 04/16] gnu: python-cvxopt: Update to 1.3.2.
Date: Sun,  9 Feb 2025 01:52:21 +0000

* gnu/packages/maths.scm (python-cvxopt): Update to 1.3.2.

Change-Id: I7924821a69e092da529a5188df3d1b2e3f4eed49
---
 gnu/packages/maths.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index bfdad0eff3..47a81a510c 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -39,7 +39,7 @@
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll <at> gmail.com>
 ;;; Copyright © 2020 Nicolò Balzarotti <nicolo <at> nixo.xyz>
 ;;; Copyright © 2020 B. Wilson <elaexuotee <at> wilsonb.com>
-;;; Copyright © 2020, 2021 Vinicius Monego <monego <at> posteo.net>
+;;; Copyright © 2020, 2021, 2025 Vinicius Monego <monego <at> posteo.net>
 ;;; Copyright © 2020 Simon Tournier <zimon.toutoune <at> gmail.com>
 ;;; Copyright © 2020 Martin Becze <mjbecze <at> riseup.net>
 ;;; Copyright © 2021 Gerd Heber <gerd.heber <at> gmail.com>
@@ -3975,7 +3975,7 @@ (define-public python-blis-for-thinc
 (define-public python-cvxopt
   (package
     (name "python-cvxopt")
-    (version "1.2.7")
+    (version "1.3.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -3984,7 +3984,7 @@ (define-public python-cvxopt
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "114z34wwx1bsv4q6xj9p5q99dffgnj9s4i4arx10g191xq9q8i5y"))))
+                "0vdfag3rr906w0gk7vxm2yxfy8y92i4wmqxi82cbykpfp5r82i36"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
2.48.1

Message #20 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 76150 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 05/16] gnu: Add msolve.
Date: Sun,  9 Feb 2025 01:52:22 +0000

* gnu/packages/maths.scm (msolve): New variable.

Change-Id: I8587f7527a6eb1cc9065751351491777c4cd00be
---
 gnu/packages/maths.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 47a81a510c..2c89451d0f 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -7095,6 +7095,40 @@ (define-public lpsolve
 revised simplex and the branch-and-bound methods.")
     (license license:lgpl2.1+)))
 
+(define-public msolve
+  (package
+    (name "msolve")
+    (version "0.7.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/algebraic-solving/msolve")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1ipsdw5sk4d344ki4r5ma9vn8gyi8hrk0n951r0720wvgxkw920p"))))
+    (build-system gnu-build-system)
+    (native-inputs (list autoconf automake libtool))
+    (inputs (list flint gmp mpfr))
+    (home-page "https://msolve.lip6.fr/")
+    (synopsis
+     "Library for polynomial system solving through algebraic methods")
+    (description "@code{msolve} is a C library implementing computer algebra
+algorithms for solving polynomial systems (with rational coefficients or
+coefficients in a prime field).
+
+Currently, with msolve, you can basically solve multivariate polynomial
+systems.  This encompasses:
+
+@itemize
+@item the computation of Groebner bases
+@item real root isolation of the solutions to polynomial systems
+@item the computation of the dimension and the degree of the solution set and
+many other things you can do using msolve.
+@end itemize")
+    (license license:gpl2+)))
+
 ;; Private Trilinos package for dealii-openmpi (similar to
 ;; trilinos-serial-xyce and trilinos-parallel-xyce).
 ;; This version is the latest known to be compatible with deal.II [1].
-- 
2.48.1

Message #23 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 76150 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 06/16] gnu: Add python-cylp.
Date: Sun,  9 Feb 2025 01:52:23 +0000

* gnu/packages/maths.scm (python-cylp): New variable.

Change-Id: Id3467bc34833472aa7fca3416801a5fbf5c033e6
---
 gnu/packages/maths.scm | 48 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 2c89451d0f..44bd1b15d9 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2739,6 +2739,54 @@ (define-public clp
 and quadratic objectives using the Simplex algorithm.")
     (license license:epl1.0)))
 
