Merge branch 'develop' into 19145

sagemath · Feb 12, 2021 · ef01fdb · ef01fdb
2 parents 539410d + 8453ffb
commit ef01fdb
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Showing 250 changed files with 2,911 additions and 1,787 deletions.
diff --git a/.github/workflows/ci-cygwin-minimal.yml b/.github/workflows/ci-cygwin-minimal.yml
diff --git a/.github/workflows/ci-cygwin-standard.yml b/.github/workflows/ci-cygwin-standard.yml
@@ -6,6 +6,8 @@ on:
   push:
     tags:
       - '*'
+  workflow_dispatch:
+    # Allow to run manually
 
 env:
   MAKE: make -j8
@@ -43,7 +45,7 @@ jobs:
       shell: bash {0}
       run: |
         choco --version
-        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/cygwin.txt ./build/pkgs/cygwin-bootstrap.txt)
+        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/_prereq/distros/cygwin.txt ./build/pkgs/_prereq/distros/cygwin-bootstrap.txt)
         choco install $PACKAGES --source cygwin
     - name: bootstrap
       run: |
@@ -113,7 +115,7 @@ jobs:
       shell: bash {0}
       run: |
         choco --version
-        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/cygwin.txt ./build/pkgs/cygwin-bootstrap.txt)
+        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/_prereq/distros/cygwin.txt ./build/pkgs/_prereq/distros/cygwin-bootstrap.txt)
         choco install $PACKAGES --source cygwin
     - name: bootstrap
       run: |
@@ -188,7 +190,7 @@ jobs:
       shell: bash {0}
       run: |
         choco --version
-        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/cygwin.txt ./build/pkgs/cygwin-bootstrap.txt)
+        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/_prereq/distros/cygwin.txt ./build/pkgs/_prereq/distros/cygwin-bootstrap.txt)
         choco install $PACKAGES --source cygwin
     - name: bootstrap
       run: |
@@ -268,7 +270,7 @@ jobs:
       shell: bash {0}
       run: |
         choco --version
-        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/cygwin.txt ./build/pkgs/cygwin-bootstrap.txt)
+        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/_prereq/distros/cygwin.txt ./build/pkgs/_prereq/distros/cygwin-bootstrap.txt)
         choco install $PACKAGES --source cygwin
     - name: bootstrap
       run: |
@@ -346,7 +348,7 @@ jobs:
       shell: bash {0}
       run: |
         choco --version
-        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/cygwin.txt ./build/pkgs/cygwin-bootstrap.txt)
+        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/_prereq/distros/cygwin.txt ./build/pkgs/_prereq/distros/cygwin-bootstrap.txt)
         choco install $PACKAGES --source cygwin
     - name: bootstrap
       run: |
@@ -424,7 +426,7 @@ jobs:
       shell: bash {0}
       run: |
         choco --version
-        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/cygwin.txt ./build/pkgs/cygwin-bootstrap.txt)
+        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/_prereq/distros/cygwin.txt ./build/pkgs/_prereq/distros/cygwin-bootstrap.txt)
         choco install $PACKAGES --source cygwin
     - name: bootstrap
       run: |
@@ -502,7 +504,7 @@ jobs:
       shell: bash {0}
       run: |
         choco --version
-        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/cygwin.txt ./build/pkgs/cygwin-bootstrap.txt)
+        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/_prereq/distros/cygwin.txt ./build/pkgs/_prereq/distros/cygwin-bootstrap.txt)
         choco install $PACKAGES --source cygwin
     - name: bootstrap
       run: |
@@ -582,7 +584,7 @@ jobs:
       shell: bash {0}
       run: |
         choco --version
-        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/cygwin.txt ./build/pkgs/cygwin-bootstrap.txt)
+        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/_prereq/distros/cygwin.txt ./build/pkgs/_prereq/distros/cygwin-bootstrap.txt)
         choco install $PACKAGES --source cygwin
     - name: bootstrap
       run: |
@@ -662,7 +664,7 @@ jobs:
       shell: bash {0}
       run: |
         choco --version
-        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/cygwin.txt ./build/pkgs/cygwin-bootstrap.txt)
+        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/_prereq/distros/cygwin.txt ./build/pkgs/_prereq/distros/cygwin-bootstrap.txt)
         choco install $PACKAGES --source cygwin
     - name: bootstrap
       run: |
@@ -740,7 +742,7 @@ jobs:
       shell: bash {0}
       run: |
         choco --version
-        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/cygwin.txt ./build/pkgs/cygwin-bootstrap.txt)
+        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/_prereq/distros/cygwin.txt ./build/pkgs/_prereq/distros/cygwin-bootstrap.txt)
         choco install $PACKAGES --source cygwin
     - name: bootstrap
       run: |
@@ -818,7 +820,7 @@ jobs:
       shell: bash {0}
       run: |
         choco --version
-        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/cygwin.txt ./build/pkgs/cygwin-bootstrap.txt)
+        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/_prereq/distros/cygwin.txt ./build/pkgs/_prereq/distros/cygwin-bootstrap.txt)
         choco install $PACKAGES --source cygwin
     - name: bootstrap
       run: |
@@ -896,7 +898,7 @@ jobs:
       shell: bash {0}
       run: |
         choco --version
-        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/cygwin.txt ./build/pkgs/cygwin-bootstrap.txt)
+        PACKAGES=$(sed 's/#.*//;' ./build/pkgs/_prereq/distros/cygwin.txt ./build/pkgs/_prereq/distros/cygwin-bootstrap.txt)
         choco install $PACKAGES --source cygwin
     - name: bootstrap
       run: |

diff --git a/.github/workflows/ci-wsl.yml b/.github/workflows/ci-wsl.yml
@@ -9,6 +9,7 @@ on:
     branches:
       - 'public/build/**wsl**'
   workflow_dispatch:
+    # Allow to run manually
 
 jobs:
   windows:

diff --git a/.github/workflows/tox-experimental.yml b/.github/workflows/tox-experimental.yml
@@ -23,6 +23,8 @@ on:
   push:
     tags:
       - '*'
+  workflow_dispatch:
+    # Allow to run manually
 
 env:
   TARGETS_PRE: build/make/Makefile

diff --git a/.github/workflows/tox-gcc_spkg.yml b/.github/workflows/tox-gcc_spkg.yml
@@ -23,6 +23,8 @@ on:
   push:
     tags:
       - '*'
+  workflow_dispatch:
+    # Allow to run manually
 
 env:
   TARGETS_PRE: sagelib-build-deps

diff --git a/.github/workflows/tox-optional.yml b/.github/workflows/tox-optional.yml
@@ -23,6 +23,8 @@ on:
   push:
     tags:
       - '*'
+  workflow_dispatch:
+    # Allow to run manually
 
 env:
   TARGETS_PRE: build/make/Makefile

diff --git a/.github/workflows/tox.yml b/.github/workflows/tox.yml
@@ -23,6 +23,8 @@ on:
   push:
     tags:
       - '*'
+  workflow_dispatch:
+    # Allow to run manually
 
 env:
   TARGETS_PRE: sagelib-build-deps

diff --git a/.zenodo.json b/.zenodo.json
@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.3.beta6", 
-    "version": "9.3.beta6", 
+    "title": "sagemath/sage: 9.3.beta7", 
+    "version": "9.3.beta7", 
     "upload_type": "software", 
-    "publication_date": "2021-01-17", 
+    "publication_date": "2021-02-07", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta6", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta7", 
             "relation": "isSupplementTo"
         }, 
         {

diff --git a/Makefile b/Makefile
@@ -169,6 +169,7 @@ PTESTALL = ./sage -t -p --all
 # https://trac.sagemath.org/ticket/25345 and
 # https://trac.sagemath.org/ticket/26110.
 TESTALL_FLAGS = --optional=sage,dochtml,optional,external,build
+TESTALL_NODOC_FLAGS = --optional=sage,optional,external,build
 
 test: all
 	$(TESTALL) --logfile=logs/test.log
@@ -208,7 +209,45 @@ ptestoptional: all
 ptestoptionallong: all
 	$(PTESTALL) --long --logfile=logs/ptestoptionallong.log
 
-configure: bootstrap src/doc/bootstrap configure.ac src/bin/sage-version.sh m4/*.m4 build/pkgs/*/spkg-configure.m4 build/pkgs/*/type build/pkgs/*.txt build/pkgs/*/distros/*.txt
+test-nodoc: build
+	$(TESTALL) --logfile=logs/test.log
+
+check-nodoc: test-nodoc
+
+testall-nodoc: build
+	$(TESTALL) $(TESTALL_NODOC_FLAGS) --logfile=logs/testall.log
+
+testlong-nodoc: build
+	$(TESTALL) --long --logfile=logs/testlong.log
+
+testalllong-nodoc: build
+	$(TESTALL) --long $(TESTALL_NODOC_FLAGS) --logfile=logs/testalllong.log
+
+ptest-nodoc: build
+	$(PTESTALL) --logfile=logs/ptest.log
+
+ptestall-nodoc: build
+	$(PTESTALL) $(TESTALL_NODOC_FLAGS) --logfile=logs/ptestall.log
+
+ptestlong-nodoc: build
+	$(PTESTALL) --long --logfile=logs/ptestlong.log
+
+ptestalllong-nodoc: build
+	$(PTESTALL) --long $(TESTALL_NODOC_FLAGS) --logfile=logs/ptestalllong.log
+
+testoptional-nodoc: build
+	$(TESTALL) --logfile=logs/testoptional.log
+
+testoptionallong-nodoc: build
+	$(TESTALL) --long --logfile=logs/testoptionallong.log
+
+ptestoptional-nodoc: build
+	$(PTESTALL) --logfile=logs/ptestoptional.log
+
+ptestoptionallong-nodoc: build
+	$(PTESTALL) --long --logfile=logs/ptestoptionallong.log
+
+configure: bootstrap src/doc/bootstrap configure.ac src/bin/sage-version.sh m4/*.m4 build/pkgs/*/spkg-configure.m4 build/pkgs/*/type build/pkgs/*/distros/*.txt
 	./bootstrap -d
 
 install: all

diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-SageMath version 9.3.beta6, Release Date: 2021-01-17
+SageMath version 9.3.beta7, Release Date: 2021-02-07
diff --git a/bootstrap b/bootstrap
@@ -85,8 +85,12 @@ bootstrap () {
                 # --enable-SPKG options for installing pip packages
                 if [ ! -f build/pkgs/$pkgname/requirements.txt ]; then
                     pkgtype="$(cat build/pkgs/$pkgname/type)"
-                    spkg_configures="$spkg_configures
-SAGE_SPKG_ENABLE([$pkgname], [$pkgtype])"
+                    # Trac #29124: Do not provide --enable-_recommended and similar
+                    case "$pkgname" in
+                        _*) ;;
+                        *)  spkg_configures="$spkg_configures
+SAGE_SPKG_ENABLE([$pkgname], [$pkgtype])" ;;
+                    esac
                 fi
     done
     for pkgname in $(./sage --package list --has-file spkg-configure.m4 | sort); do

diff --git a/build/bin/sage-dist-helpers b/build/bin/sage-dist-helpers
@@ -204,7 +204,7 @@ sdh_setup_bdist_wheel() {
     mkdir -p dist
     rm -f dist/*.whl
     BDIST_DIR="$(mktemp -d)"
-    sage-python23 setup.py --no-user-cfg \
+    python3 setup.py --no-user-cfg \
          bdist_wheel --bdist-dir "$BDIST_DIR" \
          "$@" || sdh_die "Error building a wheel for $PKG_NAME"
 }
@@ -221,7 +221,7 @@ sdh_pip_install() {
 
     mkdir -p dist
     rm -f dist/*.whl
-    sage-python23 -m pip wheel --wheel-dir=dist --no-binary :all: --verbose --no-deps --no-index --isolated --no-build-isolation "$@" || \
+    python3 -m pip wheel --wheel-dir=dist --no-binary :all: --verbose --no-deps --no-index --isolated --no-build-isolation "$@" || \
         sdh_die "Error building a wheel for $PKG_NAME"
 
     sdh_store_and_pip_install_wheel .

diff --git a/build/bin/sage-pip-install b/build/bin/sage-pip-install
@@ -14,11 +14,14 @@
 #                      ~/.pydistutils.cfg
 pip_install_flags="--ignore-installed --verbose --no-deps --no-index --isolated"
 
-# Note: We need to take care to specify the full path to Sage's Python here
-# to emphasize that this command should use it, and not the system Python;
-# see https://trac.sagemath.org/ticket/18438
-# But now we delegate this to sage-python23.
-PYTHON=sage-python23
+# Note: "sage-pip-install" is meant to be run after $(PYTHON) has
+# been installed (either as an spkg or as a venv over a system python3).
+# It is then guaranteed by sage-env that PATH is set in a way that "python3"
+# refers to the correct python3.
+#
+# All SPKGs that use this script must therefore declare $(PYTHON) as a
+# dependency.
+PYTHON=python3
 
 # The PIP variable is only used to determine the name of the lock file.
 PIP=pip3

diff --git a/build/bin/sage-pip-uninstall b/build/bin/sage-pip-uninstall
@@ -12,11 +12,11 @@ if [ "$1" != "." ]; then
     exit 1
 fi
 
-# Note: We need to take care to specify the full path to Sage's Python here
-# to emphasize that this command should use it, and not the system Python;
-# see https://trac.sagemath.org/ticket/18438
-# But now we delegate this to sage-python23.
-PYTHON=sage-python23
+# Note: "sage-pip-uninstall" is meant to be run after $(PYTHON) has
+# been installed (either as an spkg or as a venv over a system python3).
+# It is then guaranteed by sage-env that PATH is set in a way that "python3"
+# refers to the correct python3.
+PYTHON=python3
 
 # The PIP variable is only used to determine the name of the lock file.
 PIP=pip3

diff --git a/build/bin/sage-print-system-package-command b/build/bin/sage-print-system-package-command
@@ -49,6 +49,7 @@ if [ -z "$system" -o -z "$command" ]; then
 fi
 system_packages="$*"
 options=
+env=
 shopt -s extglob
 case $system:$command in
     homebrew*:setup-build-env)
@@ -73,8 +74,8 @@ case $system:$command in
         ;;
     @(debian*|ubuntu*):*)
         [ "$NO_INSTALL_RECOMMENDS" = yes ] && options="$options --no-install-recommends"
-        [ "$YES" = yes ] && options="$options --yes"
-        [ -n "$system_packages" ] && echo "${PROMPT}${SUDO}apt-get $command $options $system_packages"
+        [ "$YES" = yes ] && options="$options --yes" env="DEBIAN_FRONTEND=noninteractive "
+        [ -n "$system_packages" ] && echo "${PROMPT}${SUDO}${env}apt-get $command $options $system_packages"
         ;;
     @(fedora*|redhat*|centos*):install)
         [ "$YES" = yes ] && options="$options -y"

diff --git a/build/bin/sage-python23 b/build/bin/sage-python23
diff --git a/build/bin/sage-spkg b/build/bin/sage-spkg
@@ -857,10 +857,4 @@ else
 fi
 
 
-# Touch this file to force a sage-location run next time Sage is
-# started.  This is needed to make some of the installed libraries and
-# scripts independent of the SAGE_ROOT path.
-touch "$SAGE_LOCAL/lib/sage-force-relocate.txt"
-
-
 echo "Finished installing $PKG_NAME"