bindings generated with Clang.jl

.ci_install_p4est.sh

@@ -4,35 +4,16 @@ if [ -z "$P4EST_RELEASE" ]; then
   P4EST_RELEASE="2.8"
 fi
 
-if [ "${P4EST_TEST}" = "P4EST_JLL_USES_MPI_PRE_GENERATED_BINDINGS" ]; then
-  echo "Found 'P4EST_TEST=${P4EST_TEST}'. Nothing to do here."
+if [ "${JULIA_P4EST_TEST}" = "P4EST_JLL_MPI_DEFAULT" ]; then
+  echo "Found 'JULIA_P4EST_TEST=${JULIA_P4EST_TEST}'. Nothing to do here."
 fi
-if [ "${P4EST_TEST}" = "P4EST_JLL_USES_MPI" ]; then
-  echo "Found 'P4EST_TEST=${P4EST_TEST}'. Nothing to do here."
+if [ "${JULIA_P4EST_TEST}" = "P4EST_JLL_MPI_OPENMPIJLL" ]; then
+  echo "Found 'JULIA_P4EST_TEST=${JULIA_P4EST_TEST}'. Nothing to do here."
 fi
-if [ "${P4EST_TEST}" = "P4EST_CUSTOM_NON_MPI" ]; then
-  echo "Found 'P4EST_TEST=P4EST_CUSTOM_NON_MPI'. Installing custom p4est *without* MPI support..."
+if [ "${JULIA_P4EST_TEST}" = "P4EST_CUSTOM_MPI_CUSTOM" ]; then
+  echo "Found 'JULIA_P4EST_TEST=${JULIA_P4EST_TEST}'. Installing custom `p4est` with MPI support from the default MPI installation on the system."
   pushd `pwd`
-  export P4EST_TMP=`pwd`/libp4est_tmp_non_mpi
-  mkdir -p $P4EST_TMP
-  cd $P4EST_TMP/
-  wget https://p4est.github.io/release/p4est-${P4EST_RELEASE}.tar.gz
-  tar xf p4est-${P4EST_RELEASE}.tar.gz
-  mkdir build
-  cd build/
-  $P4EST_TMP/p4est-${P4EST_RELEASE}/configure --prefix=$P4EST_TMP/prefix
-  make -j 2
-  make install
-  ls -l $P4EST_TMP/prefix/lib/libp4est.so
-  mkdir test_tmp
-  cd test_tmp
-  $P4EST_TMP/prefix/bin/p4est_step1
-  popd
-fi
-if [ "${P4EST_TEST}" = "P4EST_CUSTOM_USES_MPI" ]; then
-  echo "Found 'P4EST_TEST=P4EST_CUSTOM_USES_MPI'. Installing custom p4est *with* MPI support..."
-  pushd `pwd`
-  export P4EST_TMP=`pwd`/libp4est_tmp_uses_mpi
+  export P4EST_TMP=`pwd`/libp4est_tmp
   mkdir -p $P4EST_TMP
   cd $P4EST_TMP/
   wget https://p4est.github.io/release/p4est-${P4EST_RELEASE}.tar.gz

.github/workflows/Documenter.yml

@@ -20,10 +20,10 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: julia-actions/setup-julia@v1
         with:
-          version: '1.6'
+          version: '1'
           show-versioninfo: true
       - uses: julia-actions/julia-buildpkg@v1
         env:

