Revert "Remove code stuff"

This reverts commit 081d622.

.codecov.yml

@@ -0,0 +1,2 @@
+github_checks:
+ annotations: false

.github/workflows/ci.yml

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+name: CI
+
+on:
+ push:
+ branches:
+ - main
+ paths-ignore:
+ - 'AUTHORS.md'
+ - 'LICENSE.md'
+ - 'README.md'
+ pull_request:
+ paths-ignore:
+ - 'AUTHORS.md'
+ - 'LICENSE.md'
+ - 'README.md'
+ workflow_dispatch:
+ inputs:
+ debug_enabled:
+ description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
+ required: false
+ default: false
+
+env:
+ # Modify this variable to change the ifort compiler version - do NOT hardcode the version
+ # anywhere else!
+ INTEL_ONEAPI_VERSION: 2023.2.1
+
+jobs:
+ test:
+ if: "!contains(github.event.head_commit.message, 'skip ci')"
+ name: ${{ matrix.os_name }} - ${{ matrix.compiler }} - ${{ matrix.test_type }} - ${{ github.event_name }}
+ runs-on: ${{ matrix.os }}
+ strategy:
+ fail-fast: false
+ matrix:
+ include:
+ # Linux
+ - os: ubuntu-22.04
+ os_name: linux
+ compiler: gfortran-9
+ shell: bash
+ test_type: regular
+ coverage: false
+ - os: ubuntu-22.04
+ os_name: linux
+ compiler: gfortran-9
+ shell: bash
+ test_type: valgrind
+ coverage: false
+ - os: ubuntu-latest
+ os_name: linux
+ compiler: gfortran-10
+ shell: bash
+ test_type: regular
+ coverage: true
+ - os: ubuntu-latest
+ os_name: linux
+ compiler: gfortran-10
+ shell: bash
+ test_type: valgrind
+ coverage: false
+ - os: ubuntu-22.04
+ os_name: linux
+ compiler: gfortran-11
+ shell: bash
+ test_type: regular
+ coverage: false
+ - os: ubuntu-22.04
+ os_name: linux
+ compiler: gfortran-11
+ shell: bash
+ test_type: valgrind
+ coverage: false
+ - os: ubuntu-latest
+ os_name: linux
+ compiler: gfortran-12
+ shell: bash
+ test_type: regular
+ coverage: false
+ - os: ubuntu-latest
+ os_name: linux
+ compiler: gfortran-12
+ shell: bash
+ test_type: valgrind
+ coverage: false
+ - os: ubuntu-24.04
+ os_name: linux
+ compiler: gfortran-13
+ shell: bash
+ test_type: regular
+ coverage: false
+ - os: ubuntu-24.04
+ os_name: linux
+ compiler: gfortran-13
+ shell: bash
+ test_type: valgrind
+ coverage: false
+ - os: ubuntu-latest
+ os_name: linux
+ compiler: ifort
+ shell: bash
+ test_type: regular
+ coverage: false
+ # macOS
+ - os: macos-latest
+ os_name: macos
+ compiler: gfortran-11
+ shell: bash
+ test_type: regular
+ coverage: false
+ - os: macos-latest
+ os_name: macos
+ compiler: gfortran-12
+ shell: bash
+ test_type: regular
+ coverage: false
+ - os: macos-latest
+ os_name: macos
+ compiler: gfortran-13
+ shell: bash
+ test_type: regular
+ coverage: false
+ # Windows
+ - os: windows-latest
+ os_name: windows
+ compiler: gfortran
+ shell: 'msys2 {0}'
+ test_type: regular
+ coverage: false
+ # Set default shell as suggested here: https://github.community/t/setting-default-shell-or-other-step-metadata-conditionally-in-workflows/154055
+ defaults:
+ run:
+ shell: ${{ matrix.shell }}
+ steps:
+ - name: Checkout repository
+ uses: actions/checkout@v4
+ # - name: Add msbuild to PATH
+ # if: ${{ matrix.os_name == 'windows-latest' }}
+ # uses: microsoft/[email protected]
+ - uses: msys2/setup-msys2@v2
+ if: ${{ matrix.os == 'windows-latest' }}
+ with:
+ update: true
+ install: git base-devel mingw-w64-x86_64-toolchain mingw-w64-x86_64-gcc-fortran
+ - uses: actions/cache@v4
+ id: cache
+ with:
+ path: /opt/intel/oneapi
+ key: ${{ matrix.os }}-${{ matrix.compiler }}-${{ env.INTEL_ONEAPI_VERSION }}
+ - name: Install Intel oneAPI Fortran compiler
+ if: matrix.compiler == 'ifort' && steps.cache.outputs.cache-hit != 'true'
+ run: |
+ # download the key to system keyring
+ wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \
+ | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
+
+ # add signed entry to apt sources and configure the APT client to use Intel repository:
+ echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
+
+ # update package index and install Fortran compiler
+ sudo apt update
+ sudo apt-get install intel-oneapi-compiler-fortran-$INTEL_ONEAPI_VERSION
+
+ # set environment variables and make them persistent across steps
+ . /opt/intel/oneapi/setvars.sh
+ env | grep oneapi >> $GITHUB_ENV
+ - name: Use existing Intel oneAPI Fortran compiler
+ if: matrix.compiler == 'ifort' && steps.cache.outputs.cache-hit == 'true'
+ run: |
+ # set environment variables and make them persistent across steps
+ . /opt/intel/oneapi/setvars.sh
+ env | grep oneapi >> $GITHUB_ENV
+ - name: Bootstrap
+ run: |
+ ./Utilities/bootstrap
+ - name: Show version information
+ run: |
+ ${{ matrix.compiler }} --version
+ - name: Build
+ run: |
+ make -j 2 FC=${{ matrix.compiler }}
+ - name: Run regular function tests
+ if: ${{ matrix.test_type == 'regular' }}
+ run: |
+ ./HOHQMesh -test
+ - name: Run memory checks with Valgrind (only Linux)
+ if: ${{ matrix.os_name == 'linux' && matrix.test_type == 'valgrind' }}
+ run: |
+ sudo apt update
+ sudo apt-get install -y valgrind
+ valgrind --error-exitcode=1 -s ./HOHQMesh -test
+ # Enable tmate debugging of manually-triggered workflows if the input option was provided
+ - name: Setup tmate session for debugging
+ if: ${{ matrix.os == 'windows-latest' && github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled && always() }}
+ uses: mxschmitt/action-tmate@v3
+ timeout-minutes: 15
+ - name: Run tests for coverage
+ if: ${{ matrix.coverage }}
+ run: |
+ sudo apt-get install -y lcov
+ FC=${{ matrix.compiler }} ./Utilities/createcoverage
+ - uses: codecov/codecov-action@v4
+ if: ${{ matrix.coverage }}
+ with:
+ files: ./lcov.info
+ flags: unittests
+ name: codecov-umbrella
+ env:
+ CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} # now required for public repos
+ - name: Coveralls
+ if: ${{ matrix.coverage }}
+ uses: coverallsapp/github-action@master
+ with:
+ github-token: ${{ secrets.GITHUB_TOKEN }}
+ path-to-lcov: ./lcov.info

.github/workflows/documentation.yml

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+name: Documentation (mkdocs)
+on:
+ push:
+ branches:
+ - master
+ - main
+jobs:
+ deploy:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v4
+ - uses: actions/setup-python@v5
+ with:
+ python-version: 3.x
+ - run: |
+ pip install mkdocs-material
+ cd Documentation
+ ./preparedocs
+ mkdocs gh-deploy --force
+

AUTHORS.md

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+# Authors
+
+HOHQMesh's development is coordinated by David A. Kopriva, who is the *principal developer*
+and main contributor. In addition, there are *contributors* who have
+provided substantial additions or modifications. Together, these two groups form
+authors as mentioned in the [LICENSE.md](LICENSE.md) file.
+
+## Principal Developers
+* [David A. Kopriva](https://www.math.fsu.edu/~kopriva),
+ Florida State University, USA
+
+## Contributors
+The following people contributed major additions or modifications to HOHQMesh and
+are listed in alphabetical order:
+
+* David A. Kopriva
+* Joseph Schoonover
+* Andrew Winters

Benchmarks/BenchmarkData/AllFeatures.txt

@@ -0,0 +1,9 @@
+ 1
+ 1690 1833 3525 2
+ 3.07838E-01
+ 1.22496E+00
+ 1.14753E+00
+ 1.44190E+00
+ 2.39601E-01
+ 7.46320E+01
+ 1.07656E+02

