sagemath · mkoeppe · Jul 19, 2023 · Jul 19, 2023 · Jul 19, 2023 · Feb 5, 2024
diff --git a/.gitignore b/.gitignore
@@ -225,6 +225,7 @@ build/pkgs/wheel/version_requirements.txt
 /pkgs/sagemath-sirocco/setup.cfg
 /pkgs/sagemath-tdlib/setup.cfg
 /pkgs/sagemath-categories/setup.cfg
+/pkgs/sagemath-cmr/setup.cfg
 /pkgs/sagemath-environment/setup.cfg
 /pkgs/sagemath-repl/setup.cfg
 /pkgs/sagemath-objects/pyproject.toml
@@ -235,6 +236,7 @@ build/pkgs/wheel/version_requirements.txt
 /pkgs/sagemath-sirocco/pyproject.toml
 /pkgs/sagemath-tdlib/pyproject.toml
 /pkgs/sagemath-categories/pyproject.toml
+/pkgs/sagemath-cmr/pyproject.toml
 /pkgs/sagemath-environment/pyproject.toml
 /pkgs/sagemath-repl/pyproject.toml
 /pkgs/sagemath-objects/requirements*.txt
@@ -245,6 +247,7 @@ build/pkgs/wheel/version_requirements.txt
 /pkgs/sagemath-sirocco/requirements*.txt
 /pkgs/sagemath-tdlib/requirements*.txt
 /pkgs/sagemath-categories/requirements*.txt
+/pkgs/sagemath-cmr/requirements*.txt
 /pkgs/sagemath-environment/requirements*.txt
 /pkgs/sagemath-repl/requirements*.txt
 /pkgs/sagemath-categories/MANIFEST.in

diff --git a/build/make/Makefile.in b/build/make/Makefile.in
@@ -142,6 +142,7 @@ PYPI_WHEEL_PACKAGES = $(PYPI_NOARCH_WHEEL_PACKAGES) \
 	sagemath_repl				\
 	sagemath_categories			\
 	sagemath_bliss 				\
+	sagemath_cmr 				\
 	sagemath_mcqd 				\
 	sagemath_tdlib				\
 	sagemath_coxeter3 			\

diff --git a/build/pkgs/cmr/SPKG.rst b/build/pkgs/cmr/SPKG.rst
@@ -0,0 +1,32 @@
+cmr: Combinatorial matrix recognition
+=====================================
+
+Description
+-----------
+
+The following matrix classes can be recognized:
+
+- Totally Unimodular Matrices
+- Network Matrices
+- Complement Totally Unimodular Matrices
+- (Strongly) k-Modular and Unimodular Matrices
+
+Moreover, representation matrices for the following matroid classes can be recognized:
+
+- Regular Matroids
+- Graphic / Cographic / Planar Matrices
+- Series-Parallel Matroids
+
+
+License
+-------
+
+MIT license
+
+
+Upstream Contact
+----------------
+
+https://discopt.github.io/cmr/
+
+https://github.com/discopt/cmr
diff --git a/build/pkgs/cmr/checksums.ini b/build/pkgs/cmr/checksums.ini
@@ -0,0 +1,4 @@
+tarball=cmr-0+VERSION.tar.gz
+sha1=05a74a210ff6ed105595c6ccd4b70ce232dc5674
+sha256=3c4d7bfd4391a2e50491b1d259465892d4a040e3355a256b85090af6787272e4
+upstream_url=https://github.com/discopt/cmr/archive/VERSION.tar.gz
diff --git a/build/pkgs/cmr/dependencies b/build/pkgs/cmr/dependencies
@@ -0,0 +1 @@
+googletest
diff --git a/build/pkgs/cmr/dependencies_order_only b/build/pkgs/cmr/dependencies_order_only
@@ -0,0 +1 @@
+cmake
diff --git a/build/pkgs/cmr/package-version.txt b/build/pkgs/cmr/package-version.txt
@@ -0,0 +1 @@
+e405fce633c4119a53249a5d0cade8a41fba081e
diff --git a/build/pkgs/cmr/patches/0001-src-cmr-seymour_internal.h-Add-missing-include.patch b/build/pkgs/cmr/patches/0001-src-cmr-seymour_internal.h-Add-missing-include.patch
@@ -0,0 +1,25 @@
+From 72a78493855add45a1ec8ddcd9c1e4d1d08e7028 Mon Sep 17 00:00:00 2001
+From: Matthias Koeppe <[email protected]>
+Date: Sun, 13 Oct 2024 16:27:44 -0700
+Subject: [PATCH] src/cmr/seymour_internal.h: Add missing include
+
+---
+ src/cmr/seymour_internal.h | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/src/cmr/seymour_internal.h b/src/cmr/seymour_internal.h
+index 8abefea3..10fc4815 100644
+--- a/src/cmr/seymour_internal.h
++++ b/src/cmr/seymour_internal.h
+@@ -1,6 +1,8 @@
+ #ifndef CMR_SEYMOUR_INTERNAL_H
+ #define CMR_SEYMOUR_INTERNAL_H
+
++#include <time.h>
++
+ #include "densematrix.h"
+
+ #include <cmr/matroid.h>
+-- 
+2.42.0
+
diff --git a/build/pkgs/cmr/spkg-check.in b/build/pkgs/cmr/spkg-check.in
@@ -0,0 +1,4 @@
+cd src
+cd build
+ctest
+ctest --rerun-failed --output-on-failure 
diff --git a/build/pkgs/cmr/spkg-install.in b/build/pkgs/cmr/spkg-install.in
@@ -0,0 +1,9 @@
+# -*- shell-script -*-
+cd src
+# Need C++14, so remove our flags that force C++11
+export CXX="$(echo "$CXX" | sed 's/-std=[a-z0-9+]*//g') -std=gnu++14"
+mkdir build
+cd build
+sdh_cmake -DGENERATORS=on -DCMAKE_SYSTEM_PREFIX_PATH="$SAGE_LOCAL" -DHAVE_FLAG_SEARCH_PATHS_FIRST=0 -DSHARED=on ..