+(define-public python-cylp
+  (package
+    (name "python-cylp")
+    (version "0.92.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "cylp" version))
+       (sha256
+        (base32 "1mhvjrhvpgnpw4zwri92dj168qvyclcpsqvzbj5maxx5cilnhkww"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags #~(list "-k" (string-append
+                                 "not " (string-join
+                                         (list
+                                          "test_removeVar2" ; AssertionError
+                                          ;; Tests below segfault
+                                          "test_dantzig"
+                                          "test_lifo"
+                                          "test_mf"
+                                          "test_pe")
+                                         " and not ")))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'pre-check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (if tests? ; rebuild extensions
+                  (invoke "python" "setup.py" "build_ext" "--inplace")))))))
+    (propagated-inputs (list python-numpy python-pytest python-scipy))
+    (inputs (list cbc))
+    (native-inputs (list pkg-config
+                         python-cython-3
+                         python-hypothesis
+                         python-numpy
+                         python-pytest
+                         python-setuptools
+                         python-wheel))
+    (home-page "https://github.com/coin-or/cylp")
+    (synopsis "Python interface for CLP, CBC, and CGL")
+    (description
+     "CyLP is a Python interface to COIN-OR’s Linear and mixed-integer program
+solvers (CLP, CBC, and CGL).  CyLP’s unique feature is that you can use it to
+alter the solution process of the solvers from within Python.  For example,
+you may define cut generators, branch-and-bound strategies, and primal/dual
+Simplex pivot rules completely in Python.")
+    (license license:epl2.0)))
+
 (define-public gecode
   (let* ((commit "f7f0d7c273d6844698f01cec8229ebe0b66a016a")
          (version (git-version "6.2.0" "1" commit)))
-- 
2.48.1

Message #26 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 76150 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 07/16] gnu: singular: Remove package labels.
Date: Sun,  9 Feb 2025 01:52:24 +0000

* gnu/packages/algebra.scm (singular)[inputs]: Remove package labels.

Change-Id: Iecdcf07df4c0f18c0305a8f990d4a2e3c832cdd6
---
 gnu/packages/algebra.scm | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 4e111a542a..bf3abaa8ed 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -619,13 +619,13 @@ (define-public singular
    (native-inputs
     (list doxygen graphviz perl))
    (inputs
-    `(("cddlib" ,cddlib)
-      ("gmp" ,gmp)
-      ("flint" ,flint)
-      ("mpfr" ,mpfr)
-      ("ntl" ,ntl)
-      ("python" ,python-2)
-      ("readline" ,readline)))
+    (list cddlib
+          gmp
+          flint
+          mpfr
+          ntl
+          python-2
+          readline))
    (arguments
     `(#:configure-flags
       (list (string-append "--with-ntl="
-- 
2.48.1

Message #29 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 76150 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 08/16] gnu: singular: Update to 4.4.0p7.
Date: Sun,  9 Feb 2025 01:52:25 +0000

* gnu/packages/algebra.scm (singular): Update to 4.4.0p7.

Change-Id: I64f74815097ca3aaeeaba9f3177580818c433a4c
---
 gnu/packages/algebra.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index bf3abaa8ed..acbc76b4ca 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -599,7 +599,7 @@ (define-public ntl
 (define-public singular
   (package
    (name "singular")
-   (version "4.3.2p16")
+   (version "4.4.0p7")
    (source
     (origin
       (method url-fetch)
@@ -613,8 +613,9 @@ (define-public singular
                                     version))
                         #\.) "-")
                       "/singular-" version ".tar.gz"))
-             (sha256 (base32
-                      "05ia8zqiddj1agg9bfdx54z0sjqcgjgi6lz7ck2ngv562fx36mv7"))))
+            (sha256
+              (base32
+               "0625541pxxhs7789i3ddf5fm1pqvf1kyljyaii41djg9j12cdhbc"))))
    (build-system gnu-build-system)
    (native-inputs
     (list doxygen graphviz perl))
-- 
2.48.1

Message #32 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 76150 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 09/16] gnu: singular: Use G-Expressions.
Date: Sun,  9 Feb 2025 01:52:26 +0000

* gnu/packages/algebra.scm (singular)[arguments]: Use
G-Expressions. Move below build-system.

