Merge remote-tracking branch 'upstream/master' into petsc_trilinos_and_kokkos

Author: masterleinad

Diff for: .clang-tidy

@@ -8,6 +8,10 @@
 # - selected modernize-* warnings:
 #   Some of these produce a lot of noise for limited utility.
 #
+# - performance-enum-size:
+#   We don't care if an enum could use a smaller base type than
+#   unsigned int.
+#
 # - performance-inefficient-string-concatenation:
 #   We don't care about "a"+to_string(5)+...
 #
@@ -33,9 +37,10 @@ Checks: >
   -modernize-use-transparent-functors,
   mpi-*,
   performance-*,
+  -performance-avoid-endl,
+  -performance-enum-size,
   -performance-inefficient-string-concatenation,
   -performance-no-automatic-move,
-  -performance-avoid-endl,
   readability-qualified-auto
 
 WarningsAsErrors: '*'

Diff for: .gitattributes

@@ -14,9 +14,11 @@ Jenkinsfile export-ignore
 
 /.github/ export-ignore
 
+# exclude most of the testsuite from the tarball:
+/tests/* export-ignore
+# but keep everything to run the "make test" target (quick_tests, examples):
 /tests/CMakeLists.txt -export-ignore
 /tests/examples -export-ignore
-/tests/* export-ignore
 /tests/quick_tests -export-ignore
 /tests/run_*.cmake -export-ignore
 /tests/scripts -export-ignore

Diff for: .github/workflows/docker.yml

@@ -19,12 +19,12 @@ jobs:
     if: (github.event_name == 'schedule' && github.repository == 'dealii/dealii') || github.event_name != 'schedule'
 
     name: build master docker ${{ matrix.ubuntu_version }} ${{ matrix.platform }}
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
 
     strategy:
       fail-fast: false
       matrix:
-        ubuntu_version: [focal, jammy]
+        ubuntu_version: [jammy, noble]
         platform: [linux/amd64]
         # Use only 2 jobs to build, as more jobs
         # would starve the github machine for memory.
@@ -93,15 +93,15 @@ jobs:
   merge:
     if: (github.event_name == 'schedule' && github.repository == 'dealii/dealii') || github.event_name != 'schedule'
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     needs:
       - build-master-docker-ubuntu
 
 # Merge all images for a specific ubuntu version
     strategy:
       fail-fast: false
       matrix:
-        ubuntu_version: [focal, jammy]
+        ubuntu_version: [jammy, noble]
 
     steps:
       - name: Download digests

Diff for: .github/workflows/indent.yml

@@ -3,7 +3,7 @@ name: indent
 on: [push, pull_request]
 
 concurrency:
-  group: ${ {github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{github.event_name == 'pull_request'}}
 
 permissions:
@@ -14,7 +14,7 @@ jobs:
     # run the indent checks
 
     name: indent
-    runs-on: [ubuntu-22.04]
+    runs-on: ubuntu-24.04
 
     steps:
     - uses: actions/checkout@v4
@@ -31,23 +31,24 @@ jobs:
     # build the documentation
 
     name: doxygen
-    runs-on: [ubuntu-22.04]
+    runs-on: ubuntu-24.04
+
+    env:
+      MAKEFLAGS: "--jobs=4"
 
     steps:
     - name: setup
       run: |
         sudo apt update
-        sudo apt install graphviz perl texlive-bibtex-extra
-    - uses: ssciwr/doxygen-install@v1
-      with:
-        version: "1.9.6"
+        sudo apt install doxygen graphviz perl texlive-bibtex-extra
+        doxygen --version
     - uses: actions/checkout@v4
     - name: build documentation
       run: |
         mkdir build
         cd build
         cmake -DDEAL_II_COMPONENT_DOCUMENTATION=ON -DDEAL_II_DOXYGEN_USE_MATHJAX=ON ..
-        make -j 2 documentation
+        make documentation
     - name: check for doxygen errors and warnings
       run: |
         cd build
@@ -63,24 +64,21 @@ jobs:
         sed -i '/^$/d' doxygen.log
         # Check if remaining log is zero size
         ! [ -s doxygen.log ] || exit 1
-    - name: compress
-      run: |
-        tar -czf doxygen_documentation.tar.gz build/doc/doxygen
-    - name: archive documentation
-      uses: actions/upload-artifact@v4
+    - uses: actions/upload-artifact@v4
       with:
-        name: doxygen_documentation.tar.gz
-        path: doxygen_documentation.tar.gz
+        name: doxygen_documentation
+        path: build/doc/doxygen
 
-  typos:
-    # check for typos
+  pre-commit:
+    # run pre-commit checks
 
-    name: typos
-    runs-on: [ubuntu-22.04]
+    name: pre-commit
+    runs-on: ubuntu-24.04
+
+    env:
+      SKIP: clang-format, no-commit-to-branch
 
     steps:
     - uses: actions/checkout@v4
-    - uses: crate-ci/[email protected]
-      with:
-        files: doc examples include source tests
-        config: ./.typos.toml
+    - run:  python -m pip install networkx
+    - uses: pre-commit/[email protected]