install python 3.10 #51
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| name: "Update Publications" | |
| on: | |
| push: | |
| branches: | |
| - dpe-1262-fix-pub-script | |
| schedule: | |
| - cron: "0 0 1 * *" | |
| workflow_dispatch: | |
| env: | |
| RETICULATE_AUTOCONFIGURE: 'FALSE' | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| update-publications: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # - name: Set up Python | |
| # uses: actions/setup-python@v4 | |
| # with: | |
| # python-version: "3.10" | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.3.1' | |
| - name: Install system dependencies | |
| run: | | |
| export DEBIAN_FRONTEND=noninteractive | |
| sudo apt-get update && \ | |
| sudo apt-get -y install libpng-dev \ | |
| pandoc \ | |
| git-core \ | |
| libv8-dev \ | |
| libxml2-dev \ | |
| libcurl4-openssl-dev \ | |
| libssl-dev \ | |
| libssh2-1-dev \ | |
| zlib1g-dev \ | |
| libgit2-dev \ | |
| python3-pip \ | |
| python3.10 \ | |
| python3.10-dev \ | |
| python3.10-venv | |
| # pandoc-citeproc | |
| - name: Install dependencies | |
| run: | | |
| install.packages('remotes') | |
| remotes::install_cran('rentrez') | |
| remotes::install_cran('librarian') | |
| remotes::install_version('rjson', version='0.2.21') | |
| remotes::install_version('reticulate', version='1.28') | |
| reticulate::install_miniconda() | |
| reticulate::use_condaenv("r-reticulate", required=TRUE) | |
| reticulate::py_config() | |
| remotes::install_cran("synapser", repos = c("http://ran.synapse.org", "https://cloud.r-project.org")) | |
| # deps <- readRDS('depends.Rds') | |
| # deps[['installed']] <- vapply(deps[['package']], remotes:::local_sha, character(1)) | |
| # update(deps) | |
| shell: Rscript {0} | |
| - name: Update OpenSSL in Conda | |
| run: | | |
| /home/runner/.local/share/r-miniconda/bin/conda install --yes -c conda-forge "openssl>=3.3.0" | |
| # - name: Install Miniconda | |
| # run: | | |
| # Rscript -e "remotes::install_github('rstudio/reticulate')" | |
| # Rscript -e "reticulate::install_miniconda()" | |
| # - name: Install Python deps | |
| # run: | | |
| # Rscript -e "reticulate::py_discover_config()" | |
| # Rscript -e "reticulate::py_install(c('pandas', 'numpy', 'boto3', 'synapseclient'), pip = TRUE)" | |
| # - name: Install porTools | |
| # run: | | |
| # Rscript -e "remotes::install_github('eliteportal/publication_scraper')" | |
| - name: Query PubMed and upload results | |
| run: | | |
| Rscript ./inst/scripts/query-pubmed-grants.R --grant_table syn51209786 --parent syn51317180 --pub_table syn51407023 --auth_token ${{ secrets.SYNAPSE_PAT }} |