Benchmarks/BenchmarkData/BoneAndMarrow.txt

@@ -0,0 +1,9 @@
+ 1
+ 928 981 1908 32
+ 6.63086E-01
+ 1.29974E+00
+ 1.24992E+00
+ 1.59842E+00
+ 5.77207E-01
+ 7.51017E+01
+ 1.06507E+02

Benchmarks/BenchmarkData/BottomFromFile.txt

@@ -0,0 +1,8 @@
+ 2
+ 144 245
+ 9.70085E-01
+ 3.83146E+00
+ 2.91848E-01
+ 6.08656E-01
+ 7.01044E-02
+ 3.19161E-01

Benchmarks/BenchmarkData/Box3D.txt

@@ -0,0 +1,8 @@
+ 2
+ 50 108
+ 1.00000E+00
+ 1.00000E+00
+ 1.00000E+00
+ 1.00000E+00
+ 0.00000E+00
+ 1.00000E+00

Benchmarks/BenchmarkData/Box3DRotated.txt

@@ -0,0 +1,8 @@
+ 2
+ 150 252
+ 1.00000E+00
+ 2.58819E+00
+ 2.00000E+00
+ 6.55346E-01
+ 1.16573E-16
+ 2.25000E+00

Benchmarks/BenchmarkData/Circles3Benchmark.txt

@@ -0,0 +1,9 @@
+ 1
+ 421 485 908 1
+ 1.38420E+00
+ 1.28311E+00
+ 1.19225E+00
+ 1.57279E+00
+ 1.04363E+00
+ 7.10372E+01
+ 1.11620E+02

Benchmarks/BenchmarkData/GingerbreadBenchmark.txt

@@ -0,0 +1,9 @@
+ 1
+ 1010 1186 2201 2
+ 1.26106E+00
+ 1.28821E+00
+ 1.19420E+00
+ 1.57163E+00
+ 9.95071E-01
+ 7.10403E+01
+ 1.11331E+02

Benchmarks/BenchmarkData/HalfCircle3DRBenchmark.txt

@@ -0,0 +1,8 @@
+ 2
+ 306 462
+ 9.67009E-01
+ 3.11936E+00
+ 3.92290E-01
+ 6.39401E-01
+ 9.30153E-02
+ 5.36944E-01

Benchmarks/BenchmarkData/HalfCircleBenchmark.txt

@@ -0,0 +1,9 @@
+ 1
+ 426 473 898 0
+ 5.89678E-02
+ 1.05369E+00
+ 1.02793E+00
+ 1.10260E+00
+ 5.65656E-02
+ 8.59605E+01
+ 9.48078E+01

Benchmarks/BenchmarkData/HalfCircleExtBenchmark.txt

@@ -0,0 +1,8 @@
+ 2
+ 204 330
+ 9.59649E-01
+ 1.72720E+00
+ 4.16281E-01
+ 8.57298E-01
+ 9.24078E-02
+ 4.88872E-01

Benchmarks/BenchmarkData/IceCreamConeWHole.txt

@@ -0,0 +1,9 @@
+ 1
+ 384 454 839 1
+ 1.16737E-01
+ 1.22951E+00
+ 1.14473E+00
+ 1.44130E+00
+ 9.73932E-02
+ 7.43684E+01
+ 1.07980E+02

Benchmarks/BenchmarkData/NACA0012.txt

@@ -0,0 +1,9 @@
+ 1
+ 692 755 1447 1
+ 2.31202E+00
+ 1.19741E+00
+ 1.13487E+00
+ 1.41233E+00
+ 2.25520E+00
+ 7.82753E+01
+ 1.02874E+02

Benchmarks/BenchmarkData/PacMan.txt

@@ -0,0 +1,9 @@
+ 1
+ 94 115 208 0
+ 3.39246E-02
+ 1.22993E+00
+ 1.11908E+00
+ 1.42737E+00
+ 2.79085E-02
+ 7.51275E+01
+ 1.07185E+02

Benchmarks/BenchmarkData/Pill.txt

@@ -0,0 +1,9 @@
+ 1
+ 657 771 1430 4
+ 1.69415E-03
+ 1.24081E+00
+ 1.17422E+00
+ 1.49304E+00
+ 1.42784E-03
+ 7.36118E+01
+ 1.07717E+02