Merge branch 'develop' into no-pari-2.17

sagemath · Oct 5, 2024 · f366e88 · f366e88
2 parents 72085e2 + b0f09d9
commit f366e88
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diff --git a/.ci/create-changes-html.sh b/.ci/create-changes-html.sh
@@ -1,11 +1,12 @@
 #!/bin/sh
 if [ $# != 2 ]; then
-    echo >&2 "usage: $0 BASE_DOC_COMMIT DOC_REPO"
-    echo >&2 "creates CHANGES.html in the current directory"
-    echo >&2 "for the diffs of DOC_REPO against BASE_DOC_COMMIT"
+    echo >&2 "Usage: $0 DIFF_TEXT DOC_REPO"
+    echo >&2 "This script generates a CHANGES.html file in the current directory"
+    echo >&2 "and adds anchor targets in the documents within DOC_REPO"
+    echo >&2 "based on the diff hunks in the DIFF_TEXT file."
     exit 1
 fi
-BASE_DOC_COMMIT="$1"
+DIFF_TEXT="$1"
 DOC_REPOSITORY="$2"
 
 # Create CHANGES.html
@@ -52,11 +53,10 @@ diffParagraphs.forEach(paragraph => {
 EOF
 echo '</head>' >> CHANGES.html
 echo '<body>' >> CHANGES.html
-(cd $DOC_REPOSITORY && git diff $BASE_DOC_COMMIT -- "*.html") > diff.txt
 python3 - << EOF
 import os, re, html
 from itertools import chain
-with open('diff.txt', 'r') as f:
+with open('$DIFF_TEXT', 'r') as f:
     diff_text = f.read()
 diff_blocks = re.split(r'^(?=diff --git)', diff_text, flags=re.MULTILINE)
 out_blocks = []
@@ -83,12 +83,21 @@ for block in diff_blocks:
                     hunk_lines = []
                 search_result = re.search(r'@@ -(\d+),(\d+) \+(\d+),(\d+)', line)
                 if search_result:
-                    line_number = int(search_result.group(3))
+                    line_number = int(search_result.group(3)) - 1
                     span = int(search_result.group(4))
                     for i in chain(range(line_number, line_number + span), range(line_number - 1, -1, -1)):
-                        if content[i].startswith('<') and not content[i].startswith('</'):
+                        try:
+                            ln = content[i]
+                        except IndexError:
+                            continue
+                        for idx, char in enumerate(ln):
+                            if not char.isspace():
+                                break
+                        else:
+                            idx = len(ln)
+                        if ln.startswith('<', idx) and not ln.startswith('</', idx):
                             count += 1
-                            content[i] = f'<span id="hunk{count}" style="visibility: hidden;"></span>' + content[i]
+                            content[i] = ln[:idx] + f'<span id="hunk{count}" style="visibility: hidden;"></span>' + ln[idx:]
                             hunks.append(f'<p class="hunk"><a href="{path}#hunk{count}" class="hunk" target="_blank">hunk #{count}</a></p>')
                             break
             hunk_lines.append(line)
@@ -107,4 +116,4 @@ EOF
 cat diff.html >> CHANGES.html
 echo '</body>' >> CHANGES.html
 echo '</html>' >> CHANGES.html
-rm diff.txt diff.html
+rm diff.html
diff --git a/.ci/retrofit-worktree.sh b/.ci/retrofit-worktree.sh
@@ -43,4 +43,4 @@ git worktree add --detach $WORKTREE_NAME
 rm -rf $WORKTREE_DIRECTORY/.git && mv $WORKTREE_NAME/.git $WORKTREE_DIRECTORY/
 rm -rf $WORKTREE_NAME && ln -s $WORKTREE_DIRECTORY $WORKTREE_NAME
 if [ ! -f $WORKTREE_NAME/.gitignore ]; then cp .gitignore $WORKTREE_NAME/; fi
-(cd $WORKTREE_NAME && git add -A && git commit --quiet --allow-empty -m "old" -a && git tag -f old && git checkout new && git status)
+(cd $WORKTREE_NAME && git add -A && git commit --quiet --allow-empty -m "old" -a && git tag -f old && git checkout -f new && git clean -fd && git status)
diff --git a/.ci/write-dockerfile.sh b/.ci/write-dockerfile.sh
@@ -283,8 +283,8 @@ $ADD .upstream.d /new/.upstream.d
 ADD .ci /.ci
 RUN if [ -d /sage ]; then                                               \
         echo "### Incremental build from \$(cat /sage/VERSION.txt)" &&  \
-        printf '/src\n!/src/doc/bootstrap\n!/src/bin\n!/src/*.m4\n!/src/*.toml\n!/src/VERSION.txt\n' >> /sage/.gitignore && \
-        printf '/src\n!/src/doc/bootstrap\n!/src/bin\n!/src/*.m4\n!/src/*.toml\n!/src/VERSION.txt\n' >> /new/.gitignore && \
+        printf '/src/*\n!/src/doc/bootstrap\n!/src/bin\n!/src/*.m4\n!/src/*.toml\n!/src/VERSION.txt\n' >> /sage/.gitignore && \
+        printf '/src/*\n!/src/doc/bootstrap\n!/src/bin\n!/src/*.m4\n!/src/*.toml\n!/src/VERSION.txt\n' >> /new/.gitignore && \
         if ! (cd /new && /.ci/retrofit-worktree.sh worktree-image /sage); then \
             echo "retrofit-worktree.sh failed, falling back to replacing /sage"; \
             for a in local logs; do                                     \

diff --git a/...eam-9-python3.9-minimal/devcontainer.json → ...centos-stream-9-minimal/devcontainer.json b/...eam-9-python3.9-minimal/devcontainer.json → ...centos-stream-9-minimal/devcontainer.json
@@ -3,12 +3,12 @@
 //      from .devcontainer/portability-devcontainer.json.in
 // See https://aka.ms/devcontainer.json for format details.
 {
-    "name": "centos-stream-9-python3.9-minimal (≥ 8-core)",
+    "name": "centos-stream-9-minimal (≥ 8-core)",
     "build": {
         "dockerfile": "portability-Dockerfile",
         // See tox.ini for definitions
         "args": {
-            "SYSTEM_FACTOR": "centos-stream-9-python3.9",
+            "SYSTEM_FACTOR": "centos-stream-9",
             "PACKAGE_FACTOR": "minimal",
             "DOCKER_TARGET": "with-targets",
             "DOCKER_TAG": "dev"

diff --git a/...-python3.9-minimal/portability-Dockerfile → ...s-stream-9-minimal/portability-Dockerfile b/...-python3.9-minimal/portability-Dockerfile → ...s-stream-9-minimal/portability-Dockerfile
diff --git a/.devcontainer/portability-centos-stream-9-python3.12-minimal/devcontainer.json b/.devcontainer/portability-centos-stream-9-python3.12-minimal/devcontainer.json
@@ -0,0 +1,25 @@
+// The command "tox -e update_docker_platforms"
+//   creates .devcontainer/portability-*-*/devcontainer.json
+//      from .devcontainer/portability-devcontainer.json.in
+// See https://aka.ms/devcontainer.json for format details.
+{
+    "name": "centos-stream-9-python3.12-minimal (≥ 8-core)",
+    "build": {
+        "dockerfile": "portability-Dockerfile",
+        // See tox.ini for definitions
+        "args": {
+            "SYSTEM_FACTOR": "centos-stream-9-python3.12",
+            "PACKAGE_FACTOR": "minimal",
+            "DOCKER_TARGET": "with-targets",
+            "DOCKER_TAG": "dev"
+        }
+    },
+    "containerEnv": {
+        "MAKE": "make -j4"
+    },
+    "onCreateCommand": ".devcontainer/onCreate.sh",
+    "updateContentCommand": ".devcontainer/portability-updateContent.sh",
+    "extensions": [
+        "ms-python.python"
+    ]
+}
diff --git a/...python3.9-standard/portability-Dockerfile → ...python3.12-minimal/portability-Dockerfile b/...python3.9-standard/portability-Dockerfile → ...python3.12-minimal/portability-Dockerfile
diff --git a/.devcontainer/portability-centos-stream-9-python3.12-standard/devcontainer.json b/.devcontainer/portability-centos-stream-9-python3.12-standard/devcontainer.json
@@ -0,0 +1,25 @@
+// The command "tox -e update_docker_platforms"
+//   creates .devcontainer/portability-*-*/devcontainer.json
+//      from .devcontainer/portability-devcontainer.json.in
+// See https://aka.ms/devcontainer.json for format details.
+{
+    "name": "centos-stream-9-python3.12-standard (≥ 8-core)",
+    "build": {
+        "dockerfile": "portability-Dockerfile",
+        // See tox.ini for definitions
+        "args": {
+            "SYSTEM_FACTOR": "centos-stream-9-python3.12",
+            "PACKAGE_FACTOR": "standard",
+            "DOCKER_TARGET": "with-targets",
+            "DOCKER_TAG": "dev"
+        }
+    },
+    "containerEnv": {
+        "MAKE": "make -j4"
+    },
+    "onCreateCommand": ".devcontainer/onCreate.sh",
+    "updateContentCommand": ".devcontainer/portability-updateContent.sh",
+    "extensions": [
+        "ms-python.python"
+    ]
+}
diff --git a/.devcontainer/portability-centos-stream-9-python3.12-standard/portability-Dockerfile b/.devcontainer/portability-centos-stream-9-python3.12-standard/portability-Dockerfile
@@ -0,0 +1 @@
+../portability-Dockerfile
diff --git a/...am-9-python3.9-standard/devcontainer.json → ...entos-stream-9-standard/devcontainer.json b/...am-9-python3.9-standard/devcontainer.json → ...entos-stream-9-standard/devcontainer.json
@@ -3,12 +3,12 @@
 //      from .devcontainer/portability-devcontainer.json.in
 // See https://aka.ms/devcontainer.json for format details.
 {
-    "name": "centos-stream-9-python3.9-standard (≥ 8-core)",
+    "name": "centos-stream-9-standard (≥ 8-core)",
     "build": {
         "dockerfile": "portability-Dockerfile",
         // See tox.ini for definitions
         "args": {
-            "SYSTEM_FACTOR": "centos-stream-9-python3.9",
+            "SYSTEM_FACTOR": "centos-stream-9",
             "PACKAGE_FACTOR": "standard",
             "DOCKER_TARGET": "with-targets",
             "DOCKER_TAG": "dev"

