Demote brial (= polybori) from standard to optional, add distribution sagemath-brial, enlarge sagemath-objects, sagemath-categories

.github/workflows/dist.yml

@@ -181,7 +181,7 @@ jobs:
       # SPKGs to install as system packages
       SPKGS: _bootstrap _prereq
       # Non-Python packages to install as spkgs
-      TARGETS_PRE: gmp mpfr mpc bliss coxeter3 mcqd meataxe sirocco boost_cropped tdlib
+      TARGETS_PRE: gmp mpfr mpc bliss coxeter3 mcqd meataxe sirocco boost_cropped tdlib brial
       CIBW_BUILD: "*${{ matrix.build }}*"
       # Disable building PyPy wheels on all platforms
       CIBW_SKIP: "pp*"
@@ -255,6 +255,10 @@ jobs:
         run: |
           "${{ steps.python.outputs.python-path }}" -m cibuildwheel unpacked/sagemath*bliss*
 
+      - name: sagemath-brial
+        run: |
+          "${{ steps.python.outputs.python-path }}" -m cibuildwheel unpacked/sagemath*brial*
+
       - name: sagemath-coxeter3
         run: |
           "${{ steps.python.outputs.python-path }}" -m cibuildwheel unpacked/sagemath*coxeter3*

.gitignore

@@ -221,6 +221,7 @@ build/pkgs/wheel/version_requirements.txt
 
 /pkgs/sagemath-objects/setup.cfg
 /pkgs/sagemath-bliss/setup.cfg
+/pkgs/sagemath-brial/setup.cfg
 /pkgs/sagemath-coxeter3/setup.cfg
 /pkgs/sagemath-mcqd/setup.cfg
 /pkgs/sagemath-meataxe/setup.cfg
@@ -231,6 +232,7 @@ build/pkgs/wheel/version_requirements.txt
 /pkgs/sagemath-repl/setup.cfg
 /pkgs/sagemath-objects/pyproject.toml
 /pkgs/sagemath-bliss/pyproject.toml
+/pkgs/sagemath-brial/pyproject.toml
 /pkgs/sagemath-coxeter3/pyproject.toml
 /pkgs/sagemath-mcqd/pyproject.toml
 /pkgs/sagemath-meataxe/pyproject.toml
@@ -241,6 +243,7 @@ build/pkgs/wheel/version_requirements.txt
 /pkgs/sagemath-repl/pyproject.toml
 /pkgs/sagemath-objects/requirements*.txt
 /pkgs/sagemath-bliss/requirements*.txt
+/pkgs/sagemath-brial/requirements*.txt
 /pkgs/sagemath-coxeter3/requirements*.txt
 /pkgs/sagemath-mcqd/requirements*.txt
 /pkgs/sagemath-meataxe/requirements*.txt

build/make/Makefile.in

@@ -146,7 +146,8 @@ PYPI_WHEEL_PACKAGES = $(PYPI_NOARCH_WHEEL_PACKAGES) \
 	sagemath_tdlib				\
 	sagemath_coxeter3 			\
 	sagemath_sirocco			\
-	sagemath_meataxe
+	sagemath_meataxe			\
+	sagemath_brial
 
 # sage_docbuild is here, not in PYPI_WHEEL_PACKAGES, because it depends on sagelib
 WHEEL_PACKAGES = $(PYPI_WHEEL_PACKAGES)		\

build/pkgs/sagelib/dependencies

@@ -1,4 +1,4 @@
-FORCE $(SCRIPTS) boost_cropped $(BLAS) brial cliquer cypari cysignals cython ecl eclib ecm flint libgd gap giac givaro glpk gmpy2 gsl iml importlib_metadata importlib_resources jupyter_core lcalc lrcalc_python libbraiding libhomfly libpng linbox m4ri m4rie memory_allocator mpc mpfi mpfr $(MP_LIBRARY) ntl numpy pari pip pkgconfig planarity ppl pplpy primesieve primecount primecountpy $(PYTHON) requests rw sage_conf singular symmetrica typing_extensions $(PCFILES) | $(PYTHON_TOOLCHAIN) sage_setup $(PYTHON) pythran
+FORCE $(SCRIPTS) boost_cropped $(BLAS) cliquer cypari cysignals cython ecl eclib ecm flint libgd gap giac givaro glpk gmpy2 gsl iml importlib_metadata importlib_resources jupyter_core lcalc lrcalc_python libbraiding libhomfly libpng linbox m4ri m4rie memory_allocator mpc mpfi mpfr $(MP_LIBRARY) ntl numpy pari pip pkgconfig planarity ppl pplpy primesieve primecount primecountpy $(PYTHON) requests rw sage_conf singular symmetrica typing_extensions $(PCFILES) | $(PYTHON_TOOLCHAIN) sage_setup $(PYTHON) pythran
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/sagelib/dependencies_optional

