Update Paper joss #149
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| name: R-test | |
| on: | |
| pull_request: | |
| branches: | |
| [main] | |
| push: | |
| branches: | |
| [main, dev] | |
| schedule: | |
| - cron: '11 1 1 * *' | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| jobs: | |
| R-test: | |
| name: python ${{ matrix.python-version }}, ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| REPO_NAME: ${{ github.event.repository.name }} | |
| strategy: | |
| matrix: | |
| os: [windows-latest, macos-latest] | |
| python-version: ['3.8', '3.9', '3.10', '3.11'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| miniforge-version: 'latest' | |
| - name: Conda install | |
| shell: bash -el {0} | |
| run: | | |
| # conda deactivate | |
| # conda rename -n test wq_harmonize | |
| conda install "pytest" "numpy<2.0" "pandas<2.0" "geopandas>=0.10.2, <0.13" "pint>=0.18" "dataretrieval>=1.0, <1.0.5" "requests" | |
| conda install pip | |
| pip install . | |
| conda create --name wq_harmonize --clone test | |
| - name: Print Conda environment | |
| shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'release' | |
| #- uses: r-lib/actions/setup-renv@v2 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: R depends | |
| shell: Rscript {0} | |
| run: | | |
| install.packages(c("knitr", "rmarkdown", "reticulate")) | |
| - name: setup r-reticulate venv & render rmd | |
| shell: Rscript {0} | |
| run: | | |
| library(reticulate) | |
| # packages = c( | |
| # "pytest", "numpy<2.0", "pandas<2.0", "geopandas>=0.10.2, <0.13", "pint>=0.18", | |
| # "dataretrieval>=1.0, <1.0.5", "requests" | |
| # ) | |
| # reticulate::install_miniconda() | |
| # reticulate::conda_create("wq_harmonize", python_version = "${{ matrix.python-version }}") | |
| # reticulate::conda_install("wq_harmonize", packages) | |
| # path_to_venv <- virtualenv_create( | |
| # envname = "wq_harmonize", | |
| # python = Sys.which("python"), # placed on PATH by the setup-python action | |
| # packages | |
| # ) | |
| # use_virtualenv("wq_harmonize") | |
| reticulate::use_condaenv("wq_harmonize") | |
| #reticulate::py_install("git+https://github.com/USEPA/harmonize-wq.git", pip = TRUE, envname = "wq_harmonize") | |
| rmarkdown::render(input = "demos/Harmonize_Pensacola.Rmd") | |
| - name: Upload artifact | |
| if: ${{ (matrix.os == 'windows-latest') && (matrix.python-version == 3.11) }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: demos-artifact | |
| # Upload entire demos folder | |
| path: './demos' |