Change-Id: I4253b8a9a9cd3b7d2b7492853323d1e8c4fbec4e
---
 gnu/packages/algebra.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index acbc76b4ca..b69b14fa28 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -617,6 +617,10 @@ (define-public singular
               (base32
                "0625541pxxhs7789i3ddf5fm1pqvf1kyljyaii41djg9j12cdhbc"))))
    (build-system gnu-build-system)
+   (arguments
+    (list
+     #:configure-flags #~(list (string-append "--with-ntl="
+                                              #$(this-package-input "ntl")))))
    (native-inputs
     (list doxygen graphviz perl))
    (inputs
@@ -627,10 +631,6 @@ (define-public singular
           ntl
           python-2
           readline))
-   (arguments
-    `(#:configure-flags
-      (list (string-append "--with-ntl="
-                           (assoc-ref %build-inputs "ntl")))))
    (synopsis "Computer algebra system for polynomial computations")
    (description
     "Singular is a computer algebra system for polynomial computations,
-- 
2.48.1

Message #35 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 76150 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 10/16] gnu: Add python-pysingular.
Date: Sun,  9 Feb 2025 01:52:27 +0000

* gnu/packages/algebra.scm (python-pysingular): New variable.

Change-Id: I57e828bd4eb2c64b2ba094ed0c9cb516fee1c5b4
---
 gnu/packages/algebra.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index b69b14fa28..6abe959343 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -642,6 +642,28 @@ (define-public singular
    (license license:gpl3)
    (home-page "https://www.singular.uni-kl.de/index.php")))
 
+(define-public python-pysingular
+  (package
+    (name "python-pysingular")
+    (version "0.9.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "PySingular" version))
+       (sha256
+        (base32 "037n3s1l08g75k22saki6813wi3ciiq45zxca11izilgagbx20ya"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:tests? #f)) ; there are no tests
+    (native-inputs (list python-setuptools python-wheel))
+    ;; XXX: GMP failed to be loaded from Singular.  Pass it here for now.
+    (inputs (list gmp singular))
+    (home-page "https://github.com/sebasguts/SingularPython")
+    (synopsis "Simple interface to Singular")
+    (description "This package provides a simple Python interface to the
+Singular computer algebra system.")
+    (license license:gpl2+)))
+
 (define-public gmp-ecm
   (package
     (name "gmp-ecm")
-- 
2.48.1

Message #38 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 76150 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 11/16] gnu: m4ri: Update to 20200125.
Date: Sun,  9 Feb 2025 01:52:28 +0000

* gnu/packages/algebra.scm (m4ri): Update to 20200125.

Change-Id: I0b6ec9c92e224fa6ac8200c8aea0abb343dae8a6
---
 gnu/packages/algebra.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 6abe959343..90cee7e2ac 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1573,7 +1573,7 @@ (define-public linbox
 (define-public m4ri
   (package
     (name "m4ri")
-    (version "20140914")
+    (version "20200125")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1582,7 +1582,7 @@ (define-public m4ri
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3"))))
+                "1dxgbv6zdyki3h61qlv7003wzhy6x14zmcaz9x19md1i7ng07w1k"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf automake libtool pkg-config))
-- 
2.48.1

Message #41 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 76150 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 12/16] gnu: m4rie: Update to 20200125.
Date: Sun,  9 Feb 2025 01:52:29 +0000

* gnu/packages/algebra.scm (m4rie): Update to 20200125.

Change-Id: I114f5c2bf3a689d8d7e66dd3a9125970852c90a6
---
 gnu/packages/algebra.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 90cee7e2ac..8175589006 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1662,7 +1662,7 @@ (define-public symmetrica
 (define-public m4rie
   (package
     (name "m4rie")
-    (version "20150908")
+    (version "20200125")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1671,7 +1671,7 @@ (define-public m4rie
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss"))))
+                "078f0b4skv1bbdj0j9b397hydj7gimhfzf407nisy2zcyp2iqc3f"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf automake libtool))
-- 
2.48.1

Message #44 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 76150 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 13/16] gnu: Add hpcombi.
Date: Sun,  9 Feb 2025 01:52:30 +0000

* gnu/packages/maths.scm (hpcombi): New variable.

Change-Id: I64eb46aa4002a2291ae59122e083998a9c846eaf
---
 gnu/packages/maths.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 44bd1b15d9..cd0a0828e1 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2976,6 +2976,32 @@ (define-public libflame
 includes a complete LAPACK implementation.")
       (license license:bsd-3))))
 
+(define-public hpcombi
+  (package
+    (name "hpcombi")
+    (version "1.0.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/libsemigroups/hpcombi")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "00mbxw5x6m61n0x68dsiyq97i7b08h3hkbj9is2w6gcg571jy319"))))
+    (arguments
+     (list #:configure-flags #~(list "-DBUILD_TESTING=ON")))
+    (native-inputs
+     (list catch2-3))
+    (build-system cmake-build-system)
+    (home-page "https://libsemigroups.github.io/HPCombi/")
+    (synopsis "Fast combinatorics in C++ using SSE/AVX instruction sets")
+    (description "HPCombi is a C++17 header-only library using the SSE and AVX
+instruction sets, and some equivalents, for very fast manipulation of
+combinatorial objects such as transformations, permutations, and boolean
+matrices of small size.")
+    (license license:gpl3+)))
+
 (define-public scasp
   (package
     (name "scasp")
-- 
2.48.1

Message #47 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 76150 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 14/16] gnu: Add libsemigroups.
Date: Sun,  9 Feb 2025 01:52:31 +0000

* gnu/packages/algebra.scm (libsemigroups): New variable.

Change-Id: I6e929fe6b479c7e7c2b5b4632759bd781af3c927
---
 gnu/packages/algebra.scm | 41 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 8175589006..9da5f0124c 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -63,6 +63,7 @@ (define-module (gnu packages algebra)
   #:use-module (gnu packages ocaml)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages pretty-print)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-build)
@@ -1836,6 +1837,46 @@ (define-public r-dtt
 (@dfn{DHT}).")
     (license license:gpl2+)))
 
+(define-public libsemigroups
+  (package
+    (name "libsemigroups")
+    (version "2.7.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/libsemigroups/libsemigroups")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0acpx6n6chqm365k71ba6lwqqzapbh6h4wzra63p6mbgb8dw9l1f"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      ;; XXX: libsemigroup's build system doesn't have an option to use
+      ;; external HPCombi.  Try to work it around in the future and skip
+      ;; support for now.
+      #:configure-flags #~(list "--enable-fmt=yes"
+                                "--enable-hpcombi=no"
+                                "--with-external-eigen=yes"
+                                "--with-external-fmt=yes")
+      #:phases #~(modify-phases %standard-phases
+                   (add-after 'unpack 'fix-version
+                     (lambda* (#:key inputs #:allow-other-keys)
+                       (substitute* "etc/version-number.sh"
+                         (("/bin/sh")
+                          (search-input-file inputs "/bin/bash"))))))))
+    (native-inputs
+     (list autoconf automake libtool pkg-config))
+    (inputs (list eigen fmt))
+    (home-page "https://github.com/libsemigroups/libsemigroups")
+    (synopsis "Library for semigroups and monoids")
+    (description
+     "@code{libsemigroups} is a C++14 library containing implementations of
+several algorithms for computing finite, and finitely presented,
+semigroups and monoids.")
+    (license license:gpl2+)))
+
 (define-public sollya
   (package
    (name "sollya")
-- 
2.48.1

Message #50 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 76150 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 15/16] gnu: Add plantri.
Date: Sun,  9 Feb 2025 01:52:32 +0000

* gnu/packages/graph.scm (plantri): New variable.

Change-Id: I976eb88437b47bc06d7b2c2f8703da217e85cc7e
---
 gnu/packages/graph.scm | 35 ++++++++++++++++++++++++++++++++++-
 1 file changed, 34 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index c8bd25af9c..5303f2e9db 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -6,7 +6,7 @@
 ;;; Copyright © 2019 Andreas Enge <andreas <at> enge.fr>
 ;;; Copyright © 2020 Alexander Krotov <krotov <at> iitp.ru>
 ;;; Copyright © 2020 Pierre Langlois <pierre.langlos <at> gmx.com>
-;;; Copyright © 2021, 2023 Vinicius Monego <monego <at> posteo.net>
+;;; Copyright © 2021, 2023, 2025 Vinicius Monego <monego <at> posteo.net>
 ;;; Copyright © 2021 Alexandre Hannud Abdo <abdo <at> member.fsf.org>
 ;;; Copyright © 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
 ;;; Copyright © 2022 Marius Bakke <marius <at> gnu.org>
@@ -783,6 +783,39 @@ (define-public edge-addition-planarity-suite
     (home-page
       "https://github.com/graph-algorithms/edge-addition-planarity-suite")))
 