@@ -0,0 +1 @@
+brial

build/pkgs/sagemath_brial/SPKG.rst

@@ -0,0 +1 @@
+src/README.rst

build/pkgs/sagemath_brial/bootstrap

@@ -0,0 +1 @@
+../sagelib/bootstrap

build/pkgs/sagemath_brial/dependencies

@@ -0,0 +1 @@
+cypari memory_allocator brial sagelib | $(PYTHON_TOOLCHAIN) sage_setup cython pkgconfig $(PYTHON)

build/pkgs/sagemath_brial/dependencies_check

@@ -0,0 +1 @@
+../sagemath_categories/dependencies_check

build/pkgs/sagemath_brial/package-version.txt

@@ -0,0 +1 @@
+src/VERSION.txt

build/pkgs/sagemath_brial/spkg-check

@@ -0,0 +1 @@
+../sagemath_objects/spkg-check

build/pkgs/sagemath_brial/spkg-install.in

@@ -0,0 +1 @@
+../sagemath_tdlib/spkg-install.in

build/pkgs/sagemath_brial/spkg-src

@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+#
+# Script to prepare an sdist tarball for sagemath-brial
+# This script is not used during build.
+#
+# HOW TO MAKE THE TARBALL:
+# ./sage --sh build/pkgs/sagemath_brial/spkg-src
+
+if [ -z "$SAGE_ROOT" ] ; then
+    echo >&2 "Error - SAGE_ROOT undefined ... exiting"
+    echo >&2 "Maybe run 'sage -sh'?"
+    exit 1
+fi
+
+# Exit on failure
+set -e
+
+cd build/pkgs/sagemath_brial
+
+cd src
+# Get rid of old *.egg-info/SOURCES.txt
+rm -Rf *.egg-info
+
+python3 -m build --sdist --no-isolation --skip-dependency-check --outdir "$SAGE_DISTFILES"

build/pkgs/sagemath_brial/src

@@ -0,0 +1 @@
+../../../pkgs/sagemath-brial

build/pkgs/sagemath_brial/type

@@ -0,0 +1 @@
+standard

build/pkgs/sagemath_brial/version_requirements.txt

@@ -0,0 +1,2 @@
+# This file is updated on every release by the sage-update-version script
+sagemath-brial

pkgs/sagemath-brial/MANIFEST.in

@@ -0,0 +1,21 @@
+prune sage
+
+include VERSION.txt
+
+graft sage/libs/polybori
+graft sage/rings/polynomial/pbori
+
+global-exclude *.c
+global-exclude *.cpp
+
+global-exclude all__sagemath_*.py
+global-include all__sagemath_brial.py
+
+global-exclude __pycache__
+global-exclude *.py[co]
+global-exclude *.bak
+global-exclude *.so
+global-exclude *~
+prune .tox
+prune build
+prune dist

pkgs/sagemath-brial/README.rst

@@ -0,0 +1,30 @@
+=========================================================================
+ Sage: Open Source Mathematics Software: Boolean Ring Algebra with BRiAl
+=========================================================================
+
+About SageMath
+--------------
+
+   "Creating a Viable Open Source Alternative to
+    Magma, Maple, Mathematica, and MATLAB"
+
+   Copyright (C) 2005-2023 The Sage Development Team
+
+   https://www.sagemath.org
+
+SageMath fully supports all major Linux distributions, recent versions of
+macOS, and Windows (using Cygwin or Windows Subsystem for Linux).
+
+The traditional and recommended way to install SageMath is from source via
+Sage-the-distribution (https://www.sagemath.org/download-source.html).
+Sage-the-distribution first builds a large number of open source packages from
+source (unless it finds suitable versions installed in the system) and then
+installs the Sage Library (sagelib, implemented in Python and Cython).
+
+
+About this pip-installable source distribution
+----------------------------------------------
+
+This pip-installable source distribution ``sagemath-brial`` provides
+a Boolean Ring Algebra implementation using binary decision diagrams,
+implemented by the BRiAl library, the successor to PolyBoRi.

