src/pyproject.toml.m4: Merge all metadata from src/setup.cfg.m4, remo…

…ve src/setup.cfg.m4, update docs

bootstrap

@@ -232,8 +232,7 @@ 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
+	src/requirements.txt
 
     # Update version
     echo "$NEWCONFVERSION" >$PKG/package-version.txt

build/bin/write-dockerfile.sh

@@ -236,7 +236,7 @@ $ADD Makefile VERSION.txt COPYING.txt condarc.yml README.md bootstrap bootstrap-
 $ADD config/config.rpath config/config.rpath
 $ADD src/doc/bootstrap src/doc/bootstrap
 $ADD src/bin src/bin
-$ADD src/Pipfile.m4 src/pyproject.toml.m4 src/requirements.txt.m4 src/setup.cfg.m4 src/VERSION.txt src/
+$ADD src/Pipfile.m4 src/pyproject.toml.m4 src/requirements.txt.m4 src/VERSION.txt src/
 $ADD m4 ./m4
 $ADD pkgs pkgs
 $ADD build ./build

build/pkgs/typing_extensions/version_requirements.txt

@@ -1,3 +1,3 @@
 # 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 >= 4.4.0; python_version<"3.11"

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)'
@@ -45,7 +45,7 @@ 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.m4` (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 +14,9 @@ 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), ``m4/pyproject_toml_metadata.m4`` (for
+the Sage library and 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

