Merge tag '9.3.beta3' into t/29314/packages/gap411

SageMath version 9.3.beta3, Release Date: 2020-12-06

Author: Matthias Koeppe

.github/workflows/ci-wsl.yml

@@ -1,11 +1,19 @@
 name: Build & Test WSL
 
-on: [push, pull_request]
+on:
+  pull_request:
+    types: [opened, synchronize]
+  push:
+    tags:
+      - '*'
+    branches:
+      - 'public/build/**wsl**'
+  workflow_dispatch:
 
 jobs:
   windows:
     runs-on: windows-latest
-    name: Windows (using WSL)
+    name: Ubuntu 20.04
     # Following https://trac.sagemath.org/ticket/25206#comment:63
     steps:
     - name: Configure git
@@ -18,22 +26,10 @@ jobs:
         Ubuntu\ubuntu2004.exe install --root
     - name: Install dependencies
       run: |
-        Function ExtractPackages
-        {
-           param($path)
-           @(Get-Content $path | Where-Object { !$_.StartsWith("#") })
-        }
-        $packages = Get-ChildItem build/pkgs -recurse -Include debian.txt, debian-bootstrap.txt | foreach-object { ExtractPackages $_.FullName } | sort -Unique
-        # Add tox which is use to build
-        $packages += 'tox'
-        echo "Install the following packages:" @packages
-        # Add deadsnakes so that libpython3.7-dev is found
-        & wsl sudo add-apt-repository ppa:deadsnakes/ppa
-        # Install
-        & wsl sudo apt-get update -y 
-        & wsl sudo apt-get install -y @packages
+        wsl sudo apt-get update -y 
+        wsl sudo apt-get install -y tox
     - name: Build
-      run: wsl tox -e local -- SAGE_NUM_THREADS=4 build
+      run: wsl tox -e local-sudo-ubuntu-standard -- SAGE_NUM_THREADS=4 build
       env:
         # WSL runs everything as root, so we have to enable build as root user
         EXTRA_CONFIGURE_ARGS: "--enable-build-as-root"
@@ -42,7 +38,7 @@ jobs:
         MAKE: "make -j2"
         WSLENV: EXTRA_CONFIGURE_ARGS:MAKE
     - name: Test
-      run: wsl tox -e local -- SAGE_NUM_THREADS=4 ptest
+      run: wsl tox -e local-sudo-ubuntu-standard -- SAGE_NUM_THREADS=4 ptest
     - name: Prepare logs artifact
       run: mkdir -p "artifacts/logs"; cp -r .tox/*/log "artifacts/logs"
       shell: bash

.github/workflows/lint.yml

@@ -0,0 +1,47 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint-pycodestyle:
+    name: Code style check with pycodestyle
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Install pycodestyle
+      run: pip install tox pycodestyle
+    - name: Lint using pycodestyle
+      run: tox -e pycodestyle
+  lint-relint:
+    name: Code style check with relint
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Install pycodestyle
+      run: pip install tox relint
+    - name: Lint using relint
+      run: tox -e relint src/
+  lint-pyright:
+    name: Static type check with pyright
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+    - name: Set up node to install pyright
+      uses: actions/setup-node@v1
+      with:
+        node-version: '12'
+    - name: Install pyright
+      run: npm install -g pyright
+    - name: Lint using pyright
+      run: pyright

.github/workflows/tox-experimental.yml

@@ -69,7 +69,7 @@ jobs:
               TOKEN="${{ secrets.GITHUB_TOKEN }}"
             fi
             if echo "$TOKEN" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin; then
-              echo "::set-env name=DOCKER_PUSH_REPOSITORY::docker.pkg.github.com/${{ github.repository }}/"
+              echo "DOCKER_PUSH_REPOSITORY=docker.pkg.github.com/${{ github.repository }}/" >> $GITHUB_ENV
             fi
       - run: |
           set -o pipefail; EXTRA_DOCKER_BUILD_ARGS="--build-arg USE_MAKEFLAGS=\"-k V=0 SAGE_NUM_THREADS=3\"" tox -e $TOX_ENV -- $TARGETS 2>&1 | sed "/^configure: notice:/s|^|::warning file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;/^configure: warning:/s|^|::warning file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;/^configure: error:/s|^|::error file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;"
@@ -99,20 +99,25 @@ jobs:
 
   local-macos:
 