pkgs/sagemath-brial/VERSION.txt

@@ -0,0 +1 @@
+../../src/VERSION.txt

pkgs/sagemath-brial/pyproject.toml.m4

@@ -0,0 +1,57 @@
+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_pkgconfig
+    SPKG_INSTALL_REQUIRES_sage_setup
+    SPKG_INSTALL_REQUIRES_sagemath_categories
+    SPKG_INSTALL_REQUIRES_sagemath_environment
+    SPKG_INSTALL_REQUIRES_sagemath_objects
+    SPKG_INSTALL_REQUIRES_cython
+    SPKG_INSTALL_REQUIRES_cysignals
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "sagemath-brial"
+description = "Sage: Open Source Mathematics Software: Boolean Ring Algebra with BRiAl"
+dependencies = [
+    SPKG_INSTALL_REQUIRES_cysignals
+]
+dynamic = ["version"]
+include(`pyproject_toml_metadata.m4')dnl'
+
+[project.readme]
+file = "README.rst"
+content-type = "text/x-rst"
+
+[project.optional-dependencies]
+test = [
+     SPKG_INSTALL_REQUIRES_sagemath_categories
+     SPKG_INSTALL_REQUIRES_sagemath_repl
+]
+
+[tool.setuptools]
+include-package-data = false
+
+[tool.setuptools.dynamic]
+version = {file = ["VERSION.txt"]}
+
+[external]
+# External dependencies in the format proposed by https://peps.python.org/pep-0725
+build-requires = [
+  "virtual:compiler/c",
+  "virtual:compiler/cpp",
+  "pkg:generic/pkg-config",
+]
+
+host-requires = [
+  "pkg:generic/brial",
+  "pkg:generic/gmp",
+  "pkg:generic/mpc",
+  "pkg:generic/mpfr",
+]
+
+dependencies = [
+]

pkgs/sagemath-brial/requirements-editable.txt.m4

@@ -0,0 +1,6 @@
+include(`sage_spkg_versions.m4')dnl
+dnl Same as setup.cfg.m4 install_requires; FIXME: should pin to built wheels.
+SPKG_INSTALL_REQUIRES_gmpy2
+SPKG_INSTALL_REQUIRES_cysignals
+-e ../sagemath-objects
+-e ../sagemath-categories

pkgs/sagemath-brial/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)')

pkgs/sagemath-brial/sage

@@ -0,0 +1 @@
+../../src/sage

pkgs/sagemath-brial/setup.py

@@ -0,0 +1,11 @@
+#!/usr/bin/env python
+
+# PEP 517 builds do not have . in sys.path
+import os
+import sys
+sys.path.insert(0, os.path.dirname(__file__))
+
+from sage_setup import sage_setup
+
+sage_setup(['sagemath-brial'],
+           required_modules=('m4ri', 'libpng'))