.github/workflows/ci.yml

@@ -27,52 +27,38 @@ concurrency:
 jobs:
   test:
     if: "!contains(github.event.head_commit.message, 'skip ci')"
-    name: ${{ matrix.os }} - ${{ matrix.p4est_test }} - Julia ${{ matrix.version }}
+    name: ${{ matrix.os }} - ${{ matrix.JULIA_P4EST_TEST }} - Julia ${{ matrix.version }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         version:
           - '1.6'
+          - '1'
           # - 'nightly'
         os:
           - ubuntu-latest
-          # - macos-latest
-          # - windows-latest
+          - macos-latest
+          - windows-latest
         arch:
           - x64
-        p4est_test:
-          - P4EST_JLL_USES_MPI_PRE_GENERATED_BINDINGS
-          - P4EST_JLL_USES_MPI
-          - P4EST_CUSTOM_NON_MPI
-          - P4EST_CUSTOM_USES_MPI
-        # Only selected tests on macOS and Windows, since not everything works everywhere yet
-        include:
+        JULIA_P4EST_TEST:
+          - P4EST_JLL_MPI_DEFAULT
+          - P4EST_CUSTOM_MPI_CUSTOM
+        exclude:
+          # Some preferences are not loaded in package tests in older versions
+          # of Julia, see
+          # https://github.com/JuliaPackaging/Preferences.jl/issues/40
+          # Thus, we need to disable this setup in CI.
           - version: '1.6'
-            os: macOS-latest
-            arch: x64
-            p4est_test: P4EST_JLL_USES_MPI_PRE_GENERATED_BINDINGS
-          - version: '1.6'
-            os: macOS-latest
-            arch: x64
-            p4est_test: P4EST_JLL_USES_MPI
-          - version: '1.6'
-            os: windows-latest
-            arch: x64
-            p4est_test: P4EST_JLL_USES_MPI_PRE_GENERATED_BINDINGS
-          # Additional tests on Julia v1.7
-          - version: '^1.7.0-0'
-            os: ubuntu-latest
-            arch: x64
-            p4est_test: P4EST_JLL_USES_MPI_PRE_GENERATED_BINDINGS
-          - version: '^1.7.0-0'
-            os: macOS-latest
-            arch: x64
-            p4est_test: P4EST_JLL_USES_MPI_PRE_GENERATED_BINDINGS
-          - version: '^1.7.0-0'
-            os: windows-latest
-            arch: x64
-            p4est_test: P4EST_JLL_USES_MPI_PRE_GENERATED_BINDINGS
+            JULIA_P4EST_TEST: P4EST_CUSTOM_MPI_CUSTOM
+          # Run only selected tests on macOS and Windows, since not everything
+          # works everywhere yet and we are most familiar with setting up custom
+          # p4est and MPI builds on Linux.
+          - os: macos-latest
+            JULIA_P4EST_TEST: P4EST_CUSTOM_MPI_CUSTOM
+          - os: windows-latest
+            JULIA_P4EST_TEST: P4EST_CUSTOM_MPI_CUSTOM
     steps:
       - uses: actions/checkout@v3
       - name: Set p4est release to run tests against
@@ -83,70 +69,54 @@ jobs:
         shell: bash
       - name: Set environment variables
         run: |
-          echo "Setting variables for '${{ matrix.p4est_test }}'..."
-          echo "P4EST_TEST=${{ matrix.p4est_test }}" >> $GITHUB_ENV
-          echo "P4EST_TEST=${{ matrix.p4est_test }}"
-          if [[ ${{ matrix.p4est_test }} == "P4EST_JLL_USES_MPI_PRE_GENERATED_BINDINGS" ]]; then
+          echo "Setting variables for '${{ matrix.JULIA_P4EST_TEST }}'..."
+          echo "JULIA_P4EST_TEST=${{ matrix.JULIA_P4EST_TEST }}" >> $GITHUB_ENV
+          echo "JULIA_P4EST_TEST=${{ matrix.JULIA_P4EST_TEST }}"
+          if [[ ${{ matrix.JULIA_P4EST_TEST }} == "P4EST_JLL_MPI_DEFAULT" ]]
+          then
             echo "(no additional environment variables required)"
-          elif [[ ${{ matrix.p4est_test }} == "P4EST_JLL_USES_MPI" ]]; then
-            echo "JULIA_P4EST_GENERATE_BINDINGS=yes" >> $GITHUB_ENV
-            echo "JULIA_P4EST_GENERATE_BINDINGS=yes"
-          elif [[ ${{ matrix.p4est_test }} == "P4EST_CUSTOM_NON_MPI" ]]; then
-            echo "JULIA_P4EST_GENERATE_BINDINGS=yes" >> $GITHUB_ENV
-            echo "JULIA_P4EST_GENERATE_BINDINGS=yes"
-            P4EST_TMP=`pwd`/libp4est_tmp_non_mpi
-            echo "P4EST_TMP=$P4EST_TMP" >> $GITHUB_ENV
-            echo "P4EST_TMP=$P4EST_TMP"
-            echo "JULIA_P4EST_LIBRARY=$P4EST_TMP/prefix/lib/libp4est.so" >> $GITHUB_ENV
-            echo "JULIA_P4EST_LIBRARY=$P4EST_TMP/prefix/lib/libp4est.so"
-            echo "JULIA_P4EST_INCLUDE=$P4EST_TMP/prefix/include" >> $GITHUB_ENV
-            echo "JULIA_P4EST_INCLUDE=$P4EST_TMP/prefix/include"
-          elif [[ ${{ matrix.p4est_test }} == "P4EST_CUSTOM_USES_MPI" ]]; then
-            echo "JULIA_P4EST_GENERATE_BINDINGS=yes" >> $GITHUB_ENV
-            echo "JULIA_P4EST_GENERATE_BINDINGS=yes"
-            P4EST_TMP=`pwd`/libp4est_tmp_uses_mpi
+          elif [[ ${{ matrix.JULIA_P4EST_TEST }} == "P4EST_CUSTOM_MPI_DEFAULT" ]] || [[ ${{ matrix.JULIA_P4EST_TEST }} == "P4EST_CUSTOM_MPI_CUSTOM" ]]
+          then
+            P4EST_TMP=`pwd`/libp4est_tmp
             echo "P4EST_TMP=$P4EST_TMP" >> $GITHUB_ENV
             echo "P4EST_TMP=$P4EST_TMP"
-            echo "JULIA_P4EST_LIBRARY=$P4EST_TMP/prefix/lib/libp4est.so" >> $GITHUB_ENV
-            echo "JULIA_P4EST_LIBRARY=$P4EST_TMP/prefix/lib/libp4est.so"
-            echo "JULIA_P4EST_INCLUDE=$P4EST_TMP/prefix/include" >> $GITHUB_ENV
-            echo "JULIA_P4EST_INCLUDE=$P4EST_TMP/prefix/include"
-            echo "JULIA_P4EST_USES_MPI=yes" >> $GITHUB_ENV
-            echo "JULIA_P4EST_USES_MPI=yes"
-            echo "JULIA_P4EST_MPI_INCLUDE=/usr/include/x86_64-linux-gnu/mpich" >> $GITHUB_ENV
-            echo "JULIA_P4EST_MPI_INCLUDE=/usr/include/x86_64-linux-gnu/mpich"
+            echo "JULIA_P4EST_TEST_LIBP4EST=$P4EST_TMP/prefix/lib/libp4est.so" >> $GITHUB_ENV
+            echo "$JULIA_P4EST_TEST_LIBP4EST=$P4EST_TMP/prefix/lib/libp4est.so"
           else
-            echo "ERROR: unknown test type ${{ matrix.p4est_test }}" >&2
+            echo "ERROR: unknown test type ${{ matrix.JULIA_P4EST_TEST }}" >&2
             exit 1
           fi
           echo "Done."
         shell: bash
-      - name: Install custom p4est libraries for testing
-        run: |
-          if [[ ${{ matrix.p4est_test }} == "P4EST_CUSTOM_USES_MPI" ]]; then
-            sudo apt-get install -y mpich libmpich-dev
-          fi
-          ./.ci_install_p4est.sh
-        shell: bash
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
           show-versioninfo: true
       - uses: julia-actions/cache@v1
+      - name: Install custom MPI library for testing
+        run: |
+          if [[ ${{ matrix.JULIA_P4EST_TEST }} == "P4EST_CUSTOM_MPI_CUSTOM" ]]
+          then
+            sudo apt-get install -y openmpi-bin libopenmpi-dev
+          fi
+        shell: bash
+      - name: Install custom p4est library for testing
+        run: |
+          ./.ci_install_p4est.sh
+        shell: bash
+      - name: Configure MPI.jl
+        shell: julia --color=yes {0}
+        run: |
+          @show pwd()
+          include(joinpath(pwd(), "test", "configure_packages.jl"))
       - uses: julia-actions/julia-buildpkg@v1
         env:
           PYTHON: ""
       - uses: julia-actions/julia-runtest@v1
         env:
           PYTHON: ""
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: coverallsapp/github-action@master
-        with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          flag-name: run-${{ matrix.os }}-${{ matrix.version }}-${{ matrix.arch }}
-          parallel: true
-          path-to-lcov: ./lcov.info
       - uses: codecov/codecov-action@v3
         with:
           token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
@@ -155,13 +125,73 @@ jobs:
           name: codecov-umbrella # optional
           fail_ci_if_error: true # optional (default = false)
           # verbose: true # optional (default = false)
+      # The standard setup of Coveralls is just annoying for parallel builds, see, e.g.,
+      # https://github.com/trixi-framework/Trixi.jl/issues/691
+      # https://github.com/coverallsapp/github-action/issues/47
+      # https://github.com/coverallsapp/github-action/issues/67
+      # This standard setup is reproduced below for completeness.
+      # - uses: coverallsapp/github-action@master
+      #   with:
+      #     github-token: ${{ secrets.GITHUB_TOKEN }}
+      #     flag-name: run-${{ matrix.JULIA_P4EST_TEST }}-${{ matrix.os }}-${{ matrix.version }}-${{ matrix.arch }}-${{ github.run_id }}
+      #     parallel: true
+      #     path-to-lcov: ./lcov.info
+      # Instead, we use a more tedious approach:
+      # - Store all individual coverage files as artifacts (directly below)
+      # - Download and merge individual coverage reports in another step
+      # - Upload only the merged coverage report to Coveralls
+      - shell: bash
+        run: |
+          cp ./lcov.info ./lcov-${{ matrix.JULIA_P4EST_TEST }}-${{ matrix.os }}-${{ matrix.version }}-${{ matrix.arch }}.info
+      - uses: actions/upload-artifact@v3
+        with:
+          name: lcov-${{ matrix.JULIA_P4EST_TEST }}-${{ matrix.os }}-${{ matrix.version }}-${{ matrix.arch }}
+          path: ./lcov-${{ matrix.JULIA_P4EST_TEST }}-${{ matrix.os }}-${{ matrix.version }}-${{ matrix.arch }}.info
 
