Add codespell (config, precommit, workflow) and make it fix typos #713
Workflow file for this run
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| name: shpc test modules | |
| on: | |
| pull_request: [] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| module: [[lmod, 8.4.27], [tcl, 4.7.1], [tcl, 5.0.1]] | |
| container_tech: [podman, singularity, docker] | |
| steps: | |
| - name: Install Dependencies | |
| run: | | |
| sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev tcsh | |
| - name: Install Environment Modules | |
| if: ${{ matrix.module[0] == 'tcl' }} | |
| env: | |
| PKG_VERSION: ${{ matrix.module[1] }} | |
| run: | | |
| curl -LJO https://github.com/cea-hpc/modules/releases/download/v${PKG_VERSION}/modules-${PKG_VERSION}.tar.gz | |
| tar xfz modules-${PKG_VERSION}.tar.gz | |
| ls | |
| cd modules-${PKG_VERSION} | |
| ./configure | |
| make | |
| sudo make install | |
| - name: Install Lmod | |
| if: ${{ matrix.module[0] == 'lmod' }} | |
| env: | |
| PKG_VERSION: ${{ matrix.module[1] }} | |
| run: | | |
| PKG_URL="https://github.com/TACC/Lmod/archive/${PKG_VERSION}.tar.gz" | |
| wget $PKG_URL | |
| tar xfz ${PKG_VERSION}.tar.gz | |
| cd Lmod-${PKG_VERSION} | |
| ./configure --prefix=/usr/share && make && make install | |
| - uses: eWaterCycle/setup-singularity@v7 | |
| if: ${{ matrix.container_tech == 'singularity' }} | |
| name: Install Singularity | |
| with: | |
| singularity-version: 3.7.1 | |
| - name: Create conda environment | |
| run: conda create --quiet -c conda-forge --name shpc spython | |
| - uses: actions/checkout@v4 | |
| - name: Install shpc | |
| run: | | |
| export PATH="/usr/share/miniconda/bin:$PATH" | |
| source activate shpc | |
| pip install -e . | |
| - name: Run python module tests (bash) | |
| shell: bash | |
| env: | |
| module_sys: ${{ matrix.module[0] }} | |
| container_tech: ${{ matrix.container_tech }} | |
| run: | | |
| case "${module_sys}" in | |
| lmod) | |
| . /usr/share/lmod/lmod/init/bash | |
| ;; | |
| tcl) | |
| . /usr/local/Modules/init/bash | |
| shopt expand_aliases || true | |
| shopt -s expand_aliases | |
| ;; | |
| esac | |
| export PATH="/usr/share/miniconda/bin:$PATH" | |
| source activate shpc | |
| shpc config set container_tech:${{ matrix.container_tech }} | |
| shpc config set module_sys:${module_sys} | |
| shpc config set enable_tty:false | |
| printf "\n\shpc test ============================================\n" | |
| shpc test python:3.9.5-alpine | |
| shpc install python:3.9.5-alpine | |
| module use ./modules | |
| module load python/3.9.5-alpine | |
| alias | |
| printf "\n\nmodule show ============================================\n" | |
| module show python/3.9.5-alpine | |
| printf "\n\nmodule whatis ==========================================\n" | |
| module whatis python/3.9.5-alpine | |
| printf "\n\nmodule help ============================================\n" | |
| module help python/3.9.5-alpine | |
| script_path=$(which python-exec) | |
| cat $script_path | |
| set -x | |
| python-exec echo donuts >test_output | |
| cat test_output | |
| grep --quiet donuts test_output | |
| python-container > container_output | |
| cat container_output | |
| python-run python --version >test_output | |
| cat test_output | |
| grep --quiet 'Python 3.9.5' test_output | |
| rm test_output | |
| mkdir -p tmp-modules | |
| shpc config set views_base:tmp-modules | |
| shpc view create noodles | |
| shpc view install noodles python:3.9.5-alpine | |
| shpc uninstall --force python:3.9.5-alpine | |
| shpc view --force delete noodles | |
| - name: Run python module tests (tcsh) | |
| shell: tcsh -e {0} | |
| env: | |
| module_sys: ${{ matrix.module[0] }} | |
| container_tech: ${{ matrix.container_tech }} | |
| run: | | |
| switch ("${module_sys}") | |
| case lmod: | |
| source /usr/share/lmod/lmod/init/tcsh | |
| breaksw | |
| case tcl: | |
| source /usr/local/Modules/init/tcsh | |
| breaksw | |
| endsw | |
| source /usr/share/miniconda/etc/profile.d/conda.csh | |
| conda activate shpc | |
| shpc config set container_tech:${{ matrix.container_tech }} | |
| shpc config set module_sys:${module_sys} | |
| shpc config set enable_tty:false | |
| shpc install python:3.9.5-alpine | |
| module use ./modules | |
| module load python/3.9.5-alpine | |
| alias | |
| printf "\n\nmodule show ============================================\n" | |
| module show python/3.9.5-alpine | |
| printf "\n\nmodule whatis ==========================================\n" | |
| module whatis python/3.9.5-alpine | |
| printf "\n\nmodule help ============================================\n" | |
| module help python/3.9.5-alpine | |
| python-container > container_output | |
| cat container_output | |
| python-exec echo donuts >test_output | |
| cat test_output | |
| grep --quiet donuts test_output | |
| python-run python --version >test_output | |
| cat test_output | |
| grep --quiet 'Python 3.9.5' test_output | |
| rm test_output | |
| mkdir -p tmp-modules | |
| shpc config set views_base:tmp-modules | |
| shpc view create noodles | |
| shpc view install noodles python:3.9.5-alpine | |
| shpc uninstall --force python:3.9.5-alpine | |
| shpc view --force delete noodles |