pkgs/sagemath-standard: Move metadata from setup.cfg to pyproject.toml

.ci/write-dockerfile.sh

@@ -275,7 +275,7 @@ $ADD Makefile VERSION.txt COPYING.txt condarc.yml README.md bootstrap bootstrap-
 $ADD config/config.rpath /new/config/config.rpath
 $ADD src/doc/bootstrap /new/src/doc/bootstrap
 $ADD src/bin /new/src/bin
-$ADD src/Pipfile.m4 src/pyproject.toml src/requirements.txt.m4 src/setup.cfg.m4 src/VERSION.txt /new/src/
+$ADD src/Pipfile.m4 src/pyproject.toml src/requirements.txt.m4 src/VERSION.txt /new/src/
 $ADD m4 /new/m4
 $ADD pkgs /new/pkgs
 $ADD build /new/build

.gitignore

@@ -185,19 +185,6 @@ __pycache__/
 build/temp.*/
 build/bin/sage-build-env-config
 
-# Generated files in build
-build/pkgs/cypari/version_requirements.txt
-build/pkgs/cysignals/version_requirements.txt
-build/pkgs/cython/version_requirements.txt
-build/pkgs/gmpy2/version_requirements.txt
-build/pkgs/jupyter_core/version_requirements.txt
-build/pkgs/memory_allocator/version_requirements.txt
-build/pkgs/numpy/version_requirements.txt
-build/pkgs/pkgconfig/version_requirements.txt
-build/pkgs/pplpy/version_requirements.txt
-build/pkgs/setuptools/version_requirements.txt
-build/pkgs/wheel/version_requirements.txt
-
 # Generated files in the top-level source trees
 /pkgs/*/build
 /pkgs/*/dist

Makefile

@@ -178,17 +178,6 @@ bootstrap-clean:
 	rm -f src/Pipfile
 	rm -f src/requirements.txt
 	rm -f src/setup.cfg
-	rm -f build/pkgs/cypari/version_requirements.txt
-	rm -f build/pkgs/cysignals/version_requirements.txt
-	rm -f build/pkgs/cython/version_requirements.txt
-	rm -f build/pkgs/gmpy2/version_requirements.txt
-	rm -f build/pkgs/jupyter_core/version_requirements.txt
-	rm -f build/pkgs/memory_allocator/version_requirements.txt
-	rm -f build/pkgs/numpy/version_requirements.txt
-	rm -f build/pkgs/pkgconfig/version_requirements.txt
-	rm -f build/pkgs/pplpy/version_requirements.txt
-	rm -f build/pkgs/setuptools/version_requirements.txt
-	rm -f build/pkgs/wheel/version_requirements.txt
 
 # Remove absolutely everything which isn't part of the git repo
 maintainer-clean: distclean bootstrap-clean

bootstrap

@@ -33,15 +33,6 @@ MAKE="${MAKE:-make}"
 
 
 bootstrap () {
-    for pkgname in cypari cysignals cython gmpy2 jupyter_core memory_allocator numpy pkgconfig pplpy setuptools wheel; do
-        # Write the version_requirements.txt files for dependencies declared in pyproject.toml
-        target=build/pkgs/${pkgname}/version_requirements.txt
-        if [ "${BOOTSTRAP_QUIET}" = "no" ]; then
-            echo "bootstrap:$LINENO: installing '"$target"'"
-        fi
-        echo "# Generated by SAGE_ROOT/bootstrap based on src/pyproject.toml; do not edit directly" > $target
-        sage-get-system-packages install-requires ${pkgname} >> $target
-    done
     for a in m4/sage_spkg_configures.m4 m4/sage_spkg_versions.m4 m4/sage_spkg_versions_toml.m4; do
         if [ "${BOOTSTRAP_QUIET}" = "no" ]; then
             echo "bootstrap:$LINENO: installing '"$a"'"
@@ -232,19 +223,7 @@ save () {
 	src/environment-optional-3.[89].yml src/environment-optional-3.1[0-9].yml \
 	src/Pipfile \
 	src/pyproject.toml \
-	src/requirements.txt \
-	src/setup.cfg \
-	build/pkgs/cypari/version_requirements.txt \
-	build/pkgs/cysignals/version_requirements.txt \
-	build/pkgs/cython/version_requirements.txt \
-	build/pkgs/gmpy2/version_requirements.txt \
-	build/pkgs/jupyter_core/version_requirements.txt \
-	build/pkgs/memory_allocator/version_requirements.txt \
-	build/pkgs/numpy/version_requirements.txt \
-	build/pkgs/pkgconfig/version_requirements.txt \
-	build/pkgs/pplpy/version_requirements.txt \
-	build/pkgs/setuptools/version_requirements.txt \
-	build/pkgs/wheel/version_requirements.txt
+	src/requirements.txt
 
