Merge branch 'master' into CGAL-reuse_compliance-lrineau

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/Remove_labels.yml

@@ -0,0 +1,33 @@
+name: remove_labels
+on:
+  pull_request_target:
+    types: [synchronize]
+  workflow_dispatch:
+jobs:
+  remove_label:
+    runs-on: ubuntu-latest
+    if: contains(github.event.pull_request.labels.*.name, 'Tested')
+    name: remove label
+    steps:
+      - name: removelabel
+        uses: actions/github-script@v6
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            github.rest.issues.removeLabel({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.issue.number,
+              name: "Tested",
+            });
+      - name: Post address
+        uses: actions/github-script@v6
+        if: ${{ success() }}
+        with:
+          script: |
+            github.rest.issues.createComment({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.issue.number,
+              body: "This pull-request was previously marked with the label `Tested`, but has been modified with new commits. That label has been removed."
+              })

.github/workflows/build_doc.yml

@@ -4,12 +4,19 @@ on:
   issue_comment:
       types: [created]
 
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
 jobs:
   build:
 
+    permissions:
+      contents: read # to fetch code (actions/checkout)
+      pull-requests: write # to create comment
+
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/github-script@v3
+      - uses: actions/github-script@v6
         id: get_round
         with:
          result-encoding: string
@@ -31,7 +38,7 @@ jobs:
              }
            }
            return 'stop'
-      - uses: actions/github-script@v3
+      - uses: actions/github-script@v6
         if: steps.get_round.outputs.result != 'stop'
         id: get_pr_number
         with:
@@ -40,24 +47,35 @@ jobs:
            //get pullrequest url
            const pr_number = context.payload.issue.number
            return pr_number
-      - uses: actions/checkout@v2
-        name: "checkout branch"
+
+      - name: Emoji-comment
+        uses: actions/github-script@v6
         if: steps.get_round.outputs.result != 'stop'
         with:
-          repository: ${{ github.repository }}
-          ref: refs/pull/${{ steps.get_pr_number.outputs.result }}/merge
-          token: ${{ secrets.PUSH_TO_CGAL_GITHUB_IO_TOKEN }}
-          fetch-depth: 2
+          script: |
+            github.rest.reactions.createForIssueComment({
+              comment_id: ${{ github.event.comment.id }},
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              content: 'rocket'
+            })
 
+      - uses: actions/checkout@v3
+        name: "checkout branch"
+        if: steps.get_round.outputs.result != 'stop'
+        with:
+           repository: ${{ github.repository }}
+           ref: refs/pull/${{ steps.get_pr_number.outputs.result }}/merge
+           fetch-depth: 2
 
       - name: install dependencies
         if: steps.get_round.outputs.result != 'stop'
         run: |
           set -x
           sudo apt-get update && sudo apt-get install -y graphviz ssh bibtex2html
           sudo pip install lxml
-          sudo pip install 'pyquery==1.4.1' # it seems to be the last py2 compatible version
-          wget --no-verbose -O doxygen_exe https://cgal.geometryfactory.com/~cgaltest/doxygen_1_8_13_patched/doxygen
+          sudo pip install pyquery
+          wget --no-verbose -O doxygen_exe https://cgal.geometryfactory.com/~cgaltest/doxygen_1_9_6_patched/doxygen
           sudo mv doxygen_exe /usr/bin/doxygen
           sudo chmod +x /usr/bin/doxygen
           git config --global user.email "[email protected]"
@@ -83,14 +101,17 @@ jobs:
             #list impacted packages
             LIST_OF_PKGS=$(git diff --name-only HEAD^1 HEAD |cut -s -d/ -f1 |sort -u | xargs -I {} echo {} && ls -d {}/package_info 2>/dev/null  |cut -d/ -f1 |egrep -v Installation||true)
             if [ "$LIST_OF_PKGS" = "" ]; then
-              echo "::set-output name=DoxygenError::No package affected."
+              echo "DoxygenError=No package affected." >> $GITHUB_OUTPUT
               exit 1
             fi
             cd build_doc && make -j2 doc
             make -j2 doc_with_postprocessing 2>tmp.log
             if [ -s tmp.log ]; then
               content=`cat ./tmp.log`
-              echo "::set-output name=DoxygenError::$(cat tmp.log)"
+              delimiter="$(openssl rand -hex 8)"
+              echo "DoxygenError<<${delimiter}" >> "${GITHUB_OUTPUT}"
+              cat tmp.log >> "${GITHUB_OUTPUT}"
+              echo "${delimiter}" >> "${GITHUB_OUTPUT}"
               exit 1
             fi
             cd ..
@@ -110,34 +131,37 @@ jobs:
             mv tmp.html index.html
             git add ${PR_NUMBER}/$ROUND index.html && git commit -q --amend -m "base commit" && git push -q -f -u origin master
           else
-            echo "::set-output name=DoxygenError::This round already exists. Overwrite it with /force-build."
+            echo "DoxygenError=This round already exists. Overwrite it with /force-build." >> $GITHUB_OUTPUT
             exit 1
           fi
 