+sdh_make VERBOSE=1
+sdh_make_install
diff --git a/build/pkgs/cmr/type b/build/pkgs/cmr/type
@@ -0,0 +1 @@
+optional
diff --git a/build/pkgs/googletest/SPKG.rst b/build/pkgs/googletest/SPKG.rst
@@ -0,0 +1,19 @@
+googletest: Google testing and mocking framework
+================================================
+
+Description
+-----------
+
+C++ test framework
+
+
+License
+-------
+
+BSD-3-Clause license
+
+
+Upstream Contact
+----------------
+
+https://github.com/google/googletest
diff --git a/build/pkgs/googletest/checksums.ini b/build/pkgs/googletest/checksums.ini
@@ -0,0 +1,4 @@
+tarball=googletest-VERSION.tar.gz
+sha1=568d58e26bd4e838449ca7ab8ebc152b3cbd210d
+sha256=7b42b4d6ed48810c5362c265a17faebe90dc2373c885e5216439d37927f02926
+upstream_url=https://github.com/google/googletest/archive/refs/tags/vVERSION.tar.gz
diff --git a/build/pkgs/googletest/dependencies_order_only b/build/pkgs/googletest/dependencies_order_only
@@ -0,0 +1 @@
+cmake
diff --git a/build/pkgs/googletest/distros/alpine.txt b/build/pkgs/googletest/distros/alpine.txt
@@ -0,0 +1 @@
+gtest-dev
diff --git a/build/pkgs/googletest/distros/arch.txt b/build/pkgs/googletest/distros/arch.txt
@@ -0,0 +1 @@
+gtest
diff --git a/build/pkgs/googletest/distros/debian.txt b/build/pkgs/googletest/distros/debian.txt
@@ -0,0 +1 @@
+googletest
diff --git a/build/pkgs/googletest/distros/fedora.txt b/build/pkgs/googletest/distros/fedora.txt
@@ -0,0 +1 @@
+gtest
diff --git a/build/pkgs/googletest/distros/freebsd.txt b/build/pkgs/googletest/distros/freebsd.txt
@@ -0,0 +1 @@
+devel/googletest
diff --git a/build/pkgs/googletest/distros/gentoo.txt b/build/pkgs/googletest/distros/gentoo.txt
@@ -0,0 +1 @@
+dev-cpp/gtest
diff --git a/build/pkgs/googletest/distros/homebrew.txt b/build/pkgs/googletest/distros/homebrew.txt
@@ -0,0 +1 @@
+googletest
diff --git a/build/pkgs/googletest/distros/nix.txt b/build/pkgs/googletest/distros/nix.txt
@@ -0,0 +1 @@
+gtest
diff --git a/build/pkgs/googletest/distros/opensuse.txt b/build/pkgs/googletest/distros/opensuse.txt
@@ -0,0 +1 @@
+googletest
diff --git a/build/pkgs/googletest/distros/repology.txt b/build/pkgs/googletest/distros/repology.txt
@@ -0,0 +1 @@
+gtest
diff --git a/build/pkgs/googletest/distros/void.txt b/build/pkgs/googletest/distros/void.txt
@@ -0,0 +1 @@
+gtest-devel
diff --git a/build/pkgs/googletest/package-version.txt b/build/pkgs/googletest/package-version.txt
@@ -0,0 +1 @@
+1.15.2
diff --git a/build/pkgs/googletest/spkg-configure.m4 b/build/pkgs/googletest/spkg-configure.m4
@@ -0,0 +1,16 @@
+SAGE_SPKG_CONFIGURE([googletest], [dnl
+    AC_MSG_CHECKING([whether googletest is available])
+    rm -rf conftest_srcdir
+    mkdir conftest_srcdir
+    cat > conftest_srcdir/CMakeLists.txt <<EOF
+cmake_minimum_required (VERSION 3.11.0)
+project(dummy)
+find_package(GTest REQUIRED)
+EOF
+    AS_IF([cmake -S conftest_srcdir -B conftest_srcdir/build >& ]AS_MESSAGE_LOG_FD[ 2>&1], [dnl
+        AC_MSG_RESULT([yes])
+    ], [dnl
+        AC_MSG_RESULT([no])
+        AS_VAR_SET([sage_spkg_install_googletest], [yes])
+    ])
+])
diff --git a/build/pkgs/googletest/spkg-install.in b/build/pkgs/googletest/spkg-install.in
@@ -0,0 +1,9 @@
+# -*- shell-script -*-
+cd src
+# Need C++14, so remove our flags that force C++11
+export CXX="$(echo "$CXX" | sed 's/-std=[a-z0-9+]*//g') -std=gnu++14"
+mkdir build
+cd build
+sdh_cmake -DBUILD_SHARED_LIBS=ON ..