+(define-public plantri
+  (package
+    (name "plantri")
+    (version "5.5")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://users.cecs.anu.edu.au/~bdm/plantri/"
+                                  "plantri" (string-join
+                                             (string-split version #\.)
+                                             "") ".tar.gz"))
+              (sha256
+               (base32
+                "1vbxpjih293d9nmb65fsh6xgg0w12kygwycg1yw4wad7ridxy74i"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f ; there are no tests
+      #:phases #~(modify-phases %standard-phases
+                   (delete 'configure)
+                   (replace 'install
+                     (lambda _
+                       (for-each
+                        (lambda (bin)
+                          (install-file bin (string-append #$output "/bin")))
+                        '("fullgen" "plantri")))))))
+    (home-page "https://users.cecs.anu.edu.au/~bdm/plantri/")
+    (synopsis "Generate certain types of planar graphs")
+    (description
+     "@code{plantri} and @code{fullgen} are programs for generation of certain
+types of planar graphs.  Graphs are generated in such a way that exactly one
+member of each isomorphism class is output without the need for storing them.")
+    (license license:asl2.0)))
+
 (define-public rw
   (package
     (name "rw")
-- 
2.48.1

Message #53 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 76150 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 16/16] gnu: Add glucose.
Date: Sun,  9 Feb 2025 01:52:33 +0000

* gnu/packages/maths.scm (glucose): New variable.

Change-Id: I8e9031db55aa98ddde82ea676d3287656f7c4288
---
Is it OK to use -DCMAKE_BUILD_RPATH here? I don't see anyone doing it this way, it usually has a dedicated phase but it's more verbose that way.
 gnu/packages/maths.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index cd0a0828e1..1856a68d10 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2899,6 +2899,45 @@ (define-public libfixmath
 fixed point (16.16) format.")
       (license license:expat))))
 
+(define-public glucose
+  (package
+    (name "glucose")
+    (version "4.2.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/audemard/glucose")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0zrn4hnkf8k95dc3s3acydl1bqkr8a0axw56g7n562lx7zj7sd62"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:tests? #f ; there are no tests
+      #:configure-flags
+      #~(list "-DBUILD_SHARED_LIBS=ON"
+              (string-append "-DCMAKE_BUILD_RPATH=" #$output "/lib"))
+      #:phases #~(modify-phases %standard-phases
+                   (replace 'install
+                     (lambda _
+                       (for-each
+                        (lambda (bin)
+                          (install-file bin (string-append #$output "/bin")))
+                        '("glucose-simp" "glucose-syrup"))
+                       (for-each
+                        (lambda (lib)
+                          (install-file lib (string-append #$output "/lib")))
+                        '("libglucose.so" "libglucosep.so")))))))
+    (inputs (list zlib))
+    (home-page "https://www.labri.fr/perso/lsimon/research/glucose/")
+    (synopsis "SAT Solver")
+    (description "Glucose is a SAT solver based on a scoring scheme introduced
+in 2009 for the clause learning mechanism of so called “Modern” SAT solvers.
+It is designed to be parallel.")
+    (license license:expat)))
+
 (define-public libflame
   ;; The latest release (5.2.0) dates back to 2019.  Use a newer one, which
   ;; among other things provides extra LAPACK symbols, such as 'dgemlq_'
-- 
2.48.1

Message #56 received at 76150 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Vinicius Monego <monego <at> posteo.net>
Cc: 76150 <at> debbugs.gnu.org, vicvbcun <guix <at> ikherbers.com>,
 Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: Re: Fwd: [PATCH 00/16] More patches towards SageMath.
Date: Sun, 9 Feb 2025 10:41:13 +0100

Thanks for the patches! I have built and applied the first two, and will
continue working on the others as time permits, probably starting
tomorrow.

Andreas

Message #61 received at 76150-done <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Vinicius Monego <monego <at> posteo.net>
Cc: 76150-done <at> debbugs.gnu.org, vicvbcun <guix <at> ikherbers.com>,
 Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: Re: Fwd: [PATCH 00/16] More patches towards SageMath.
Date: Mon, 10 Feb 2025 14:49:00 +0100

Hello!

All packages are pushed to master now. I have changed the licence of
libsemigroups (it is gpl3+) and updated it to the latest version.
For good measure, I have also updated eclib.

Thanks for all these high quality patches!

Closing this bug report.

Andreas

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