Merge #32899

.github/workflows/tox-experimental.yml

@@ -41,7 +41,7 @@ jobs:
         # This list is different from the one in tox.yml:
         # Trac #31526 switches gcc 4.x-based distributions to using the gcc_spkg configuration factor
         # Trac #32281 removes gcc 4.x-based distributions whose binutils are unusable
-        tox_system_factor: [ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie-gcc_spkg, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7-gcc_spkg, centos-8, gentoo, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386-gcc_spkg]
+        tox_system_factor: [ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie-gcc_spkg, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7-gcc_spkg, centos-8, gentoo-python3.9, gentoo-python3.10, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386-gcc_spkg]
         tox_packages_factor: [maximal]
         targets_pattern: [0-g, h-o, p, q-z]
     env:

.github/workflows/tox-optional.yml

@@ -41,7 +41,7 @@ jobs:
         # This list is different from the one in tox.yml:
         # Trac #31526 switches gcc 4.x-based distributions to using the gcc_spkg configuration factor
         # Trac #32281 removes gcc 4.x-based distributions whose binutils are unusable
-        tox_system_factor: [ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie-gcc_spkg, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7-gcc_spkg, centos-8, gentoo, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386-gcc_spkg]
+        tox_system_factor: [ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie-gcc_spkg, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7-gcc_spkg, centos-8, gentoo-python3.9, gentoo-python3.10, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386-gcc_spkg]
         tox_packages_factor: [maximal]
         targets_pattern: [0-g, h-o, p, q-z]
     env:

.github/workflows/tox.yml

@@ -38,7 +38,7 @@ jobs:
       fail-fast: false
       max-parallel: 20
       matrix:
-        tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, ubuntu-impish, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, linuxmint-20.2, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, fedora-35, centos-7, centos-8, gentoo, gentoo-python3.7, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386]
+        tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, ubuntu-impish, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, linuxmint-20.2, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, fedora-35, centos-7, centos-8, gentoo-python3.9, gentoo-python3.10, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386]
         tox_packages_factor: [minimal, standard]
     env:
       TOX_ENV: docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.5.beta6", 
-    "version": "9.5.beta6", 
+    "title": "sagemath/sage: 9.5.beta7", 
+    "version": "9.5.beta7", 
     "upload_type": "software", 
-    "publication_date": "2021-11-12", 
+    "publication_date": "2021-11-18", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.5.beta6", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.5.beta7", 
             "relation": "isSupplementTo"
         }, 
         {

README.md

@@ -349,54 +349,72 @@ Simplified directory layout (only essential files/directories):
 SAGE_ROOT                 Root directory (sage-x.y.z in Sage tarball)
 ├── build
 │   └── pkgs              Every package is a subdirectory here
-│       ├── 4ti2
+│       ├── 4ti2/
 │       …
-│       └── zn_poly
+│       └── zn_poly/
 ├── configure             Top-level configure script
 ├── COPYING.txt           Copyright information
 ├── pkgs                  Source trees of Python distribution packages
 │   ├── sage-conf
 │   │   ├── sage_conf.py
 │   │   └── setup.py
 │   ├── sage-docbuild
-│   │   ├── sage_docbuild
+│   │   ├── sage_docbuild/
+│   │   └── setup.py
+│   ├── sage-setup
+│   │   ├── sage_setup/
 │   │   └── setup.py
 │   ├── sage-sws2rst
-│   │   ├── sage_sws2rst
+│   │   ├── sage_sws2rst/
 │   │   └── setup.py
 │   └── sagemath-standard
-│       ├── bin
-│       ├── sage
+│       ├── bin/
