update actions (#136)

* python up one version, remove sklearn dependancy from actions * add uv for setting up python env * fix codecov
OHDSI · Dec 17, 2024 · d926034 · d926034
1 parent 4b99d90
commit d926034
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Showing 3 changed files with 22 additions and 27 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -15,3 +15,4 @@
 ^Meta$
 ^Dockerfile$
 ^.devcontainer
+^.venv/
diff --git a/.github/workflows/R_CDM_check_hades.yaml b/.github/workflows/R_CDM_check_hades.yaml
@@ -43,6 +43,7 @@ jobs:
       CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
       CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
       CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
+      UV_SYSTEM_PYTHON: 1
 
     steps:
       - uses: actions/checkout@v4
@@ -58,7 +59,13 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
-
+
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: "latest"
+          python-version: "3.11"
+
       - name: Install system requirements
         if: runner.os == 'Linux'
         run: |
@@ -75,38 +82,25 @@ jobs:
           extra-packages: any::rcmdcheck
           needs: check
 
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.11'
-
       - name: setup r-reticulate venv
-        shell: Rscript {0}
-        run: |
-          python_packages <- 
-            c("polars", "tqdm", "connectorx", "pyarrow", "pynvml", "numpy")
-          
-          library(reticulate)
-          virtualenv_create("r-reticulate", Sys.which("python"), packages=python_packages)
-          virtualenv_install("r-reticulate", "torch", pip_options = c("--index-url https://download.pytorch.org/whl/cpu"))
+        run: | 
+          uv pip install polars tqdm connectorx pyarrow pynvml numpy
+          uv pip install torch --index https://download.pytorch.org/whl/cpu/
           
-          path_to_python <- virtualenv_python("r-reticulate")
-          writeLines(sprintf("RETICULATE_PYTHON=%s", path_to_python),
-                     Sys.getenv("GITHUB_ENV"))
-      
       - uses: r-lib/actions/check-r-package@v2
         with:
           args: 'c("--no-manual", "--as-cran")'
           error-on: '"warning"'
           check-dir: '"check"'
 
       - name: Install covr
-        if: runner.os == 'ubuntu-24.04'
+        if: runner.os == 'Linux'
         run: |
           remotes::install_cran("covr")
         shell: Rscript {0}
 
       - name: Test coverage
-        if: runner.os == 'ubuntu-24.04'
+        if: runner.os == 'Linux'
         run: covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")
         shell: Rscript {0}
 

diff --git a/.github/workflows/R_CMD_check_main_weekly.yaml b/.github/workflows/R_CMD_check_main_weekly.yaml
@@ -47,18 +47,17 @@ jobs:
       WEBAPI_TEST_SECURE_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_SECURE_WEBAPI_URL }}
       WEBAPI_TEST_ADMIN_USER_NAME: ${{ secrets.WEBAPI_TEST_ADMIN_USER_NAME }}
       WEBAPI_TEST_ADMIN_USER_PASSWORD: ${{ secrets.WEBAPI_TEST_ADMIN_USER_PASSWORD }}
-      TORCH_INSTALL: '1'
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.10' 
+          python-version: '3.11' 
 
       - uses: r-lib/actions/setup-tinytex@v2
 
@@ -73,12 +72,13 @@ jobs:
         shell: Rscript {0}
         run: |
           python_packages <- 
-            c("polars", "tqdm", "connectorx", "pyarrow", "scikit-learn")
+            c("polars", "tqdm", "connectorx", "pyarrow")
           
           library(reticulate)
-          virtualenv_create("r-reticulate", Sys.which("python"))
-          virtualenv_install("r-reticulate", python_packages)
-          virtualenv_install("r-reticulate", "torch", pip_options = c("--index-url https://download.pytorch.org/whl/cpu"))
+          virtualenv_create("r-reticulate", Sys.which("python"),
+            packages=python_packages)
+          virtualenv_install("r-reticulate", "torch", 
+            pip_options = c("--index-url https://download.pytorch.org/whl/cpu"))
           
           path_to_python <- virtualenv_python("r-reticulate")
           writeLines(sprintf("RETICULATE_PYTHON=%s", path_to_python),
-Original file line number
+Diff line change
@@ Expand Up / @@ -15,3 +15,4 @@ @@
     ^Meta$
     ^Dockerfile$
     ^.devcontainer
+    ^.venv/