Merge branch 'master' into Gaussian_map_3-efif

.github/dependabot.yml

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

.github/install.sh

@@ -1,12 +1,29 @@
 #!/bin/bash
-sudo add-apt-repository ppa:mikhailnov/pulseeffects -y
+
+set -ex
+
 sudo apt-get update
-sudo apt-get install -y  libmpfr-dev \
- libeigen3-dev qtbase5-dev libqt5sql5-sqlite libqt5opengl5-dev qtscript5-dev \
- libqt5svg5-dev qttools5-dev qttools5-dev-tools libboost-dev libinsighttoolkit4-dev zsh
-#update cmake to 3.18.4
+sudo apt-get install -y \
+ libmpfr-dev \
+ libtbb-dev \
+ libmetis-dev \
+ libssh-dev \
+ libeigen3-dev \
+ qtbase5-dev libqt5sql5-sqlite libqt5opengl5-dev qtscript5-dev libqt5websockets5-dev \
+ libqt5svg5-dev qttools5-dev qttools5-dev-tools \
+ libboost-dev libboost-serialization-dev libboost-iostreams-dev libboost-filesystem-dev libboost-filesystem-dev \
+ libvtk9-dev libgdcm-tools libvtkgdcm-dev libunwind-dev \
+ libinsighttoolkit5-dev \
+ libceres-dev \
+ libglpk-dev \
+ libopencv-dev \
+ zsh \
+ qt6-base-dev qt6-declarative-dev libqt6svg6-dev libqt6websockets6-dev
+
+#update CMake
 sudo apt purge --auto-remove cmake
 cd /tmp
-wget https://cmake.org/files/v3.18/cmake-3.18.4-Linux-x86_64.sh
-sudo sh cmake-3.18.4-Linux-x86_64.sh --skip-license --prefix=/usr/local
-rm cmake-3.18.4-Linux-x86_64.sh
+CMAKE_VER=$(curl --silent https://cmake.org/files/LatestRelease/cmake-latest-files-v1.json | jq -r .version.string)
+wget https://cmake.org/files/LatestRelease/cmake-$CMAKE_VER-linux-x86_64.sh
+sudo sh cmake-*.sh --skip-license --prefix=/usr/local
+rm cmake-*.sh

.github/test.sh

@@ -3,11 +3,10 @@
 FACTOR=$1
 set -ex
 cd Polyhedron/demo
-LIST_OF_PLUGINS=$(/usr/local/bin/cmake --build . -t help | egrep 'plugin$' |& cut -d\  -f2)
+/usr/local/bin/cmake -S Polyhedron -B build -DCGAL_DIR=$2
+LIST_OF_PLUGINS=$(/usr/local/bin/cmake --build build -t help | egrep 'plugin$' |& cut -d\  -f2)
 PLUGINS_ARRAY=(${LIST_OF_PLUGINS});
 NB_OF_PLUGINS=${#PLUGINS_ARRAY[@]}
 DEL=$(($NB_OF_PLUGINS / 4))
-mkdir build
 cd build
-/usr/local/bin/cmake -DCGAL_DIR=$2 ../Polyhedron
 make -j2 ${PLUGINS_ARRAY[@]:$(($FACTOR * $DEL)):$((($FACTOR + 1) * $DEL))}

.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@v7
+        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@v7
+        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@v7
         id: get_round
         with:
          result-encoding: string
@@ -31,7 +38,7 @@ jobs:
              }
            }
            return 'stop'
-      - uses: actions/github-script@v3
+      - uses: actions/github-script@v7
         if: steps.get_round.outputs.result != 'stop'
         id: get_pr_number
         with:
@@ -40,28 +47,39 @@ 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@v7
         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@v4
+        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/~mgimeno/doxygen/build_1_8_13/bin/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 "maxime.gimeno@geometryfactory.com"
-          git config --global user.name "Maxime Gimeno"
+          git config --global user.email "cgal@geometryfactory.com"
+          git config --global user.name "cgaltest"
 
       - name: configure all
         if: steps.get_round.outputs.result != 'stop'
@@ -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@v7
         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@v7
         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

@@ -1,27 +1,30 @@
 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@v4
     - name: install dependencies
       run: |
         .github/install.sh
         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/~mgimeno/doxygen/build_1_8_13/bin/doxygen
+        wget --no-verbose -O doxygen_exe https://cgal.geometryfactory.com/~cgaltest/doxygen_1_8_13_patched/doxygen
         sudo mv doxygen_exe /usr/bin/doxygen
         sudo chmod +x /usr/bin/doxygen
-        git config --global user.email "maxime.gimeno@geometryfactory.com"
-        git config --global user.name "Maxime Gimeno"
-        
+        git config --global user.email "cgal@geometryfactory.com"
+        git config --global user.name "cgaltest"
+
     - name: Run checks
       run: |
         zsh Scripts/developer_scripts/test_merge_of_branch HEAD

.github/workflows/cmake-all.yml

@@ -1,32 +1,35 @@
 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@v4
     - name: install dependencies
       run: sudo apt-get install -y libboost-dev libboost-program-options-dev libmpfr-dev libeigen3-dev
     - name: configure all
       run: |
         set -e
-        mkdir build && cd build && CXX=clang++ cmake -DWITH_examples=ON -DWITH_tests=ON -DWITH_demos=ON -DBUILD_TESTING=ON ..
+        mkdir build && cd build && CXX=clang++ cmake -DWITH_examples=ON -DWITH_tests=ON -DWITH_demos=ON -DCGAL_ENABLE_TESTING=ON ..
         ctest -L Installation -j $(getconf _NPROCESSORS_ONLN)
 
-  cmake-testsuite-with-qt5:
+  cmake-testsuite-with-qt:
 
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2.0.0
+    - uses: actions/checkout@v4
     - name: install dependencies
       run: sudo bash -e .github/install.sh
     - name: configure all
       run: |
         set -e
-        mkdir build && cd build && CXX=clang++ cmake -DWITH_examples=ON -DWITH_tests=ON -DWITH_demos=ON -DBUILD_TESTING=ON ..
+        mkdir build && cd build && CXX=clang++ cmake -DWITH_examples=ON -DWITH_tests=ON -DWITH_demos=ON -DCGAL_ENABLE_TESTING=ON ..
         ctest -L Installation -j $(getconf _NPROCESSORS_ONLN)

.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@v4
     - name: delete directory
       run: |
          set -x
-         git config --global user.email "maxime.gimeno@geometryfactory.com"
-         git config --global user.name "Maxime Gimeno"
-         git clone https://maxGimeno:${{ secrets.PUSH_TO_CGAL_GITHUB_IO_TOKEN }}@github.com/CGAL/cgal.github.io.git --depth=5
+         git config --global user.email "cgal@geometryfactory.com"
+         git config --global user.name "cgaltest"
+         git clone https://CGAL:${{ 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@v4
     - 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@v4
     - 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@v4
     - 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@v4
     - name: install dependencies
       run: .github/install.sh
     - name: run4