Run sage doc server for notebooks

.codecov.yml

@@ -0,0 +1 @@
+comment: false

.github/workflows/ci-cygwin-standard.yml

@@ -59,11 +59,13 @@ jobs:
     needs: [cygwin-stage-i-a, cygwin-stage-i-b]
 
   cygwin-stage-ii-e:
-    uses: ./.github/workflows/cygwin.yml
-    with:
-      stage: ii-e
-      previous_stages: i-*
-      targets: threejs tachyon pillow jmol m4rie sympy lrcalc lcalc symmetrica cliquer libbraiding planarity rw elliptic_curves combinatorial_designs sympow
+    env:
+      STAGE: ii-e
+      PREVIOUS_STAGES: i-*
+      TARGETS: threejs tachyon pillow jmol m4rie sympy lrcalc lcalc symmetrica cliquer libbraiding planarity rw elliptic_curves combinatorial_designs sympow
+      LOCAL_ARTIFACT_NAME: sage-local-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
+      LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
+
     needs: [cygwin-stage-i-a, cygwin-stage-i-b]
 
 ############################################## stage-iii ##########################################

.github/workflows/ci-linux.yml

@@ -162,3 +162,41 @@ jobs:
           ["maximal"]
       docker_targets: "with-targets-optional"
       targets_optional: '$(echo $(export PATH=build/bin:$PATH && sage-package list :experimental: --has-file "spkg-install.in|spkg-install|requirements.txt" --no-file "huge|has_nonfree_dependencies" | grep -v sagemath_doc | grep ^[p-z]))'
+
+  local-ubuntu:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      max-parallel: 1
+      matrix:
+        tox_system_factor: [conda-forge-ubuntu]
+        tox_packages_factor: [minimal, standard, environment, environment-optional]
+    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 }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install test prerequisites
+        run: |
+          sudo DEBIAN_FRONTEND=noninteractive apt-get update
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
+      - name: Build and test with tox
+        # We use a high parallelization on purpose in order to catch possible parallelization bugs in the build scripts.
+        # For doctesting, we use a lower parallelization to avoid timeouts.
+        run: |
+          MAKE="make -j12" tox -e $TOX_ENV -- SAGE_NUM_THREADS=4 $TARGETS
+      - name: Prepare logs artifact
+        run: |
+          mkdir -p "artifacts/$LOGS_ARTIFACT_NAME"; cp -r .tox/*/log "artifacts/$LOGS_ARTIFACT_NAME"
+        if: always()
+      - uses: actions/upload-artifact@v3
+        with:
+          path: artifacts
+          name: ${{ env.LOGS_ARTIFACT_NAME }}
+        if: always()
+      - name: Print out logs for immediate inspection
+        # and markup the output with GitHub Actions logging commands
+        run: |
+          .github/workflows/scan-logs.sh "artifacts/$LOGS_ARTIFACT_NAME"
+        if: always()

.github/workflows/doc-build.yml

@@ -15,13 +15,14 @@ jobs:
   build-docs:
     runs-on: ubuntu-latest
     container: ghcr.io/sagemath/sage/sage-docker-ubuntu-focal-standard-with-targets:dev
+    env:
+      CAN_DEPLOY: ${{ secrets.NETLIFY_AUTH_TOKEN != '' }}
     steps:
       - name: Checkout
         uses: actions/checkout@v3
 
       - name: Prepare
         run: |
-          apt-get update && apt-get install -y zip
           # Reuse built SAGE_LOCAL contained in the Docker image
           ./bootstrap
           ./configure --enable-build-as-root --prefix=/sage/local --with-sage-venv --enable-download-from-upstream-url
@@ -33,17 +34,43 @@ jobs:
           SAGE_NUM_THREADS: 2
 
       - name: Copy docs
+        if: env.CAN_DEPLOY == 'true'
         run: |
           # For some reason the deploy step below cannot find /sage/...
           # So copy everything from there to local folder
           # We also need to replace the symlinks because netlify is not following them
           mkdir -p ./docs
           cp -r -L /sage/local/share/doc/sage/html/en/* ./docs
-          # Zip everything for increased performance
-          zip -r docs.zip docs
 