+│       ├── sage -> ../../src/sage
 │       └── setup.py
-├── local  (SAGE_LOCAL)   Compiled packages are installed here
+├── local  (SAGE_LOCAL)   Installation hierarchy for non-Python packages
 │   ├── bin               Executables
 │   ├── include           C/C++ headers
-│   ├── lib               Shared libraries
+│   ├── lib               Shared libraries, architecture-dependent data
 │   ├── share             Databases, architecture-independent data, docs
 │   │   └── doc           Viewable docs of Sage and of some components
 │   └── var
-│       ├── lib/sage      List of installed packages
-│       └── tmp/sage      Temporary files when building Sage
+│       ├── lib/sage
+│       │   ├── installed/
+│       │   │             Records of installed non-Python packages
+│       │   ├── scripts/  Scripts for uninstalling installed packages
+│       │   └── venv-python3.9  (SAGE_VENV)
+│       │       │         Installation hierarchy (virtual environment)
+│       │       │         for Python packages
+│       │       ├── bin/  Executables and installed scripts
+│       │       ├── lib/python3.9/site-packages/
+│       │       │         Python modules/packages are installed here
+│       │       └── var/lib/sage/
+│       │           └── wheels/
+│       │                 Python wheels for all installed Python packages
+│       │
+│       └── tmp/sage/     Temporary files when building Sage
 ├── logs
 │   ├── dochtml.log       Log of the documentation build
 │   ├── install.log       Full install log
 │   └── pkgs              Build logs of individual packages
 │       ├── alabaster-0.7.12.log
 │       …
 │       └── zn_poly-0.9.2.log
-├── m4                    M4 macros for configure
+├── m4                    M4 macros for generating the configure script
 │   └── *.m4
 ├── Makefile              Running "make" uses this file
+├── prefix -> SAGE_LOCAL  Convenience symlink to the installation tree
 ├── README.md             This file
 ├── sage                  Script to start Sage
 ├── src                   Monolithic Sage library source tree
-│   ├── bin               Scripts that Sage uses internally
-│   ├── doc               Sage documentation sources
-│   └── sage              The Sage library source code
+│   ├── bin/              Scripts that Sage uses internally
+│   ├── doc/              Sage documentation sources
+│   └── sage/             The Sage library source code
 ├── upstream              Source tarballs of packages
 │   ├── Babel-2.9.1.tar.gz
 │   …
 │   └── zn_poly-0.9.2.tar.gz
+├── venv -> SAGE_VENV     Convenience symlink to the virtual environment
 └── VERSION.txt
 ```
 For more details see [our Developer's Guide](https://doc.sagemath.org/html/en/developer/coding_basics.html#files-and-directory-structure).

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.5.beta6, Release Date: 2021-11-12
+SageMath version 9.5.beta7, Release Date: 2021-11-18

build/bin/sage-bootstrap-python

@@ -40,7 +40,19 @@ if [ "$LC_ALL" = "C" -o "$LANG" = "C" -o "$LC_CTYPE" = "C" ]; then
     export LANG
 fi
 
-PYTHONS="python python3 python3.8 python3.7 python2.7 python3.6 python2"
+PYTHONS="python python3 python3.10 python3.9 python3.8 python3.7 python2.7 python3.6 python2"
+# Trac #32405: Prefer a Python that provides ssl with SNI, which allows developers
+# to download from upstream URLs (configure --enable-download-from-upstream-url),
+# in particular from PyPI, which requires SNI.
+for PY in $PYTHONS; do
+    PYTHON="$(PATH="$SAGE_ORIG_PATH" command -v $PY)"
+    if [ -n "$PYTHON" ]; then
+        if "$PYTHON" -c "import argparse; import urllib; from hashlib import sha1; from ssl import HAS_SNI; assert HAS_SNI; from os import listdir; listdir(\"$(pwd)\");" 2>/dev/null; then
+            exec "$PYTHON" "$@"
+        fi
+    fi
+done
+# Second round, no ssl/SNI test.
 for PY in $PYTHONS; do
     PYTHON="$(PATH="$SAGE_ORIG_PATH" command -v $PY)"
     if [ -n "$PYTHON" ]; then

build/bin/sage-dist-helpers

@@ -268,6 +268,12 @@ sdh_pip_install() {
     sdh_store_and_pip_install_wheel $install_options .