diff --git a/.devcontainer/portability-centos-stream-9-standard/portability-Dockerfile b/.devcontainer/portability-centos-stream-9-standard/portability-Dockerfile
@@ -0,0 +1 @@
+../portability-Dockerfile
diff --git a/.devcontainer/portability-fedora-41-minimal/devcontainer.json b/.devcontainer/portability-fedora-41-minimal/devcontainer.json
@@ -0,0 +1,25 @@
+// The command "tox -e update_docker_platforms"
+//   creates .devcontainer/portability-*-*/devcontainer.json
+//      from .devcontainer/portability-devcontainer.json.in
+// See https://aka.ms/devcontainer.json for format details.
+{
+    "name": "fedora-41-minimal (≥ 8-core)",
+    "build": {
+        "dockerfile": "portability-Dockerfile",
+        // See tox.ini for definitions
+        "args": {
+            "SYSTEM_FACTOR": "fedora-41",
+            "PACKAGE_FACTOR": "minimal",
+            "DOCKER_TARGET": "with-targets",
+            "DOCKER_TAG": "dev"
+        }
+    },
+    "containerEnv": {
+        "MAKE": "make -j4"
+    },
+    "onCreateCommand": ".devcontainer/onCreate.sh",
+    "updateContentCommand": ".devcontainer/portability-updateContent.sh",
+    "extensions": [
+        "ms-python.python"
+    ]
+}
diff --git a/.devcontainer/portability-fedora-41-minimal/portability-Dockerfile b/.devcontainer/portability-fedora-41-minimal/portability-Dockerfile
@@ -0,0 +1 @@
+../portability-Dockerfile
diff --git a/.devcontainer/portability-fedora-41-standard/devcontainer.json b/.devcontainer/portability-fedora-41-standard/devcontainer.json
@@ -0,0 +1,25 @@
+// The command "tox -e update_docker_platforms"
+//   creates .devcontainer/portability-*-*/devcontainer.json
+//      from .devcontainer/portability-devcontainer.json.in
+// See https://aka.ms/devcontainer.json for format details.
+{
+    "name": "fedora-41-standard (≥ 8-core)",
+    "build": {
+        "dockerfile": "portability-Dockerfile",
+        // See tox.ini for definitions
+        "args": {
+            "SYSTEM_FACTOR": "fedora-41",
+            "PACKAGE_FACTOR": "standard",
+            "DOCKER_TARGET": "with-targets",
+            "DOCKER_TAG": "dev"
+        }
+    },
+    "containerEnv": {
+        "MAKE": "make -j4"
+    },
+    "onCreateCommand": ".devcontainer/onCreate.sh",
+    "updateContentCommand": ".devcontainer/portability-updateContent.sh",
+    "extensions": [
+        "ms-python.python"
+    ]
+}
diff --git a/.devcontainer/portability-fedora-41-standard/portability-Dockerfile b/.devcontainer/portability-fedora-41-standard/portability-Dockerfile
@@ -0,0 +1 @@
+../portability-Dockerfile
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -46,9 +46,8 @@ body:
           - **OS**: Ubuntu 20.04
           - Sage Version: 9.2
       value: |
-          - **OS**:
-          - **Sage Version**:
-      render: markdown
+          - **OS**: 
+          - **Sage Version**: 
     validations:
       required: true
   - type: checkboxes

diff --git a/.github/ISSUE_TEMPLATE/failure_building_from_source.yml b/.github/ISSUE_TEMPLATE/failure_building_from_source.yml
@@ -17,9 +17,8 @@ body:
           - **OS**: Ubuntu 20.04
           - Sage Version: 9.2
       value: |
-          - **OS**:
+          - **OS**: 
           - **Sage Version**: 
-      render: markdown
     validations:
       required: true
   - type: textarea

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -102,7 +102,7 @@ jobs:
         uses: actions/checkout@v4
       - name: Get changed files and packages
         id: changed-files
-        uses: tj-actions/changed-files@v44
+        uses: tj-actions/changed-files@v45
         with:
           # File extensions for doctests per sage.doctest.control.skipfile
           files_yaml: |
@@ -176,7 +176,7 @@ jobs:
 
       - name: Build Docker image
         id: image
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           # push and load may not be set together at the moment
           #
@@ -291,7 +291,7 @@ jobs:
 
       - name: Build Docker image
         id: image
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           push:       true
           load:       false
@@ -389,7 +389,7 @@ jobs:
 
       - name: Build Docker image
         id: image
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           push:       true
           load:       false
@@ -442,8 +442,11 @@ jobs:
         if: (success() || failure()) && steps.container.outcome == 'success'
         uses: actions/upload-artifact@v4
         with:
+          # The path .coverage is a directory that contains the combined coverage
+          # data file .coverage, which is a hidden file because of the leading dot
           name: coverage-${{ steps.copy-coverage.outputs.tests_id }}
           path: .coverage
+          include-hidden-files: true
 
   coverage-report:
     runs-on: ubuntu-latest
@@ -503,7 +506,7 @@ jobs:
 
       - name: Build Docker image
         id: image
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           push:       true
           load:       false
@@ -530,11 +533,11 @@ jobs:
       # Combining
 
       - name: Download coverage artifacts
+        if: (success() || failure()) && steps.container.outcome == 'success'
         uses: actions/download-artifact@v4
         with:
           path: .coverage
           pattern: coverage-*
-        if: (success() || failure()) && steps.container.outcome == 'success'
 
       - name: Coverage report
         if: (success() || failure()) && steps.container.outcome == 'success'

diff --git a/.github/workflows/ci-linux-incremental.yml b/.github/workflows/ci-linux-incremental.yml
@@ -46,7 +46,7 @@ jobs:
       - uses: actions/checkout@v4
       - name: Get all packages that have changed
         id: changed-files
-        uses: tj-actions/changed-files@v44
+        uses: tj-actions/changed-files@v45
         with:
           files_yaml: |
             configures:
@@ -60,9 +60,9 @@ jobs:
           uninstall_targets=$(echo $(for a in '' ${{ steps.changed-files.outputs.configures_all_changed_files }}; do echo $a | sed -E 's,build/pkgs/([a-z0-9][_.a-z0-9]*)/spkg-configure[.]m4 *,\1-uninstall,'; done | sort -u))
           build_targets=$(echo $(for a in '' ${{ steps.changed-files.outputs.pkgs_all_changed_files }}; do SPKG=$(echo $a | sed -E 's,-,_,g;s,(build/)?pkgs/([a-z0-9][-_.a-z0-9]*)/[^ ]* *,\2,;'); if [ -f "build/pkgs/$SPKG/checksums.ini" -o -f "build/pkgs/$SPKG/requirements.txt" -o -f "build/pkgs/$SPKG/spkg-install" ]; then echo "$SPKG-ensure"; fi; done | sort -u))
           if [ -n "$uninstall_targets" ]; then
-              echo "build_targets=$uninstall_targets reconfigure $build_targets ci-build-with-fallback" >> $GITHUB_OUTPUT
+              echo "build_targets=$uninstall_targets reconfigure $build_targets" >> $GITHUB_OUTPUT
           else
-              echo "build_targets=$build_targets ci-build-with-fallback" >> $GITHUB_OUTPUT
+              echo "build_targets=$build_targets" >> $GITHUB_OUTPUT
           fi
           cat $GITHUB_OUTPUT
       - uses: actions/checkout@v4
@@ -92,7 +92,7 @@ jobs:
       from_docker_target: "with-targets"
       from_docker_tag: "dev"
       docker_targets: "with-targets"
-      targets: "${{needs.changed_files.outputs.build_targets}} doc-html ptest-nodoc"
+      targets: "${{needs.changed_files.outputs.build_targets}} ci-build-with-fallback doc-html ptest-nodoc"
       tox_system_factors: >-
         ["ubuntu-focal",
          "ubuntu-noble",
@@ -108,6 +108,29 @@ jobs:
       docker_push_repository: ghcr.io/${{ github.repository }}/
       max_parallel: 8
 
+  constraints_pkgs-norequirements:
+    needs: [changed_files]
+    uses: ./.github/workflows/docker.yml
+    with:
+      # Build incrementally from published Docker image
+      incremental: true
+      free_disk_space: true
+      from_docker_repository: ghcr.io/sagemath/sage/
+      from_docker_target: "with-targets-pre"
+      from_docker_tag: "dev"
+      docker_targets: "with-targets-pre"
+      targets_pre: "${{needs.changed_files.outputs.build_targets}} all-sage-local python3-ensure tox-ensure sagelib-tox-sagepython-constraints_pkgs-norequirements"
+      tox_system_factors: >-
+        ["ubuntu-focal",
+         "ubuntu-noble",
+         "debian-bookworm",
+         "fedora-40",
+         "debian-bullseye-i386"]
+      tox_packages_factors: >-
+          ["standard"]
+      docker_push_repository: ghcr.io/${{ github.repository }}/
+      max_parallel: 16
+
   site:
     needs: [changed_files]
     uses: ./.github/workflows/docker.yml