Merge branch 'develop' into public/sparse_strategies_for_composite_el…

…liptic_curve_isogenies

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,6 +1,11 @@
+<!-- ^^^^^
+Please provide a concise, informative and self-explanatory title.
+Don't put issue numbers in there, do this in the PR body below.
+For example, instead of "Fixes #1234" use "Introduce new method to calculate 1+1"
+-->
 ### 📚 Description
 
-<!-- Describe your changes in detail -->
+<!-- Describe your changes here in detail -->
 <!-- Why is this change required? What problem does it solve? -->
 <!-- If it resolves an open issue, please link to the issue here. For example "Closes #1337" -->
 
@@ -10,6 +15,7 @@
 <!-- If your change requires a documentation PR, please link it appropriately -->
 <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! -->
 
+- [ ] I have made sure that the title is self-explanatory and the description concisely explains the PR.
 - [ ] I have linked an issue or discussion.
 - [ ] I have created tests covering the changes.
 - [ ] I have updated the documentation accordingly.

.github/workflows/doc-build.yml

@@ -15,14 +15,13 @@ 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
@@ -34,43 +33,17 @@ 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: Deploy to Netlify preview
-        id: preview-netlify
-        if: env.CAN_DEPLOY == 'true' && github.ref != 'refs/heads/develop'
-        uses: netlify/actions/cli@master
+      - name: Upload docs
+        uses: actions/upload-artifact@v3
         with:
-          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 }}"
+          name: docs
+          path: docs.zip

.github/workflows/doc-publish.yml

@@ -0,0 +1,95 @@
+# Triggers after the documentation build has finished, 
+# taking the artifact and uploading it to netlify
+name: Publish documentation
+
+on:
+  workflow_run:
+    workflows: ["Build documentation"]
+    types:
+      - completed
+
+permissions:
+  statuses: write
+  checks: write
+  pull-requests: write
+
+jobs:
+  upload-docs:
+    runs-on: ubuntu-latest
+    if: github.event.workflow_run.conclusion == 'success'
+    steps:
+      - name: Get information about workflow origin
+        uses: potiuk/get-workflow-origin@v1_5
+        id: source-run-info
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          sourceRunId: ${{ github.event.workflow_run.id }}
+
+      # Once https://github.com/actions/download-artifact/issues/172 and/or https://github.com/actions/download-artifact/issues/60 is implemented, we can use the official download-artifact action
+      # For now use the solution from https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#using-data-from-the-triggering-workflow
+      - name: Download docs
+        uses: actions/github-script@v3.1.0
+        with:
+          script: |
+            var artifacts = await github.actions.listWorkflowRunArtifacts({
+               owner: context.repo.owner,
+               repo: context.repo.repo,
+               run_id: ${{github.event.workflow_run.id }},
+            });
+            var matchArtifact = artifacts.data.artifacts.filter((artifact) => {
+              return artifact.name == "docs"
+            })[0];
+            var download = await github.actions.downloadArtifact({
+               owner: context.repo.owner,
+               repo: context.repo.repo,
+               artifact_id: matchArtifact.id,
+               archive_format: 'zip',
+            });
+            var fs = require('fs');
+            fs.writeFileSync('${{github.workspace}}/docs.zip', Buffer.from(download.data));
+      
+      - name: Extract docs
+        run: unzip docs.zip -d docs && unzip docs/docs.zip -d docs/docs
+
+      - name: Deploy to Netlify
+        id: deploy-netlify
+        uses: netlify/actions/cli@master
+        with:
+          args: deploy --dir=docs/docs/docs ${NETLIFY_PRODUCTION:+"--prod"} --message ${NETLIFY_MESSAGE} --alias ${NETLIFY_ALIAS}
+        env:
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+          NETLIFY_PRODUCTION: ${{ github.ref == 'refs/heads/develop' }}
+          NETLIFY_MESSAGE: ${{ steps.source-run-info.outputs.pullRequestNumber }}
+          NETLIFY_ALIAS: deploy-preview-${{ steps.source-run-info.outputs.pullRequestNumber }}
+
+      # Add deployment as status check, PR comment and annotation
+      # we could use the nwtgck/actions-netlify action for that, except for that it is not (yet) working in workflow_run context: https://github.com/nwtgck/actions-netlify/issues/545
+      - name: Add/Update deployment status PR comment
+        uses: marocchino/sticky-pull-request-comment@v2
+        with:
+          number: ${{ steps.source-run-info.outputs.pullRequestNumber }}
+          header: preview-comment
+          recreate: true
+          message: |
+            [Documentation preview for this PR](${{ steps.deploy-netlify.outputs.NETLIFY_URL }}) is ready! :tada:
+            Built with commit: ${{ steps.source-run-info.outputs.sourceHeadSha }}
+      
+      - name: Update deployment status PR check
+        uses: myrotvorets/set-commit-status-action@1.1.6
+        if: ${{ always() }}
+        env:
+          DEPLOY_SUCCESS: Successfully deployed preview.
+          DEPLOY_FAILURE: Failed to deploy preview.
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          status: ${{ job.status == 'success' && 'success' || 'failure' }}
+          sha: ${{ github.event.workflow_run.head_sha }}
+          context: Deploy Documentation
+          targetUrl: ${{ steps.deploy-netlify.outputs.NETLIFY_URL }}
+          description: ${{ job.status == 'success' && env.DEPLOY_SUCCESS || env.DEPLOY_FAILURE }}
+
+      - name: Report deployment url
+        run: |
+          echo "::notice::The documentation has being automatically deployed to Netlify. %0A ✅ Preview: ${{ 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: 9.8.rc1", 
-    "version": "9.8.rc1", 
+    "title": "sagemath/sage: 10.0.beta0", 
+    "version": "10.0.beta0", 
     "upload_type": "software", 
-    "publication_date": "2023-02-05", 
+    "publication_date": "2023-02-12", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.8.rc1", 
+            "identifier": "https://github.com/sagemath/sage/tree/10.0.beta0", 
             "relation": "isSupplementTo"
         }, 
         {