     # Update version; this re-computes the checksum
     sage-package update configure "$NEWCONFVERSION"

build/bin/sage-get-system-packages

@@ -101,9 +101,14 @@ for PKG_BASE in $SPKGS; do
             *pyproject.toml)
                 SYSTEM_PACKAGES_FILE="$SAGE_ROOT"/$NAME
                 if [ -f "$SYSTEM_PACKAGES_FILE" ]; then
-                    # Extract from the "requires" block in src/pyproject.toml
+                    # Extract from src/pyproject.toml:
+                    #  - from the "[build-system] requires" value
+                    #  - from "[project] dependencies",
+                    #  - from "[project.optional-dependencies]"
                     # Packages are in the format "'sage-conf ~= 10.3b3',"
-                    PACKAGE_INFO=$(sed -n '/requires *= *\[/,/^\]/s/^ *'\''\('$PKG_BASE'.*\)'\'',/\1/p' "$SAGE_ROOT/src/pyproject.toml")
+                    # Accept dashes and underscores in package names as equivalent:
+                    PKG_REGEX=$(echo $PKG_BASE | sed 's/[-_]/[-_]/g')
+                    PACKAGE_INFO=$(sed -En '/(requires|dependencies|R) *= *\[/,/^\]/s/^ *'\''('$PKG_REGEX'.*)'\'',/\1/p' "$SAGE_ROOT/src/pyproject.toml" | sort -u)
                     if [ -n "$PACKAGE_INFO" ]; then
                         echo "$PACKAGE_INFO" | ${STRIP_COMMENTS}
                         [ $SYSTEM = versions ] || break

build/pkgs/conway_polynomials/version_requirements.txt

@@ -1 +1 @@
-conway-polynomials >=0.8
+conway-polynomials

build/pkgs/cypari/version_requirements.txt

@@ -0,0 +1 @@
+cypari2

build/pkgs/cysignals/version_requirements.txt

@@ -0,0 +1 @@
+cysignals

build/pkgs/cython/version_requirements.txt

@@ -0,0 +1 @@
+cython

build/pkgs/fpylll/version_requirements.txt

@@ -1 +1 @@
-fpylll >=0.5.9
+fpylll

build/pkgs/gmpy2/version_requirements.txt

@@ -0,0 +1 @@
+gmpy2

build/pkgs/importlib_metadata/version_requirements.txt

@@ -1,3 +1 @@
-# According to https://pypi.org/project/importlib-metadata/,
-# 4.13 provides the features of Python 3.11 importlib.metadata
-importlib_metadata >=4.13; python_version<"3.11"
+importlib_metadata

build/pkgs/importlib_resources/version_requirements.txt

@@ -1,3 +1 @@
-# According to https://pypi.org/project/importlib-resources/,
-# version 5.7 provides the features of Python 3.11 importlib.resources
-importlib_resources >= 5.7; python_version<"3.11"
+importlib_resources

build/pkgs/ipykernel/version_requirements.txt

@@ -1 +1 @@
-ipykernel >=5.2.1
+ipykernel

build/pkgs/ipython/version_requirements.txt

@@ -1 +1 @@
-ipython >=7.13.0
+ipython

build/pkgs/ipywidgets/version_requirements.txt

@@ -1 +1 @@
-ipywidgets >=7.5.1
+ipywidgets

build/pkgs/jupyter_core/version_requirements.txt

@@ -0,0 +1 @@
+jupyter-core

build/pkgs/lrcalc_python/version_requirements.txt

@@ -1 +1 @@
-lrcalc ~=2.1
+lrcalc

build/pkgs/matplotlib/version_requirements.txt

@@ -1,3 +1 @@
-# Issue #33642: Set lower bound for use of matplotlib color maps introduced in #33491,
-# and to suppress deprecation warnings (https://github.com/matplotlib/matplotlib/pull/21073)
-matplotlib >=3.5.1
+matplotlib