-      - name: Upload docs
-        uses: actions/upload-artifact@v3
+      - name: Deploy to Netlify preview
+        id: preview-netlify
+        if: env.CAN_DEPLOY == 'true' && github.ref != 'refs/heads/develop'
+        uses: netlify/actions/cli@master
         with:
-          name: docs
-          path: docs.zip
+          args: deploy --dir=docs --alias="${NETLIFY_ALIAS}"
+        env:
+          # Set deployment url to commit hash to easily link from the trac.
+          # We could also set NETLIFY_ALIAS to the branch name.
+          # However, netlify currently doesn't support updates to a deployment with the same alias
+          # https://github.com/netlify/cli/issues/948
+          # https://github.com/netlify/cli/issues/1984
+          # Note that even if this feature is implemented, one would also need to first process the branch name
+          # to workaround the bug https://github.com/netlify/cli/issues/969.
+          NETLIFY_ALIAS: ${{ github.sha }}
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+
+      - name: Deploy to Netlify production
+        id: deploy-netlify
+        if: env.CAN_DEPLOY == 'true' && github.ref == 'refs/heads/develop'
+        uses: netlify/actions/cli@master
+        with:
+          args: deploy --dir=docs --prod
+        env:
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+
+      - name: Report deployment url
+        if: env.CAN_DEPLOY == 'true'
+        run: |
+          echo "::notice::The documentation has being automatically deployed to Netlify. %0A ✅ Preview: ${{ steps.preview-netlify.outputs.NETLIFY_URL || steps.deploy-netlify.outputs.NETLIFY_URL }}"

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 10.0.beta0", 
-    "version": "10.0.beta0", 
+    "title": "sagemath/sage: 9.8.rc1", 
+    "version": "9.8.rc1", 
     "upload_type": "software", 
-    "publication_date": "2023-02-12", 
+    "publication_date": "2023-02-05", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/10.0.beta0", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.8.rc1", 
             "relation": "isSupplementTo"
         }, 
         {

VERSION.txt

@@ -1 +1 @@
-SageMath version 10.0.beta0, Release Date: 2023-02-12
+SageMath version 9.8.rc1, Release Date: 2023-02-05

build/bin/sage-bootstrap-python

@@ -53,7 +53,7 @@ if [ "$LC_ALL" = "C" -o "$LANG" = "C" -o "$LC_CTYPE" = "C" ]; then
     export LANG
 fi
 
-PYTHONS="python python3 python3.12 python3.11 python3.10 python3.9 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.

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=fc9c71ad5be4e3197007ddb150cba47d15716d89
-md5=0a707bcc4316b8c3e3faca6330fc5dc2
-cksum=3972886119
+sha1=6e536cb217dd823f547403263fc7d1b21578eaef
+md5=83b833531d8bf1689f3368c47374f5e1
+cksum=2145026758

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-785ddef6338073b27082bb675446e3ae111b3b5d
+2d3c71b03b2c11caceac69da380dab3ef4374519

build/pkgs/ore_algebra/requirements.txt

@@ -1 +1 @@
-git+https://github.com/mkauers/ore_algebra@01c357f590685ff362c008229681ee08269457da#egg=ore_algebra
+git+https://github.com/mkauers/ore_algebra@cfcb386f2cc1d3e044c71dfb149444355b16d775#egg=ore_algebra

build/pkgs/sage_conf/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-conf ~= 10.0b0
+sage-conf ~= 9.8rc1

build/pkgs/sage_docbuild/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-docbuild ~= 10.0b0
+sage-docbuild ~= 9.8rc1

build/pkgs/sage_setup/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-setup ~= 10.0b0
+sage-setup ~= 9.8rc1

build/pkgs/sage_sws2rst/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-sws2rst ~= 10.0b0
+sage-sws2rst ~= 9.8rc1

build/pkgs/sagelib/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagelib ~= 10.0b0
+sagelib ~= 9.8rc1

build/pkgs/sagemath_categories/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-categories ~= 10.0b0
+sagemath-categories ~= 9.8rc1

build/pkgs/sagemath_environment/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-environment ~= 10.0b0
+sagemath-environment ~= 9.8rc1

build/pkgs/sagemath_objects/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-objects ~= 10.0b0
+sagemath-objects ~= 9.8rc1

build/pkgs/sagemath_repl/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-repl ~= 10.0b0
+sagemath-repl ~= 9.8rc1

