From 0c1b76c7d1380b593695c4caf1d2eb64d47c9023 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 10 Apr 2024 00:35:25 -0500 Subject: [PATCH 01/10] reuse same test definition in daily and weekly workflows --- .github/workflows/ci-weekly.yml | 51 ++----------------------- .github/workflows/ci.yml | 50 ++---------------------- .github/workflows/reused/test.yml | 63 +++++++++++++++++++++++++++++++ 3 files changed, 71 insertions(+), 93 deletions(-) create mode 100644 .github/workflows/reused/test.yml diff --git a/.github/workflows/ci-weekly.yml b/.github/workflows/ci-weekly.yml index 57cf83456d8..4062c4bcc2b 100644 --- a/.github/workflows/ci-weekly.yml +++ b/.github/workflows/ci-weekly.yml @@ -14,59 +14,16 @@ env: CI: true jobs: - # ---------------------------------------------------------------------- - # R TEST - # ---------------------------------------------------------------------- test: - if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build') - runs-on: ubuntu-latest - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - strategy: fail-fast: false matrix: R: - "devel" - - services: - postgres: - image: mdillon/postgis:9.5 - options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5 - - container: - image: pecan/depends:R${{ matrix.R }} - - steps: - # checkout source code - - name: work around https://github.com/actions/checkout/issues/766 - run: git config --global --add safe.directory "$GITHUB_WORKSPACE" - - uses: actions/checkout@v4 - with: - set-safe-directory: false - - # install additional tools needed - - name: install utils - run: apt-get update && apt-get install -y postgresql-client qpdf - - name: update dependency lists - run: Rscript scripts/generate_dependencies.R - - name: check for out-of-date dependencies files - uses: infotroph/tree-is-clean@v1 - - name: install newly-added dependencies - working-directory: docker/depends - run: Rscript pecan.depends.R - - # initialize database - - name: db setup - uses: docker://pecan/db:ci - - name: add models to db - run: ./scripts/add.models.sh - - # run PEcAn tests - - name: test - run: make -j1 test - - name: check for out-of-date files - uses: infotroph/tree-is-clean@v1 + uses: ./.github/workflows/reused/test.yml + with: + R-version: ${{ matrix.R }} + secrets: inherit # ---------------------------------------------------------------------- # R CHECK diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2389fedbc86..19792e5a769 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -25,60 +25,18 @@ env: CI: true jobs: - # ---------------------------------------------------------------------- - # R TEST - # ---------------------------------------------------------------------- test: if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build') - runs-on: ubuntu-latest - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - strategy: fail-fast: false matrix: R: - "4.2" - "4.1" - - services: - postgres: - image: mdillon/postgis:9.5 - options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5 - - container: - image: pecan/depends:R${{ matrix.R }} - - steps: - # checkout source code - - name: work around https://github.com/actions/checkout/issues/766 - run: git config --global --add safe.directory "$GITHUB_WORKSPACE" - - uses: actions/checkout@v4 - with: - set-safe-directory: false - - # install additional tools needed - - name: install utils - run: apt-get update && apt-get install -y postgresql-client qpdf - - name: update dependency lists - run: Rscript scripts/generate_dependencies.R - - name: check for out-of-date dependencies files - uses: infotroph/tree-is-clean@v1 - - name: install newly-added dependencies - working-directory: docker/depends - run: Rscript pecan.depends.R - - # initialize database - - name: db setup - uses: docker://pecan/db:ci - - name: add models to db - run: ./scripts/add.models.sh - - # run PEcAn tests - - name: test - run: make -j1 test - - name: check for out-of-date files - uses: infotroph/tree-is-clean@v1 + uses: ./.github/workflows/reused/test.yml + with: + R-version: ${{ matrix.R }} + secrets: inherit # ---------------------------------------------------------------------- # R CHECK diff --git a/.github/workflows/reused/test.yml b/.github/workflows/reused/test.yml new file mode 100644 index 00000000000..54f0a2b1f4f --- /dev/null +++ b/.github/workflows/reused/test.yml @@ -0,0 +1,63 @@ +name: test + +on: + workflow_call: + inputs: + R-version: + required: true + type: string + secrets: + GITHUB_TOKEN: + required: true + +env: + R_LIBS_USER: /usr/local/lib/R/site-library + LC_ALL: en_US.UTF-8 + NCPUS: 2 + PGHOST: postgres + CI: true + +jobs: + test: + runs-on: ubuntu-latest + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + services: + postgres: + image: mdillon/postgis:9.5 + options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5 + + container: + image: pecan/depends:R${{ inputs.R-version }} + + steps: + # checkout source code + - name: work around https://github.com/actions/checkout/issues/766 + run: git config --global --add safe.directory "$GITHUB_WORKSPACE" + - uses: actions/checkout@v4 + with: + set-safe-directory: false + + # install additional tools needed + - name: install utils + run: apt-get update && apt-get install -y postgresql-client qpdf + - name: update dependency lists + run: Rscript scripts/generate_dependencies.R + - name: check for out-of-date dependencies files + uses: infotroph/tree-is-clean@v1 + - name: install newly-added dependencies + run: Rscript docker/depends/pecan.depends.R + + # initialize database + - name: db setup + uses: docker://pecan/db:ci + - name: add models to db + run: ./scripts/add.models.sh + + # run PEcAn tests + - name: test + run: make -j1 test + - name: check for out-of-date files + uses: infotroph/tree-is-clean@v1 From 1307bac2d3c31dd1818fdbf5664753f2cf4263c5 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 10 Apr 2024 00:55:42 -0500 Subject: [PATCH 02/10] reuse check definition too --- .github/workflows/ci-weekly.yml | 48 +++----------------- .github/workflows/ci.yml | 57 +++-------------------- .github/workflows/reused/check.yml | 72 ++++++++++++++++++++++++++++++ 3 files changed, 82 insertions(+), 95 deletions(-) create mode 100644 .github/workflows/reused/check.yml diff --git a/.github/workflows/ci-weekly.yml b/.github/workflows/ci-weekly.yml index 4062c4bcc2b..a5a079ea0d0 100644 --- a/.github/workflows/ci-weekly.yml +++ b/.github/workflows/ci-weekly.yml @@ -25,55 +25,17 @@ jobs: R-version: ${{ matrix.R }} secrets: inherit - # ---------------------------------------------------------------------- - # R CHECK - # ---------------------------------------------------------------------- check: - if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build') - runs-on: ubuntu-latest - strategy: fail-fast: false matrix: R: - "devel" - - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - _R_CHECK_LENGTH_1_CONDITION_: true - _R_CHECK_LENGTH_1_LOGIC2_: true - # Avoid compilation check warnings that come from the system Makevars - # See https://stat.ethz.ch/pipermail/r-package-devel/2019q2/003898.html - _R_CHECK_COMPILATION_FLAGS_KNOWN_: -Wformat -Werror=format-security -Wdate-time - # Keep R checks from trying to consult the very flaky worldclockapi.com - _R_CHECK_SYSTEM_CLOCK_: 0 - - container: - image: pecan/depends:R${{ matrix.R }} - - steps: - # checkout source code - - name: work around https://github.com/actions/checkout/issues/766 - run: git config --global --add safe.directory "$GITHUB_WORKSPACE" - - uses: actions/checkout@v4 - with: - set-safe-directory: false - - # install additional tools needed - - name: install utils - run: apt-get update && apt-get install -y postgresql-client