build/pkgs/memory_allocator/version_requirements.txt

@@ -0,0 +1 @@
+memory_allocator

build/pkgs/mpmath/version_requirements.txt

@@ -1 +1 @@
-mpmath >=1.1.0
+mpmath

build/pkgs/networkx/version_requirements.txt

@@ -1 +1 @@
-networkx >=2.4
+networkx

build/pkgs/numpy/version_requirements.txt

@@ -0,0 +1 @@
+numpy

build/pkgs/pexpect/version_requirements.txt

@@ -1 +1 @@
-pexpect >=4.8.0
+pexpect

build/pkgs/pillow/version_requirements.txt

@@ -1 +1 @@
-pillow >=7.2.0
+pillow

build/pkgs/pkgconfig/version_requirements.txt

@@ -0,0 +1 @@
+pkgconfig

build/pkgs/pplpy/version_requirements.txt

@@ -0,0 +1 @@
+pplpy

build/pkgs/ptyprocess/version_requirements.txt

@@ -1 +1 @@
-ptyprocess > 0.5
+ptyprocess

build/pkgs/requests/version_requirements.txt

@@ -1 +1 @@
-requests >=2.13.0
+requests

build/pkgs/rpy2/version_requirements.txt

@@ -1 +1 @@
-rpy2 >=3.3
+rpy2

build/pkgs/scipy/version_requirements.txt

@@ -1,7 +1 @@
-# 1.8 is known good version.
-# Per https://docs.scipy.org/doc/scipy/dev/core-dev/index.html#version-numbering
-# and https://docs.scipy.org/doc/scipy/dev/core-dev/index.html#deprecations,
-# deprecations cannot be introduced in micro releases.
-# SciPy devs wait "at least 6 months", "in practice two (minor) releases"
-# from deprecation to removal of a feature.
-scipy >=1.5
+scipy

build/pkgs/setuptools/version_requirements.txt

@@ -0,0 +1 @@
+setuptools

build/pkgs/six/version_requirements.txt

@@ -1 +1 @@
-six >=1.15.0
+six

build/pkgs/sympy/version_requirements.txt

@@ -1 +1 @@
-sympy >=1.6, <2.0
+sympy

build/pkgs/typing_extensions/version_requirements.txt

@@ -1,3 +1 @@
-# According to https://github.com/python/typing_extensions/blob/main/CHANGELOG.md,
-# version 4.4.0 adds another Python 3.11 typing backport
-typing_extensions >= 4.4.0; python_version<'3.11'
+typing_extensions

build/pkgs/wheel/version_requirements.txt

@@ -0,0 +1 @@
+wheel

pkgs/sagemath-standard/tox.ini

@@ -17,7 +17,7 @@
 [tox]
 envlist =
     # Build and test without using the concrete dependencies specified by requirements.txt,
-    # using the dependencies declared in pyproject.toml and setup.cfg (install-requires) only:
+    # using the dependencies declared in pyproject.toml (build-system requires, dependencies) only:
     # Still use ONLY the wheels built and stored by the Sage distribution (no PyPI).
     #
     #   ./sage -sh -c '(cd pkgs/sagemath-standard && tox -v -v -v -e sagepython-sagewheels-nopypi-norequirements)'
@@ -58,7 +58,7 @@ envlist =
     #
     #   ./sage -sh -c '(cd pkgs/sagemath-standard && tox -v -v -v -e sagepython-sagewheels-pipenv-dist)'
     #
-    # Build using the dependencies declared in pyproject.toml and setup.cfg (install-requires) only.
+    # Build using the dependencies declared in pyproject.toml (build-system requires, dependencies) only:
     # Use the wheels built and stored by the Sage distribution,
     # and additionally allow packages from PyPI.
     #

src/Pipfile.m4

@@ -6,17 +6,17 @@ url = "https://pypi.org/simple"
 verify_ssl = true
 
 [dev-packages]
-## We do not list packages that are already declared as install_requires
-## in setup.cfg
+## We do not list packages that are already declared as dependencies (install_requires)
+## in pyproject.toml
 pycodestyle = "*"
 tox = "*"
 pytest = "*"
 rope = "*"
 six = "*"
 
 [packages]
-## We do not list packages that are already declared as install_requires
-## in setup.cfg
+## We do not list packages that are already declared as dependencies (install_requires)
+## in pyproject.toml
 
 [packages.e1839a8]
 path = "."

src/doc/en/developer/coding_basics.rst

@@ -193,8 +193,8 @@ included in one of the following places:
   This practice is deprecated, see :issue:`33037`.
 
 In all cases, the files must be listed (explicitly or via wildcards) in
-the section ``options.package_data`` of the file
-:sage_root:`pkgs/sagemath-standard/setup.cfg.m4` (or the corresponding
+the section ``[tool.setuptools.package-data]`` of the file
+:sage_root:`SAGE_ROOT/pkgs/sagemath-standard/pyproject.toml` (or the corresponding
 file of another distribution).
 