-    runs-on: macos-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       max-parallel: 3
       matrix:
+        os: [ macos-10.15, macos-11.0 ]
         tox_system_factor: [homebrew-macos, homebrew-macos-python3_xcode, homebrew-macos-python3_xcode-nokegonly, homebrew-macos-python3_pythonorg, conda-forge-macos]
         tox_packages_factor: [maximal]
         targets_pattern: [0-g, h-o, p, q-z]
+        xcode_version_factor: [11.7, default, 12.3]
     env:
       TOX_ENV: local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
-      LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
+      LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}-${{ matrix.os }}-xcode_${{ matrix.xcode_version_factor }}
       TARGETS_OPTIONAL: "$( echo $(PATH=build/bin:$PATH build/bin/sage-package list :experimental: | grep -v  database_stein_watkins\\$ | grep -v polytopes_db_4d | grep '^[${{ matrix.targets_pattern }}]' ) )"
     steps:
       - uses: actions/checkout@v2
+      - name: Select Xcode version
+        run: |
+          if [ ${{ matrix.xcode_version_factor }} != default ]; then sudo xcode-select -s /Applications/Xcode_${{ matrix.xcode_version_factor }}.app; fi
       - name: Install test prerequisites
         run: |
           brew install tox

.github/workflows/tox-gcc_spkg.yml

@@ -67,7 +67,7 @@ jobs:
               TOKEN="${{ secrets.GITHUB_TOKEN }}"
             fi
             if echo "$TOKEN" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin; then
-              echo "::set-env name=DOCKER_PUSH_REPOSITORY::docker.pkg.github.com/${{ github.repository }}/"
+              echo "DOCKER_PUSH_REPOSITORY=docker.pkg.github.com/${{ github.repository }}/" >> $GITHUB_ENV
             fi
       - run: |
           set -o pipefail; EXTRA_DOCKER_BUILD_ARGS="--build-arg USE_MAKEFLAGS=\"-k V=0 SAGE_NUM_THREADS=3\"" tox -e $TOX_ENV -- $TARGETS 2>&1 | sed "/^configure: notice:/s|^|::warning file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;/^configure: warning:/s|^|::warning file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;/^configure: error:/s|^|::error file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;"

.github/workflows/tox-optional.yml

@@ -71,7 +71,7 @@ jobs:
               TOKEN="${{ secrets.GITHUB_TOKEN }}"
             fi
             if echo "$TOKEN" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin; then
-              echo "::set-env name=DOCKER_PUSH_REPOSITORY::docker.pkg.github.com/${{ github.repository }}/"
+              echo "DOCKER_PUSH_REPOSITORY=docker.pkg.github.com/${{ github.repository }}/" >> $GITHUB_ENV
             fi
       - run: |
           set -o pipefail; EXTRA_DOCKER_BUILD_ARGS="--build-arg USE_MAKEFLAGS=\"-k V=0 SAGE_NUM_THREADS=3\"" tox -e $TOX_ENV -- $TARGETS 2>&1 | sed "/^configure: notice:/s|^|::warning file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;/^configure: warning:/s|^|::warning file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;/^configure: error:/s|^|::error file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;"
@@ -101,22 +101,27 @@ jobs:
 
   local-macos:
 
-    runs-on: macos-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       max-parallel: 3
       matrix:
+        os: [ macos-10.15, macos-11.0 ]
         tox_system_factor: [homebrew-macos, homebrew-macos-python3_xcode, homebrew-macos-python3_xcode-nokegonly, homebrew-macos-python3_pythonorg, conda-forge-macos]
         tox_packages_factor: [maximal]
         targets_pattern: [0-g, h-o, p, q-z]
+        xcode_version_factor: [11.7, default, 12.3]
     env:
       TOX_ENV: local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
-      LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
+      LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}-${{ matrix.os }}-xcode_${{ matrix.xcode_version_factor }}
       # Test all optional packages, but do not test huge packages
       # and do not test packages that require external software
       TARGETS_OPTIONAL: "$( echo $(PATH=build/bin:$PATH build/bin/sage-package list :optional: | grep -v  database_stein_watkins\\$ | grep -v polytopes_db_4d | grep -v cplex | grep -v gurobi | grep '^[${{ matrix.targets_pattern }}]' ) )"
     steps:
       - uses: actions/checkout@v2
+      - name: Select Xcode version
+        run: |
+          if [ ${{ matrix.xcode_version_factor }} != default ]; then sudo xcode-select -s /Applications/Xcode_${{ matrix.xcode_version_factor }}.app; fi
       - name: Install test prerequisites
         run: |
           brew install tox

.github/workflows/tox.yml

@@ -67,7 +67,7 @@ jobs:
               TOKEN="${{ secrets.GITHUB_TOKEN }}"
             fi
             if echo "$TOKEN" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin; then
-              echo "::set-env name=DOCKER_PUSH_REPOSITORY::docker.pkg.github.com/${{ github.repository }}/"
+              echo "DOCKER_PUSH_REPOSITORY=docker.pkg.github.com/${{ github.repository }}/" >> $GITHUB_ENV
             fi
       - run: |
           set -o pipefail; EXTRA_DOCKER_BUILD_ARGS="--build-arg USE_MAKEFLAGS=\"-k V=0 SAGE_NUM_THREADS=3\"" tox -e $TOX_ENV -- $TARGETS 2>&1 | sed "/^configure: notice:/s|^|::warning file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;/^configure: warning:/s|^|::warning file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;/^configure: error:/s|^|::error file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;"
@@ -97,17 +97,18 @@ jobs:
 
   local-macos:
 
-    runs-on: macos-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       max-parallel: 4
       matrix:
+        os: [ macos-10.15, macos-11.0 ]
         tox_system_factor: [homebrew-macos, homebrew-macos-python3_xcode, homebrew-macos-python3_xcode-nokegonly, homebrew-macos-python3_pythonorg, homebrew-macos-python3_xcode-gcc_spkg, conda-forge-macos]
         tox_packages_factor: [minimal, standard]
-        xcode_version_factor: [default, 12]
+        xcode_version_factor: [11.7, default, 12.3]
     env:
       TOX_ENV: local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
-      LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}-xcode_${{ matrix.xcode_version_factor }}
+      LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}-${{ matrix.os }}-xcode_${{ matrix.xcode_version_factor }}
     steps:
       - uses: actions/checkout@v2
       - name: Select Xcode version
@@ -214,11 +215,12 @@ jobs:
 
     needs: [dist]
 
-    runs-on: macos-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       max-parallel: 4
       matrix:
+        os: [ macos-10.15, macos-11.0 ]
         tox_system_factor: [macos-nobootstrap, macos-nobootstrap-python3_pythonorg]
         tox_packages_factor: [minimal]
         xcode_version_factor: [default, 12]

.gitignore

@@ -18,6 +18,11 @@
 # no longer generated, but may still be in user worktrees
 /src/lib/pkgconfig
 
+/environment.yml
+/environment-optional.yml
+/src/environment.yml
+/src/environment-optional.yml
+
 # Various editors
 *~
 

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.3.beta1", 
-    "version": "9.3.beta1", 
+    "title": "sagemath/sage: 9.3.beta3", 
+    "version": "9.3.beta3", 
     "upload_type": "software", 
-    "publication_date": "2020-11-07", 
+    "publication_date": "2020-12-06", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta1", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta3", 
             "relation": "isSupplementTo"
         }, 
         {

Makefile

@@ -64,11 +64,11 @@ build/make/Makefile: configure $(SPKG_COLLECT_FILES) $(CONFIG_FILES:%=%.in)
 buildbot-python3:
 	$(MAKE)
 
-# Preemptively download all standard upstream source tarballs.
+# Preemptively download all source tarballs of normal packages.
 download:
 	export SAGE_ROOT=$$(pwd) && \
-	export PATH=$$SAGE_ROOT/src/bin:$$PATH && \
-	./src/bin/sage-download-upstream
+	export PATH=$$SAGE_ROOT/build/bin:$$PATH && \
+	sage-package download :all:
 
 dist: build/make/Makefile
 	./sage --sdist
@@ -111,6 +111,10 @@ bootstrap-clean:
 	rm -f src/doc/en/installation/*.txt
 	rm -rf src/doc/en/reference/spkg/*.rst
 	rm -f src/doc/en/reference/repl/*.txt
+	rm -f environment.yml
+	rm -f src/environment.yml
+	rm -f environment-optional.yml
+	rm -f src/environment-optional.yml
 
 # Remove absolutely everything which isn't part of the git repo
 maintainer-clean: distclean bootstrap-clean
@@ -147,15 +151,15 @@ micro_release:
 
 # Leaves everything that is needed to make the next "make" fast but removes
 # all the cheap build artifacts that can be quickly regenerated.
+# Trac #30960: We no longer uninstall sagelib.
 fast-rebuild-clean: misc-clean
 	rm -rf upstream/
-	rm -rf src/build/temp.*
-	# Without site-packages/sage sage does not start but copying/compiling
-	# them from src/build is very fast.
-	rm -rf local/lib/python*/site-packages/sage
+	rm -rf build/pkgs/sagelib/src/build/temp.*
 	# The .py files in src/build are restored from src/sage without their
 	# mtimes changed.
-	find src/build -name '*.py' -exec rm \{\} \;
+	-find build/pkgs/sagelib/src/build -name '*.py' -exec rm \{\} \;
+	# Remove leftovers from ancient branches
+	rm -rf src/build
 
 TESTALL = ./sage -t --all
 PTESTALL = ./sage -t -p --all

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.3.beta1, Release Date: 2020-11-07
+SageMath version 9.3.beta3, Release Date: 2020-12-06