+sdh_make
+sdh_make_install
diff --git a/build/pkgs/googletest/type b/build/pkgs/googletest/type
@@ -0,0 +1 @@
+optional
diff --git a/build/pkgs/sagemath_cmr/SPKG.rst b/build/pkgs/sagemath_cmr/SPKG.rst
@@ -0,0 +1 @@
+src/README.rst
diff --git a/build/pkgs/sagemath_cmr/bootstrap b/build/pkgs/sagemath_cmr/bootstrap
@@ -0,0 +1 @@
+../sagelib/bootstrap
diff --git a/build/pkgs/sagemath_cmr/dependencies b/build/pkgs/sagemath_cmr/dependencies
@@ -0,0 +1 @@
+$(PYTHON) cmr cysignals $(SAGE_ROOT)/pkgs/sagemath-cmr/sage/libs/cmr/*.pxd $(SAGE_ROOT)/pkgs/sagemath-cmr/sage/matrix/matrix_cmr*.pyx $(SAGE_ROOT)/pkgs/sagemath-cmr/sage/matrix/seymour*.pyx | $(PYTHON_TOOLCHAIN) sage_setup sagemath_environment cython
diff --git a/build/pkgs/sagemath_cmr/package-version.txt b/build/pkgs/sagemath_cmr/package-version.txt
@@ -0,0 +1 @@
+src/VERSION.txt
diff --git a/build/pkgs/sagemath_cmr/spkg-install.in b/build/pkgs/sagemath_cmr/spkg-install.in
@@ -0,0 +1 @@
+../sagemath_bliss/spkg-install.in
diff --git a/build/pkgs/sagemath_cmr/spkg-src b/build/pkgs/sagemath_cmr/spkg-src
@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+#
+# Script to prepare an sdist tarball for sagemath-cmr
+# This script is not used during build.
+#
+# HOW TO MAKE THE TARBALL:
+# ./sage --sh build/pkgs/sagemath_cmr/spkg-src
+
+if [ -z "$SAGE_ROOT" ] ; then
+    echo >&2 "Error - SAGE_ROOT undefined ... exiting"
+    echo >&2 "Maybe run 'sage -sh'?"
+    exit 1
+fi
+
+# Exit on failure
+set -e
+
+cd build/pkgs/sagemath_cmr
+
+cd src
+# Get rid of old *.egg-info/SOURCES.txt
+rm -Rf *.egg-info
+
+python3 -m build --sdist --no-isolation --skip-dependency-check --outdir "$SAGE_DISTFILES"
diff --git a/build/pkgs/sagemath_cmr/src b/build/pkgs/sagemath_cmr/src
@@ -0,0 +1 @@
+../../../pkgs/sagemath-cmr
diff --git a/build/pkgs/sagemath_cmr/type b/build/pkgs/sagemath_cmr/type
@@ -0,0 +1 @@
+optional
diff --git a/build/pkgs/sagemath_cmr/version_requirements.txt b/build/pkgs/sagemath_cmr/version_requirements.txt
@@ -0,0 +1,2 @@
+# This file is updated on every release by the sage-update-version script
+sagemath-cmr ~= 10.1
diff --git a/build/pkgs/sagemath_doc_html/dependencies_optional b/build/pkgs/sagemath_doc_html/dependencies_optional
@@ -1 +1 @@
-jupyter_sphinx
+jupyter_sphinx sagemath_cmr
diff --git a/pkgs/sagemath-cmr/MANIFEST.in b/pkgs/sagemath-cmr/MANIFEST.in
@@ -0,0 +1,21 @@
+include VERSION.txt
+
+graft sage/libs/cmr
+include sage/matrix/*_cmr_*.p*
+include sage/matrix/seymour_*.p*
+
+global-exclude *.c
+global-exclude *.cpp
+
+global-exclude __pycache__
+global-exclude *.py[co]
+global-exclude *.bak
+global-exclude *.so
+global-exclude *~
+
+global-exclude all__*.py
+global-include all__sagemath_cmr.py
+
+prune .tox
+prune build
+prune dist
diff --git a/pkgs/sagemath-cmr/README.rst b/pkgs/sagemath-cmr/README.rst
@@ -0,0 +1,37 @@
+==========================================================================
+ Sage: Open Source Mathematics Software: Combinatorial matrix recognition
+==========================================================================
+
+About SageMath
+--------------
+
+   "Creating a Viable Open Source Alternative to
+    Magma, Maple, Mathematica, and MATLAB"
+
+   Copyright (C) 2005-2024 The Sage Development Team
+
+   https://www.sagemath.org
+
+SageMath fully supports all major Linux distributions, recent versions of
+macOS, and Windows (Windows Subsystem for Linux).