pkgs/sagemath-brial/tox.ini

@@ -0,0 +1,120 @@
+# To build and test in the tox environment:
+#
+# ./sage -sh -c '(cd pkgs/sagemath-brial && tox -v -v -v -e sagepython)'
+#
+# To test interactively:
+#
+# pkgs/sagemath-brial/.tox/sagepython/bin/python
+#
+[tox]
+envlist =
+    sagepython-sagewheels-nopypi-norequirements
+
+requires =
+    # Auto-provision a modern tox.
+    # [pkgenv] added in 4.2 - https://tox.wiki/en/latest/upgrading.html#packaging-configuration-and-inheritance
+    # Because of https://github.com/tox-dev/tox/issues/3238, need <4.14.1
+    tox>=4.2
+    tox<4.14.1
+
+[pkgenv]
+# Environment in which to build the sdist.
+# https://tox.wiki/en/latest/upgrading.html#packaging-environments
+passenv =
+    # Variables set by .homebrew-build-env
+                             CPATH
+                             LIBRARY_PATH
+                             PKG_CONFIG_PATH
+    # Parallel build
+                             SAGE_NUM_THREADS
+                             SAGE_NUM_THREADS_PARALLEL
+                             MAKEFLAGS
+    # SAGE_VENV only for referring to the basepython or finding the wheels
+    sagepython, sagewheels:  SAGE_VENV
+    # Location of the wheels
+    sagewheels:              SAGE_SPKG_WHEELS
+
+setenv =
+    # We supply pip options by environment variables so that they
+    # apply both to the installation of the dependencies and of the package
+    sagewheels:              PIP_FIND_LINKS=file://{env:SAGE_SPKG_WHEELS:{env:SAGE_VENV:{toxinidir}/../../../../venv}/var/lib/sage/wheels}
+    nopypi:                  PIP_NO_INDEX=true
+
+[testenv]
+deps =
+    !norequirements:         -rrequirements.txt
+
+extras = test
+
+passenv =                    {[pkgenv]passenv}
+
+setenv =                     {[pkgenv]setenv}
+    # Sage scripts such as sage-runtests like to use $HOME/.sage
+                             HOME={envdir}
+    # Stop 'sage -t --installed' from picking up doc installed in SAGE_LOCAL
+                             SAGE_DOC=/doesnotexist
+                             KNOWN_TEST_FAILURES={toxinidir}/known-test-failures.json
+    # See src/bin/sage-env
+                             PYDEVD_DISABLE_FILE_VALIDATION=1
+
+allowlist_externals =
+    bash
+
+commands =
+    # Beware of the treacherous non-src layout. "./sage/" shadows the installed sage package.
+    {envpython} -c 'import sys; "" in sys.path and sys.path.remove(""); import sage.all__sagemath_brial; import sage.rings.polynomial.pbori'
+
+[testenv:.tox]
+# Allow access to PyPI for auto-provisioning a suitable tox version
+passenv =
+setenv =                     PIP_NO_INDEX=false
+
+[testenv:.pkg-sagepython]
+# Environment in which to build the sdist.
+# inherits from [pkgenv] - https://tox.wiki/en/latest/upgrading.html#packaging-environments
+basepython = {env:SAGE_VENV}/bin/python3
+
+[testenv:.pkg-sagepython-sagewheels-nopypi]
+passenv =                    {[pkgenv]passenv}
+                             SAGE_VENV
+                             SAGE_SPKG_WHEELS
+
+setenv =                     {[pkgenv]setenv}
+                             PIP_FIND_LINKS=file://{env:SAGE_SPKG_WHEELS:{env:SAGE_VENV:{toxinidir}/../../../../venv}/var/lib/sage/wheels}
+                             PIP_NO_INDEX=true
+
+basepython = {env:SAGE_VENV}/bin/python3
+
+[testenv:.pkg-sagepython-sagewheels-nopypi-editable]
+config_settings_build_editable =
+                             editable_mode = strict
+
+
+[testenv:sagepython]
+basepython = {env:SAGE_VENV}/bin/python3
+package_env = .pkg-sagepython
+
+[testenv:sagepython-sagewheels-nopypi]
+basepython = {env:SAGE_VENV}/bin/python3
+package_env = .pkg-sagepython-sagewheels-nopypi
+
+[testenv:sagepython-sagewheels]
+basepython = {env:SAGE_VENV}/bin/python
+package_env = .pkg-sagepython
+
+[testenv:sagepython-norequirements]
+basepython = {env:SAGE_VENV}/bin/python3
+package_env = .pkg-sagepython
+
+
+[testenv:sagepython-sagewheels-nopypi-norequirements]
+basepython = {env:SAGE_VENV}/bin/python3
+package_env = .pkg-sagepython-sagewheels-nopypi
+
+[testenv:sagepython-sagewheels-nopypi-editable]
+basepython = {env:SAGE_VENV}/bin/python3
+package_env = .pkg-sagepython-sagewheels-nopypi-editable
+package = editable
+deps = -r requirements-editable.txt
+config_settings_build_editable =
+                             editable_mode = strict