From 7c86c210ea066667ba70d0545e73a432223b1dd6 Mon Sep 17 00:00:00 2001 From: sbidari Date: Tue, 14 Jan 2025 15:30:29 -0500 Subject: [PATCH 1/8] add setup-r --- .github/workflows/pre-commit.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml index 71789f9b..e823c865 100644 --- a/.github/workflows/pre-commit.yaml +++ b/.github/workflows/pre-commit.yaml @@ -13,6 +13,9 @@ jobs: - uses: actions/setup-python@v5 with: python-version: "3.12" + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true - uses: actions/cache@v4 with: path: | From a39e6d7dc2ac6e984446ef536da82d2dc6ad3d1b Mon Sep 17 00:00:00 2001 From: "Dylan H. Morris" Date: Tue, 14 Jan 2025 16:07:57 -0500 Subject: [PATCH 2/8] Update pipeline-run-check.yaml --- .github/workflows/pipeline-run-check.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/pipeline-run-check.yaml b/.github/workflows/pipeline-run-check.yaml index 1e6c1a77..7e10b7c9 100644 --- a/.github/workflows/pipeline-run-check.yaml +++ b/.github/workflows/pipeline-run-check.yaml @@ -26,8 +26,6 @@ jobs: run: pip install poetry - name: "Install pyrenew-hew" run: poetry install - - name: "Set up Quarto" - uses: quarto-dev/quarto-actions/setup@v2 - name: "Set up dependencies for hewr" uses: r-lib/actions/setup-r-dependencies@v2 with: From c5cfa4dee152d55d45c874834e9134167c695473 Mon Sep 17 00:00:00 2001 From: "Dylan H. Morris" Date: Tue, 14 Jan 2025 16:17:21 -0500 Subject: [PATCH 3/8] Update pipeline-run-check.yaml --- .github/workflows/pipeline-run-check.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/pipeline-run-check.yaml b/.github/workflows/pipeline-run-check.yaml index 7e10b7c9..1913cfd0 100644 --- a/.github/workflows/pipeline-run-check.yaml +++ b/.github/workflows/pipeline-run-check.yaml @@ -22,6 +22,8 @@ jobs: with: r-version: "release" use-public-rspm: true + - name: "Set up Quarto" + uses: quarto-dev/quarto-actions/setup@v2 - name: "Install poetry" run: pip install poetry - name: "Install pyrenew-hew" From cdd31bdce6af6eb3a1d6c893d413031dc200265b Mon Sep 17 00:00:00 2001 From: "Dylan H. Morris" Date: Tue, 14 Jan 2025 16:32:03 -0500 Subject: [PATCH 4/8] pin pygit2 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index e561d840..b1b51463 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,7 @@ ipykernel = "^6.29.5" polars = "^1.5.0" pypdf = "^5.1.0" pyarrow = "^18.0.0" -pygit2 = "^1.16.0" +pygit2 = "1.16.0" azuretools = {git = "https://github.com/cdcgov/cfa-azuretools"} forecasttools = {git = "https://github.com/CDCgov/forecasttools-py"} tomli-w = "^1.1.0" From cc0a636d37d8de95e014dc7cd559d56b1c43cac5 Mon Sep 17 00:00:00 2001 From: "Dylan H. Morris" Date: Wed, 15 Jan 2025 13:52:59 -0500 Subject: [PATCH 5/8] Unpin pygit2 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index b1b51463..c705a0de 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,7 @@ ipykernel = "^6.29.5" polars = "^1.5.0" pypdf = "^5.1.0" pyarrow = "^18.0.0" -pygit2 = "1.16.0" +pygit2 = "^1.17.0" azuretools = {git = "https://github.com/cdcgov/cfa-azuretools"} forecasttools = {git = "https://github.com/CDCgov/forecasttools-py"} tomli-w = "^1.1.0" From d8403dfc6e12668c6a0ae288bd8708607fd83be1 Mon Sep 17 00:00:00 2001 From: "Dylan H. Morris" Date: Wed, 15 Jan 2025 14:04:02 -0500 Subject: [PATCH 6/8] Run with debug --- pipelines/diagnostic_report/render_diagnostic_report.R | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/pipelines/diagnostic_report/render_diagnostic_report.R b/pipelines/diagnostic_report/render_diagnostic_report.R index 2c18d6a3..13dbb44f 100644 --- a/pipelines/diagnostic_report/render_diagnostic_report.R +++ b/pipelines/diagnostic_report/render_diagnostic_report.R @@ -36,7 +36,10 @@ render_webpage <- function(model_run_dir, template_qmd_path) { quarto_render( input = page_qmd, - execute_params = list(model_dir_raw = model_run_dir) + execute_params = list( + model_dir_raw = model_run_dir, + execute_debug = TRUE + ) ) message("rendered ", page_html) From 21c3497c801cb9bc2e70ddcf6efb4729099371ae Mon Sep 17 00:00:00 2001 From: "Dylan H. Morris" Date: Wed, 15 Jan 2025 14:21:10 -0500 Subject: [PATCH 7/8] Matrix end-to-end --- .github/workflows/pipeline-run-check.yaml | 6 +++++- pipelines/diagnostic_report/render_diagnostic_report.R | 3 +-- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pipeline-run-check.yaml b/.github/workflows/pipeline-run-check.yaml index 1913cfd0..5ed07610 100644 --- a/.github/workflows/pipeline-run-check.yaml +++ b/.github/workflows/pipeline-run-check.yaml @@ -7,7 +7,11 @@ on: jobs: run-pipeline: - runs-on: ubuntu-latest + strategy: + matrix: + os: [ubuntu-latest, ubuntu-22.04, macos-latest] + runs-on: ${{matrix.os}} + env: NHSN_API_KEY_ID: ${{ secrets.NHSN_API_KEY_ID }} NHSN_API_KEY_SECRET: ${{ secrets.NHSN_API_KEY_SECRET }} diff --git a/pipelines/diagnostic_report/render_diagnostic_report.R b/pipelines/diagnostic_report/render_diagnostic_report.R index 13dbb44f..25ca5f89 100644 --- a/pipelines/diagnostic_report/render_diagnostic_report.R +++ b/pipelines/diagnostic_report/render_diagnostic_report.R @@ -37,8 +37,7 @@ render_webpage <- function(model_run_dir, template_qmd_path) { quarto_render( input = page_qmd, execute_params = list( - model_dir_raw = model_run_dir, - execute_debug = TRUE + model_dir_raw = model_run_dir ) ) message("rendered ", page_html) From 98fb748c068e57fba722499d28fa3c0acaea800e Mon Sep 17 00:00:00 2001 From: "Dylan H. Morris" Date: Wed, 15 Jan 2025 14:27:53 -0500 Subject: [PATCH 8/8] Do not run on Ubuntu-latest --- .github/workflows/pipeline-run-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-run-check.yaml b/.github/workflows/pipeline-run-check.yaml index 5ed07610..6e7a03d9 100644 --- a/.github/workflows/pipeline-run-check.yaml +++ b/.github/workflows/pipeline-run-check.yaml @@ -9,7 +9,7 @@ jobs: run-pipeline: strategy: matrix: - os: [ubuntu-latest, ubuntu-22.04, macos-latest] + os: [ubuntu-22.04, macos-latest] runs-on: ${{matrix.os}} env: