Refactor sagemath-standard through sagemath-{categories,environment,repl}

.gitignore

@@ -177,6 +177,7 @@ build/bin/sage-build-env-config
 /pkgs/sagemath-objects/setup.cfg
 /pkgs/sagemath-categories/setup.cfg
 /pkgs/sagemath-environment/setup.cfg
+/pkgs/sagemath-standard/setup.cfg
 /pkgs/sagemath-repl/setup.cfg
 /pkgs/sagemath-objects/pyproject.toml
 /pkgs/sagemath-categories/pyproject.toml

build/pkgs/sagelib/dependencies

@@ -1,4 +1,4 @@
-FORCE $(SCRIPTS) arb boost_cropped $(BLAS) brial cliquer cypari cysignals cython ecl eclib ecm flint libgd gap giac givaro glpk gmpy2 gsl iml importlib_metadata importlib_resources jinja2 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 pycygwin $(PYTHON) requests rw sage_conf singular symmetrica typing_extensions $(PCFILES) | $(PYTHON_TOOLCHAIN) sage_setup
+FORCE $(SCRIPTS) arb boost_cropped $(BLAS) brial cliquer cypari cysignals cython ecl eclib ecm flint libgd gap giac givaro glpk gmpy2 gsl iml importlib_metadata importlib_resources jinja2 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 pycygwin $(PYTHON) requests rw sage_conf $(and $(or $(findstring yes,$(SAGE_WHEELS)),$(findstring no,$(SAGE_EDITABLE))), sagemath_objects sagemath_categories sagemath_environment sagemath_repl) singular symmetrica typing_extensions $(PCFILES) | $(PYTHON_TOOLCHAIN) python_build sage_setup
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/sagelib/spkg-install

@@ -65,7 +65,10 @@ if [ "$SAGE_EDITABLE" = yes ]; then
 
     if [ "$SAGE_WHEELS" = yes ]; then
         # Additionally build a wheel (for use in other venvs)
-        cd $SAGE_PKGS/sagelib/src && time sdh_setup_bdist_wheel && sdh_store_wheel .
+        cd $SAGE_PKGS/sagelib/src
+        DIST_DIR="$(mktemp -d)"
+        python3 -m build --no-isolation --outdir "$DIST_DIR"/dist . || sdh_die "Failure building sdist and wheel"
+        wheel=$(cd "$DIST_DIR" && sdh_store_and_pip_install_wheel . && echo $wheel)
     fi
 else
     # Make sure that an installed old version of sagelib in which sage is an ordinary package
@@ -75,10 +78,17 @@ else
     (cd "$SITEPACKAGESDIR" && rm -f sagemath-standard.egg-link)
 
     if [ "$SAGE_WHEELS" = yes ]; then
+        # First build the sdist, then build the wheel from the sdist.
+        # https://pypa-build.readthedocs.io/en/latest/#python--m-build
+        # (Important because sagemath-objects uses MANIFEST.in for filtering.)
+        DIST_DIR="$(mktemp -d)"
         # Use --no-build-isolation to avoid rebuilds because of dependencies:
         # Compiling sage/interfaces/sagespawn.pyx because it depends on /private/var/folders/38/wnh4gf1552g_crsjnv2vmmww0000gp/T/pip-build-env-609n5985/overlay/lib/python3.10/site-packages/Cython/Includes/posix/unistd.pxd
-        time sdh_pip_install --no-build-isolation .
+        python3 -m build --no-isolation --outdir "$DIST_DIR"/dist . || sdh_die "Failure building sdist and wheel"
+        wheel=$(cd "$DIST_DIR" && sdh_store_and_pip_install_wheel . && echo $wheel)
     else
+        # TODO: Deprecate this installation mode.
+        # Note this no longer does any cleaning!
         time python3 -u setup.py --no-user-cfg build install || exit 1
     fi
 fi

build/pkgs/sagemath_categories/type

@@ -1 +1 @@
-experimental
+standard

build/pkgs/sagemath_environment/type

@@ -1 +1 @@
-experimental
+standard

build/pkgs/sagemath_objects/spkg-install

@@ -17,11 +17,10 @@ export PIP_FIND_LINKS="file://$SAGE_SPKG_WHEELS"
 # First build the sdist, then build the wheel from the sdist.
 # https://pypa-build.readthedocs.io/en/latest/#python--m-build
 # (Important because sagemath-objects uses MANIFEST.in for filtering.)
-# Do not install the wheel.
 DIST_DIR="$(mktemp -d)"
 python3 -m build --outdir "$DIST_DIR"/dist . || sdh_die "Failure building sdist and wheel"
 
-wheel=$(cd "$DIST_DIR" && sdh_store_wheel . && echo $wheel)
+wheel=$(cd "$DIST_DIR" && sdh_store_and_pip_install_wheel . 1>&2 && echo $wheel)
 ls -l "$wheel"
 
 if [ "$SAGE_CHECK" != no ]; then

build/pkgs/sagemath_objects/type

@@ -1 +1 @@
-experimental
+standard

build/pkgs/sagemath_repl/type

@@ -1 +1 @@
-experimental
+standard

pkgs/sagemath-standard/MANIFEST.in

@@ -0,0 +1,85 @@
+include VERSION.txt
+
+global-include *.pxi *.pxd *.h *.hpp
+
+prune sage/ext/interpreters   # In particular, __init__.py must not be present in the distribution; or sage_setup.autogen.interpreters.rebuild will not generate the code
+prune sage_setup
+prune sage_docbuild
+prune doc
+
+#
+# Most C and C++ files are generated by Cython and should not
+# be included in the sdist.
+#
+global-exclude *.c
+global-exclude *.cpp
+
+#
+# List of C and C++ files that are actual source files,
+# NOT generated by Cython. The same list appears in SAGE_ROOT/.gitignore
+#
+include sage/cpython/debugimpl.c
+include sage/graphs/base/boost_interface.cpp
+include sage/graphs/cliquer/cl.c
+include sage/graphs/graph_decompositions/sage_tdlib.cpp
+include sage/libs/eclib/wrap.cpp
+include sage/libs/linkages/padics/relaxed/flint_helper.c
+include sage/misc/inherit_comparison_impl.c
+include sage/modular/arithgroup/farey.cpp
+include sage/modular/arithgroup/sl2z.cpp
+include sage/rings/bernmm/bern_modp.cpp
+include sage/rings/bernmm/bern_modp_util.cpp
+include sage/rings/bernmm/bern_rat.cpp
+include sage/rings/bernmm/bernmm-test.cpp
+include sage/rings/padics/transcendantal.c
+include sage/rings/polynomial/weil/power_sums.c
+include sage/schemes/hyperelliptic_curves/hypellfrob/hypellfrob.cpp
+include sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_ntl.cpp
+include sage/stats/distributions/dgs_bern.c
+include sage/stats/distributions/dgs_gauss_dp.c
+include sage/stats/distributions/dgs_gauss_mp.c
+include sage/symbolic/ginac/*.cpp
+# Also actual C++ source files.
+include sage/geometry/triangulation/triangulations.cc
+include sage/geometry/triangulation/data.cc
+include sage/geometry/triangulation/functions.cc
+
+# Exclude what is already shipped in sagemath-objects, sagemath-categories, sagemath-environment, sagemath-repl
+global-exclude all__*.py
+prune sage/misc
+include sage/misc/all.py
+include sage/misc/allocator.pxd
+include sage/misc/allocator.pyx
+include sage/misc/binary_tree.pxd
+include sage/misc/binary_tree.pyx
+include sage/misc/search.pxd
+include sage/misc/search.pyx
+# Exclude what is shipped in sagemath-objects
+prune sage/cpython
+prune sage/structure
+prune sage/libs/gmp
+# Exclude what is shipped in sagemath-categories
+prune sage/categories
+exclude sage/rings/ideal.*
+exclude sage/rings/ring.*
+prune sage/typeset
+# Exclude what is shipped in sagemath-environment
+exclude sage/env.py
+exclude sage/version.py
+prune sage/features
+# Exclude what is shipped in sagemath-repl
+prune sage/doctest
+prune sage/repl
+exclude sage/misc/banner.py
+exclude sage/misc/sagedoc.py
+exclude sage/misc/sage_input.py
+exclude sage/misc/sage_eval.py
+
+global-exclude __pycache__
+global-exclude *.py[co]
+global-exclude *.bak
+global-exclude *.so
+global-exclude *~
+prune .tox
+prune build
+prune dist