+
+See https://doc.sagemath.org/html/en/installation/index.html
+for general installation instructions.
+
+
+About this pip-installable source distribution
+----------------------------------------------
+
+This pip-installable source distribution ``sagemath-cmr`` is a small
+optional distribution for use with ``sagemath-standard``.
+
+It provides a Cython interface to the CMR library (https://github.com/discopt/cmr),
+providing recognition and decomposition algorithms for:
+
+- Totally Unimodular Matrices
+- Network Matrices
+- Complement Totally Unimodular Matrices
+- (Strongly) k-Modular and Unimodular Matrices
+- Regular Matroids
+- Graphic / Cographic / Planar Matrices
+- Series-Parallel Matroids
diff --git a/pkgs/sagemath-cmr/VERSION.txt b/pkgs/sagemath-cmr/VERSION.txt
@@ -0,0 +1 @@
+10.0
diff --git a/pkgs/sagemath-cmr/pyproject.toml.m4 b/pkgs/sagemath-cmr/pyproject.toml.m4
@@ -0,0 +1,36 @@
+include(`sage_spkg_versions_toml.m4')dnl' -*- conf-toml -*-
+[build-system]
+# Minimum requirements for the build system to execute.
+requires = [
+    SPKG_INSTALL_REQUIRES_setuptools
+    SPKG_INSTALL_REQUIRES_sage_conf
+    SPKG_INSTALL_REQUIRES_sage_setup
+    SPKG_INSTALL_REQUIRES_sagemath_environment
+    SPKG_INSTALL_REQUIRES_cython
+    SPKG_INSTALL_REQUIRES_cysignals
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "sagemath-cmr"
+description = "Sage: Open Source Mathematics Software: Combinatorial matrix recognition"
+dependencies = [
+    SPKG_INSTALL_REQUIRES_cysignals
+]
+dynamic = ["version"]
+include(`pyproject_toml_metadata.m4')dnl'
+
+[project.optional-dependencies]
+test = [
+    SPKG_INSTALL_REQUIRES_sagemath_repl
+]
+
+[project.readme]
+file = "README.rst"
+content-type = "text/x-rst"
+
+[tool.setuptools]
+include-package-data = false
+
+[tool.setuptools.dynamic]
+version = {file = ["VERSION.txt"]}
diff --git a/pkgs/sagemath-cmr/requirements.txt.m4 b/pkgs/sagemath-cmr/requirements.txt.m4
@@ -0,0 +1,2 @@
+Cython==esyscmd(`printf $(sed "s/[.]p.*//;" ../cython/package-version.txt)')
+sagemath-standard==esyscmd(`printf $(sed "s/[.]p.*//;" ../sagelib/package-version.txt)')
diff --git a/pkgs/sagemath-cmr/sage b/pkgs/sagemath-cmr/sage
@@ -0,0 +1 @@
+../../src/sage
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		$(PYTHON) cmr cysignals $(SAGE_ROOT)/pkgs/sagemath-cmr/sage/libs/cmr/.pxd $(SAGE_ROOT)/pkgs/sagemath-cmr/sage/matrix/matrix_cmr.pyx $(SAGE_ROOT)/pkgs/sagemath-cmr/sage/matrix/seymour*.pyx \| $(PYTHON_TOOLCHAIN) sage_setup sagemath_environment cython
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		# This file is updated on every release by the sage-update-version script
		sagemath-cmr ~= 10.1
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		Cython==esyscmd(`printf $(sed "s/[.]p.*//;" ../cython/package-version.txt)')
		sagemath-standard==esyscmd(`printf $(sed "s/[.]p.*//;" ../sagelib/package-version.txt)')