Update publications #44
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| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: '0 5 1 * *' | |
| name: Update publications | |
| jobs: | |
| update-bibtex: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| install-r: false | |
| use-public-rspm: true | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libcurl4-openssl-dev | |
| - uses: r-lib/actions/setup-renv@v2 | |
| - name: Create bibtex file with selected entries | |
| run: | | |
| last_comment_pubs <- gh::gh( | |
| "/repos/{gh_repo}/issues/{issue_number}/comments", | |
| gh_repo = "${{ github.repository }}", | |
| issue_number = 3, | |
| .accept = "application/vnd.github.v3.full+json" | |
| ) |> | |
| purrr::keep(~ .x$user$login == "github-actions[bot]") |> | |
| tail(1) |> | |
| purrr::map_chr("body_html") |> | |
| xml2::read_html() | |
| last_comment_pubs |> | |
| xml2::xml_find_first("//details") |> | |
| xml2::xml_text() |> | |
| write("bibentries_previous_month.bib") | |
| bibentries_previous_month <- bibtex::read.bib("bibentries_previous_month.bib") | |
| selected <- last_comment_pubs |> | |
| xml2::xml_find_first("//ul") |> | |
| xml2::xml_find_all("//input") |> | |
| xml2::xml_has_attr("checked") | |
| selected_bibentries <- bibentries_previous_month[selected] | |
| bib_new <- vapply(selected_bibentries, format, style = "Bibtex", character(1)) | |
| bib_old <- readLines("_data/papers.bib") | |
| bib <- paste(c(bib_old, bib_new), collapse = "\n") | |
| write(bib, "_data/papers.bib") | |
| shell: Rscript {0} | |
| - uses: peter-evans/create-pull-request@v5 | |
| id: cpr | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| commit-message: Automated update of team publications | |
| committer: epiforecasts-bot <[email protected]> | |
| author: epiforecasts-bot <[email protected]> | |
| branch: pubs | |
| branch-suffix: timestamp | |
| add-paths: _data/papers.bib | |
| title: Automated update of team publications | |
| delete-branch: true | |
| fetch-new-papers: | |
| needs: update-bibtex | |
| if: always() | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| install-r: false | |
| use-public-rspm: true | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libcurl4-openssl-dev | |
| - uses: r-lib/actions/setup-renv@v2 | |
| - name: Post a comment listing new papers | |
| run: | | |
| options(width = 10000) # do not hard-wrap formatted citations | |
| source("_automation/get_new_papers.R") | |
| month_1st <- format(lubridate::floor_date(lubridate::today()-1, "month")) | |
| new_papers <- get_new_papers_team(from_date = month_1st) | |
| if (nrow(new_papers) > 0) { | |
| bibentries_new <- create_bibentries(new_papers) | |
| saveRDS(bibentries_new, paste0("bibentries_previous_month.rds")) | |
| bibentries_new_checklist <- paste("- [ ]", vapply(bibentries_new, format, character(1))) | |
| bibentries_comment <- paste( | |
| c( | |
| "Papers published last month:", | |
| bibentries_new_checklist, | |
| "<details>", | |
| "", | |
| "```", | |
| vapply(bibentries_new, format, character(1), "bibtex"), | |
| "```", | |
| "</details>" | |
| ), | |
| collapse = "\n" | |
| ) | |
| gh::gh( | |
| "POST /repos/{gh_repo}/issues/{issue_number}/comments", | |
| gh_repo = "${{ github.repository }}", | |
| issue_number = 3, | |
| body = bibentries_comment | |
| ) | |
| } | |
| shell: Rscript {0} |