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Merge pull request #17 from hrlai/olivuntu-zip-zinb
Refactor ZIP and ZINB
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| 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 | ||
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| permissions: read-all | ||
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| jobs: | ||
| test-coverage: | ||
| runs-on: macOS-latest | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
|
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| - uses: r-lib/actions/setup-r@v1 | ||
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| - uses: r-lib/actions/setup-pandoc@v1 | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
|
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| - name: Query dependencies | ||
| run: | | ||
| install.packages('remotes') | ||
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
| writeLines(sprintf("R-%i.%i", getRversion()$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 | ||
|
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| - 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} | ||
|
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| - 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} | ||
|
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| # 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} | ||
|
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| - 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: ${{ secrets.CODECOV_TOKEN }} | ||
|
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| - name: Show testthat output | ||
| if: always() | ||
| run: | | ||
| Rscript -e 'tensorflow::tf_config()' | ||
| Rscript -e 'tensorflow::tf_version()' | ||
| Rscript -e 'reticulate::py_module_available("tensorflow_probability")' | ||
| Rscript -e 'reticulate::py_config()' | ||
| ### | ||
| ## -------------------------------------------------------------------- | ||
| find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true | ||
| shell: bash | ||
|
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| - 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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,8 @@ | ||
| # Generated by roxygen2: do not edit by hand | ||
|
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| export(zero_inflated_negative_binomial) | ||
| export(zero_inflated_poisson) | ||
| importFrom(R6,R6Class) | ||
| importFrom(greta,.internals) | ||
| importFrom(tensorflow,tf) | ||
| importFrom(utils,globalVariables) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| #' @title Extends Distributions Available in the `greta` package | ||
| #' @name greta.distributions | ||
| #' | ||
| #' @description describe your package here, you can re-use the text from DESCRIPTION | ||
| #' @keywords internal | ||
| "_PACKAGE" | ||
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| ## usethis namespace: start | ||
| #' @importFrom tensorflow tf | ||
| #' @importFrom greta .internals | ||
| #' @importFrom R6 R6Class | ||
| #' @importFrom utils globalVariables | ||
| ## usethis namespace: end | ||
| NULL | ||
|
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| globalVariables( | ||
| c( | ||
| "as_2d_array", | ||
| "as_data", | ||
| "calculate", | ||
| "initials", | ||
| "prep_initials", | ||
| "variable" | ||
| ) | ||
| ) |
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