       - name: Post address
-        uses: actions/github-script@v3
+        uses: actions/github-script@v6
         if: ${{ success() && steps.get_round.outputs.result != 'stop' }}
         with:
           script: |
             const tmp_round = "${{ steps.get_round.outputs.result }}";
             const id = tmp_round.indexOf(":");
             const round = tmp_round.substring(0,id);
             const address = "The documentation is built. It will be available, after a few minutes, here: https://cgal.github.io/${{ steps.get_pr_number.outputs.result }}/"+round+"/Manual/index.html"
-            github.issues.createComment({
+            github.rest.issues.createComment({
               owner: "CGAL",
               repo: "cgal",
               issue_number: ${{ github.event.issue.number }},
               body: address
             });
 
       - name: Post error
-        uses: actions/github-script@v3
+        env:
+          ERRORMSG: ${{steps.build_and_run.outputs.DoxygenError}}
+        uses: actions/github-script@v6
         if: ${{ failure() && steps.get_round.outputs.result != 'stop' }}
         with:
           script: |
-            const error = "${{steps.build_and_run.outputs.DoxygenError}}"
-            const msg = "There was an error while building the doc: \n"+error
-            github.issues.createComment({
+            const error = process.env.ERRORMSG
+            const job_url = `${context.serverUrl}/CGAL/cgal/actions/runs/${context.runId}`
+            const msg = "There was an error while building the doc: \n```\n"+error + "\n```\n" + job_url
+            github.rest.issues.createComment({
               owner: "CGAL",
               repo: "cgal",
               issue_number: ${{ github.event.issue.number }},

.github/workflows/checks.yml

@@ -1,14 +1,17 @@
 name: CMake Test Merge Branch
 
-on: [push, pull_request]
+on: [push, pull_request, workflow_dispatch]
+
+permissions:
+  contents: read
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2.0.0
+    - uses: actions/checkout@v3
     - name: install dependencies
       run: |
         .github/install.sh

.github/workflows/cmake-all.yml

@@ -1,14 +1,17 @@
 name: CMake Testsuite
 
-on: [push, pull_request]
+on: [push, pull_request, workflow_dispatch]
+
+permissions:
+  contents: read
 
 jobs:
   cmake-testsuite:
 
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2.0.0
+    - uses: actions/checkout@v3
     - name: install dependencies
       run: sudo apt-get install -y libboost-dev libboost-program-options-dev libmpfr-dev libeigen3-dev
     - name: configure all
@@ -22,7 +25,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2.0.0
+    - uses: actions/checkout@v3
     - name: install dependencies
       run: sudo bash -e .github/install.sh
     - name: configure all

.github/workflows/delete_doc.yml

@@ -2,20 +2,25 @@ name: Documentation Removal
 
 on:
   pull_request_target:
-    types: [closed, removed]
+    types: [closed, removed, workflow_dispatch]
+permissions:
+  contents: read
+
 jobs:
   build:
 
+    permissions:
+      contents: write  # for Git to git push
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2.0.0
+    - uses: actions/checkout@v3
     - name: delete directory
       run: |
          set -x
          git config --global user.email "[email protected]"
          git config --global user.name "cgaltest"
-         git clone https://maxGimeno:${{ secrets.PUSH_TO_CGAL_GITHUB_IO_TOKEN }}@github.com/CGAL/cgal.github.io.git --depth=5
+         git clone https://CGAL:${{ secrets.PUSH_TO_CGAL_GITHUB_IO_TOKEN }}@github.com/CGAL/cgal.github.io.git
          PR_NUMBER=$(python -c "import json; import os; y = json.load(open(os.environ['GITHUB_EVENT_PATH'])); print(y[\"number\"])")
          cd cgal.github.io/
          egrep -v " ${PR_NUMBER}\." index.html > tmp.html || true

.github/workflows/demo.yml

@@ -1,36 +1,39 @@
 name: Test Polyhedron Demo
 
-on: [push, pull_request]
+on: [push, pull_request,workflow_dispatch]
+
+permissions:
+  contents: read
 
 jobs:
   batch_1:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2.0.0
+    - uses: actions/checkout@v3
     - name: install dependencies
       run: .github/install.sh
     - name: run1
       run: ./.github/test.sh 0 ${{ github.workspace }}
   batch_2:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2.0.0
+    - uses: actions/checkout@v3
     - name: install dependencies
       run: .github/install.sh
     - name: run2
       run: ./.github/test.sh 1 ${{ github.workspace }}
   batch_3:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2.0.0
+    - uses: actions/checkout@v3
     - name: install dependencies
       run: .github/install.sh
     - name: run3
       run: ./.github/test.sh 2 ${{ github.workspace }}
   batch_4:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2.0.0
+    - uses: actions/checkout@v3
     - name: install dependencies
       run: .github/install.sh
     - name: run4

.github/workflows/filter_testsuite.yml

@@ -3,13 +3,18 @@ name: Filter Testsuite
 on:
   issue_comment:
       types: [created]
+  workflow_dispatch:
 
+permissions: {}
 jobs:
   build:
+    permissions:
+      pull-requests: write # to create comment
+
     if: (github.event.comment.user.login == 'sloriot' || github.event.comment.user.login == 'lrineau') && contains(github.event.comment.body, '/testme')
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/github-script@v3
+      - uses: actions/github-script@v6
         id: get_label
         with:
          result-encoding: string
@@ -58,7 +63,7 @@ jobs:
             ssh ${HOST} "${PATH_TO_SCRIPT}/run_testsuite_from_branch_name.sh $USER_NAME $BRANCH_NAME $BASE $PR_NUMBER"
           done
       - name: Post address
-        uses: actions/github-script@v3
+        uses: actions/github-script@v6
         with:
           script: |
             const address = "Testsuite launched. Results will appear on the following page: https://cgal.geometryfactory.com/~cgaltest/test_suite/TESTRESULTS/index.shtml "

.github/workflows/list_workflow_last_run.css

@@ -0,0 +1,30 @@
+table {
+    margin-left: auto;
+    margin-right: auto;
+    margin-bottom: 24px;
+    border-spacing: 0;
+    border-bottom: 2px solid black;
+    border-top: 2px solid black;
+}
+table th {
+    padding: 3px 10px;
+    background-color: white;
+    border-top: none;
+    border-left: none;
+    border-right: none;
+    border-bottom: 1px solid black;
+}
+table td {
+    padding: 3px 10px;
+    border-top: none;
+    border-left: none;
+    border-bottom: none;
+    border-right: none;
+}
+
+table tr.odd {
+    background-color: #f0f0f0;
+}
+table tr.even {
+    background-color: #e0e0e0;
+}