try uv for python

OHDSI · Dec 17, 2024 · b623f7a · b623f7a
1 parent d5301ea
commit b623f7a
Showing 1 changed file with 11 additions and 19 deletions.
diff --git a/.github/workflows/R_CDM_check_hades.yaml b/.github/workflows/R_CDM_check_hades.yaml
@@ -55,10 +55,12 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: actions/setup-python@v5
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v4
         with:
-          python-version: '3.11'
-
+          version: "latest"
+          python-version: "3.11"
+
       - name: Install system requirements
         if: runner.os == 'Linux'
         run: |
@@ -75,24 +77,14 @@ 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 venv -p 3.11 \
+          uv pip install polars tqdm connectorx pyarrow pynvml numpy \
+          uv pip install torch --index https://download.pytorch.org/whl/cpu/
+        env: 
+          UV_SYSTEM_PYTHON: 1
 
-          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")'