From 2a835ba91ad916c784a3d7ff72fc802e9df602ae Mon Sep 17 00:00:00 2001 From: gitHub Actions Date: Tue, 30 Sep 2025 16:58:18 +0000 Subject: [PATCH 01/18] Add the test coverage.html to test_coverage directory --- .../NEONprocIS.stat-coverage.html | 7731 +++++++++++++++++ 1 file changed, 7731 insertions(+) create mode 100644 pack/test_coverage/NEONprocIS.stat-coverage.html diff --git a/pack/test_coverage/NEONprocIS.stat-coverage.html b/pack/test_coverage/NEONprocIS.stat-coverage.html new file mode 100644 index 000000000..1855819af --- /dev/null +++ b/pack/test_coverage/NEONprocIS.stat-coverage.html @@ -0,0 +1,7731 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + +
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NEONprocIS.stat coverage - 97.14%

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NEONprocIS.wq coverage - 95.85%

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+ + From 1790af7ff587389f3fccd626856b9a69e8eebceb Mon Sep 17 00:00:00 2001 From: Ivan Date: Thu, 30 Oct 2025 17:29:08 -0600 Subject: [PATCH 03/18] Updated file 'NEON-IS-data-processing.github/actions/run-IS-unit-tests/action.yml' to generate test report --- .github/actions/run-IS-unit-tests/action.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/actions/run-IS-unit-tests/action.yml b/.github/actions/run-IS-unit-tests/action.yml index 0016fae47..b5478ddea 100644 --- a/.github/actions/run-IS-unit-tests/action.yml +++ b/.github/actions/run-IS-unit-tests/action.yml @@ -49,6 +49,9 @@ runs: packages: | fs devtools + testthat + covr + report rapportools arrow@19.0.1.1 dplyr@1.1.3 @@ -84,6 +87,9 @@ runs: library("NEONprocIS.cal") } # + library(testthat) + library(covr) + library(report) library(dplyr) library(arrow) library(jsonlite) From 56161a15c2469dab519612b26d3e8be9ddefd522 Mon Sep 17 00:00:00 2001 From: Justin Wright Date: Fri, 31 Oct 2025 13:50:31 -0600 Subject: [PATCH 04/18] Test cleaned up test workflow --- .github/actions/run-IS-unit-tests/action.yml | 59 ++++--------------- .github/workflows/IS_pack_base_unit_tests.yml | 59 ++----------------- 2 files changed, 14 insertions(+), 104 deletions(-) diff --git a/.github/actions/run-IS-unit-tests/action.yml b/.github/actions/run-IS-unit-tests/action.yml index b5478ddea..b54485ff1 100644 --- a/.github/actions/run-IS-unit-tests/action.yml +++ b/.github/actions/run-IS-unit-tests/action.yml @@ -3,41 +3,7 @@ description: "Run R unit tests on IS package" runs: using: "composite" - steps: - - id: "auth" - uses: "google-github-actions/auth@v2" - with: - workload_identity_provider: ${{ env.GCP_PROVIDER }} - service_account: ${{ env.GCP_SERVICE_ACCOUNT }} - # - - name: "Set up Cloud SDK" - uses: "google-github-actions/setup-gcloud@v2" - # - - name: "Docker auth" - shell: bash - run: gcloud auth configure-docker ${{ env.GCP_ARTIFACT_HOST }} --quiet - # - # setup-buildx-action for Docker - - name: Setup Docker buildx - uses: docker/setup-buildx-action@v3 - # - # Login to github registry - - name: Log into github registry ${{ env.GHCR_REGISTRY }} - uses: docker/login-action@v3 - with: - registry: ${{ env.GHCR_REGISTRY }} - username: ${{ github.actor }} - password: ${{ env.GITHUB_TOKEN }} - # - # Build and push Docker image with Buildx (don't push on PR) with multiple tags - # https://github.com/docker/build-push-action - - name: Build Docker image - id: build - uses: docker/build-push-action@v5 - with: - context: ./ - file: ${{ env.MODULE_PATH }}/Dockerfile - + steps: - name: Set up R uses: r-lib/actions/setup-r@v2 with: @@ -72,9 +38,6 @@ runs: shell: bash run: sudo apt install libavro23 - - name: check out repository - uses: actions/checkout@v3 - - name: Run ${{ env.MODULE_NAME }} unit test coverage using covr package shell: Rscript {0} run: | @@ -107,7 +70,7 @@ runs: covr::report(cov, file="${{ env.MODULE_NAME }}-coverage.html") # Generates a Cobertura XML file covr::to_cobertura(cov, filename = "test-summary.xml") - # + # Generate Markdown Summary - name: Code Coverage Summary Report uses: irongut/CodeCoverageSummary@v1.3.0 @@ -117,8 +80,8 @@ runs: hide_complexity: false format: markdown output: both - # - # # Display in Job Summary + + # Display in Job Summary - name: Add coverage summary to job summary shell: bash run: cat code-coverage-results.md >> $GITHUB_STEP_SUMMARY @@ -130,7 +93,7 @@ runs: file: ./test-summary.xml flags: unittests name: codecov-umbrella - # + # Uploads the coverage.html file as a workflow artifact # Find the r-coverage-report artifact on the workflow run details page. # Download the artifact and open the coverage.html file in your browser @@ -150,13 +113,11 @@ runs: IFS=$'\n\t' git config --local user.email "actions@github.com" git config --local user.name "gitHub Actions" - git config push.default current - git pull - git add "${{ env.MODULE_NAME }}-coverage.html" echo "Attempting to create a test_coverage directory" mkdir -p pack/test_coverage echo "Directory creation successful (or already existed)." - git mv "${{ env.MODULE_NAME }}-coverage.html" ./pack/test_coverage/ - git commit -m "Add the test coverage.html to test_coverage directory" || echo "No coveage added" - git push origin || echo "No changes to commit" - + mv "${{ env.MODULE_NAME }}-coverage.html" ./pack/test_coverage/ + git add "./pack/test_coverage/${{ env.MODULE_NAME }}-coverage.html" + git commit -m "Add the test coverage.html to test_coverage directory" || echo "No coverage added" + git status +# git push origin || echo "No changes to commit" diff --git a/.github/workflows/IS_pack_base_unit_tests.yml b/.github/workflows/IS_pack_base_unit_tests.yml index d703e831d..ee6b32a75 100644 --- a/.github/workflows/IS_pack_base_unit_tests.yml +++ b/.github/workflows/IS_pack_base_unit_tests.yml @@ -10,73 +10,22 @@ on: workflow_dispatch: {} # Allows trigger of workflow from web interface env: - GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }} - # Use github and google registries - GHCR_REGISTRY: ghcr.io - # GHCR_NS, i.e, NEONSciene, in lowercase - # GHCR_NS: ${{ github.repository_owner }} - GHCR_NS: ${{ vars.SHARED_WIF_REPO }} - GCP_ARTIFACT_HOST: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev - GCP_REGISTRY: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev/${{ vars.SHARED_WIF_PROJECT }}/${{ vars.SHARED_WIF_REPO }} - GCP_PROVIDER: ${{ vars.SHARED_WIF_PROVIDER }} - GCP_SERVICE_ACCOUNT: ${{ vars.SHARED_WIF_SERVICE_ACCOUNT }} - # Use docker.io for Docker Hub if empty - REGISTRY: ghcr.io - REPO_NAME: neon-is-data-processing # IS package name MODULE_BASE_NAME: NEONprocIS.base MODULE_BASE_PATH: ./pack/NEONprocIS.base MODULE_NAME: NEONprocIS.base MODULE_PATH: ./pack/NEONprocIS.base - IMAGE_NAME: neon-is-pack-base-r jobs: run-unit-test: runs-on: ubuntu-latest permissions: - contents: 'write' - security-events: write - packages: write - id-token: 'write' - pull-requests: 'write' + contents: write + pull-requests: write steps: - - name: "Checkout" - uses: "actions/checkout@v4.1.4" - with: - ref: 'master' - fetch-depth: '0' - - # Note: must clone other repos AFTER checking out the repo where the action is run from. - # Otherwise, previously cloned repos are removed. - - name: "Clone avro" - uses: actions/checkout@v4 - with: - # Repository name with owner. For example, actions/checkout - # Default: ${{ github.repository }} - repository: 'BattelleEcology/avro' - - # The branch, tag or SHA to checkout. When checking out the repository that - # triggered a workflow, this defaults to the reference or SHA for that event. - # Otherwise, uses the default branch. - ref: 'release-1.10.0' - #fetch-depth: '0' - - # SSH key used to fetch the repository. The SSH key is configured with the local - # git config, which enables your scripts to run authenticated git commands. The - # post-job step removes the SSH key. - # - # We recommend using a service account with the least permissions necessary. - # - # [Learn more about creating and using encrypted secrets](https://help.github.com/en/actions/automating-your-workflow-with-github-actions/creating-and-using-encrypted-secrets) - # Note: when generating the key, use the following: ssh-keygen -t ed25519 -C "git@github.com" - ssh-key: ${{ secrets.BE_GITHUB_KEY }} - - # Relative path under $GITHUB_WORKSPACE to place the repository - path: './avro' - - - name: Get short SHA - run: echo "short_sha=$(git rev-parse --short HEAD)" >> $GITHUB_ENV + - name: Checkout + uses: actions/checkout@v5 - name: Run IS ${{ env.MODULE_NAME }} unit tests uses: ./.github/actions/run-IS-unit-tests From e4311eb46775e14b0c1d3ef792b5a4e20d252775 Mon Sep 17 00:00:00 2001 From: Justin Wright Date: Fri, 31 Oct 2025 14:09:32 -0600 Subject: [PATCH 05/18] Remove report package --- .github/actions/run-IS-unit-tests/action.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/actions/run-IS-unit-tests/action.yml b/.github/actions/run-IS-unit-tests/action.yml index b54485ff1..dd4634500 100644 --- a/.github/actions/run-IS-unit-tests/action.yml +++ b/.github/actions/run-IS-unit-tests/action.yml @@ -17,13 +17,11 @@ runs: devtools testthat covr - report rapportools arrow@19.0.1.1 dplyr@1.1.3 jsonlite@1.8.7 extra-packages: | - any::covr any::xml2 needs: coverage cache: always @@ -52,7 +50,6 @@ runs: # library(testthat) library(covr) - library(report) library(dplyr) library(arrow) library(jsonlite) From f3d65f296a482fee77b4ce663ee28c0f8e005e6b Mon Sep 17 00:00:00 2001 From: Justin Wright Date: Mon, 3 Nov 2025 09:29:11 -0700 Subject: [PATCH 06/18] Tweak coverage step --- .github/actions/run-IS-unit-tests/action.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/actions/run-IS-unit-tests/action.yml b/.github/actions/run-IS-unit-tests/action.yml index dd4634500..46e83d19c 100644 --- a/.github/actions/run-IS-unit-tests/action.yml +++ b/.github/actions/run-IS-unit-tests/action.yml @@ -115,6 +115,7 @@ runs: echo "Directory creation successful (or already existed)." mv "${{ env.MODULE_NAME }}-coverage.html" ./pack/test_coverage/ git add "./pack/test_coverage/${{ env.MODULE_NAME }}-coverage.html" - git commit -m "Add the test coverage.html to test_coverage directory" || echo "No coverage added" + git commit -m "Add the test coverage.html to test_coverage directory" + git log git status # git push origin || echo "No changes to commit" From 5be0d34a60728b533b35fe2784df9ba9b86b779f Mon Sep 17 00:00:00 2001 From: Justin Wright Date: Mon, 3 Nov 2025 10:03:37 -0700 Subject: [PATCH 07/18] Tweak git coverage report step --- .github/actions/run-IS-unit-tests/action.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/actions/run-IS-unit-tests/action.yml b/.github/actions/run-IS-unit-tests/action.yml index 46e83d19c..064b9b53a 100644 --- a/.github/actions/run-IS-unit-tests/action.yml +++ b/.github/actions/run-IS-unit-tests/action.yml @@ -115,7 +115,5 @@ runs: echo "Directory creation successful (or already existed)." mv "${{ env.MODULE_NAME }}-coverage.html" ./pack/test_coverage/ git add "./pack/test_coverage/${{ env.MODULE_NAME }}-coverage.html" - git commit -m "Add the test coverage.html to test_coverage directory" - git log - git status -# git push origin || echo "No changes to commit" + git commit -m "Add ${{ env.MODULE_NAME }}-coverage.html to test_coverage directory" + git push From d6eafadf17c4c09961463f2e1d7146bd3bfd0d9e Mon Sep 17 00:00:00 2001 From: gitHub Actions Date: Mon, 3 Nov 2025 17:16:25 +0000 Subject: [PATCH 08/18] Add NEONprocIS.base-coverage.html to test_coverage directory --- pack/test_coverage/NEONprocIS.base-coverage.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pack/test_coverage/NEONprocIS.base-coverage.html b/pack/test_coverage/NEONprocIS.base-coverage.html index 5a0dbb15a..b5893bf65 100644 --- a/pack/test_coverage/NEONprocIS.base-coverage.html +++ b/pack/test_coverage/NEONprocIS.base-coverage.html @@ -107,8 +107,8 @@

