Merge tag '9.3.beta1' into t/30559/refine_python3_s_sage_spkg_depcheck

SageMath version 9.3.beta1, Release Date: 2020-11-07

.ci/build-docker.sh

@@ -26,7 +26,7 @@ docker_build() {
     # Docker's --cache-from does not really work with multi-stage builds: https://github.com/moby/moby/issues/34715
     # So we just have to rely on the local cache.
     time docker build -f docker/Dockerfile \
---build-arg "--build-arg "MAKEFLAGS=${MAKEFLAGS}" --build-arg "SAGE_NUM_THREADS=${SAGE_NUM_THREADS}" --build-arg "MAKEFLAGS_DOCBUILD=${MAKEFLAGS}" --build-arg "SAGE_NUM_THREADS_DOCBUILD=${SAGE_NUM_THREADS_DOCBUILD}" --build-arg ARTIFACT_BASE=$ARTIFACT_BASE $@
+--build-arg "MAKEFLAGS=${MAKEFLAGS}" --build-arg "SAGE_NUM_THREADS=${SAGE_NUM_THREADS}" --build-arg "MAKEFLAGS_DOCBUILD=${MAKEFLAGS}" --build-arg "SAGE_NUM_THREADS_DOCBUILD=${SAGE_NUM_THREADS_DOCBUILD}" --build-arg ARTIFACT_BASE=$ARTIFACT_BASE $@
 }
 
 # We use a multi-stage build /docker/Dockerfile. For the caching to be
@@ -53,7 +53,7 @@ docker tag "$DOCKER_IMAGE_CLI" "$DOCKER_IMAGE_BINDER"
 # Display the layers of this image
 docker history "$DOCKER_IMAGE_CLI"
 # Build the developer image with the build artifacts intact.
-# Note: It's important to build the dev image last because it might be tagged as ARTIFACT_BASE.
+# Note: It is important to build the dev image last because it might be tagged as ARTIFACT_BASE.
 docker_build --target sagemath-dev --tag "$DOCKER_IMAGE_DEV" .
 # Display the layers of this image
 docker history "$DOCKER_IMAGE_DEV"

.ci/update-env.sh

@@ -27,8 +27,6 @@ if [ -n "$CI_MONKEY_PATCH" ]; then
     $SCRIPT
 fi
 
-WITH_PYTHON=${WITH_PYTHON:-2}
-
 # From the docker documentation: "A tag name must be valid ASCII and may
 # contain lowercase and uppercase letters, digits, underscores, periods and
 # dashes. A tag name may not start with a period or a dash and may contain a
@@ -38,10 +36,6 @@ export DOCKER_TAG=`echo $DOCKER_TAG | tr -d '[:space:]' | tr -c '[:alnum:]_.-' '
 [[ -z "$DOCKER_TAG" ]] && export DOCKER_TAG=none
 [[ "$DOCKER_TAG" = "master" ]] && export DOCKER_TAG=latest
 
-if [ $WITH_PYTHON = 3 ]; then
-    export DOCKER_TAG=${DOCKER_TAG}-py3
-fi
-
 export DOCKER_IMAGE_CLI=${DOCKER_NAMESPACE:-sagemath}/sagemath:$DOCKER_TAG
 export DOCKER_IMAGE_DEV=${DOCKER_NAMESPACE:-sagemath}/sagemath-dev:$DOCKER_TAG
 

.gitignore

@@ -4,9 +4,7 @@
 /logs
 /upstream
 
-#############################
-# Autotools generated files #
-#############################
+# Autotools generated files
 /aclocal.m4
 /autom4te.cache/
 /config/
@@ -20,10 +18,6 @@
 # no longer generated, but may still be in user worktrees
 /src/lib/pkgconfig
 
-###################
-# Temporary Files #
-###################
-
 # Various editors
 *~
 
@@ -43,7 +37,7 @@
 .iml
 
 # VSCode
-.vscode
+.vscode/*
 
 # XCode
 xcuserdata/
@@ -77,43 +71,79 @@ $RECYCLE.BIN/
 # SublimeText
 *.sublime-workspace
 
-# mypy
-**/.mypy_cache/
-
-#################
-# SageMathCloud #
-#################
+# SageMathCloud
 *.sage-chat
 *.sage-history
 *.syncdoc*
 
-###########
-# Jupyter #
-###########
+# Jupyter
 .ipynb_checkpoints
 Untitled*.ipynb
 
-#############################
-# GitLab CI generated files #
-#############################
+# GitLab CI generated files
 gitlab-build-docker.log
 
-/src/.cython_version
-/src/build
-/src/Makefile
-/src/bin/sage-env-config
-/build/bin/sage-build-env-config
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Generated Cython files
+*.so
+src/sage/**/*.c
+src/sage/**/*.cpp
+src/sage/modular/arithgroup/farey_symbol.h
+!src/sage/cpython/debugimpl.c
+!src/sage/graphs/base/boost_interface.cpp
+!src/sage/graphs/cliquer/cl.c
+!src/sage/graphs/graph_decompositions/tdlib/sage_tdlib.cpp
+!src/sage/libs/eclib/wrap.cpp
+!src/sage/misc/inherit_comparison_impl.c
+!src/sage/modular/arithgroup/farey.cpp
+!src/sage/modular/arithgroup/sl2z.cpp
+!src/sage/rings/bernmm/bern_modp.cpp
+!src/sage/rings/bernmm/bern_modp_util.cpp
+!src/sage/rings/bernmm/bern_rat.cpp
+!src/sage/rings/bernmm/bernmm-test.cpp
+!src/sage/rings/padics/transcendantal.c
+!src/sage/rings/polynomial/weil/power_sums.c
+!src/sage/schemes/hyperelliptic_curves/hypellfrob/hypellfrob.cpp
+!src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_ntl.cpp
+!src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_zn_poly.cpp
+!src/sage/stats/distributions/dgs_bern.c
+!src/sage/stats/distributions/dgs_gauss_dp.c
+!src/sage/stats/distributions/dgs_gauss_mp.c
+
+# Temporary build files
+build/temp.*/
+build/bin/sage-build-env-config
 
 /build/pkgs/*/src/build
 /build/pkgs/*/src/dist
 /build/pkgs/*/src/MANIFEST
 /build/pkgs/*/src/*.egg-info
 /build/pkgs/*/src/.tox
 
-#######################
-# tox generated files #
-#######################
+# Distribution / packaging
+src/*.egg-info/
+/src/.cython_version
+/src/build
+/src/Makefile
+/src/bin/sage-env-config
+
+# Virtual environments
+src/.env
+src/.venv
+src/env/
+src/venv/
+src/ENV/
+src/env.bak/
+src/venv.bak/
+
+# mypy
+**/.mypy_cache/
 
+# tox generated files
 /.tox
 /prefix
 worktree*

.homebrew-build-env

@@ -2,7 +2,7 @@
 # that activate keg-only homebrew package installations
 
 HOMEBREW=`brew --prefix` || return 1
-for l in gettext bzip2; do
+for l in gettext bzip2 texinfo; do
     if [ -d "$HOMEBREW/opt/$l/bin" ]; then
         PATH="$HOMEBREW/opt/$l/bin:$PATH"
     fi

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.3.beta0", 
-    "version": "9.3.beta0", 
+    "title": "sagemath/sage: 9.3.beta1", 
+    "version": "9.3.beta1", 
     "upload_type": "software", 
-    "publication_date": "2020-11-01", 
+    "publication_date": "2020-11-07", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta0", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta1", 
             "relation": "isSupplementTo"
         }, 
         {

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.3.beta0, Release Date: 2020-11-01
+SageMath version 9.3.beta1, Release Date: 2020-11-07

bootstrap

@@ -256,13 +256,6 @@ MAKE_SILENT=""
 $MAKE ${MAKE_SILENT} bootstrap-clean 2>/dev/null
 mkdir config 2>/dev/null
 
-# If Sage has not been built yet, this will fail due to a missing
-# sage-env-config.
-if [ -f src/bin/sage-env-config ]; then
-    . src/bin/sage-env-config
-    . src/bin/sage-env
-fi
-
 if [ $ALWAYSDOWNLOAD = yes ]; then
     if [ -n "$CONFTARBALL_URL" ]; then
         URL="$CONFTARBALL_URL"/configure-$CONFVERSION.tar.gz

build/bin/sage-guess-package-system

@@ -3,7 +3,7 @@
 # First test for user-installable package systems, then system package systems
 if conda --version > /dev/null 2>&1; then
     if [ -z "$CONDA_DEFAULT_ENV" ]; then
-        echo >&2 -n "(ignoring conda because no environment is active) "
+        printf >&2 "(ignoring conda because no environment is active) "
     else
         echo conda
         exit

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=8e62a22481989ce61bb06adab0ce926c555604c5
-md5=3ea78ce307e26ca687652bc8d6bde85d
-cksum=791004627
+sha1=13ac5ae7fa66fb0f1dc4fb09b4c5c6d72918a3ef
+md5=67b20028087b39225833e6a7fe2553fe
+cksum=832894188

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-f1e553872604276da99fb4dc017b515766c38532
+8e72e1b9c9b3e9b84c29245666493e0a1bd48cab

build/pkgs/fplll/distros/conda.txt

@@ -0,0 +1 @@
+fplll

build/pkgs/gmp/checksums.ini

@@ -1,4 +1,5 @@
-tarball=gmp-VERSION.tar.bz2
-sha1=366ded6a44cd108ba6b3f5b9a252eab3f3a95cdf
-md5=8ddbb26dc3bd4e2302984debba1406a5
-cksum=2451242108
+tarball=gmp-VERSION.tar.xz
+sha1=052a5411dc74054240eec58132d2cf41211d0ff6
+md5=a325e3f09e6d91e62101e59f9bda3ec1
+cksum=942462047
+upstream_url=https://gmplib.org/download/gmp/gmp-VERSION.tar.xz

build/pkgs/gmp/package-version.txt

@@ -1 +1 @@
-6.1.2
+6.2.0

build/pkgs/libhomfly/distros/debian.txt

@@ -1 +1 @@
-libhomfly
+libhomfly-dev

build/pkgs/libsemigroups/distros/conda.txt

@@ -0,0 +1 @@
+libsemigroups

build/pkgs/sage_conf/src/setup.cfg.in

@@ -7,7 +7,7 @@ description = Sage: Open Source Mathematics Software: Configuration for sagelib
 long_description = file: README.rst
 license = GNU General Public License (GPL) v3 or later
 author = The Sage Developers
-author_email = https://groups.google.com/group/sage-support
+author_email = sage-support@googlegroups.com
 url = https://www.sagemath.org
 
 [options]

build/pkgs/sage_sws2rst/src/setup.cfg

@@ -6,7 +6,7 @@ long_description = file: README.rst
 long_description_content_type = text/x-rst
 license = GNU General Public License (GPL) v3 or later
 author = The Sage Developers
-author_email = https://groups.google.com/group/sage-support
+author_email = sage-support@googlegroups.com
 url = https://www.sagemath.org
 
 [options]

build/pkgs/sagelib/package-version.txt

@@ -1 +1 @@
-9.3.beta0
+9.3.beta1

pyrightconfig.json

@@ -0,0 +1,16 @@
+{
+    "include": [
+      "src/sage/manifolds"
+    ],
+    "executionEnvironments": [
+      {
+        "root": "src"
+      }
+    ],  
+    "pythonVersion": "3.7",
+
+    "reportMissingImports": "warning",
+    "reportGeneralTypeIssues": "warning",
+    "reportUnboundVariable": "warning",
+    "reportDuplicateImport": "error"
+}

src/bin/sage-version.sh

@@ -1,5 +1,5 @@
 # Sage version information for shell scripts
 # This file is auto-generated by the sage-update-version script, do not edit!
-SAGE_VERSION='9.3.beta0'
-SAGE_RELEASE_DATE='2020-11-01'
-SAGE_VERSION_BANNER='SageMath version 9.3.beta0, Release Date: 2020-11-01'
+SAGE_VERSION='9.3.beta1'
+SAGE_RELEASE_DATE='2020-11-07'
+SAGE_VERSION_BANNER='SageMath version 9.3.beta1, Release Date: 2020-11-07'

src/doc/ca/intro/conf.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-#
 # Sage documentation build configuration file, created by
 # sphinx-quickstart on Thu Aug 21 20:15:55 2008.
 #
@@ -14,8 +12,15 @@
 from sage.docs.conf import release
 from sage.docs.conf import *  # NOQA
 
+# Add any paths that contain custom static files (such as style sheets),
+# relative to this directory to html_static_path. They are copied after the
+# builtin static files, so a file named "default.css" will overwrite the
+# builtin "default.css". html_common_static_path imported from sage.docs.conf
+# contains common paths.
+html_static_path = [] + html_common_static_path
+
 # General information about the project.
-project = u"Introducció de Sage"
+project = "Introducció de Sage"
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
@@ -27,6 +32,6 @@
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, document class [howto/manual]).
 latex_documents = [
-  ('index', 'TutorialdeSage.tex', u'Introducció de Sage',
-   u'The Sage Development Team', 'manual'),
+  ('index', 'TutorialdeSage.tex', 'Introducció de Sage',
+   'The Sage Development Team', 'manual'),
 ]

src/doc/de/a_tour_of_sage/conf.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-#
 # Numerical Sage documentation build configuration file, created by
 # sphinx-quickstart on Sat Dec  6 11:08:04 2008.
 #
@@ -16,22 +14,29 @@
 from sage.docs.conf import release
 from sage.docs.conf import *  # NOQA
 
+# Add any paths that contain custom static files (such as style sheets),
+# relative to this directory to html_static_path. They are copied after the
+# builtin static files, so a file named "default.css" will overwrite the
+# builtin "default.css". html_common_static_path imported from sage.docs.conf
+# contains common paths.
+html_static_path = [] + html_common_static_path
+
 # General information about the project.
-project = u"Ein Rundgang durch Sage"
+project = "Ein Rundgang durch Sage"
 name = "a_tour_of_sage"
 language = 'de'
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
 html_title = project + " v" + release
-html_short_title = u"Sage Rundgang v" + release
+html_short_title = "Sage Rundgang v" + release
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = name
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, document class [howto/manual]).
 latex_documents = [
-  ("index", name + ".tex", u"Ein Rundgang durch Sage",
-   u"The Sage Development Team", "manual"),
+  ("index", name + ".tex", "Ein Rundgang durch Sage",
+   "The Sage Development Team", "manual"),
 ]