Merge pull request sagemath#303 from passagemath/sagemath-gfan

pkgs/sagemath-gfan: New

build/pkgs/sagemath_gfan/SPKG.rst

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

build/pkgs/sagemath_gfan/bootstrap

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+../sagelib/bootstrap

build/pkgs/sagemath_gfan/dependencies

@@ -0,0 +1 @@
+$(SAGE_ROOT)/pkgs/sagemath-gfan/pyproject.toml $(SAGE_ROOT)/pkgs/sagemath-gfan/MANIFEST.in  gfan cysignals | $(PYTHON_TOOLCHAIN) sage_setup sage_conf sagemath_environment cython pkgconfig $(PYTHON)

build/pkgs/sagemath_gfan/dependencies_check

@@ -0,0 +1 @@
+tox sagemath_modules sagemath_repl

build/pkgs/sagemath_gfan/package-version.txt

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

build/pkgs/sagemath_gfan/spkg-check

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+../sagemath_objects/spkg-check

build/pkgs/sagemath_gfan/spkg-install.in

@@ -0,0 +1,9 @@
+cd src
+
+export PIP_NO_INDEX=true
+export PIP_FIND_LINKS="file://$SAGE_SPKG_WHEELS"
+
+# Modularized install via wheels
+# --no-build-isolation so that declared build dependencies,
+# in particular sagemath-environment do not have to be present as wheels.
+sdh_pip_install --no-build-isolation .

build/pkgs/sagemath_gfan/spkg-src

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

build/pkgs/sagemath_gfan/src

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+../../../pkgs/sagemath-gfan

build/pkgs/sagemath_gfan/type

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+optional

build/pkgs/sagemath_gfan/version_requirements.txt

@@ -0,0 +1,2 @@
+# This file is updated on every release by the sage-update-version script
+passagemath-gfan ~= 10.4.44.0

pkgs/sagemath-gfan/MANIFEST.in

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

pkgs/sagemath-gfan/README.rst

@@ -0,0 +1,25 @@
+===========================================================
+passagemath: Groebner fans and tropical varieties with gfan
+===========================================================
+
+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 distribution package
+-----------------------------------------------
+
+This pip-installable source distribution ``passagemath-gfan`` provides an interface to gfan.

pkgs/sagemath-gfan/VERSION.txt

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

pkgs/sagemath-gfan/pyproject.toml.m4

@@ -0,0 +1,71 @@
+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_environment
+    SPKG_INSTALL_REQUIRES_cython
+    SPKG_INSTALL_REQUIRES_cysignals
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "passagemath-gfan"
+description = "passagemath: Groebner fans and tropical varieties with gfan"
+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_modules
+    SPKG_INSTALL_REQUIRES_sagemath_repl
+]
+
+[tool.cibuildwheel.linux]
+# Unfortunately CIBW_REPAIR_WHEEL_COMMAND does not expand {project} (and other placeholders),
+# so there is no clean way to refer to the repair_wheel.py script
+# https://github.com/pypa/cibuildwheel/issues/1931
+repair-wheel-command = [
+    'python3 -m pip install passagemath-conf',
+    'python3 pkgs/sagemath-gfan/repair_wheel.py {wheel}',
+    'auditwheel repair -w {dest_dir} {wheel}',
+]
+[tool.cibuildwheel.macos]
+repair-wheel-command = [
+    'python3 -m pip install passagemath-conf',
+    'python3 pkgs/sagemath-gfan/repair_wheel.py {wheel}',
+    'delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}',
+]
+
+[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/gfan",
+  "pkg:generic/gmp",
+  "pkg:generic/mpc",
+  "pkg:generic/mpfr",
+]
+
+dependencies = [
+]

pkgs/sagemath-gfan/repair_wheel.py

@@ -0,0 +1,17 @@
+# Add Maxima data to the wheel
+
+import os
+import shlex
+import sys
+
+from pathlib import Path
+
+from sage_conf import SAGE_LOCAL
+
+wheel = sys.argv[1]
+
+# SAGE_LOCAL/bin/gfan* --> sage_wheels/bin/gfan*
+command = f'ln -sf {shlex.quote(SAGE_LOCAL)} sage_wheels && zip -r {shlex.quote(wheel)} sage_wheels/bin/gfan*'
+print(f'Running {command}')
+sys.stdout.flush()
+os.system(command)

pkgs/sagemath-gfan/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-gfan/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-gfan/sage

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+../../src/sage

pkgs/sagemath-gfan/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-gfan'],
+           spkgs=['gfan'])

pkgs/sagemath-gfan/tox.ini

@@ -0,0 +1,123 @@
+# To build and test in the tox environment:
+#
+# ./sage -sh -c '(cd pkgs/sagemath-gfan && tox -v -v -v -e sagepython)'
+#
+# To test interactively:
+#
+# pkgs/sagemath-gfan/.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_gfan; import sage.rings.polynomial.gfan'
+
+    bash -c 'cd $(python -c "import sys; \"\" in sys.path and sys.path.remove(\"\"); from sage.env import SAGE_LIB; print(SAGE_LIB)") \
+        && sage-runtests -p --force-lib --initial --environment=sage.all__sagemath_gfan --probe all --baseline-stats-path=$KNOWN_TEST_FAILURES --optional=sage sage/rings/polynomial/groebner_fan.py sage/interfaces/gfan.py'
+
+[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

pkgs/sagemath-polyhedra/MANIFEST.in

@@ -5,7 +5,6 @@ include VERSION.txt
 exclude *.m4
 include requirements.txt
 
-include sage/interfaces/gfan.p*
 include sage/interfaces/polymake.p*
 
 graft sage/geometry
@@ -26,7 +25,6 @@ exclude sage/numerical/gauss_legendre.p*                # sagemath-modules
 exclude sage/numerical/optimize.p*                      # sagemath-modules
 exclude sage/numerical/backends/glpk*.p*                # sagemath-glpk
 
-include sage/rings/polynomial/groebner_fan.p*
 include sage/rings/polynomial/omega.py
 
 graft sage/schemes/toric

src/sage/all__sagemath_gfan.py

@@ -0,0 +1 @@
+# sage_setup: distribution = sagemath-gfan

src/sage/interfaces/all__sagemath_gfan.py

@@ -0,0 +1 @@
+# sage_setup: distribution = sagemath-gfan

src/sage/interfaces/gfan.py

@@ -1,4 +1,4 @@
-# sage_setup: distribution = sagemath-polyhedra
+# sage_setup: distribution = sagemath-gfan
 r"""
 Interface to Groebner Fan
 

src/sage/libs/all__sagemath_gfan.py

@@ -0,0 +1 @@
+# sage_setup: distribution = sagemath-gfan

src/sage/libs/gfan.pyx

@@ -0,0 +1 @@
+# sage_setup: distribution = sagemath-gfan

src/sage/rings/all__sagemath_gfan.py

@@ -0,0 +1 @@
+# sage_setup: distribution = sagemath-gfan

src/sage/rings/polynomial/all__sagemath_gfan.py

@@ -0,0 +1 @@
+# sage_setup: distribution = sagemath-gfan

src/sage/rings/polynomial/groebner_fan.py

@@ -1,4 +1,4 @@
-# sage_setup: distribution = sagemath-polyhedra
+# sage_setup: distribution = sagemath-gfan
 r"""
 Groebner Fans