src/pyproject.toml.m4

@@ -1,29 +1,161 @@
+include(`sage_spkg_versions_toml.m4')dnl' -*- conf-toml -*-
 [build-system]
 # Minimum requirements for the build system to execute.
 requires = [
     "sage_setup[autogen]",
     # Some version of sage-conf is required.
     # Note that PEP517/518 have no notion of optional sage_spkg dependencies:
     # https://github.com/pypa/pip/issues/6144
-     esyscmd(`sage-get-system-packages install-requires-toml \
-        sage_conf      \
-        setuptools \
-        wheel          \
-        sage_setup     \
-        cypari         \
-        cysignals      \
-        cython         \
-        gmpy2          \
-        jinja2         \
-        jupyter_core   \
-        numpy          \
-        pkgconfig      \
-        pplpy          \
-        memory_allocator \
-                    ')]
+    SPKG_INSTALL_REQUIRES_sage_conf
+    SPKG_INSTALL_REQUIRES_setuptools
+    SPKG_INSTALL_REQUIRES_wheel
+    SPKG_INSTALL_REQUIRES_sage_setup
+    SPKG_INSTALL_REQUIRES_cypari
+    SPKG_INSTALL_REQUIRES_cysignals
+    SPKG_INSTALL_REQUIRES_cython
+    SPKG_INSTALL_REQUIRES_gmpy2
+    SPKG_INSTALL_REQUIRES_jupyter_core
+    SPKG_INSTALL_REQUIRES_memory_allocator
+    SPKG_INSTALL_REQUIRES_numpy
+    SPKG_INSTALL_REQUIRES_pkgconfig
+    SPKG_INSTALL_REQUIRES_pplpy
+]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "sagemath-standard"
+description = "Sage: Open Source Mathematics Software: Standard Python Library"
+dependencies = [
+    SPKG_INSTALL_REQUIRES_sage_conf
+    SPKG_INSTALL_REQUIRES_six
+dnl From build/pkgs/sagelib/dependencies
+    SPKG_INSTALL_REQUIRES_conway_polynomials
+    SPKG_INSTALL_REQUIRES_cypari
+    SPKG_INSTALL_REQUIRES_cysignals
+    SPKG_INSTALL_REQUIRES_cython
+    SPKG_INSTALL_REQUIRES_gmpy2
+    SPKG_INSTALL_REQUIRES_importlib_metadata
+    SPKG_INSTALL_REQUIRES_importlib_resources
+    SPKG_INSTALL_REQUIRES_jupyter_core
+    SPKG_INSTALL_REQUIRES_lrcalc_python
+    SPKG_INSTALL_REQUIRES_memory_allocator
+    SPKG_INSTALL_REQUIRES_numpy
+    SPKG_INSTALL_REQUIRES_pkgconfig
+    SPKG_INSTALL_REQUIRES_pplpy
+    SPKG_INSTALL_REQUIRES_primecountpy
+    SPKG_INSTALL_REQUIRES_requests
+    SPKG_INSTALL_REQUIRES_typing_extensions
+dnl From Makefile.in: SAGERUNTIME
+    SPKG_INSTALL_REQUIRES_ipython
+    SPKG_INSTALL_REQUIRES_pexpect
+dnl From Makefile.in: DOC_DEPENDENCIES
+    SPKG_INSTALL_REQUIRES_sphinx
+    SPKG_INSTALL_REQUIRES_networkx
+    SPKG_INSTALL_REQUIRES_scipy
+    SPKG_INSTALL_REQUIRES_sympy
+    SPKG_INSTALL_REQUIRES_matplotlib
+    SPKG_INSTALL_REQUIRES_pillow
+    SPKG_INSTALL_REQUIRES_mpmath
+    SPKG_INSTALL_REQUIRES_ipykernel
+    SPKG_INSTALL_REQUIRES_jupyter_client
+    SPKG_INSTALL_REQUIRES_ipywidgets
+    SPKG_INSTALL_REQUIRES_fpylll
+dnl pycryptosat  # Sage distribution installs it as part of cryptominisat. According to its README on https://pypi.org/project/pycryptosat/: "The pycryptosat python package compiles while compiling CryptoMiniSat. It cannot be compiled on its own, it must be compiled at the same time as CryptoMiniSat."
+dnl Packages with important upper version bounds
+    SPKG_INSTALL_REQUIRES_ptyprocess
+]
+dynamic = ["version"]
+include(`pyproject_toml_metadata.m4')dnl'
+
+[project.optional-dependencies]
+R = [
+    SPKG_INSTALL_REQUIRES_rpy2
+]
+
+[project.readme]
+file = "README.rst"
+content-type = "text/x-rst"
+
 [tool.conda-lock]
 platforms = [
     'osx-64', 'linux-64', 'linux-aarch64', 'osx-arm64'
 ]
+
+[tool.setuptools]
+script-files = [
+    # The sage script
+    "bin/sage",
+    # Other scripts that should be in the path also for OS packaging of sage:
+    "bin/sage-eval",
+    # Included because it is useful for doctesting/coverage testing user scripts too:
+    "bin/sage-runtests",
+    "bin/sage-fixdoctests",
+    "bin/sage-coverage",
+    # The following is deprecated but might still be used in user package install scripts
+    "bin/sage-cython",
+    # Helper scripts invoked by sage script
+    # (they would actually belong to something like libexec)
+    "bin/sage-cachegrind",
+    "bin/sage-callgrind",
+    "bin/sage-massif",
+    "bin/sage-omega",
+    "bin/sage-valgrind",
+    "bin/sage-venv-config",
+    "bin/sage-version.sh",
+    "bin/sage-cleaner",
+    # Only makes sense in sage-the-distribution. TODO: Move to another installation script.
+    "bin/sage-list-packages",
+    # Uncategorized scripts in alphabetical order
+    "bin/math-readline",
+    "bin/sage-env",
+    # sage-env-config -- installed by sage_conf
+    # sage-env-config.in -- not to be installed
+    "bin/sage-grep",
+    "bin/sage-grepdoc",
+    "bin/sage-inline-fortran",
+    "bin/sage-ipynb2rst",
+    "bin/sage-ipython",
+    "bin/sage-notebook",
+    "bin/sage-num-threads.py",
+    "bin/sage-preparse",
+    "bin/sage-python",
+    "bin/sage-run",
+    "bin/sage-run-cython",
+    "bin/sage-startuptime.py",
+    "bin/sage-update-version",
+]
+license-files = ["LICENSE.txt"]
+include-package-data = false
+
+[tool.setuptools.package-data]
+"sage.libs.gap" = ["sage.gaprc"]
+"sage.interfaces" = ["sage-maxima.lisp"]
+"sage.doctest" = ["tests/*"]
+"sage.repl.rich_output" = ["example*"]
+sage = [
+    "ext_data/*",
+    "ext_data/kenzo/*",
+    "ext_data/singular/*",
+    "ext_data/singular/function_field/*",
+    "ext_data/images/*",
+    "ext_data/doctest/*",
+    "ext_data/doctest/invalid/*",
+    "ext_data/gap/*",
+    "ext_data/gap/joyner/*",
+    "ext_data/mwrank/*",
+    "ext_data/notebook-ipython/*",
+    "ext_data/nbconvert/*",
+    "ext_data/graphs/*",
+    "ext_data/pari/*",
+    "ext_data/pari/dokchitser/*",
+    "ext_data/pari/buzzard/*",
+    "ext_data/pari/simon/*",
+    "ext_data/magma/*",
+    "ext_data/magma/latex/*",
+    "ext_data/magma/sage/*",
+    "ext_data/valgrind/*",
+    "ext_data/threejs/*",
+]
+
+[tool.setuptools.dynamic]
+version = {file = ["VERSION.txt"]}