qpdf - - name: install new dependencies - run: Rscript scripts/generate_dependencies.R && cd docker/depends && Rscript pecan.depends.R - - # run PEcAn checks - - name: check - run: make -j1 check - env: - REBUILD_DOCS: "FALSE" - RUN_TESTS: "FALSE" - - name: check for out-of-date files - uses: infotroph/tree-is-clean@v1 - + uses: ./.github/workflows/reused/check.yml + with: + R-version: ${{ matrix.R }} + make-grouping: ${{ matrix.package }} + secrets: inherit # ---------------------------------------------------------------------- # SIPNET TESTS diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 19792e5a769..f82e8629dd4 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -38,13 +38,8 @@ jobs: R-version: ${{ matrix.R }} secrets: inherit - # ---------------------------------------------------------------------- - # R CHECK - # ---------------------------------------------------------------------- check: if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build') - runs-on: ubuntu-latest - strategy: fail-fast: false matrix: @@ -52,53 +47,11 @@ jobs: R: - "4.2" - "4.1" - - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - _R_CHECK_LENGTH_1_CONDITION_: true - _R_CHECK_LENGTH_1_LOGIC2_: true - # Avoid compilation check warnings that come from the system Makevars - # See https://stat.ethz.ch/pipermail/r-package-devel/2019q2/003898.html - _R_CHECK_COMPILATION_FLAGS_KNOWN_: -Wformat -Werror=format-security -Wdate-time - # Keep R checks from trying to consult the very flaky worldclockapi.com - _R_CHECK_SYSTEM_CLOCK_: 0 - - container: - image: pecan/depends:R${{ matrix.R }} - - steps: - # checkout source code - - name: work around https://github.com/actions/checkout/issues/766 - run: git config --global --add safe.directory "$GITHUB_WORKSPACE" - - uses: actions/checkout@v4 - with: - set-safe-directory: false - - # Forbid spaces in names. Yes, *we* know it's not 1980 anymore, but Make doesn't. - - name: check for filenames that would confuse Make - run: | - SPACENAMES=`find . -name '* *'` - if [ -n "$SPACENAMES" ]; then - echo "::error file=${SPACENAMES}::Spaces in filename(s): ${SPACENAMES}. Please rename these files by converting spaces to underscores." - exit 1 - fi - - # install additional tools needed - - name: install utils - run: apt-get update && apt-get install -y postgresql-client qpdf - - name: install new dependencies - run: Rscript scripts/generate_dependencies.R && cd docker/depends/ && Rscript pecan.depends.R - - # run PEcAn checks - # The package names of base, modules, and models are passed as matrix variables to avoid repeatability of code - - name: check - run: make -j1 ${{ matrix.package }} - env: - REBUILD_DOCS: "FALSE" - RUN_TESTS: "FALSE" - - - name: check for out-of-date files - uses: infotroph/tree-is-clean@v1 + uses: ./.github/workflows/reused/check.yml + with: + R-version: ${{ matrix.R }} + make-grouping: ${{ matrix.package }} + secrets: inherit # ---------------------------------------------------------------------- diff --git a/.github/workflows/reused/check.yml b/.github/workflows/reused/check.yml new file mode 100644 index 00000000000..4060efa6137 --- /dev/null +++ b/.github/workflows/reused/check.yml @@ -0,0 +1,72 @@ +name: check + +on: + workflow_call: + inputs: + R-version: + required: true + type: string + make-grouping: + required: true + type: string + secrets: + GITHUB_TOKEN: + required: true + +env: + R_LIBS_USER: /usr/local/lib/R/site-library + LC_ALL: en_US.UTF-8 + NCPUS: 2 + PGHOST: postgres + CI: true + +jobs: + check: + runs-on: ubuntu-latest + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + _R_CHECK_LENGTH_1_CONDITION_: true + _R_CHECK_LENGTH_1_LOGIC2_: true + # Avoid compilation check warnings that come from the system Makevars + # See https://stat.ethz.ch/pipermail/r-package-devel/2019q2/003898.html + _R_CHECK_COMPILATION_FLAGS_KNOWN_: -Wformat -Werror=format-security -Wdate-time + # Keep R checks from trying to consult the very flaky worldclockapi.com + _R_CHECK_SYSTEM_CLOCK_: 0 + + container: + image: pecan/depends:R${{ inputs.R-version }} + + steps: + # checkout source code + - name: work around https://github.com/actions/checkout/issues/766 + run: git config --global --add safe.directory "$GITHUB_WORKSPACE" + - uses: actions/checkout@v4 + with: + set-safe-directory: false + + # Forbid spaces in names. Yes, *we* know it's not 1980 anymore, but Make doesn't. + - name: check for filenames that would confuse Make + run: | + SPACENAMES=`find . -name '* *'` + if [ -n "$SPACENAMES" ]; then + echo "::error file=${SPACENAMES}::Spaces in filename(s): ${SPACENAMES}. Please rename these files by converting spaces to underscores." + exit 1 + fi + + # install additional tools needed + - name: install utils + run: apt-get update && apt-get install -y postgresql-client qpdf + - name: install new dependencies + run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R + + # run PEcAn checks + # The package names of base, modules, and models are passed as matrix variables to avoid repeatability of code + - name: check + run: make -j1 ${{ inputs.make-grouping }} + env: + REBUILD_DOCS: "FALSE" + RUN_TESTS: "FALSE" + + - name: check for out-of-date files + uses: infotroph/tree-is-clean@v1 From bfd764b97081d2cab8860765be466b45d5f824bf Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 10 Apr 2024 01:06:28 -0500 Subject: [PATCH 03/10] and sipnet --- .github/workflows/ci-weekly.yml | 60 ++---------------------- .github/workflows/ci.yml | 60 ++---------------------- .github/workflows/reused/sipnet.yml | 72 +++++++++++++++++++++++++++++ 3 files changed, 80 insertions(+), 112 deletions(-) create mode 100644 .github/workflows/reused/sipnet.yml diff --git a/.github/workflows/ci-weekly.yml b/.github/workflows/ci-weekly.yml index a5a079ea0d0..4846e54c5a7 100644 --- a/.github/workflows/ci-weekly.yml +++ b/.github/workflows/ci-weekly.yml @@ -37,65 +37,13 @@ jobs: make-grouping: ${{ matrix.package }} secrets: inherit - # ---------------------------------------------------------------------- - # SIPNET TESTS - # ---------------------------------------------------------------------- sipnet: - if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build') - runs-on: ubuntu-latest - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - strategy: fail-fast: false matrix: R: - "devel" - - services: - postgres: - image: mdillon/postgis:9.5 - options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5 - - container: - image: pecan/depends:R${{ matrix.R }} - - steps: - # checkout source code - - name: work around https://github.com/actions/checkout/issues/766 - run: git config --global --add safe.directory "$GITHUB_WORKSPACE" - - uses: actions/checkout@v4 - with: - set-safe-directory: false - - # install additional tools needed - - name: install utils - run: apt-get update && apt-get install -y postgresql-client qpdf - - name: install new dependencies - run: Rscript scripts/generate_dependencies.R && cd docker/depends && Rscript pecan.depends.R - - # initialize database - - name: db setup - uses: docker://pecan/db:ci - - name: add models to db - run: ./scripts/add.models.sh - - # install sipnet - - name: Check out SIPNET - uses: actions/checkout@v4 - with: - repository: PecanProject/sipnet - path: sipnet - set-safe-directory: false - - name: install sipnet - run: | - cd ${GITHUB_WORKSPACE}/sipnet - make - - # compile PEcAn code - - name: build - run: make -j1 - - # run SIPNET test - - name: integration test - run: ./tests/integration.sh ghaction + uses: ./.github/workflows/reused/sipnet.yml + with: + R-version: ${{ matrix.R }} + secrets: inherit diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f82e8629dd4..3b48eb99384 