VERSION.txt

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

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 python3.10 python3.9 python3.8 python3.7 python2.7 python3.6 python2"
+PYTHONS="python python3 python3.12 python3.11 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=6e536cb217dd823f547403263fc7d1b21578eaef
-md5=83b833531d8bf1689f3368c47374f5e1
-cksum=2145026758
+sha1=fc9c71ad5be4e3197007ddb150cba47d15716d89
+md5=0a707bcc4316b8c3e3faca6330fc5dc2
+cksum=3972886119

build/pkgs/configure/package-version.txt

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

build/pkgs/ore_algebra/requirements.txt

@@ -1 +1 @@
-git+https://github.com/mkauers/ore_algebra@cfcb386f2cc1d3e044c71dfb149444355b16d775#egg=ore_algebra
+git+https://github.com/mkauers/ore_algebra@01c357f590685ff362c008229681ee08269457da#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 ~= 9.8rc1
+sage-conf ~= 10.0b0

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 ~= 9.8rc1
+sage-docbuild ~= 10.0b0

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 ~= 9.8rc1
+sage-setup ~= 10.0b0

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 ~= 9.8rc1
+sage-sws2rst ~= 10.0b0

build/pkgs/sagelib/install-requires.txt

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

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 ~= 9.8rc1
+sagemath-categories ~= 10.0b0

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 ~= 9.8rc1
+sagemath-environment ~= 10.0b0

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 ~= 9.8rc1
+sagemath-objects ~= 10.0b0

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 ~= 9.8rc1
+sagemath-repl ~= 10.0b0

build/pkgs/singular/checksums.ini

@@ -1,5 +1,5 @@
 tarball=singular-VERSION.tar.gz
-sha1=6c2b622d3681e2de3d58d30c654d43d3e32b720c
-md5=abb1e37c794472e7760655358ab66054
-cksum=17455733
+sha1=28bb3ee97ef48d04dfa96de182fd93eebe08426c
+md5=fc0a4f5720dadba45a52ee94324ce00c
+cksum=1573851737
 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 @@
-4.3.1p1
+4.3.1p3

pkgs/sage-conf/VERSION.txt

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

pkgs/sage-conf_pypi/VERSION.txt

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

pkgs/sage-docbuild/VERSION.txt

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

pkgs/sage-setup/VERSION.txt

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

pkgs/sage-sws2rst/VERSION.txt

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

pkgs/sagemath-categories/VERSION.txt

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

pkgs/sagemath-environment/VERSION.txt

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

pkgs/sagemath-objects/VERSION.txt

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

pkgs/sagemath-repl/VERSION.txt

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

src/.relint.yml

@@ -46,7 +46,9 @@
 - 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: 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
   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 @@
-9.8.rc1
+10.0.beta0

src/bin/sage

@@ -479,6 +479,13 @@ 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"
@@ -974,6 +981,11 @@ 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

src/bin/sage-version.sh

@@ -4,6 +4,6 @@
 # which stops "setup.py develop" from rewriting it as a Python file.
 :
 # This file is auto-generated by the sage-update-version script, do not edit!
-SAGE_VERSION='9.8.rc1'
-SAGE_RELEASE_DATE='2023-02-05'
-SAGE_VERSION_BANNER='SageMath version 9.8.rc1, Release Date: 2023-02-05'
+SAGE_VERSION='10.0.beta0'
+SAGE_RELEASE_DATE='2023-02-12'
+SAGE_VERSION_BANNER='SageMath version 10.0.beta0, Release Date: 2023-02-12'

src/doc/en/developer/packaging_sage_library.rst

@@ -274,6 +274,10 @@ distribution -- which then must be declared as a run-time dependency.
   the ``sage:`` prompt. In particular, no Sage library code should import from
   :mod:`sage.rings.all`.
 
+  To audit the Sage library for such imports, use ``sage --tox -e relint``.
+  In most cases, the imports can be fixed automatically using the
+  tool ``sage --fiximports``.
+
 - Replace module-level imports by method-level imports.  Note that
   this comes with a small runtime overhead, which can become
   noticeable if the method is called in tight inner loops.

src/doc/en/reference/combinat/module_list.rst

@@ -145,6 +145,7 @@ Comprehensive Module List
     sage/combinat/k_regular_sequence
     sage/combinat/k_tableau
     sage/combinat/kazhdan_lusztig
+    sage/combinat/key_polynomial
     sage/combinat/knutson_tao_puzzles
     sage/combinat/matrices/all
     sage/combinat/matrices/dancing_links

src/doc/en/reference/groups/index.rst

@@ -19,11 +19,13 @@ Groups
    sage/groups/cubic_braid
    sage/groups/indexed_free_group
    sage/groups/raag
+   sage/groups/cactus_group
    sage/groups/group_exp
    sage/groups/group_semidirect_product
    sage/groups/misc_gps/misc_groups
    sage/groups/semimonomial_transformations/semimonomial_transformation_group
    sage/groups/semimonomial_transformations/semimonomial_transformation
+   sage/groups/kernel_subgroup
    sage/groups/class_function
    sage/groups/conjugacy_classes