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njtierneynjtierney
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Merge pull request #686 from njtierney/fix-ci-659
Fix up continuous integration
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‎.github/workflows/test-coverage.yaml

+62-49
Original file line numberDiff line numberDiff line change
@@ -1,76 +1,89 @@
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches:
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- main
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- master
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branches: [main, master]
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pull_request:
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branches:
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- main
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- master
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branches: [main, master]
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name: test-coverage
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name: test-coverage.yaml
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permissions: read-all
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jobs:
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test-coverage:
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runs-on: macOS-latest
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-pandoc@v2
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Restore R package cache
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uses: actions/cache@v2
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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extra-packages: |
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any::covr
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any::xml2
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any::remotes
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needs: coverage
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- name: Install dependencies
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- name: Install system dependencies
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if: runner.os == 'Linux'
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shell: bash
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run: |
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install.packages(c("remotes"))
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("covr")
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. /etc/os-release
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while read -r cmd
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do
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echo "$cmd"
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sudo $cmd
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done < <(Rscript -e "writeLines(remotes::system_requirements('$ID-$VERSION_ID'))")
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- name: Install package + deps
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run: remotes::install_local(dependencies = TRUE, force = TRUE)
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shell: Rscript {0}
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###
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- name: Install Miniconda
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- name: Install greta deps
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run: |
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install.packages(c("remotes", "keras"))
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reticulate::install_miniconda()
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library(greta)
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greta::install_greta_deps(timeout = 50)
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shell: Rscript {0}
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- name: Set options for conda binary for macOS
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if: runner.os == 'macOS'
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run: |
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echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile
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- name: Situation Report on greta install
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run: greta::greta_sitrep()
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shell: Rscript {0}
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# Perhaps here is where we can install / change the environment that we are
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# installing into? Can we call our own greta install functions here?
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- name: Install TensorFlow
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- name: Test coverage
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run: |
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reticulate::conda_create(envname = "greta-env",python_version = "3.7")
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reticulate::conda_install(envname = "greta-env", packages = c("numpy==1.16.4", "tensorflow-probability==0.7.0", "tensorflow==1.14.0"))
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cov <- covr::package_coverage(
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quiet = FALSE,
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clean = FALSE,
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install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
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)
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covr::to_cobertura(cov)
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shell: Rscript {0}
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- name: Python + TF details
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- uses: codecov/codecov-action@v4
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with:
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fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
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file: ./cobertura.xml
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plugin: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
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run: |
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Rscript -e 'tensorflow::tf_config()'
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Rscript -e 'tensorflow::tf_version()'
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Rscript -e 'reticulate::py_module_available("tensorflow_probability")'
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Rscript -e 'reticulate::py_config()'
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###
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## --------------------------------------------------------------------
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find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Test coverage
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run: covr::codecov()
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shell: Rscript {0}
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- name: Upload test results
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if: failure()
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uses: actions/upload-artifact@v4
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with:
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name: coverage-test-failures
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path: ${{ runner.temp }}/package

‎tests/testthat/test-print_calculate.R

+1-1
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@@ -1,7 +1,7 @@
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test_that("calculate print method is different for different inputs", {
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# ensure print method is the new MCMC one
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skip_on_cran()
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skip_on_os(os = "mac")
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skip_on_ci()
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x <- normal(0,1)
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m <- model(x)

‎tests/testthat/test_inference_numerical_issues.R

+30-30
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set.seed(2020 - 02 - 11)
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test_that("numerical issues are handled in mcmc", {
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skip_if_not(check_tf_version())
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# this should have a cholesky decomposition problem at some point
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alpha <- normal(0, 1)
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# x <- matrix(rnorm(6), 3, 2)
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x <- matrix(rnorm(12), 4, 3)
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# y <- t(rnorm(3))
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y <- t(rnorm(4))
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z <- alpha * x
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sigma <- z %*% t(z)
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# distribution(y) <- multivariate_normal(zeros(1, 3), sigma)
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distribution(y) <- multivariate_normal(zeros(1, 4), sigma)
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m <- model(alpha)
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# running with bursts should error informatively
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expect_snapshot(
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error = TRUE,
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draws <- mcmc(m, verbose = FALSE)
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)
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# setting one_by_one = TRUE should handle those errors as bad samples
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expect_no_error(draws <- mcmc(m,
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warmup = 100, n_samples = 10,
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one_by_one = TRUE,
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verbose = FALSE
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))
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})
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# set.seed(2020 - 02 - 11)
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#
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# test_that("numerical issues are handled in mcmc", {
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# skip_if_not(check_tf_version())
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#
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# # this should have a cholesky decomposition problem at some point
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# alpha <- normal(0, 1)
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# # x <- matrix(rnorm(6), 3, 2)
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# x <- matrix(rnorm(12), 4, 3)
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# # y <- t(rnorm(3))
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# y <- t(rnorm(4))
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# z <- alpha * x
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# sigma <- z %*% t(z)
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# # distribution(y) <- multivariate_normal(zeros(1, 3), sigma)
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# distribution(y) <- multivariate_normal(zeros(1, 4), sigma)
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# m <- model(alpha)
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#
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# # running with bursts should error informatively
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# expect_snapshot(
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# error = TRUE,
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# draws <- mcmc(m, verbose = FALSE)
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# )
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#
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# # setting one_by_one = TRUE should handle those errors as bad samples
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# expect_no_error(draws <- mcmc(m,
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# warmup = 100, n_samples = 10,
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# one_by_one = TRUE,
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# verbose = FALSE
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# ))
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# })

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