pkgs/sagemath-standard/setup-monolithic.cfg.m4

@@ -0,0 +1 @@
+../../src/setup.cfg.m4

pkgs/sagemath-standard/setup.cfg.m4

@@ -0,0 +1,171 @@
+# -*- conf-unix -*-
+[metadata]
+name = sagemath-standard
+version = file: VERSION.txt
+description = Sage: Open Source Mathematics Software: Standard Python Library
+long_description = file: README.rst
+long_description_content_type = text/x-rst
+license = GNU General Public License (GPL) v2 or later
+license_files = LICENSE.txt
+author = The Sage Developers
+author_email = [email protected]
+url = https://www.sagemath.org
+
+classifiers =
+    Development Status :: 6 - Mature
+    Intended Audience :: Education
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
+    Operating System :: POSIX
+    Operating System :: MacOS :: MacOS X
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: Implementation :: CPython
+    Topic :: Scientific/Engineering :: Mathematics
+
+[options]
+python_requires = >=3.8, <3.12
+install_requires =
+    esyscmd(`sage-get-system-packages install-requires \
+        sagemath_objects \
+        sagemath_categories \
+        sagemath_environment \
+        sagemath_repl \
+        sage_conf \
+        six \
+        | sed "2,\$s/^/    /;"')dnl'
+dnl From build/pkgs/sagelib/dependencies
+    esyscmd(`sage-get-system-packages install-requires \
+        cypari         \
+        cysignals      \
+        cython         \
+        gmpy2          \
+        jinja2         \
+        jupyter_core   \
+        lrcalc_python  \
+        memory_allocator \
+        numpy          \
+        pkgconfig      \
+        pplpy          \
+        primecountpy   \
+        requests       \
+        | sed "2,\$s/^/    /;"')dnl'
+dnl From Makefile.in: SAGERUNTIME
+    esyscmd(`sage-get-system-packages install-requires \
+        ipython        \
+        pexpect        \
+        | sed "2,\$s/^/    /;"')dnl'
+dnl From Makefile.in: DOC_DEPENDENCIES
+    esyscmd(`sage-get-system-packages install-requires \
+        sphinx         \
+        networkx       \
+        scipy          \
+        sympy          \
+        matplotlib     \
+        pillow         \
+        mpmath         \
+        ipykernel      \
+        jupyter_client \
+        ipywidgets     \
+        | sed "2,\$s/^/    /;"')dnl'
+dnl Other Python packages that are standard spkg, used in doctests
+    esyscmd(`sage-get-system-packages install-requires \
+        fpylll         \
+        | sed "2,\$s/^/    /;"')dnl'
+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
+    esyscmd(`sage-get-system-packages install-requires \
+        ptyprocess     \
+        | sed "2,\$s/^/    /;"')dnl'
+
+scripts =
+    # The sage script
+    # bin/sage                          -- installed by sagemath-environment
+    # Other scripts that should be in the path also for OS packaging of sage:
+    # bin/sage-eval                     -- installed by sagemath-repl
+    # Included because it is useful for doctesting/coverage testing user scripts too:
+    # bin/sage-runtests                 -- installed by sagemath-repl
+    # bin/sage-fixdoctests              -- installed by sagemath-repl
+    # bin/sage-coverage                 -- installed by sagemath-repl
+    # 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               -- installed by sagemath-repl
+    # bin/sage-callgrind                -- installed by sagemath-repl
+    # bin/sage-massif                   -- installed by sagemath-repl
+    # bin/sage-omega                    -- installed by sagemath-repl
+    # bin/sage-valgrind                 -- installed by sagemath-repl
+    # bin/sage-venv-config              -- installed by sagemath-environment
+    # bin/sage-version.sh               -- installed by sagemath-environment
+    # bin/sage-cleaner                  -- installed by sagemath-repl
+    # 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                      -- installed by sagemath-environment
+    # 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           -- installed by sagemath-repl
+    # bin/sage-ipynb2rst                -- installed by sagemath-repl
+    # bin/sage-ipython                  -- installed by sagemath-repl
+    # bin/sage-notebook                 -- installed by sagemath-repl
+    # bin/sage-num-threads.py           -- installed by sagemath-environment
+    # bin/sage-preparse                 -- installed by sagemath-repl
+    # bin/sage-python                   -- installed by sagemath-environment
+    bin/sage-rebase.bat
+    bin/sage-rebase.sh
+    bin/sage-rebaseall.bat
+    bin/sage-rebaseall.sh
+    # bin/sage-run                      -- installed by sagemath-repl
+    # bin/sage-run-cython               -- installed by sagemath-repl
+    # bin/sage-startuptime.py           -- installed by sagemath-repl
+    bin/sage-update-version
+
+[options.package_data]
+
+sage.libs.gap =
+    sage.gaprc
+
+sage.interfaces =
+    sage-maxima.lisp
+
+# sage.doctest =                        -- installed by sagemath-repl
+#     tests/*
+
+# sage.repl.rich_output =               -- installed by sagemath-repl
+#     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/*
+
+[options.extras_require]
+R = esyscmd(`sage-get-system-packages install-requires \
+        rpy2           \
+        | sed "2,\$s/^/    /;"')dnl'

src/pyproject.toml.m4

@@ -5,6 +5,9 @@ requires = [
     # 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 \
+        sagemath_environment \
+        sagemath_objects \
+        sagemath_categories \
         sage_conf      \
         setuptools     \
         wheel          \

src/sage/cpython/python_debug.pxd

@@ -9,7 +9,7 @@
 
 from cpython.ref cimport PyObject, PyTypeObject
 
-cdef extern from "sage/cpython/python_debug.h":
+cdef extern from "python_debug.h":
 
     # This is what is generally meant by "a debug build" of Python.
     # Implies Py_REF_DEBUG, Py_TRACE_REFS, and PYMALLOC_DEBUG (if

src/sage_setup/command/sage_install.py

@@ -93,9 +93,8 @@ def clean_stale_files(self):
         nobase_data_files = [(src_dir, [os.path.join(src_dir, filename) for filename in filenames])
                              for package, src_dir, build_dir, filenames in cmd_build_py.data_files]
 
-        # Clean install directory (usually, purelib and platlib are the same)
-        # and build directory.
-        output_dirs = [self.install_purelib, self.install_platlib, self.build_lib]
+        # Clean build directory.
+        output_dirs = [self.build_lib]
         from sage_setup.clean import clean_install_dir
         for output_dir in set(output_dirs):
             log.info('- cleaning {0}'.format(output_dir))