build/pkgs/singular/checksums.ini

@@ -1,5 +1,5 @@
 tarball=singular-VERSION.tar.gz
-sha1=28bb3ee97ef48d04dfa96de182fd93eebe08426c
-md5=fc0a4f5720dadba45a52ee94324ce00c
-cksum=1573851737
+sha1=6c2b622d3681e2de3d58d30c654d43d3e32b720c
+md5=abb1e37c794472e7760655358ab66054
+cksum=17455733
 upstream_url=ftp://jim.mathematik.uni-kl.de/pub/Math/Singular/SOURCES/4-3-1/singular-VERSION.tar.gz

build/pkgs/singular/package-version.txt

@@ -1 +1 @@
-4.3.1p3
+4.3.1p1

pkgs/sage-conf/VERSION.txt

@@ -1 +1 @@
-10.0.beta0
+9.8.rc1

pkgs/sage-conf_pypi/VERSION.txt

@@ -1 +1 @@
-10.0.beta0
+9.8.rc1

pkgs/sage-docbuild/VERSION.txt

@@ -1 +1 @@
-10.0.beta0
+9.8.rc1

pkgs/sage-setup/VERSION.txt

@@ -1 +1 @@
-10.0.beta0
+9.8.rc1

pkgs/sage-sws2rst/VERSION.txt

@@ -1 +1 @@
-10.0.beta0
+9.8.rc1

pkgs/sagemath-categories/VERSION.txt

@@ -1 +1 @@
-10.0.beta0
+9.8.rc1

pkgs/sagemath-environment/VERSION.txt

@@ -1 +1 @@
-10.0.beta0
+9.8.rc1

pkgs/sagemath-objects/VERSION.txt

@@ -1 +1 @@
-10.0.beta0
+9.8.rc1

pkgs/sagemath-repl/VERSION.txt

@@ -1 +1 @@
-10.0.beta0
+9.8.rc1

src/.relint.yml

@@ -46,9 +46,7 @@
 - name: 'namespace_pkg_all_import: import from .all of a namespace package'
   hint: |
     Sage library code should not import from sage.PAC.KAGE.all when sage.PAC.KAGE is an implicit
-    Hint: namespace package. Type import_statements("SOME_IDENTIFIER") to find a more specific import,
-    Hint: or use 'sage --fiximports' to fix automatically in the source file.
-  # Keep in sync with SAGE_ROOT/src/sage/misc/replace_dot_all.py
+    Hint: namespace package. Type import_statements("SOME_IDENTIFIER") to find a more specific import.
   pattern: 'from\s+sage(|[.](arith|categories|combinat|ext|graphs(|[.]decompositions)|interfaces|libs|matrix|misc|numerical(|[.]backends)|rings|sets))[.]all\s+import'
   filePattern: '.*[.](py|pyx|pxi)$'
   error: false # Make this a warning instead of an error for now

src/VERSION.txt

@@ -1 +1 @@
-10.0.beta0
+9.8.rc1

src/bin/sage

@@ -479,13 +479,6 @@ usage_advanced() {
         echo "                         Sage documentation for \"string\"."
         echo "  --search_src ...    -- same as --grep"
         echo "  --search_doc ...    -- same as --grepdoc"
-        echo "  --fixdoctests file.py"
-        echo "                      -- Run doctests and replace output of failing doctests"
-        echo "                         with actual output."
-        echo "  --fiximports <files|dir>"
-        echo "                      -- Replace imports from sage.PAC.KAGE.all by specific"
-        echo "                         imports when sage.PAC.KAGE is an implicit namespace"
-        echo "                         package"
     fi
     echo "  --sh [...]         -- run a shell with Sage environment variables"
     echo "                        as they are set in the runtime of Sage"
@@ -981,11 +974,6 @@ if [ "$1" = '-startuptime' -o "$1" = '--startuptime' ]; then
     exec sage-startuptime.py "$@"
 fi
 
-if [ "$1" = '-fiximports' -o "$1" = '--fiximports' ]; then
-    shift
-    exec sage-python -m sage.misc.replace_dot_all "$@"
-fi
-
 if [ "$1" = '-tox' -o "$1" = '--tox' ]; then
     shift
     if [ -n "$SAGE_SRC" -a -f "$SAGE_SRC/tox.ini" ]; then