   finish:
     needs: test
     runs-on: ubuntu-latest
     steps:
-    - name: Coveralls Finished
-      uses: coverallsapp/github-action@master
-      with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        parallel-finished: true
+      # The standard setup of Coveralls is just annoying for parallel builds, see, e.g.,
+      # https://github.com/trixi-framework/Trixi.jl/issues/691
+      # https://github.com/coverallsapp/github-action/issues/47
+      # https://github.com/coverallsapp/github-action/issues/67
+      # This standard setup is reproduced below for completeness.
+      # - name: Coveralls Finished
+      #   uses: coverallsapp/github-action@master
+      #   with:
+      #     github-token: ${{ secrets.GITHUB_TOKEN }}
+      #     parallel-finished: true
+      # Instead, we use the more tedious approach described above.
+      # At first, we check out the repository and download all artifacts
+      # (and list files for debugging).
+      - uses: actions/checkout@v3
+      - uses: actions/download-artifact@v3
+      - run: ls -R
+      # Next, we merge the individual coverage files and upload
+      # the combined results to Coveralls.
+      - name: Merge lcov files using Coverage.jl
+        shell: julia --color=yes {0}
+        run: |
+          using Pkg
+          Pkg.activate(temp=true)
+          Pkg.add("Coverage")
+          using Coverage
+          coverage = LCOV.readfolder(".")
+          for cov in coverage
+            cov.filename = replace(cov.filename, "\\" => "/")
+          end
+          coverage = merge_coverage_counts(coverage)
+          @show covered_lines, total_lines = get_summary(coverage)
+          LCOV.writefile("./lcov.info", coverage)
+      - uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: ./lcov.info
+      # Upload merged coverage data as artifact for debugging
+      - uses: actions/upload-artifact@v3
+        with:
+          name: lcov
+          path: ./lcov.info
+      # That's it
+      - run: echo "Finished testing P4est"

.gitignore

@@ -1,9 +1,13 @@
 *.mem
 **/Manifest.toml
+dev/p4est_include
 docs/build
+docs/src/authors.md
+docs/src/contributing.md
+docs/src/index.md
+docs/src/license.md
 public/
 coverage/
 coverage_report/
 **/*.jl.*.cov
-deps/libp4est.jl
-deps/*.log
+

AUTHORS.md

@@ -0,0 +1,22 @@
+# Authors
+
+The development of P4est.jl is coordinated by a group of *principal developers*,
+who are also its main contributors and who can be contacted in case of
+questions about P4est.jl. In addition, there are *contributors* who have
+provided substantial additions or modifications. Together, these two groups form
+"The P4est.jl Authors" as mentioned in the [LICENSE.md](LICENSE.md) file.
+
+## Principal Developers
+
+- [Michael Schlottke-Lakemper](https://lakemper.eu)
+- [Hendrik Ranocha](https://ranocha.de)
+
+## Contributors
+
+The following people contributed major additions or modifications to Trixi and
+are listed in alphabetical order:
+
+- Alexander Astanin
+- Lars Christmann
+- Joshua Lampert
+- Lucas C Wilcox

CONTRIBUTING.md

@@ -4,7 +4,7 @@ P4est.jl is an open-source project and we are very happy to accept contributions
 from the community. Please feel free to open issues or submit patches (preferably
 as merge requests) any time. For planned larger contributions, it is often
 beneficial to get in contact with one of the principal developers first (see
-[README.md](README.md)).
+[AUTHORS.md](AUTHORS.md)).
 
 P4est.jl and its contributions are licensed under the MIT license (see
 [LICENSE.md](LICENSE.md)). As a contributor, you certify that all your

LICENSE.md

@@ -1,21 +1,21 @@
 MIT License
 
-Copyright (c) 2020-present Michael Schlottke-Lakemper, Hendrik Ranocha, and Alexander Astanin
+Copyright (c) 2020-present The P4est.jl Authors (see [AUTHORS.md](AUTHORS.md))
 
-Permission is hereby granted, free of charge, to any person obtaining a copy  
-of this software and associated documentation files (the "Software"), to deal  
-in the Software without restriction, including without limitation the rights  
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell  
-copies of the Software, and to permit persons to whom the Software is  
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
 furnished to do so, subject to the following conditions:
 
-The above copyright notice and this permission notice shall be included in all  
+The above copyright notice and this permission notice shall be included in all
 copies or substantial portions of the Software.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR  
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,  
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE  
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER  
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,  
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE  
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.