 Large data files should not be added to the Sage source tree. Instead, it

src/doc/en/developer/coding_in_python.rst

@@ -14,8 +14,10 @@ Python language standard
 
 Sage library code needs to be compatible with all versions of Python
 that Sage supports.  The information regarding the supported versions
-can be found in the files ``build/pkgs/python3/spkg-configure.m4`` and
-``src/setup.cfg.m4``.
+can be found in the files ``build/pkgs/python3/spkg-configure.m4``
+(for the Sage distribution), ``src/pyproject.toml`` (for the Sage
+library), and ``m4/pyproject_toml_metadata.m4`` (for most other
+distribution packages in ``pkgs/``).
 
 Python 3.9 is the oldest supported version.  Hence,
 all language and library features that are available in Python 3.9 can

src/doc/en/developer/packaging_sage_library.rst

@@ -174,8 +174,7 @@ The source directory of a distribution package, such as
 
     $ ./sage --fixdistributions --set all --from-egg-info
 
-- `pyproject.toml <https://pip.pypa.io/en/stable/reference/build-system/pyproject-toml/>`_,
-  `setup.cfg <https://setuptools.pypa.io/en/latest/userguide/declarative_config.html>`_,
+- `pyproject.toml <https://pip.pypa.io/en/stable/reference/build-system/pyproject-toml/>`_
   and `requirements.txt <https://pip.pypa.io/en/stable/user_guide/#requirements-files>`_ --
   standard Python packaging metadata, declaring the distribution name, dependencies,
   etc.
@@ -288,8 +287,9 @@ modules must be part of the distribution, or provided by another
 distribution -- which then must be declared as a run-time dependency.
 
 *Declaring run-time dependencies:* These dependencies are declared in
-``setup.cfg`` (generated from ``setup.cfg.m4``) as
-`install_requires <https://setuptools.pypa.io/en/latest/userguide/dependency_management.html#declaring-required-dependency>`_.
+``pyproject.toml`` (generated from ``pyproject.toml.m4``) as
+`[project] dependencies <https://setuptools.pypa.io/en/latest/userguide/dependency_management.html#declaring-required-dependency>`_ (in the older terminology of ``setup.cfg`` and ``setup.py``,
+these dependencies were known as ``install_requires``).
 
 *Reducing module-level run-time dependencies:*
 
@@ -467,14 +467,17 @@ features, which will only be working if the user also has installed
 **sagemath-symbolics**.
 
 *Declaring optional run-time dependencies:* It is possible to declare
-such optional dependencies as `extras_require <https://setuptools.pypa.io/en/latest/userguide/dependency_management.html#optional-dependencies>`_ in ``setup.cfg``
-(generated from ``setup.cfg.m4``).  This is a very limited mechanism
+such dependencies as `[project.optional-dependencies] <https://setuptools.pypa.io/en/latest/userguide/dependency_management.html#optional-dependencies>`_ in ``pyproject.toml``
+(generated from ``pyproject.toml.m4``).
+(In the older terminology of ``setup.cfg`` and ``setup.py``,
+these optional dependencies were known as ``extras_require``.)
+This is a very limited mechanism
 -- in particular it does not affect the build phase of the
 distribution in any way. It basically only provides a way to give a
 nickname to a distribution that can be installed as an add-on.
 
-In our example, we could declare an ``extras_require`` so that users
-could use ``pip install sagemath-coding[symbolics]``.
+In our example, we could declare an optional dependency so that users
+could use ``pip install "sagemath-coding[symbolics]"``.
 
 
 Doctest-only dependencies
@@ -516,7 +519,7 @@ The version information for dependencies comes from the files
 ``build/pkgs/*/package-version.txt``.  We use the
 `m4 <https://www.gnu.org/software/m4/manual/html_node/index.html>`_
 macro processor to insert the version information in the generated files
-``pyproject.toml``, ``setup.cfg``, ``requirements.txt``.
+``pyproject.toml`` and ``requirements.txt``.
 
 
 Hierarchy of distribution packages
@@ -546,8 +549,8 @@ Hierarchy of distribution packages
     sphinx_plot(g, figsize=(8, 4), axes=False)
 
 
-Solid arrows indicate ``install_requires``, i.e., a declared runtime dependency.
-Dashed arrows indicate ``extras_require``, i.e., a declared optional runtime dependency.
+Solid arrows indicate declared runtime dependencies (``install_requires``).
+Dashed arrows indicate declared optional runtime dependencies (``extras_require``).
 Not shown in the diagram are build dependencies and optional dependencies for testing.
 
 - `sage_conf <https://pypi.org/project/sage-conf/>`_ is a configuration