Merge branch 'develop' of https://github.com/sagemath/sage into publi…

…c/build/doc_build_ci

.gitignore

@@ -163,6 +163,14 @@ build/bin/sage-build-env-config
 /pkgs/*/*.egg-info
 /pkgs/*/.tox
 
+/pkgs/sagemath-objects/setup.cfg
+/pkgs/sagemath-categories/setup.cfg
+/pkgs/sagemath-objects/pyproject.toml
+/pkgs/sagemath-categories/pyproject.toml
+/pkgs/sagemath-objects/requirements.txt
+/pkgs/sagemath-categories/requirements.txt
+/pkgs/sagemath-categories/MANIFEST.in
+
 # same for old locations - before Trac #31577
 /build/pkgs/*/src/build
 /build/pkgs/*/src/dist

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.5", 
-    "version": "9.5", 
+    "title": "sagemath/sage: 9.6.beta0", 
+    "version": "9.6.beta0", 
     "upload_type": "software", 
-    "publication_date": "2022-01-30", 
+    "publication_date": "2022-02-06", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.5", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.6.beta0", 
             "relation": "isSupplementTo"
         }, 
         {

Makefile

@@ -85,6 +85,8 @@ pypi-sdists: sage_setup
 	./sage --sh build/pkgs/sage_docbuild/spkg-src
 	./sage --sh build/pkgs/sage_setup/spkg-src
 	./sage --sh build/pkgs/sagelib/spkg-src
+	./sage --sh build/pkgs/sagemath_objects/spkg-src
+	./sage --sh build/pkgs/sagemath_categories/spkg-src
 	@echo "Built sdists are in upstream/"
 
 # ssl: build Sage, and also install pyOpenSSL. This is necessary for
@@ -228,7 +230,7 @@ PTESTALL = ./sage -t -p --all
 # When the documentation is installed, "optional" also includes all tests marked 'sagemath_doc_html',
 # see https://trac.sagemath.org/ticket/25345, https://trac.sagemath.org/ticket/26110, and
 # https://trac.sagemath.org/ticket/32759
-TESTALL_FLAGS = --optional=sage,optional,external,build
+TESTALL_FLAGS = --optional=sage,optional,external
 
 test: all
 	$(TESTALL) --logfile=logs/test.log

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.5, Release Date: 2022-01-30
+SageMath version 9.6.beta0, Release Date: 2022-02-06

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=4406875a18bd9487a85484a2917a276e85f9b31e
-md5=c665b2fdf3f2a7325d4d4a8d34d1073f
-cksum=3749171882
+sha1=345924fc41ea858557c397fb38060606c868b0bd
+md5=2e5d32301a1c1debf4ec508ebc157ec2
+cksum=1618326589

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-2e5d421a71304586f059863c84e61e5d0de00be9
+f0df3d8b40169709426fd20a9f71cdcb30851c90

build/pkgs/cython/checksums.ini

@@ -1,5 +1,5 @@
 tarball=Cython-VERSION.tar.gz
-sha1=21187175b7da94020e662c04f805d580f1071880
-md5=81aff945f5bfdfb86e7a5d24f5467668
-cksum=2423037501
+sha1=bda825a34f18c11889562466264e29a8cb0e8806
+md5=1e1edbb3d41e0e5a0eec98288ce113f2
+cksum=169454778
 upstream_url=https://pypi.io/packages/source/C/Cython/Cython-VERSION.tar.gz

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-0.29.24
+0.29.25

build/pkgs/igraph/checksums.ini

@@ -1,5 +1,5 @@
 tarball=igraph-VERSION.tar.gz
-sha1=754908e45b31883107b802470779310cbb7c64d4
-md5=b063648d9a0a8de11b3fa886837f1819
-cksum=3580664179
+sha1=34aa12fbb76bf383e6c80d3935351d63b7d09c10
+md5=81f181c39a066075acb8aa0a087b97a0
+cksum=1808520323
 upstream_url=https://github.com/igraph/igraph/releases/download/VERSION/igraph-VERSION.tar.gz

build/pkgs/igraph/dependencies

@@ -1,4 +1,4 @@
-$(MP_LIBRARY) glpk $(BLAS) libxml2
+$(MP_LIBRARY) glpk $(BLAS) libxml2 suitesparse | cmake
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/igraph/package-version.txt

@@ -1 +1 @@
-0.8.3
+0.9.5

build/pkgs/igraph/spkg-install.in

@@ -1,5 +1,21 @@
 export CFLAGS="$CFLAGS -Wno-strict-prototypes -Wno-implicit-function-declaration"
 cd src
-sdh_configure --with-external-blas --with-external-lapack --with-external-glpk
+mkdir build
+cd build
+# https://igraph.org/c/doc/igraph-Installation.html
+sdh_cmake -DCMAKE_VERBOSE_MAKEFILE=ON \
+          -DBUILD_STATIC_LIBS=OFF \
+          -DBUILD_SHARED_LIBS=ON \
+          -DIGRAPH_USE_INTERNAL_GLPK=OFF \
+          -DIGRAPH_USE_INTERNAL_GMP=OFF \
+          -DBLA_VENDOR=OpenBLAS \
+          -DBLAS_LIBRARIES="$(pkg-config --libs blas)" \
+          -DLAPACK_LIBRARIES="$(pkg-config --libs lapack)" \
+          -DIGRAPH_USE_INTERNAL_BLAS=OFF \
+          -DIGRAPH_USE_INTERNAL_LAPACK=OFF \
+          -DIGRAPH_USE_INTERNAL_SUITESPARSE=OFF \
+          -DIGRAPH_GLPK_SUPPORT=ON \
+          -DIGRAPH_GRAPHML_SUPPORT=ON \
+          ..
 sdh_make
-sdh_make_install -j1
+sdh_make_install

build/pkgs/pari_jupyter/SPKG.rst

@@ -0,0 +1,27 @@
+pari_jupyter: A Jupyter kernel for PARI/GP
+==========================================
+
+Description
+-----------
+
+A Jupyter kernel for PARI/GP
+
+License
+-------
+
+GPL version 3 or later
+
+
+Upstream Contact
+----------------
+
+-  https://github.com/sagemath/pari-jupyter
+
+Dependencies
+------------
+
+-  Python >= 3.6.1
+-  Jupyter 4
+-  PARI version 2.13 or later
+-  Readline (any version which works with PARI)
+-  Optional: Cython version 0.25 or later

build/pkgs/pari_jupyter/checksums.ini

@@ -0,0 +1,5 @@
+tarball=pari-jupyter-VERSION.tar.gz
+sha1=442ab166c9229df1ad1b40e26fb6d0c23b8282f4
+md5=2fdaa74ca8502aa8832c4c3eeb49d8c3
+cksum=1047550915
+upstream_url=https://pypi.io/packages/source/p/pari_jupyter/pari-jupyter-VERSION.tar.gz

build/pkgs/pari_jupyter/dependencies

@@ -0,0 +1 @@
+$(PYTHON) pari | $(PYTHON_TOOLCHAIN) cython notebook jupyter_core

build/pkgs/pari_jupyter/distros/conda.txt

@@ -0,0 +1 @@
+pari_jupyter

build/pkgs/pari_jupyter/distros/repology.txt

@@ -0,0 +1,2 @@
+pari-jupyter
+python:pari-jupyter

build/pkgs/pari_jupyter/install-requires.txt

@@ -0,0 +1 @@
+pari_jupyter >=1.3.2

build/pkgs/pari_jupyter/package-version.txt

@@ -0,0 +1 @@
+1.4.0

build/pkgs/pari_jupyter/spkg-install.in

@@ -0,0 +1 @@
+cd src && sdh_pip_install .

build/pkgs/pari_jupyter/type

@@ -0,0 +1 @@
+optional

build/pkgs/python_igraph/checksums.ini

@@ -1,5 +1,5 @@
 tarball=python-igraph-VERSION.tar.gz
-sha1=c54c5f5b533979f93172b75e422508973e6a4f54
-md5=dcc3b722a9772b43a769940815c501f7
-cksum=794576917
-upstream_url=https://github.com/igraph/python-igraph/releases/download/VERSION/python-igraph-VERSION.tar.gz
+sha1=42f92301e3a02bc1bb9d8ceb15dd31a350863cb5
+md5=047e02f58142210a26c190ed6b617aef
+cksum=3702659607
+upstream_url=https://pypi.io/packages/source/i/igraph/igraph-VERSION.tar.gz

build/pkgs/python_igraph/install-requires.txt

@@ -1 +1 @@
-python_igraph >=0.7.1999
+igraph

build/pkgs/python_igraph/package-version.txt

@@ -1 +1 @@
-0.8.3
+0.9.8

build/pkgs/sage_setup/install-requires.txt

@@ -1 +1 @@
-sage-setup
+sage-setup ~= 9.5.b6

build/pkgs/sagelib/bootstrap

@@ -4,7 +4,7 @@ for infile in src/*.m4; do
     if [ -f "$infile" ]; then
         outfile="src/$(basename $infile .m4)"
         if [ "${BOOTSTRAP_QUIET}" = "no" ]; then
-            echo "$0: installing build/pkgs/sagelib/$outfile"
+            echo "$0: installing $(pwd)/$outfile"
         fi
         m4 "$infile" > "$outfile"
     fi

build/pkgs/sagelib/package-version.txt

@@ -1 +1 @@
-9.5
+9.6.beta0

build/pkgs/sagelib/spkg-install

@@ -14,8 +14,7 @@ fi
 ## Building takes places in the build/ subdirectory.
 ##
 ## As a special exception, we feed SAGE_PKGS and SAGE_SPKG_INST.
-## They are needed by src/sage_setup/optional_extension.py
-## via src/sage/misc/package.py.  See meta-ticket #28815 for planned changes to this.
+## They are needed by src/sage/misc/package.py.  See meta-ticket #28815 for planned changes to this.
 
 export SAGE_PKGS="$SAGE_ROOT"/build/pkgs
 export SAGE_ROOT=/doesnotexist

build/pkgs/sagemath_categories/SPKG.rst

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

build/pkgs/sagemath_categories/bootstrap

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

build/pkgs/sagemath_categories/dependencies

@@ -0,0 +1 @@
+../sagemath_objects/dependencies

build/pkgs/sagemath_categories/package-version.txt

@@ -0,0 +1 @@
+../sagelib/package-version.txt

build/pkgs/sagemath_categories/spkg-install

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

build/pkgs/sagemath_categories/spkg-src

@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+#
+# Script to prepare an sdist tarball for sagemath-categories
+# This script is not used during build.
+#
+# HOW TO MAKE THE TARBALL:
+# ./sage --sh build/pkgs/sagemath_categories/spkg-src
+
+if [ -z "$SAGE_ROOT" ] ; then
+    echo >&2 "Error - SAGE_ROOT undefined ... exiting"
+    echo >&2 "Maybe run 'sage -sh'?"
+    exit 1
+fi
+
+# Exit on failure
+set -e
+
+cd build/pkgs/sagemath_categories
+
+cd src
+python3 -u setup.py --no-user-cfg sdist --dist-dir "$SAGE_DISTFILES"

build/pkgs/sagemath_categories/src

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

build/pkgs/sagemath_categories/type

@@ -0,0 +1 @@
+experimental

build/pkgs/sagemath_objects/SPKG.rst

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

build/pkgs/sagemath_objects/bootstrap

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

build/pkgs/sagemath_objects/dependencies

@@ -0,0 +1,4 @@
+FORCE $(PYTHON) cysignals gmpy2 ipython | $(PYTHON_TOOLCHAIN) cython pkgconfig $(and $(filter-out no,$(SAGE_CHECK)), tox)
+
+# FORCE: Always run the spkg-install script
+# ipython - for the doctester

build/pkgs/sagemath_objects/package-version.txt

@@ -0,0 +1 @@
+../sagelib/package-version.txt

build/pkgs/sagemath_objects/spkg-install

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+cd src
+
+if [ "$SAGE_CHECK" != no ]; then
+    tox
+fi
+# We skip the install for now.
+exit 0

build/pkgs/sagemath_objects/spkg-src

@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+#
+# Script to prepare an sdist tarball for sagemath-objects
+# This script is not used during build.
+#
+# HOW TO MAKE THE TARBALL:
+# 1) ./sage --sh build/pkgs/sagemath_objects/spkg-src
+
+if [ -z "$SAGE_ROOT" ] ; then
+    echo >&2 "Error - SAGE_ROOT undefined ... exiting"
+    echo >&2 "Maybe run 'sage -sh'?"
+    exit 1
+fi
+
+# Exit on failure
+set -e
+
+cd build/pkgs/sagemath_objects
+
+cd src
+python3 -u setup.py --no-user-cfg sdist --dist-dir "$SAGE_DISTFILES"

build/pkgs/sagemath_objects/src

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

build/pkgs/sagemath_objects/type

@@ -0,0 +1 @@
+experimental

build/pkgs/sphinx/SPKG.rst

@@ -27,21 +27,11 @@ Upstream Contact
 Dependencies
 ------------
 
--  six >= 1.4
 -  Jinja2 >= 2.3
 -  Pygments >= 2.0
--  docutils >= 0.11
+-  docutils < 0.18
 -  snowballstemmer >= 1.1
 -  babel >= 1.3
 -  setuptools / distribute
 -  Python
 -  GNU patch (shipped with Sage)
-
-
-Special Update/Build Instructions
----------------------------------
-
--  The script create_grammar_pickle.py creates the file
-   Grammar2.7.pickle in site-packages/Sphinx-.../sphinx/pycode/. This
-   helps to avoid race conditions when building the documentation in
-   parallel.