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annakrystalliannakrystalli
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Merge pull request #159 from hubverse-org/158/ci-testhub-val
158/ Move testhub config validation to CI
2 parents 246369f + b3b1db5 commit bc38209

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‎.github/workflows/validate-flusight-testhub-config.yaml

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name: Hub Config Validation (R)
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on:
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workflow_dispatch:
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pull_request:
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branches: main
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paths:
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- 'inst/testhubs/flusight/hub-config/**'
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- '!inst/testhubs/flusight/**README**'
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jobs:
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validate-hub-config:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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PR_NUMBER: ${{ github.event.number }}
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HUB_PATH: "inst/testhubs/flusight"
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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install-r: false
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use-public-rspm: true
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extra-repositories: 'https://hubverse-org.r-universe.dev'
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- name: Update R
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run: |
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sudo apt-get update
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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cache: 'always'
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packages: |
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any::hubAdmin
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any::sessioninfo
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- name: Run validations
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id: validate
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run: |
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hub_path <- Sys.getenv("HUB_PATH")
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diff <- file.path(hub_path, "diff.md")
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output <- Sys.getenv("GITHUB_OUTPUT")
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timestamp <- function(outfile) {
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stamp <- format(Sys.time(), usetz = TRUE, tz = "UTC")
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cat(stamp, "\n", file = outfile, sep = "", append = TRUE)
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}
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v <- hubAdmin::validate_hub_config(
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hub_path = hub_path
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)
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# check if there were any failures
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invalid <- any(vapply(v, isFALSE, logical(1)))
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if (invalid) {
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cat("result=false", "\n", file = output, sep = "", append = TRUE)
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# write output to HTML
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tbl <- hubAdmin::view_config_val_errors(v)
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writeLines("## :x: Invalid Configuration\n", diff)
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cat("\nErrors were detected in one or more config files in `hub-config/`. Details about the exact locations of the errors can be found in the table below.\n", file = diff, append = TRUE)
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cat(gt::as_raw_html(tbl), "\n", file = diff, sep = "", append = TRUE)
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timestamp(diff)
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} else {
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cat("result=true", "\n", file = output, sep = "", append = TRUE)
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writeLines(":white_check_mark: Hub correctly configured!\n", diff)
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timestamp(diff)
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}
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shell: Rscript {0}
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- name: "Comment on PR"
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id: comment-diff
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if: ${{ github.event_name != 'workflow_dispatch' }}
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uses: carpentries/actions/comment-diff@main
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with:
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pr: ${{ env.PR_NUMBER }}
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path: ${{ env.HUB_PATH }}/diff.md
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- name: Error on Failure
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if: ${{ steps.validate.outputs.result == 'false' }}
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run: |
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echo "::error title=Invalid Configuration::Errors were detected in one or more config files in 'hub-config/'"
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exit 1
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‎.github/workflows/validate-simple-testhub-config.yaml

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name: Hub Config Validation (R)
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on:
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workflow_dispatch:
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pull_request:
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branches: main
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paths:
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- 'inst/testhubs/simple/hub-config/**'
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- '!inst/testhubs/simple/**README**'
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jobs:
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validate-hub-config:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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PR_NUMBER: ${{ github.event.number }}
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HUB_PATH: "inst/testhubs/simple"
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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install-r: false
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use-public-rspm: true
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extra-repositories: 'https://hubverse-org.r-universe.dev'
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- name: Update R
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run: |
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sudo apt-get update
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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cache: 'always'
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packages: |
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any::hubAdmin
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any::sessioninfo
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- name: Run validations
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id: validate
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run: |
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hub_path <- Sys.getenv("HUB_PATH")
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diff <- file.path(hub_path, "diff.md")
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output <- Sys.getenv("GITHUB_OUTPUT")
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timestamp <- function(outfile) {
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stamp <- format(Sys.time(), usetz = TRUE, tz = "UTC")
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cat(stamp, "\n", file = outfile, sep = "", append = TRUE)
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}
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v <- hubAdmin::validate_hub_config(
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hub_path = hub_path
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)
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# check if there were any failures
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invalid <- any(vapply(v, isFALSE, logical(1)))
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if (invalid) {
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cat("result=false", "\n", file = output, sep = "", append = TRUE)
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# write output to HTML
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tbl <- hubAdmin::view_config_val_errors(v)
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writeLines("## :x: Invalid Configuration\n", diff)
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cat("\nErrors were detected in one or more config files in `hub-config/`. Details about the exact locations of the errors can be found in the table below.\n", file = diff, append = TRUE)
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cat(gt::as_raw_html(tbl), "\n", file = diff, sep = "", append = TRUE)
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timestamp(diff)
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} else {
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cat("result=true", "\n", file = output, sep = "", append = TRUE)
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writeLines(":white_check_mark: Hub correctly configured!\n", diff)
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timestamp(diff)
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}
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shell: Rscript {0}
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- name: "Comment on PR"
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id: comment-diff
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if: ${{ github.event_name != 'workflow_dispatch' }}
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uses: carpentries/actions/comment-diff@main
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with:
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pr: ${{ env.PR_NUMBER }}
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path: ${{ env.HUB_PATH }}/diff.md
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- name: Error on Failure
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if: ${{ steps.validate.outputs.result == 'false' }}
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run: |
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echo "::error title=Invalid Configuration::Errors were detected in one or more config files in 'hub-config/'"
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exit 1
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‎DESCRIPTION

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Package: hubUtils
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Title: Utility Functions for Infectious Disease Modeling Hubs
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Version: 0.1.0
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Version: 0.1.1
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Authors@R: c(
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person("Anna", "Krystalli", , "[email protected]", role = c("aut", "cre"),
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comment = c(ORCID = "0000-0002-2378-4915")),
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utils
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Suggests:
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dplyr,
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hubAdmin,
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hubData,
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knitr,
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rmarkdown,
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testthat (>= 3.2.0)
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Additional_repositories: https://hubverse-org.r-universe.dev/
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Remotes:
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hubverse-org/hubAdmin,
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hubverse-org/hubData
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Config/Needs/website: hubverse-org/hubStyle
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Config/testthat/edition: 3

‎NEWS.md

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# hubUtils 0.1.1
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* Remove `hubAdmin` Suggests dependency by moving test hub configuration validation to CI
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(resolved: @annakrystalli, https://github.com/hubverse-org/hubUtils/issues/158)
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# hubUtils 0.1.0
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* Add `read_config_file()` helper function to read a JSON config file from a file path.

‎tests/testthat/test-validate-inst-hubs.R

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