generated from greta-dev/greta.template
-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
various changes from merging into main
Merge commit '9b72b8a0cee89664e0944e22dd7155b05a6bda7e' #Conflicts: # NAMESPACE # R/package.R
- Loading branch information
Showing
23 changed files
with
949 additions
and
297 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -6,3 +6,6 @@ | |
| ^codecov\.yml$ | ||
| ^CODE_OF_CONDUCT\.md$ | ||
| ^\.github$ | ||
| ^_pkgdown\.yml$ | ||
| ^docs$ | ||
| ^pkgdown$ | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,49 @@ | ||
| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | ||
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | ||
| on: | ||
| push: | ||
| branches: [main, master] | ||
| pull_request: | ||
| release: | ||
| types: [published] | ||
| workflow_dispatch: | ||
|
|
||
| name: pkgdown.yaml | ||
|
|
||
| permissions: read-all | ||
|
|
||
| jobs: | ||
| pkgdown: | ||
| runs-on: ubuntu-latest | ||
| # Only restrict concurrency for non-PR jobs | ||
| concurrency: | ||
| group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| permissions: | ||
| contents: write | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
|
|
||
| - uses: r-lib/actions/setup-pandoc@v2 | ||
|
|
||
| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
|
|
||
| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: any::pkgdown, local::. | ||
| needs: website | ||
|
|
||
| - name: Build site | ||
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Deploy to GitHub pages 🚀 | ||
| if: github.event_name != 'pull_request' | ||
| uses: JamesIves/[email protected] | ||
| with: | ||
| clean: false | ||
| branch: gh-pages | ||
| folder: docs |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,76 +1,89 @@ | ||
| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | ||
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| - master | ||
| branches: [main, master] | ||
| pull_request: | ||
| branches: | ||
| - main | ||
| - master | ||
| branches: [main, master] | ||
|
|
||
| name: test-coverage | ||
| name: test-coverage.yaml | ||
|
|
||
| permissions: read-all | ||
|
|
||
| jobs: | ||
| test-coverage: | ||
| runs-on: macOS-latest | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
|
|
||
| - uses: r-lib/actions/setup-r@v1 | ||
|
|
||
| - uses: r-lib/actions/setup-pandoc@v1 | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
|
|
||
| - name: Query dependencies | ||
| run: | | ||
| install.packages('remotes') | ||
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | ||
| shell: Rscript {0} | ||
| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
|
|
||
| - name: Restore R package cache | ||
| uses: actions/cache@v2 | ||
| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| path: ${{ env.R_LIBS_USER }} | ||
| key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- | ||
| extra-packages: | | ||
| any::covr | ||
| any::xml2 | ||
| any::remotes | ||
| needs: coverage | ||
|
|
||
| - name: Install dependencies | ||
| - name: Install system dependencies | ||
| if: runner.os == 'Linux' | ||
| shell: bash | ||
| run: | | ||
| install.packages(c("remotes")) | ||
| remotes::install_deps(dependencies = TRUE) | ||
| remotes::install_cran("covr") | ||
| . /etc/os-release | ||
| while read -r cmd | ||
| do | ||
| echo "$cmd" | ||
| sudo $cmd | ||
| done < <(Rscript -e "writeLines(remotes::system_requirements('$ID-$VERSION_ID'))") | ||
| - name: Install package + deps | ||
| run: remotes::install_local(dependencies = TRUE, force = TRUE) | ||
| shell: Rscript {0} | ||
|
|
||
| ### | ||
| - name: Install Miniconda | ||
| - name: Install greta deps | ||
| run: | | ||
| install.packages(c("remotes", "keras")) | ||
| reticulate::install_miniconda() | ||
| library(greta) | ||
| greta::install_greta_deps(timeout = 50) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Set options for conda binary for macOS | ||
| if: runner.os == 'macOS' | ||
| run: | | ||
| echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile | ||
| - name: Situation Report on greta install | ||
| run: greta::greta_sitrep() | ||
| shell: Rscript {0} | ||
|
|
||
| # Perhaps here is where we can install / change the environment that we are | ||
| # installing into? Can we call our own greta install functions here? | ||
| - name: Install TensorFlow | ||
| - name: Test coverage | ||
| run: | | ||
| reticulate::conda_create(envname = "greta-env",python_version = "3.7") | ||
| reticulate::conda_install(envname = "greta-env", packages = c("numpy==1.16.4", "tensorflow-probability==0.7.0", "tensorflow==1.14.0")) | ||
| cov <- covr::package_coverage( | ||
| quiet = FALSE, | ||
| clean = FALSE, | ||
| install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | ||
| ) | ||
| covr::to_cobertura(cov) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Python + TF details | ||
| - uses: codecov/codecov-action@v4 | ||
| with: | ||
| fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} | ||
| file: ./cobertura.xml | ||
| plugin: noop | ||
| disable_search: true | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
|
|
||
| - name: Show testthat output | ||
| if: always() | ||
| run: | | ||
| Rscript -e 'tensorflow::tf_config()' | ||
| Rscript -e 'tensorflow::tf_version()' | ||
| Rscript -e 'reticulate::py_module_available("tensorflow_probability")' | ||
| Rscript -e 'reticulate::py_config()' | ||
| ### | ||
| ## -------------------------------------------------------------------- | ||
| find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true | ||
| shell: bash | ||
|
|
||
| - name: Test coverage | ||
| run: covr::codecov() | ||
| shell: Rscript {0} | ||
| - name: Upload test results | ||
| if: failure() | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: coverage-test-failures | ||
| path: ${{ runner.temp }}/package |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| .Rhistory | ||
| .RData | ||
| .Rproj.user | ||
| docs |
Oops, something went wrong.