👷 Testing all reactive notebooks #81
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| name: Test | |
| run-name: 👷 Testing all reactive notebooks | |
| on: [pull_request] | |
| env: | |
| JOLIN_SITE: "nosite.nosite" | |
| JOLIN_ENVIRONMENT: "test" | |
| JOLINPLUTOCICD_VERSION: "0.1.19" | |
| defaults: | |
| run: | |
| shell: bash # we want to use bash as the default shell | |
| jobs: | |
| job-matrix: | |
| runs-on: ubuntu-latest | |
| container: jolincompany/jolin_cloud_cicd:latest | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: List all notebooks. | |
| id: set-matrix | |
| run: | | |
| echo matrix=$(julia -e ' | |
| import Pkg | |
| Pkg.Registry.add("General") | |
| Pkg.Registry.add(Pkg.RegistrySpec(url="https://github.com/jolin-io/JolinRegistry.jl")) | |
| Pkg.add(name="JolinPlutoCICD", version=ENV["JOLINPLUTOCICD_VERSION"]) | |
| using JolinPlutoCICD | |
| print(JolinPlutoCICD.json_common_prefix_common_suffix_and_all_notebook_paths(ARGS[1])) | |
| ' .) >> "$GITHUB_OUTPUT" | |
| job-run: | |
| name: ${{ matrix.notebook_path }} | |
| runs-on: ubuntu-latest | |
| container: jolincompany/jolin_cloud_cicd:latest | |
| needs: job-matrix | |
| strategy: | |
| matrix: ${{ fromJSON(needs.job-matrix.outputs.matrix) }} | |
| permissions: | |
| id-token: write # This is required for requesting the JWT | |
| contents: read # This is required for actions/checkout | |
| steps: | |
| - uses: actions/checkout@v3 | |
| # set JOLIN_REPO environment variable | |
| - name: Set environment variable "JOLIN_REPO". | |
| run: echo "JOLIN_REPO=github.com/${GITHUB_REPOSITORY#*/}" >> $GITHUB_ENV | |
| - name: Add julia registries and JolinPlutoCICD (our cicd helper). | |
| run: | | |
| julia -e ' | |
| import Pkg | |
| Pkg.Registry.add("General") | |
| Pkg.Registry.add(Pkg.RegistrySpec(url="https://github.com/jolin-io/JolinRegistry.jl")) | |
| # Pkg.Registry.update() # not needed because the registries are added the first time | |
| Pkg.add("JolinPlutoCICD") | |
| ' | |
| # we need to create temporary environment under GITHUB_WORKSPACE, because only files under this directory can be hashed | |
| # see https://docs.github.com/en/actions/learn-github-actions/expressions#hashfiles | |
| - name: Setup julia project environment for the notebook and export the directory to environment variable "notebook_env". | |
| run: | | |
| echo notebook_env=$(julia -e ' | |
| using JolinPlutoCICD | |
| env_dir = JolinPlutoCICD.create_pluto_env(ARGS[1], parentdir=joinpath(ENV["GITHUB_WORKSPACE"], "_temp_envs")) | |
| # we want to cache .CondaPkg, hence it already needs to exist | |
| mkpath(joinpath(env_dir, ".CondaPkg")) | |
| # we need to strip the GITHUB_WORKSPACE because hashFiles only works with paths relative to GITHUB_WORKSPACE | |
| # Char(47) == "/" (as char, but we cannot easily use single quotes here) | |
| env_dir_relative = lstrip(env_dir[begin+length(ENV["GITHUB_WORKSPACE"]) : end], Char(47)) | |
| print(env_dir_relative) | |
| ' "${{ matrix.prefix }}${{ matrix.notebook_path }}${{ matrix.suffix }}") >> "$GITHUB_ENV" | |
| # fixing permission error for hashfiles (actually works) | |
| # adapted from https://github.com/cypress-io/github-action/issues/446#issuecomment-968192021 | |
| - name: Fix caching. | |
| run: chown -R 1001:1001 $GITHUB_WORKSPACE/$notebook_env | |
| - name: Apply caching. | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ~/.julia | |
| $GITHUB_WORKSPACE/$notebook_env/.CondaPkg | |
| key: ${{ runner.os }}-${{ hashFiles(format('{0}/*.toml', env.notebook_env)) }} | |
| restore-keys: ${{ runner.os }}- | |
| - name: Instantiate (i.e. download and install) julia project and conda packages. | |
| run: | | |
| # initialize conda first, because RCall cannot be build without R_HOME being set (pseudo R_HOME also do not work) | |
| # we cannot do this inside the notebook_env because adding JolinPlutoCICD would already trigger a build of RCall if it is there in the Manifest.toml | |
| julia -e ' | |
| # because of the caching we need to reinstall JolinPlutoCICD | |
| # (alternatively we could merge old and new .julia folder) | |
| import Pkg | |
| Pkg.Registry.add("General") | |
| Pkg.Registry.add(Pkg.RegistrySpec(url="https://github.com/jolin-io/JolinRegistry.jl")) | |
| Pkg.Registry.update() # needed because registries might already exist with outdated information | |
| Pkg.add(name="JolinPlutoCICD", version=ENV["JOLINPLUTOCICD_VERSION"]) | |
| import JolinPlutoCICD | |
| eval(JolinPlutoCICD.expr_resolve_condapkg(ARGS[1])) | |
| ' "$GITHUB_WORKSPACE/$notebook_env" | |
| # set R_HOME if conda was actually initialized - needed before Pkg.instantiate() | |
| if [ -d "$GITHUB_WORKSPACE/$notebook_env/.CondaPkg" ]; then | |
| echo R_HOME="$GITHUB_WORKSPACE/$notebook_env/.CondaPkg/env/lib/R" >> "$GITHUB_ENV" | |
| fi | |
| # this will build RCall if it is a dependency and will fail if R_HOME is not correct | |
| julia --project="$GITHUB_WORKSPACE/$notebook_env" -e ' | |
| import Pkg | |
| Pkg.instantiate() | |
| ' | |
| - name: Run notebook. | |
| working-directory: ./ | |
| run: | | |
| FILE="${{ matrix.prefix }}${{ matrix.notebook_path }}${{ matrix.suffix }}" | |
| if [[ "$FILE" == *.jl ]]; then | |
| JULIA_PROJECT="$GITHUB_WORKSPACE/$notebook_env" julia "$FILE" | |
| elif [[ "$FILE" == *.py ]]; then | |
| # we need to start python from julia, because of https://github.com/JuliaPy/PythonCall.jl/issues/426 | |
| # and because PythonCall sets up a pseudo juliacall without actually loading the juliacall package | |
| JULIA_PROJECT="$GITHUB_WORKSPACE/$notebook_env" julia -e ' | |
| import PythonCall | |
| PythonCall.pyexec(@NamedTuple{}, readchomp(ARGS[1]), Main) | |
| ' "$FILE" | |
| elif [[ "$FILE" == *.R ]] || [[ "$FILE" == *.r ]]; then | |
| JULIA_PROJECT="$GITHUB_WORKSPACE/$notebook_env" "$GITHUB_WORKSPACE/$notebook_env/.CondaPkg/env/bin/Rscript" "$FILE" | |
| fi |