 }
 
+sdh_pip_editable_install() {
+    echo "Installing $PKG_NAME (editable mode)"
+    python3 -m pip install --verbose --no-deps --no-index --no-build-isolation --isolated --editable "$@" || \
+        sdh_die "Error installing $PKG_NAME"
+}
+
 sdh_store_wheel() {
     if [ -n "$SAGE_DESTDIR" ]; then
         local sudo=""

build/make/Makefile.in

@@ -52,6 +52,10 @@ SAGE_SPKG = sage-spkg
 # These are added to SAGE_SPKG in the call
 SAGE_SPKG_OPTIONS = @SAGE_SPKG_OPTIONS@
 
+# Where the Sage distribution installs documentation.
+# set to empty if --disable-doc is used
+SAGE_DOCS = $(SAGE_LOCAL)
+
 # Where the Sage distribution installs Python packages.
 # This can be overridden by 'make SAGE_VENV=/some/venv'.
 SAGE_VENV = @SAGE_VENV@
@@ -142,7 +146,7 @@ SCRIPT_PACKAGES = @SAGE_SCRIPT_PACKAGES@
 # inst_git = $(INST)/.dummy
 
 $(foreach pkgname,$(BUILT_PACKAGES),\
-	$(eval inst_$(pkgname) = $(foreach tree, $(trees_$(pkgname)), $($(tree))/$(SPKG_INST_RELDIR)/$(pkgname)-$(vers_$(pkgname)))))
+	$(eval inst_$(pkgname) = $(foreach tree, $(trees_$(pkgname)), $(and $($(tree)), $($(tree))/$(SPKG_INST_RELDIR)/$(pkgname)-$(vers_$(pkgname))))))
 $(foreach pkgname,$(DUMMY_PACKAGES),\
 	$(eval inst_$(pkgname) = $(SAGE_LOCAL)/$(SPKG_INST_RELDIR)/.dummy))
 
@@ -157,7 +161,7 @@ $(SAGE_LOCAL)/$(SPKG_INST_RELDIR)/.dummy:
 
 
 # Filtered by installation tree
-$(foreach tree,SAGE_LOCAL SAGE_VENV, \
+$(foreach tree,SAGE_LOCAL SAGE_VENV SAGE_DOCS, \
     $(eval $(tree)_INSTALLED_PACKAGE_INSTS = \
                $(foreach pkgname,$(INSTALLED_PACKAGES), \
                          $(if $(findstring $(tree),$(trees_$(pkgname))), \
@@ -228,11 +232,11 @@ build-start: all-build
 base-toolchain: _clean-broken-gcc base
 	+$(MAKE_REC) toolchain
 
-# All targets except for the base packages
+# All targets except for the base packages and except the documentation
 all-sage: \
 		sagelib \
-		$(INSTALLED_PACKAGE_INSTS) \
-                $(UNINSTALLED_PACKAGES_CLEANS)
+		$(SAGE_LOCAL_INSTALLED_PACKAGE_INSTS) $(SAGE_LOCAL_UNINSTALLED_PACKAGES_CLEANS) \
+		$(SAGE_VENV_INSTALLED_PACKAGE_INSTS)  $(SAGE_VENV_UNINSTALLED_PACKAGES_CLEANS)
 
 # Same but filtered by installation trees:
 all-build-local: toolchain-deps
@@ -245,6 +249,11 @@ all-build-venv: toolchain-deps
 
 all-sage-venv:  $(SAGE_VENV_INSTALLED_PACKAGE_INSTS)  $(SAGE_VENV_UNINSTALLED_PACKAGES_CLEANS)
 
+all-build-docs: toolchain-deps
+	+$(MAKE_REC) all-sage-docs
+
+all-sage-docs:  $(SAGE_DOCS_INSTALLED_PACKAGE_INSTS) $(SAGE_DOCS_UNINSTALLED_PACKAGES_CLEANS)
+
 # Download all packages which should be inside an sdist tarball (the -B
 # option to make forces all targets to be built unconditionally)
 download-for-sdist:
@@ -316,35 +325,28 @@ base: $(inst_patch) $(inst_pkgconf)
 #
 # $ ./sage --docbuild -H
 
-# Building the documentation has many dependencies, because all
-# documented modules are imported and because we use matplotlib to
-# produce plots.