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -53,67 +53,15 @@ jobs: make-grouping: ${{ matrix.package }} secrets: inherit - - # ---------------------------------------------------------------------- - # SIPNET TESTS - # ---------------------------------------------------------------------- sipnet: if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build') - runs-on: ubuntu-latest - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - strategy: fail-fast: false matrix: R: - "4.2" - "4.1" - - services: - postgres: - image: mdillon/postgis:9.5 - options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5 - - container: - image: pecan/depends:R${{ matrix.R }} - - steps: - # checkout source code - - name: work around https://github.com/actions/checkout/issues/766 - run: git config --global --add safe.directory "$GITHUB_WORKSPACE" - - uses: actions/checkout@v4 - with: - set-safe-directory: false - - # install additional tools needed - - name: install utils - run: apt-get update && apt-get install -y postgresql-client qpdf - - name: install new dependencies - run: Rscript scripts/generate_dependencies.R && cd docker/depends/ && Rscript pecan.depends.R - - # initialize database - - name: db setup - uses: docker://pecan/db:ci - - name: add models to db - run: ./scripts/add.models.sh - - # install sipnet - - name: Check out SIPNET - uses: actions/checkout@v4 - with: - repository: PecanProject/sipnet - path: sipnet - set-safe-directory: false - - name: install sipnet - run: | - cd ${GITHUB_WORKSPACE}/sipnet - make - - # compile PEcAn code - - name: build - run: make -j1 - - # run SIPNET test - - name: integration test - run: ./tests/integration.sh ghaction + uses: ./.github/workflows/reused/sipnet.yml + with: + R-version: ${{ matrix.R }} + secrets: inherit diff --git a/.github/workflows/reused/sipnet.yml b/.github/workflows/reused/sipnet.yml new file mode 100644 index 00000000000..49482510274 --- /dev/null +++ b/.github/workflows/reused/sipnet.yml @@ -0,0 +1,72 @@ +name: sipnet + +on: + workflow_call: + inputs: + R-version: + required: true + type: string + secrets: + GITHUB_TOKEN: + required: true + +env: + R_LIBS_USER: /usr/local/lib/R/site-library + LC_ALL: en_US.UTF-8 + NCPUS: 2 + PGHOST: postgres + CI: true + +jobs: + sipnet: + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + services: + postgres: + image: mdillon/postgis:9.5 + options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5 + + container: + image: pecan/depends:R${{ inputs.R-version }} + + steps: + # checkout source code + - name: work around https://github.com/actions/checkout/issues/766 + run: git config --global --add safe.directory "$GITHUB_WORKSPACE" + - uses: actions/checkout@v4 + with: + set-safe-directory: false + + # install additional tools needed + - name: install utils + run: apt-get update && apt-get install -y postgresql-client qpdf + - name: install new dependencies + run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R + + # initialize database + - name: db setup + uses: docker://pecan/db:ci + - name: add models to db + run: ./scripts/add.models.sh + + # install sipnet + - name: Check out SIPNET + uses: actions/checkout@v4 + with: + repository: PecanProject/sipnet + path: sipnet + set-safe-directory: false + - name: install sipnet + run: | + cd ${GITHUB_WORKSPACE}/sipnet + make + + # compile PEcAn code + - name: build + run: make -j1 + + # run SIPNET test + - name: integration test + run: ./tests/integration.sh ghaction From cb5368e1cac45ea64c3ae1d1a412dda10b5120fd Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 10 Apr 2024 01:09:45 -0500 Subject: [PATCH 04/10] these are set in reused workflows now --- .github/workflows/ci-weekly.yml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/.github/workflows/ci-weekly.yml b/.github/workflows/ci-weekly.yml index 4846e54c5a7..48649e934c0 