NEONprocIS.base coverage - 94.96%

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From 23fd540a4985427dd9131caa65706e27d2ed3c86 Mon Sep 17 00:00:00 2001 From: Justin Wright Date: Mon, 3 Nov 2025 10:35:44 -0700 Subject: [PATCH 09/18] Update unit test workflows --- .github/actions/run-IS-unit-tests/action.yml | 7 +- .github/workflows/IS_pack_base_unit_tests.yml | 7 +- .github/workflows/IS_pack_cal_unit_tests.yml | 66 ++---------------- .github/workflows/IS_pack_pub_unit_tests.yml | 67 ++----------------- .github/workflows/IS_pack_qaqc_unit_tests.yml | 66 ++---------------- .github/workflows/IS_pack_stat_unit_tests.yml | 66 ++---------------- .github/workflows/IS_pack_wq_unit_tests.yml | 66 ++---------------- 7 files changed, 36 insertions(+), 309 deletions(-) diff --git a/.github/actions/run-IS-unit-tests/action.yml b/.github/actions/run-IS-unit-tests/action.yml index 064b9b53a..66ae200a7 100644 --- a/.github/actions/run-IS-unit-tests/action.yml +++ b/.github/actions/run-IS-unit-tests/action.yml @@ -83,7 +83,8 @@ runs: shell: bash run: cat code-coverage-results.md >> $GITHUB_STEP_SUMMARY - # Upload Coverage Report + # Upload Coverage Report to codecov.io + # - Currently fails due to missing token - name: Upload coverage to Codecov uses: codecov/codecov-action@v3 with: @@ -95,14 +96,14 @@ runs: # Find the r-coverage-report artifact on the workflow run details page. # Download the artifact and open the coverage.html file in your browser # to explore the detailed test coverage report, including line-by-line coverage information. - - name: Upload coverage.html artifact uses: actions/upload-artifact@v4 with: name: r-coverage-report path: ${{ env.MODULE_NAME }}-coverage.html retention-days: 1 # Adjust retention days as needed - + + # Commit HTML coverage report to test_coverage directory in repo - name: Add/update the test coverage.html to ./pack/test_coverage/ shell: bash run: | diff --git a/.github/workflows/IS_pack_base_unit_tests.yml b/.github/workflows/IS_pack_base_unit_tests.yml index ee6b32a75..2eebca3a7 100644 --- a/.github/workflows/IS_pack_base_unit_tests.yml +++ b/.github/workflows/IS_pack_base_unit_tests.yml @@ -3,10 +3,9 @@ name: "Run IS base package unit tests" on: push: branches: - - 'master' + - master paths: - - 'pack/NEONprocIS.base/**' - + - pack/NEONprocIS.base/** workflow_dispatch: {} # Allows trigger of workflow from web interface env: @@ -21,8 +20,6 @@ jobs: runs-on: ubuntu-latest permissions: contents: write - pull-requests: write - steps: - name: Checkout uses: actions/checkout@v5 diff --git a/.github/workflows/IS_pack_cal_unit_tests.yml b/.github/workflows/IS_pack_cal_unit_tests.yml index 5c57deb51..6af61747b 100644 --- a/.github/workflows/IS_pack_cal_unit_tests.yml +++ b/.github/workflows/IS_pack_cal_unit_tests.yml @@ -3,80 +3,26 @@ name: "Run IS cal package unit tests" on: push: branches: - - 'master' + - master paths: - - 'pack/NEONprocIS.cal/**' - + - pack/NEONprocIS.cal/** workflow_dispatch: {} # Allows trigger of workflow from web interface env: - GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }} - # Use github and google registries - GHCR_REGISTRY: ghcr.io - # GHCR_NS, i.e, NEONSciene, in lowercase - # GHCR_NS: ${{ github.repository_owner }} - GHCR_NS: ${{ vars.SHARED_WIF_REPO }} - GCP_ARTIFACT_HOST: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev - GCP_REGISTRY: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev/${{ vars.SHARED_WIF_PROJECT }}/${{ vars.SHARED_WIF_REPO }} - GCP_PROVIDER: ${{ vars.SHARED_WIF_PROVIDER }} - GCP_SERVICE_ACCOUNT: ${{ vars.SHARED_WIF_SERVICE_ACCOUNT }} - # Use docker.io for Docker Hub if empty - REGISTRY: ghcr.io - REPO_NAME: neon-is-data-processing # IS package name MODULE_BASE_NAME: NEONprocIS.base MODULE_BASE_PATH: ./pack/NEONprocIS.base - MODULE_PATH: ./pack/NEONprocIS.cal MODULE_NAME: NEONprocIS.cal - IMAGE_NAME: neon-is-pack-cal-r + MODULE_PATH: ./pack/NEONprocIS.cal jobs: run-unit-test: runs-on: ubuntu-latest permissions: - contents: 'write' - security-events: write - packages: write - id-token: 'write' - pull-requests: 'write' - + contents: write steps: - - name: "Checkout" - uses: "actions/checkout@v4.1.4" - with: - ref: 'master' - fetch-depth: '0' - - # Note: must clone other repos AFTER checking out the repo where the action is run from. - # Otherwise, previously cloned repos are removed. - - name: "Clone avro" - uses: actions/checkout@v4 - with: - # Repository name with owner. For example, actions/checkout - # Default: ${{ github.repository }} - repository: 'BattelleEcology/avro' - - # The branch, tag or SHA to checkout. When checking out the repository that - # triggered a workflow, this defaults to the reference or SHA for that event. - # Otherwise, uses the default branch. - ref: 'release-1.10.0' - #fetch-depth: '0' - - # SSH key used to fetch the repository. The SSH key is configured with the local - # git config, which enables your scripts to run authenticated git commands. The - # post-job step removes the SSH key. - # - # We recommend using a service account with the least permissions necessary. - # - # [Learn more about creating and using encrypted secrets](https://help.github.com/en/actions/automating-your-workflow-with-github-actions/creating-and-using-encrypted-secrets) - # Note: when generating the key, use the following: ssh-keygen -t ed25519 -C "git@github.com" - ssh-key: ${{ secrets.BE_GITHUB_KEY }} - - # Relative path under $GITHUB_WORKSPACE to place the repository - path: './avro' - - - name: Get short SHA - run: echo "short_sha=$(git rev-parse --short HEAD)" >> $GITHUB_ENV + - name: Checkout + uses: actions/checkout@v5 - name: Run IS ${{ env.MODULE_NAME }} unit tests uses: ./.github/actions/run-IS-unit-tests diff --git a/.github/workflows/IS_pack_pub_unit_tests.yml b/.github/workflows/IS_pack_pub_unit_tests.yml index ee3afab56..efea861e1 100644 --- a/.github/workflows/IS_pack_pub_unit_tests.yml +++ b/.github/workflows/IS_pack_pub_unit_tests.yml @@ -3,81 +3,26 @@ name: "Run IS pub package unit tests" on: push: branches: - - 'master' + - master paths: - - 'pack/NEONprocIS.pub/**' - + - pack/NEONprocIS.pub/** workflow_dispatch: {} # Allows trigger of workflow from web interface env: - GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }} - # Use github and google registries - GHCR_REGISTRY: ghcr.io - # GHCR_NS, i.e, NEONSciene, in lowercase - # GHCR_NS: ${{ github.repository_owner }} - GHCR_NS: ${{ vars.SHARED_WIF_REPO }} - GCP_ARTIFACT_HOST: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev - GCP_REGISTRY: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev/${{ vars.SHARED_WIF_PROJECT }}/${{ vars.SHARED_WIF_REPO }} - GCP_PROVIDER: ${{ vars.SHARED_WIF_PROVIDER }} - GCP_SERVICE_ACCOUNT: ${{ vars.SHARED_WIF_SERVICE_ACCOUNT }} - # Use docker.io for Docker Hub if empty - REGISTRY: ghcr.io - REPO_NAME: neon-is-data-processing # IS package name MODULE_BASE_NAME: NEONprocIS.base MODULE_BASE_PATH: ./pack/NEONprocIS.base - MODULE_PATH: ./pack/NEONprocIS.pub MODULE_NAME: NEONprocIS.pub - IMAGE_NAME: neon-is-pack-pub-r + MODULE_PATH: ./pack/NEONprocIS.pub jobs: run-unit-test: runs-on: ubuntu-latest permissions: - contents: 'write' - security-events: write - packages: write - id-token: 'write' - pull-requests: 'write' - + contents: write steps: - - name: "Checkout" - uses: "actions/checkout@v4.1.4" - with: - ref: 'master' - fetch-depth: '0' - - # Note: must clone other repos AFTER checking out the repo where the action is run from. - # Otherwise, previously cloned repos are removed. - - name: "Clone avro" - uses: actions/checkout@v4 - with: - # Repository name with owner. For example, actions/checkout - # Default: ${{ github.repository }} - repository: 'BattelleEcology/avro' - - # The branch, tag or SHA to checkout. When checking out the repository that - # triggered a workflow, this defaults to the reference or SHA for that event. - # Otherwise, uses the default branch. - ref: 'release-1.10.0' - #fetch-depth: '0' - - # SSH key used to fetch the repository. The SSH key is configured with the local - # git config, which enables your scripts to run authenticated git commands. The - # post-job step removes the SSH key. - # - # We recommend using a service account with the least permissions necessary. - # - # [Learn more about creating and using encrypted secrets](https://help.github.com/en/actions/automating-your-workflow-with-github-actions/creating-and-using-encrypted-secrets) - # Note: when generating the key, use the following: ssh-keygen -t ed25519 -C "git@github.com" - ssh-key: ${{ secrets.BE_GITHUB_KEY }} - - # Relative path under $GITHUB_WORKSPACE to place the repository - path: './avro' - - - name: Get short SHA - run: echo "short_sha=$(git rev-parse --short HEAD)" >> $GITHUB_ENV + - name: Checkout + uses: actions/checkout@v5 - name: Run IS ${{ env.MODULE_NAME }} unit tests uses: ./.github/actions/run-IS-unit-tests - diff --git a/.github/workflows/IS_pack_qaqc_unit_tests.yml b/.github/workflows/IS_pack_qaqc_unit_tests.yml index 2306357a9..7958a8f04 100644 --- a/.github/workflows/IS_pack_qaqc_unit_tests.yml +++ b/.github/workflows/IS_pack_qaqc_unit_tests.yml @@ -3,80 +3,26 @@ name: "Run IS qaqc package unit tests" on: push: branches: - - 'master' + - master paths: - - 'pack/NEONprocIS.qaqc/**' - + - pack/NEONprocIS.qaqc/** workflow_dispatch: {} # Allows trigger of workflow from web interface env: - GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }} - # Use github and google registries - GHCR_REGISTRY: ghcr.io - # GHCR_NS, i.e, NEONSciene, in lowercase - # GHCR_NS: ${{ github.repository_owner }} - GHCR_NS: ${{ vars.SHARED_WIF_REPO }} - GCP_ARTIFACT_HOST: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev - GCP_REGISTRY: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev/${{ vars.SHARED_WIF_PROJECT }}/${{ vars.SHARED_WIF_REPO }} - GCP_PROVIDER: ${{ vars.SHARED_WIF_PROVIDER }} - GCP_SERVICE_ACCOUNT: ${{ vars.SHARED_WIF_SERVICE_ACCOUNT }} - # Use docker.io for Docker Hub if empty - REGISTRY: ghcr.io - REPO_NAME: neon-is-data-processing # IS package name MODULE_BASE_NAME: NEONprocIS.base MODULE_BASE_PATH: ./pack/NEONprocIS.base - MODULE_PATH: ./pack/NEONprocIS.qaqc MODULE_NAME: NEONprocIS.qaqc - IMAGE_NAME: neon-is-pack-qaqc-r + MODULE_PATH: ./pack/NEONprocIS.qaqc jobs: run-unit-test: runs-on: ubuntu-latest permissions: - contents: 'write' - security-events: write - packages: write - id-token: 'write' - pull-requests: 'write' - + contents: write steps: - - name: "Checkout" - uses: "actions/checkout@v4.1.4" - with: - ref: 'master' - fetch-depth: '0' - - # Note: must clone other repos AFTER checking out the repo where the action is run from. - # Otherwise, previously cloned repos are removed. - - name: "Clone avro" - uses: actions/checkout@v4 - with: - # Repository name with owner. For example, actions/checkout - # Default: ${{ github.repository }} - repository: 'BattelleEcology/avro' - - # The branch, tag or SHA to checkout. When checking out the repository that - # triggered a workflow, this defaults to the reference or SHA for that event. - # Otherwise, uses the default branch. - ref: 'release-1.10.0' - #fetch-depth: '0' - - # SSH key used to fetch the repository. The SSH key is configured with the local - # git config, which enables your scripts to run authenticated git commands. The - # post-job step removes the SSH key. - # - # We recommend using a service account with the least permissions necessary. - # - # [Learn more about creating and using encrypted secrets](https://help.github.com/en/actions/automating-your-workflow-with-github-actions/creating-and-using-encrypted-secrets) - # Note: when generating the key, use the following: ssh-keygen -t ed25519 -C "git@github.com" - ssh-key: ${{ secrets.BE_GITHUB_KEY }} - - # Relative path under $GITHUB_WORKSPACE to place the repository - path: './avro' - - # - name: Get short SHA - # run: echo "short_sha=$(git rev-parse --short HEAD)" >> $GITHUB_ENV + - name: Checkout + uses: actions/checkout@v5 - name: Run IS ${{ env.MODULE_NAME }} unit tests uses: ./.github/actions/run-IS-unit-tests diff --git a/.github/workflows/IS_pack_stat_unit_tests.yml b/.github/workflows/IS_pack_stat_unit_tests.yml index ab6a5c2af..3917b97e8 100644 --- a/.github/workflows/IS_pack_stat_unit_tests.yml +++ b/.github/workflows/IS_pack_stat_unit_tests.yml @@ -3,80 +3,26 @@ name: "Run IS stat package unit tests" on: push: branches: - - 'master' + - master paths: - - 'pack/NEONprocIS.stat/**' - + - pack/NEONprocIS.stat/** workflow_dispatch: {} # Allows trigger of workflow from web interface env: - GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }} - # Use github and google registries - GHCR_REGISTRY: ghcr.io - # GHCR_NS, i.e, NEONSciene, in lowercase - # GHCR_NS: ${{ github.repository_owner }} - GHCR_NS: ${{ vars.SHARED_WIF_REPO }} - GCP_ARTIFACT_HOST: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev - GCP_REGISTRY: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev/${{ vars.SHARED_WIF_PROJECT }}/${{ vars.SHARED_WIF_REPO }} - GCP_PROVIDER: ${{ vars.SHARED_WIF_PROVIDER }} - GCP_SERVICE_ACCOUNT: ${{ vars.SHARED_WIF_SERVICE_ACCOUNT }} - # Use docker.io for Docker Hub if empty - REGISTRY: ghcr.io - REPO_NAME: neon-is-data-processing # IS package name MODULE_BASE_NAME: NEONprocIS.base MODULE_BASE_PATH: ./pack/NEONprocIS.base - MODULE_PATH: ./pack/NEONprocIS.stat MODULE_NAME: NEONprocIS.stat - IMAGE_NAME: neon-is-pack-stat-r + MODULE_PATH: ./pack/NEONprocIS.stat jobs: run-unit-test: runs-on: ubuntu-latest permissions: - contents: 'write' - security-events: write - packages: write - id-token: 'write' - pull-requests: 'write' - + contents: write steps: - - name: "Checkout" - uses: "actions/checkout@v4.1.4" - with: - ref: 'master' - fetch-depth: '0' - - # Note: must clone other repos AFTER checking out the repo where the action is run from. - # Otherwise, previously cloned repos are removed. - - name: "Clone avro" - uses: actions/checkout@v4 - with: - # Repository name with owner. For example, actions/checkout - # Default: ${{ github.repository }} - repository: 'BattelleEcology/avro' - - # The branch, tag or SHA to checkout. When checking out the repository that - # triggered a workflow, this defaults to the reference or SHA for that event. - # Otherwise, uses the default branch. - ref: 'release-1.10.0' - #fetch-depth: '0' - - # SSH key used to fetch the repository. The SSH key is configured with the local - # git config, which enables your scripts to run authenticated git commands. The - # post-job step removes the SSH key. - # - # We recommend using a service account with the least permissions necessary. - # - # [Learn more about creating and using encrypted secrets](https://help.github.com/en/actions/automating-your-workflow-with-github-actions/creating-and-using-encrypted-secrets) - # Note: when generating the key, use the following: ssh-keygen -t ed25519 -C "git@github.com" - ssh-key: ${{ secrets.BE_GITHUB_KEY }} - - # Relative path under $GITHUB_WORKSPACE to place the repository - path: './avro' - - - name: Get short SHA - run: echo "short_sha=$(git rev-parse --short HEAD)" >> $GITHUB_ENV + - name: Checkout + uses: actions/checkout@v5 - name: Run IS ${{ env.MODULE_NAME }} unit tests uses: ./.github/actions/run-IS-unit-tests diff --git a/.github/workflows/IS_pack_wq_unit_tests.yml b/.github/workflows/IS_pack_wq_unit_tests.yml index efab415f5..73d33234a 100644 --- a/.github/workflows/IS_pack_wq_unit_tests.yml +++ b/.github/workflows/IS_pack_wq_unit_tests.yml @@ -3,80 +3,26 @@ name: "Run IS wq package unit tests" on: push: branches: - - 'master' + - master paths: - - 'pack/NEONprocIS.wq/**' - + - pack/NEONprocIS.wq/** workflow_dispatch: {} # Allows trigger of workflow from web interface env: - GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }} - # Use github and google registries - GHCR_REGISTRY: ghcr.io - # GHCR_NS, i.e, NEONSciene, in lowercase - # GHCR_NS: ${{ github.repository_owner }} - GHCR_NS: ${{ vars.SHARED_WIF_REPO }} - GCP_ARTIFACT_HOST: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev - GCP_REGISTRY: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev/${{ vars.SHARED_WIF_PROJECT }}/${{ vars.SHARED_WIF_REPO }} - GCP_PROVIDER: ${{ vars.SHARED_WIF_PROVIDER }} - GCP_SERVICE_ACCOUNT: ${{ vars.SHARED_WIF_SERVICE_ACCOUNT }} - # Use docker.io for Docker Hub if empty - REGISTRY: ghcr.io - REPO_NAME: neon-is-data-processing # IS package name MODULE_BASE_NAME: NEONprocIS.base MODULE_BASE_PATH: ./pack/NEONprocIS.base - MODULE_PATH: ./pack/NEONprocIS.wq MODULE_NAME: NEONprocIS.wq - IMAGE_NAME: neon-is-pack-wq-r + MODULE_PATH: ./pack/NEONprocIS.wq jobs: run-unit-test: runs-on: ubuntu-latest permissions: - contents: 'write' - security-events: write - packages: write - id-token: 'write' - pull-requests: 'write' - + contents: write steps: - - name: "Checkout" - uses: "actions/checkout@v4.1.4" - with: - ref: 'master' - fetch-depth: '0' - - # Note: must clone other repos AFTER checking out the repo where the action is run from. - # Otherwise, previously cloned repos are removed. - - name: "Clone avro" - uses: actions/checkout@v4 - with: - # Repository name with owner. For example, actions/checkout - # Default: ${{ github.repository }} - repository: 'BattelleEcology/avro' - - # The branch, tag or SHA to checkout. When checking out the repository that - # triggered a workflow, this defaults to the reference or SHA for that event. - # Otherwise, uses the default branch. - ref: 'release-1.10.0' - #fetch-depth: '0' - - # SSH key used to fetch the repository. The SSH key is configured with the local - # git config, which enables your scripts to run authenticated git commands. The - # post-job step removes the SSH key. - # - # We recommend using a service account with the least permissions necessary. - # - # [Learn more about creating and using encrypted secrets](https://help.github.com/en/actions/automating-your-workflow-with-github-actions/creating-and-using-encrypted-secrets) - # Note: when generating the key, use the following: ssh-keygen -t ed25519 -C "git@github.com" - ssh-key: ${{ secrets.BE_GITHUB_KEY }} - - # Relative path under $GITHUB_WORKSPACE to place the repository - path: './avro' - - - name: Get short SHA - run: echo "short_sha=$(git rev-parse --short HEAD)" >> $GITHUB_ENV + - name: Checkout + uses: actions/checkout@v5 - name: Run IS ${{ env.MODULE_NAME }} unit tests uses: ./.github/actions/run-IS-unit-tests From 0f8c99b07e4ee98e4283312b4c260a01ca7ae9d8 Mon Sep 17 00:00:00 2001 From: gitHub Actions Date: Mon, 3 Nov 2025 17:50:56 +0000 Subject: [PATCH 10/18] Add NEONprocIS.stat-coverage.html to test_coverage directory --- pack/test_coverage/NEONprocIS.stat-coverage.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pack/test_coverage/NEONprocIS.stat-coverage.html b/pack/test_coverage/NEONprocIS.stat-coverage.html index 1855819af..46ca0ecd2 100644 --- a/pack/test_coverage/NEONprocIS.stat-coverage.html +++ b/pack/test_coverage/NEONprocIS.stat-coverage.html @@ -107,8 +107,8 @@

NEONprocIS.stat coverage - 97.14%

-
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From dfb8870d3a7e72dda3fcc2db9ae29e56403ccf88 Mon Sep 17 00:00:00 2001 From: gitHub Actions Date: Mon, 3 Nov 2025 18:06:23 +0000 Subject: [PATCH 11/18] Add NEONprocIS.stat-coverage.html to test_coverage directory --- pack/test_coverage/NEONprocIS.stat-coverage.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pack/test_coverage/NEONprocIS.stat-coverage.html b/pack/test_coverage/NEONprocIS.stat-coverage.html index 46ca0ecd2..be5cc0985 100644 --- a/pack/test_coverage/NEONprocIS.stat-coverage.html +++ b/pack/test_coverage/NEONprocIS.stat-coverage.html @@ -107,8 +107,8 @@

NEONprocIS.stat coverage - 97.14%

-
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+
From e672985e8cc2430a5dcd755d09e283de82f6fd04 Mon Sep 17 00:00:00 2001 From: Justin Wright Date: Mon, 3 Nov 2025 11:12:37 -0700 Subject: [PATCH 12/18] Remove commit step and increase artifact retention --- .github/actions/run-IS-unit-tests/action.yml | 30 ++++++++++---------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/.github/actions/run-IS-unit-tests/action.yml b/.github/actions/run-IS-unit-tests/action.yml index 66ae200a7..20a177589 100644 --- a/.github/actions/run-IS-unit-tests/action.yml +++ b/.github/actions/run-IS-unit-tests/action.yml @@ -101,20 +101,20 @@ runs: with: name: r-coverage-report path: ${{ env.MODULE_NAME }}-coverage.html - retention-days: 1 # Adjust retention days as needed + retention-days: 30 # Adjust retention days as needed # Commit HTML coverage report to test_coverage directory in repo - - name: Add/update the test coverage.html to ./pack/test_coverage/ - shell: bash - run: | - set -euo pipefail - IFS=$'\n\t' - git config --local user.email "actions@github.com" - git config --local user.name "gitHub Actions" - echo "Attempting to create a test_coverage directory" - mkdir -p pack/test_coverage - echo "Directory creation successful (or already existed)." - mv "${{ env.MODULE_NAME }}-coverage.html" ./pack/test_coverage/ - git add "./pack/test_coverage/${{ env.MODULE_NAME }}-coverage.html" - git commit -m "Add ${{ env.MODULE_NAME }}-coverage.html to test_coverage directory" - git push + # - name: Add/update the test coverage.html to ./pack/test_coverage/ + # shell: bash + # run: | + # set -euo pipefail + # IFS=$'\n\t' + # git config --local user.email "actions@github.com" + # git config --local user.name "gitHub Actions" + # echo "Attempting to create a test_coverage directory" + # mkdir -p pack/test_coverage + # echo "Directory creation successful (or already existed)." + # mv "${{ env.MODULE_NAME }}-coverage.html" ./pack/test_coverage/ + # git add "./pack/test_coverage/${{ env.MODULE_NAME }}-coverage.html" + # git commit -m "Add ${{ env.MODULE_NAME }}-coverage.html to test_coverage directory" + # git push From a07c4348143a5b4a61967ee64b5ab9730a559f67 Mon Sep 17 00:00:00 2001 From: Justin Wright Date: Mon, 3 Nov 2025 13:32:55 -0700 Subject: [PATCH 13/18] Test without Avro or LIBR_DIR steps --- .github/actions/run-IS-unit-tests/action.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/actions/run-IS-unit-tests/action.yml b/.github/actions/run-IS-unit-tests/action.yml index 20a177589..1b1b578ab 100644 --- a/.github/actions/run-IS-unit-tests/action.yml +++ b/.github/actions/run-IS-unit-tests/action.yml @@ -26,15 +26,15 @@ runs: needs: coverage cache: always - - name: Add libR.so to LD_LIBRARY_PATH - shell: bash - run: | - LIBR_DIR=$(dirname $(find /opt -name "libR.so" | head -n 1)) - echo "LD_LIBRARY_PATH=$LIBR_DIR:$LD_LIBRARY_PATH" >> $GITHUB_ENV + # - name: Add libR.so to LD_LIBRARY_PATH + # shell: bash + # run: | + # LIBR_DIR=$(dirname $(find /opt -name "libR.so" | head -n 1)) + # echo "LD_LIBRARY_PATH=$LIBR_DIR:$LD_LIBRARY_PATH" >> $GITHUB_ENV - - name: Install Avro - shell: bash - run: sudo apt install libavro23 + # - name: Install Avro + # shell: bash + # run: sudo apt install libavro23 - name: Run ${{ env.MODULE_NAME }} unit test coverage using covr package shell: Rscript {0} From ef3b830543e71d6d2bbec32b284410808e781c16 Mon Sep 17 00:00:00 2001 From: Justin Wright Date: Mon, 3 Nov 2025 14:01:33 -0700 Subject: [PATCH 14/18] Test base with Avro install --- .github/actions/run-IS-unit-tests/action.yml | 28 ++++++++----------- .github/workflows/IS_pack_base_unit_tests.yml | 3 ++ 2 files changed, 15 insertions(+), 16 deletions(-) diff --git a/.github/actions/run-IS-unit-tests/action.yml b/.github/actions/run-IS-unit-tests/action.yml index 1b1b578ab..93015fdd8 100644 --- a/.github/actions/run-IS-unit-tests/action.yml +++ b/.github/actions/run-IS-unit-tests/action.yml @@ -26,15 +26,11 @@ runs: needs: coverage cache: always - # - name: Add libR.so to LD_LIBRARY_PATH - # shell: bash - # run: | - # LIBR_DIR=$(dirname $(find /opt -name "libR.so" | head -n 1)) - # echo "LD_LIBRARY_PATH=$LIBR_DIR:$LD_LIBRARY_PATH" >> $GITHUB_ENV - - # - name: Install Avro - # shell: bash - # run: sudo apt install libavro23 + - name: Add libR.so to LD_LIBRARY_PATH + shell: bash + run: | + LIBR_DIR=$(dirname $(find /opt -name "libR.so" | head -n 1)) + echo "LD_LIBRARY_PATH=$LIBR_DIR:$LD_LIBRARY_PATH" >> $GITHUB_ENV - name: Run ${{ env.MODULE_NAME }} unit test coverage using covr package shell: Rscript {0} @@ -84,13 +80,13 @@ runs: run: cat code-coverage-results.md >> $GITHUB_STEP_SUMMARY # Upload Coverage Report to codecov.io - # - Currently fails due to missing token - - name: Upload coverage to Codecov - uses: codecov/codecov-action@v3 - with: - file: ./test-summary.xml - flags: unittests - name: codecov-umbrella + # Currently fails due to missing token + # - name: Upload coverage to Codecov + # uses: codecov/codecov-action@v3 + # with: + # file: ./test-summary.xml + # flags: unittests + # name: codecov-umbrella # Uploads the coverage.html file as a workflow artifact # Find the r-coverage-report artifact on the workflow run details page. diff --git a/.github/workflows/IS_pack_base_unit_tests.yml b/.github/workflows/IS_pack_base_unit_tests.yml index 2eebca3a7..1f57159fe 100644 --- a/.github/workflows/IS_pack_base_unit_tests.yml +++ b/.github/workflows/IS_pack_base_unit_tests.yml @@ -24,5 +24,8 @@ jobs: - name: Checkout uses: actions/checkout@v5 + - name: Install Avro + run: sudo apt install libavro23 + - name: Run IS ${{ env.MODULE_NAME }} unit tests uses: ./.github/actions/run-IS-unit-tests From 7fc5c8f1f86f3e56590e6dbc0bfcb61564555d4d Mon Sep 17 00:00:00 2001 From: Justin Wright Date: Mon, 3 Nov 2025 15:45:28 -0700 Subject: [PATCH 15/18] Remove code coverage reports from repo --- .github/actions/run-IS-unit-tests/action.yml | 25 - .../NEONprocIS.base-coverage.html | 37798 ---------------- .../NEONprocIS.cal-coverage.html | 23107 ---------- .../NEONprocIS.qaqc-coverage.html | 9551 ---- .../NEONprocIS.stat-coverage.html | 7731 ---- .../test_coverage/NEONprocIS.wq-coverage.html | 3097 -- 6 files changed, 81309 deletions(-) delete mode 100644 pack/test_coverage/NEONprocIS.base-coverage.html delete mode 100644 pack/test_coverage/NEONprocIS.cal-coverage.html delete mode 100644 pack/test_coverage/NEONprocIS.qaqc-coverage.html delete mode 100644 pack/test_coverage/NEONprocIS.stat-coverage.html delete mode 100644 pack/test_coverage/NEONprocIS.wq-coverage.html diff --git a/.github/actions/run-IS-unit-tests/action.yml b/.github/actions/run-IS-unit-tests/action.yml index 93015fdd8..642346519 100644 --- a/.github/actions/run-IS-unit-tests/action.yml +++ b/.github/actions/run-IS-unit-tests/action.yml @@ -78,15 +78,6 @@ runs: - name: Add coverage summary to job summary shell: bash run: cat code-coverage-results.md >> $GITHUB_STEP_SUMMARY - - # Upload Coverage Report to codecov.io - # Currently fails due to missing token - # - name: Upload coverage to Codecov - # uses: codecov/codecov-action@v3 - # with: - # file: ./test-summary.xml - # flags: unittests - # name: codecov-umbrella # Uploads the coverage.html file as a workflow artifact # Find the r-coverage-report artifact on the workflow run details page. @@ -98,19 +89,3 @@ runs: name: r-coverage-report path: ${{ env.MODULE_NAME }}-coverage.html retention-days: 30 # Adjust retention days as needed - - # Commit HTML coverage report to test_coverage directory in repo - # - name: Add/update the test coverage.html to ./pack/test_coverage/ - # shell: bash - # run: | - # set -euo pipefail - # IFS=$'\n\t' - # git config --local user.email "actions@github.com" - # git config --local user.name "gitHub Actions" - # echo "Attempting to create a test_coverage directory" - # mkdir -p pack/test_coverage - # echo "Directory creation successful (or already existed)." - # mv "${{ env.MODULE_NAME }}-coverage.html" ./pack/test_coverage/ - # git add "./pack/test_coverage/${{ env.MODULE_NAME }}-coverage.html" - # git commit -m "Add ${{ env.MODULE_NAME }}-coverage.html to test_coverage directory" - # git push diff --git a/pack/test_coverage/NEONprocIS.base-coverage.html b/pack/test_coverage/NEONprocIS.base-coverage.html deleted file mode 100644 index b5893bf65..000000000 --- a/pack/test_coverage/NEONprocIS.base-coverage.html +++ /dev/null @@ -1,37798 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - -
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NEONprocIS.base coverage - 94.96%

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NEONprocIS.cal coverage - 93.89%

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NEONprocIS.qaqc coverage - 96.46%

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NEONprocIS.stat coverage - 97.14%

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NEONprocIS.wq coverage - 95.85%

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- - From 61fe535be882a8b2866e648d58f15c0c9e367f1d Mon Sep 17 00:00:00 2001 From: Justin Wright Date: Tue, 4 Nov 2025 10:28:26 -0700 Subject: [PATCH 16/18] Add missing HTML report artifacts --- .github/actions/run-IS-unit-tests/action.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/actions/run-IS-unit-tests/action.yml b/.github/actions/run-IS-unit-tests/action.yml index 642346519..8a1ee6ab6 100644 --- a/.github/actions/run-IS-unit-tests/action.yml +++ b/.github/actions/run-IS-unit-tests/action.yml @@ -79,7 +79,7 @@ runs: shell: bash run: cat code-coverage-results.md >> $GITHUB_STEP_SUMMARY - # Uploads the coverage.html file as a workflow artifact + # Uploads the HTML report as a workflow artifact # Find the r-coverage-report artifact on the workflow run details page. # Download the artifact and open the coverage.html file in your browser # to explore the detailed test coverage report, including line-by-line coverage information. @@ -87,5 +87,7 @@ runs: uses: actions/upload-artifact@v4 with: name: r-coverage-report - path: ${{ env.MODULE_NAME }}-coverage.html + path: | + ${{ env.MODULE_NAME }}-coverage.html + lib/ retention-days: 30 # Adjust retention days as needed From 4a7c99d47cd0a0f4e0f4997a0f1de1a4dff4f6ac Mon Sep 17 00:00:00 2001 From: Justin Wright Date: Tue, 4 Nov 2025 11:19:04 -0700 Subject: [PATCH 17/18] Use default artifact retention --- .github/actions/run-IS-unit-tests/action.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/actions/run-IS-unit-tests/action.yml b/.github/actions/run-IS-unit-tests/action.yml index 8a1ee6ab6..14d83c3f3 100644 --- a/.github/actions/run-IS-unit-tests/action.yml +++ b/.github/actions/run-IS-unit-tests/action.yml @@ -90,4 +90,3 @@ runs: path: | ${{ env.MODULE_NAME }}-coverage.html lib/ - retention-days: 30 # Adjust retention days as needed From f37fc3c29eb0d4f46d5b96484743a75712af576e Mon Sep 17 00:00:00 2001 From: Justin Wright Date: Tue, 4 Nov 2025 11:25:28 -0700 Subject: [PATCH 18/18] Remove test permissions, not needed --- .github/workflows/IS_pack_base_unit_tests.yml | 2 -- .github/workflows/IS_pack_cal_unit_tests.yml | 2 -- .github/workflows/IS_pack_pub_unit_tests.yml | 2 -- .github/workflows/IS_pack_qaqc_unit_tests.yml | 2 -- .github/workflows/IS_pack_stat_unit_tests.yml | 2 -- .github/workflows/IS_pack_wq_unit_tests.yml | 2 -- 6 files changed, 12 deletions(-) diff --git a/.github/workflows/IS_pack_base_unit_tests.yml b/.github/workflows/IS_pack_base_unit_tests.yml index 1f57159fe..cc03c73da 100644 --- a/.github/workflows/IS_pack_base_unit_tests.yml +++ b/.github/workflows/IS_pack_base_unit_tests.yml @@ -18,8 +18,6 @@ env: jobs: run-unit-test: runs-on: ubuntu-latest - permissions: - contents: write steps: - name: Checkout uses: actions/checkout@v5 diff --git a/.github/workflows/IS_pack_cal_unit_tests.yml b/.github/workflows/IS_pack_cal_unit_tests.yml index 6af61747b..fb3632f1c 100644 --- a/.github/workflows/IS_pack_cal_unit_tests.yml +++ b/.github/workflows/IS_pack_cal_unit_tests.yml @@ -18,8 +18,6 @@ env: jobs: run-unit-test: runs-on: ubuntu-latest - permissions: - contents: write steps: - name: Checkout uses: actions/checkout@v5 diff --git a/.github/workflows/IS_pack_pub_unit_tests.yml b/.github/workflows/IS_pack_pub_unit_tests.yml index efea861e1..98626591d 100644 --- a/.github/workflows/IS_pack_pub_unit_tests.yml +++ b/.github/workflows/IS_pack_pub_unit_tests.yml @@ -18,8 +18,6 @@ env: jobs: run-unit-test: runs-on: ubuntu-latest - permissions: - contents: write steps: - name: Checkout uses: actions/checkout@v5 diff --git a/.github/workflows/IS_pack_qaqc_unit_tests.yml b/.github/workflows/IS_pack_qaqc_unit_tests.yml index 7958a8f04..dae259880 100644 --- a/.github/workflows/IS_pack_qaqc_unit_tests.yml +++ b/.github/workflows/IS_pack_qaqc_unit_tests.yml @@ -18,8 +18,6 @@ env: jobs: run-unit-test: runs-on: ubuntu-latest - permissions: - contents: write steps: - name: Checkout uses: actions/checkout@v5 diff --git a/.github/workflows/IS_pack_stat_unit_tests.yml b/.github/workflows/IS_pack_stat_unit_tests.yml index 3917b97e8..bb2fd3ecf 100644 --- a/.github/workflows/IS_pack_stat_unit_tests.yml +++ b/.github/workflows/IS_pack_stat_unit_tests.yml @@ -18,8 +18,6 @@ env: jobs: run-unit-test: runs-on: ubuntu-latest - permissions: - contents: write steps: - name: Checkout uses: actions/checkout@v5 diff --git a/.github/workflows/IS_pack_wq_unit_tests.yml b/.github/workflows/IS_pack_wq_unit_tests.yml index 73d33234a..52c192c75 100644 --- a/.github/workflows/IS_pack_wq_unit_tests.yml +++ b/.github/workflows/IS_pack_wq_unit_tests.yml @@ -18,8 +18,6 @@ env: jobs: run-unit-test: runs-on: ubuntu-latest - permissions: - contents: write steps: - name: Checkout uses: actions/checkout@v5