-DOC_DEPENDENCIES = sagelib sage_docbuild $(inst_sphinx) \
-	| $(SAGERUNTIME) $(inst_maxima) $(inst_networkx) $(inst_scipy) $(inst_sympy) \
-	$(inst_matplotlib) $(inst_pillow) $(inst_mathjax) $(inst_mpmath) \
-	$(inst_ipykernel) $(inst_jupyter_client) $(inst_conway_polynomials) \
-	$(inst_tachyon) $(inst_jmol) $(inst_thebe) $(inst_ipywidgets)
-
-doc: doc-html
+doc: $(SAGE_DOCS_INSTALLED_PACKAGE_INSTS) $(SAGE_DOCS_UNINSTALLED_PACKAGES_CLEANS)
 
-doc-html: $(DOC_DEPENDENCIES)
-	$(AM_V_at)cd "$(SAGE_SRC)/doc" && sage-logger -p "$(MAKE) doc-html" $(SAGE_ROOT)/logs/dochtml.log
+# All doc-building is delegated to the script packages
+# sagemath_doc_html, sagemath_doc_pdf
+doc-html: sagemath_doc_html
 
 # 'doc-html-no-plot': build docs without building the graphics coming
 # from the '.. plot' directive, in case you want to save a few
 # megabytes of disk space. 'doc-clean' is a prerequisite because the
 # presence of graphics is cached in src/doc/output.
 doc-html-no-plot: doc-clean
-	$(AM_V_at)sage-logger -p "$(MAKE) SAGE_DOCBUILD_OPTS=\"$(SAGE_DOCBUILD_OPTS) --no-plot\" doc-html" $(SAGE_ROOT)/logs/dochtml.log
+	+$(MAKE_REC) SAGE_DOCBUILD_OPTS="$(SAGE_DOCBUILD_OPTS) --no-plot" doc-html
 
+# Using mathjax is actually the default, but this target can be used
+# to override an environment setting of SAGE_DOC_MATHJAX=no
 doc-html-mathjax:
-	$(AM_V_at)sage-logger -p "$(MAKE) SAGE_DOCBUILD_OPTS=\"$(SAGE_DOCBUILD_OPTS) -j\" doc-html" $(SAGE_ROOT)/logs/dochtml.log
+	+$(MAKE_REC) SAGE_DOCBUILD_OPTS="$(SAGE_DOCBUILD_OPTS) -j" doc-html
 
 # Keep target 'doc-html-jsmath' for backwards compatibility.
 doc-html-jsmath: doc-html-mathjax
 
-doc-pdf: $(DOC_DEPENDENCIES)
-	$(AM_V_at)cd "$(SAGE_SRC)/doc" && sage-logger -p "$(MAKE) doc-pdf" $(SAGE_ROOT)/logs/docpdf.log
+doc-pdf: sagemath_doc_pdf
 
 doc-clean: doc-src-clean doc-output-clean
 

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=bdfd5753a2548365230216455d9a543fe238f092
-md5=49ffa01e32a876dd4feea975d822351e
-cksum=3517586928
+sha1=d9fff88398cb15f16c7dcb3b6180163bb206a699
+md5=585dece094717b58049a2bfaf9811162
+cksum=3669459096

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-fda367752b5e7afa3ec0fda483b162645192e008
+cdb3614b34926cee3c4cc918313678d3deea4e8d

build/pkgs/flit_core/spkg-install.in

@@ -1,2 +1,3 @@
 cd src
-sdh_pip_install .
+# We use --no-deps to suppress a warning regarding tomli.
+sdh_pip_install --no-deps .

build/pkgs/gmp/checksums.ini

@@ -1,5 +1,5 @@
 tarball=gmp-VERSION.tar.xz
-sha1=052a5411dc74054240eec58132d2cf41211d0ff6
-md5=a325e3f09e6d91e62101e59f9bda3ec1
-cksum=942462047
+sha1=0578d48607ec0e272177d175fd1807c30b00fdf2
+md5=0b82665c4a92fd2ade7440c13fcaa42b
+cksum=1546558141
 upstream_url=https://gmplib.org/download/gmp/gmp-VERSION.tar.xz

build/pkgs/gmp/package-version.txt

@@ -1 +1 @@
-6.2.0
+6.2.1

build/pkgs/memory_allocator/distros/conda.txt

@@ -0,0 +1 @@
+memory-allocator

build/pkgs/networkx/checksums.ini

@@ -1,5 +1,5 @@
 tarball=networkx-VERSION.tar.gz
-sha1=5a39af7b0b6a6180b733c280b0ee70b9868a8566
-md5=ac9cf192fc525bb877a042a684091d72
-cksum=1918700937
+sha1=659f640c03fe52c98fa7a1d03fe3a6f6bbce2015
+md5=407eb28c54e08725559754ca7ab185e0
+cksum=3378468789
 upstream_url=https://pypi.io/packages/source/n/networkx/networkx-VERSION.tar.gz

build/pkgs/networkx/package-version.txt

@@ -1 +1 @@
-2.6.2
+2.6.3

build/pkgs/numpy/checksums.ini

@@ -1,5 +1,5 @@
 tarball=numpy-VERSION.zip
-sha1=c7eb91a2232f7843301c355795860baaa0280909
-md5=5638d5dae3ca387be562912312db842e
-cksum=2204147896
+sha1=91a1faeb617601453ebf6e2855e5ce6bf94d3588
+md5=b3c4477a027d5b6fba5e1065064fd076
+cksum=1917168823
 upstream_url=https://pypi.io/packages/source/n/numpy/numpy-VERSION.zip

build/pkgs/numpy/package-version.txt

@@ -1 +1 @@
-1.21.2
+1.21.4

build/pkgs/python3/trees.txt

@@ -0,0 +1 @@
+SAGE_VENV

build/pkgs/sage_conf/spkg-install

@@ -9,4 +9,9 @@ if [ $? -ne 0 ]; then
     echo >&2 "Is $SAGE_ROOT the correct SAGE_ROOT?"
     exit 1
 fi
-cd src && sdh_pip_install .
+cd src
+if [ "$SAGE_EDITABLE" = yes ]; then
+    sdh_pip_editable_install .
+else
+    sdh_pip_install .
+fi

build/pkgs/sage_docbuild/spkg-install

@@ -9,4 +9,9 @@ if [ $? -ne 0 ]; then
     echo >&2 "Is $SAGE_ROOT the correct SAGE_ROOT?"
     exit 1
 fi
-cd src && sdh_pip_install .
+cd src
+if [ "$SAGE_EDITABLE" = yes ]; then
+    sdh_pip_editable_install .
+else
+    sdh_pip_install .
+fi

build/pkgs/sage_setup/spkg-install

@@ -9,4 +9,9 @@ if [ $? -ne 0 ]; then
     echo >&2 "Is $SAGE_ROOT the correct SAGE_ROOT?"
     exit 1
 fi
-cd src && sdh_pip_install .
+cd src
+if [ "$SAGE_EDITABLE" = yes ]; then
+    sdh_pip_editable_install .
+else
+    sdh_pip_install .
+fi

build/pkgs/sagelib/package-version.txt

@@ -1 +1 @@
-9.5.beta6
+9.5.beta7

build/pkgs/sagemath_doc_html/SPKG.rst

@@ -0,0 +1,10 @@
+sagemath_doc_html: SageMath documentation in HTML format
+========================================================
+
+Upon installation, this package builds the SageMath documentation
+in HTML format.
+
+It is a standard package.  It is built on every invocation
+of ``make`` or ``make all``, but not on ``make build``.
+The documentation build can also be run separately using
+``make doc-html``.

build/pkgs/sagemath_doc_html/dependencies

@@ -0,0 +1,5 @@
+sagelib sphinx | $(SAGERUNTIME) maxima networkx scipy sympy matplotlib pillow mathjax mpmath ipykernel jupyter_client conway_polynomials tachyon jmol thebe ipywidgets sage_docbuild
+
+# Building the documentation has many dependencies, because all
+# documented modules are imported and because we use matplotlib to
+# produce plots.