100644 --- a/.github/workflows/ci-weekly.yml +++ b/.github/workflows/ci-weekly.yml @@ -6,13 +6,6 @@ on: schedule: - cron: '30 4 * * 1' -env: - R_LIBS_USER: /usr/local/lib/R/site-library - LC_ALL: en_US.UTF-8 - NCPUS: 2 - PGHOST: postgres - CI: true - jobs: test: strategy: From 0ccf099634b4aeee23a2deb88cd10b1bb9b5dedf Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 10 Apr 2024 02:00:01 -0500 Subject: [PATCH 05/10] subdirs not supported --- .github/workflows/{reused => }/check.yml | 0 .github/workflows/ci-weekly.yml | 6 +++--- .github/workflows/ci.yml | 6 +++--- .github/workflows/{reused => }/sipnet.yml | 0 .github/workflows/{reused => }/test.yml | 0 5 files changed, 6 insertions(+), 6 deletions(-) rename .github/workflows/{reused => }/check.yml (100%) rename .github/workflows/{reused => }/sipnet.yml (100%) rename .github/workflows/{reused => }/test.yml (100%) diff --git a/.github/workflows/reused/check.yml b/.github/workflows/check.yml similarity index 100% rename from .github/workflows/reused/check.yml rename to .github/workflows/check.yml diff --git a/.github/workflows/ci-weekly.yml b/.github/workflows/ci-weekly.yml index 48649e934c0..88a1b8f758a 100644 --- a/.github/workflows/ci-weekly.yml +++ b/.github/workflows/ci-weekly.yml @@ -13,7 +13,7 @@ jobs: matrix: R: - "devel" - uses: ./.github/workflows/reused/test.yml + uses: ./.github/workflows/test.yml with: R-version: ${{ matrix.R }} secrets: inherit @@ -24,7 +24,7 @@ jobs: matrix: R: - "devel" - uses: ./.github/workflows/reused/check.yml + uses: ./.github/workflows/check.yml with: R-version: ${{ matrix.R }} make-grouping: ${{ matrix.package }} @@ -36,7 +36,7 @@ jobs: matrix: R: - "devel" - uses: ./.github/workflows/reused/sipnet.yml + uses: ./.github/workflows/sipnet.yml with: R-version: ${{ matrix.R }} secrets: inherit diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 3b48eb99384..1e8426443e6 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -33,7 +33,7 @@ jobs: R: - "4.2" - "4.1" - uses: ./.github/workflows/reused/test.yml + uses: ./.github/workflows/test.yml with: R-version: ${{ matrix.R }} secrets: inherit @@ -47,7 +47,7 @@ jobs: R: - "4.2" - "4.1" - uses: ./.github/workflows/reused/check.yml + uses: ./.github/workflows/check.yml with: R-version: ${{ matrix.R }} make-grouping: ${{ matrix.package }} @@ -61,7 +61,7 @@ jobs: R: - "4.2" - "4.1" - uses: ./.github/workflows/reused/sipnet.yml + uses: ./.github/workflows/sipnet.yml with: R-version: ${{ matrix.R }} secrets: inherit diff --git a/.github/workflows/reused/sipnet.yml b/.github/workflows/sipnet.yml similarity index 100% rename from .github/workflows/reused/sipnet.yml rename to .github/workflows/sipnet.yml diff --git a/.github/workflows/reused/test.yml b/.github/workflows/test.yml similarity index 100% rename from .github/workflows/reused/test.yml rename to .github/workflows/test.yml From 59347ca3b2f0585605e02de1e8f7e2ba11616b37 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 10 Apr 2024 02:12:18 -0500 Subject: [PATCH 06/10] inherited secrets are passed implicitly, no definition allowed --- .github/workflows/check.yml | 3 --- .github/workflows/sipnet.yml | 3 --- .github/workflows/test.yml | 3 --- 3 files changed, 9 deletions(-) diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml index 4060efa6137..751bac459c3 100644 --- a/.github/workflows/check.yml +++ b/.github/workflows/check.yml @@ -9,9 +9,6 @@ on: make-grouping: required: true type: string - secrets: - GITHUB_TOKEN: - required: true env: R_LIBS_USER: /usr/local/lib/R/site-library diff --git a/.github/workflows/sipnet.yml b/.github/workflows/sipnet.yml index 49482510274..c17e520f5df 100644 --- a/.github/workflows/sipnet.yml +++ b/.github/workflows/sipnet.yml @@ -6,9 +6,6 @@ on: R-version: required: true type: string - secrets: - GITHUB_TOKEN: - required: true env: R_LIBS_USER: /usr/local/lib/R/site-library diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 54f0a2b1f4f..7a10c6e8947 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -6,9 +6,6 @@ on: R-version: required: true type: string - secrets: - GITHUB_TOKEN: - required: true env: R_LIBS_USER: /usr/local/lib/R/site-library From da3a0fb94219fd341ff0d06fec8cfb811728ea0a Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 10 Apr 2024 02:20:15 -0500 Subject: [PATCH 07/10] oops, old paths --- .github/workflows/check.yml | 2 +- .github/workflows/sipnet.yml | 2 +- .github/workflows/test.yml | 3 ++- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml index 751bac459c3..4e40e19ce5f 100644 --- a/.github/workflows/check.yml +++ b/.github/workflows/check.yml @@ -55,7 +55,7 @@ jobs: - name: install utils run: apt-get update && apt-get install -y postgresql-client qpdf - name: install new dependencies - run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R + run: Rscript scripts/generate_dependencies.R && cd docker/depends && Rscript pecan.depends.R # run PEcAn checks # The package names of base, modules, and models are passed as matrix variables to avoid repeatability of code diff --git a/.github/workflows/sipnet.yml b/.github/workflows/sipnet.yml index c17e520f5df..b1b3eeca8d6 100644 --- a/.github/workflows/sipnet.yml +++ b/.github/workflows/sipnet.yml @@ -40,7 +40,7 @@ jobs: - name: install utils run: apt-get update && apt-get install -y postgresql-client qpdf - name: install new dependencies - run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R + run: Rscript scripts/generate_dependencies.R && cd docker/depends && Rscript pecan.depends.R # initialize database - name: db setup diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 7a10c6e8947..dc92869d6f4 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -45,7 +45,8 @@ jobs: - name: check for out-of-date dependencies files uses: infotroph/tree-is-clean@v1 - name: install newly-added dependencies - run: Rscript docker/depends/pecan.depends.R + working-directory: docker/depends + run: Rscript pecan.depends.R # initialize database - name: db setup From 69bd4b9372fbecd581715faa658859f9eb313bee Mon Sep 17 00:00:00 2001 From: Chris Black Date: Tue, 7 May 2024 21:38:30 -0700 Subject: [PATCH 08/10] specify check cmd for weekly --- .github/workflows/ci-weekly.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci-weekly.yml b/.github/workflows/ci-weekly.yml index 88a1b8f758a..c3ac65cc75b 100644 --- a/.github/workflows/ci-weekly.yml +++ b/.github/workflows/ci-weekly.yml @@ -22,6 +22,7 @@ jobs: strategy: fail-fast: false matrix: + package: [check] R: - "devel" uses: ./.github/workflows/check.yml From d2eb5982f60add9ad892d150b5f755a31f52c679 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Tue, 7 May 2024 21:40:31 -0700 Subject: [PATCH 09/10] changed my mind, no need for one-item matrix --- .github/workflows/ci-weekly.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci-weekly.yml b/.github/workflows/ci-weekly.yml index c3ac65cc75b..88a1b8f758a 100644 --- a/.github/workflows/ci-weekly.yml +++ b/.github/workflows/ci-weekly.yml @@ -22,7 +22,6 @@ jobs: strategy: fail-fast: false matrix: - package: [check] R: - "devel" uses: ./.github/workflows/check.yml From 40436d10ca5fb5ffb4a3aa7a05046454b5fd03d4 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Tue, 7 May 2024 21:42:24 -0700 Subject: [PATCH 10/10] package is same for all weekly runs --- .github/workflows/ci-weekly.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-weekly.yml b/.github/workflows/ci-weekly.yml index 88a1b8f758a..b503589156d 100644 --- a/.github/workflows/ci-weekly.yml +++ b/.github/workflows/ci-weekly.yml @@ -27,7 +27,7 @@ jobs: uses: ./.github/workflows/check.yml with: R-version: ${{ matrix.R }} - make-grouping: ${{ matrix.package }} + make-grouping: "check" secrets: inherit sipnet: