Fixing MacOs

SABS-R3-Epidemiology · Jan 13, 2025 · 598a633 · 598a633
1 parent 27bf65d
commit 598a633
Showing 1 changed file with 26 additions and 48 deletions.
diff --git a/.github/workflows/test_macos.yml b/.github/workflows/test_macos.yml
@@ -16,6 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         R: ['4.1.0']
+        python-version: ['3.10']  # Explicitly define Python version in matrix
 
     steps:
       - name: Checkout repository
@@ -30,15 +31,16 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
 
       - name: Query dependencies
         run: |
           install.packages('remotes')
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
 
-      - name: cache R installed packages
+      - name: Cache R packages
         uses: actions/cache@v2
         id: cache
         with:
@@ -54,67 +56,43 @@ jobs:
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
-      - name: setup r-reticulate venv
+      - name: Setup Python environment
         shell: Rscript {0}
         run: |
           library(reticulate)
-
-          reticulate::py_run_string("
-          import sys
-          import subprocess
-          subprocess.check_call([sys.executable, '-m', 'pip', 'install', '--upgrade', 'pip'])
-          ")
           
-          # Install required packages
-          reticulate::py_run_string("
-          import sys
-          import subprocess
+          # Use the GitHub Actions Python
+          Sys.setenv(RETICULATE_PYTHON = Sys.which("python"))
           
-          # Install basic packages
-          packages = ['numpy', 'pandas', 'matplotlib']
-          for package in packages:
-              subprocess.check_call([sys.executable, '-m', 'pip', 'install', '--upgrade', package])
+          # Install pip packages
+          system2("pip", c("install", "--upgrade", "pip"))
+          system2("pip", c("install", "--upgrade", "numpy", "pandas", "matplotlib"))
+          system2("pip", c("install", "--upgrade", "git+https://github.com/SABS-R3-Epidemiology/epiabm.git@main#egg=pyEpiabm&subdirectory=pyEpiabm"))
           
-          # Install pyEpiabm from GitHub
-          subprocess.check_call([
-              sys.executable, '-m', 'pip', 'install', '--upgrade',
-              'git+https://github.com/SABS-R3-Epidemiology/epiabm.git@main#egg=pyEpiabm&subdirectory=pyEpiabm'
-          ])
-          ")
+          # Verify Python configuration
+          py_config <- reticulate::py_config()
+          message("Python configuration:")
+          message(paste("Python version:", py_config$version))
+          message(paste("Python path:", py_config$python))
           
-          env_name <- "r-py-env"
-          python_version = "3.9"
-          tryCatch({
-            # Check if virtualenv package is available
-            if (!reticulate::virtualenv_exists(env_name)) {
-              message(sprintf("Creating new Python virtual environment: %s", env_name))
-              
-              # Create virtual environment with system site packages to help with SSL
-              reticulate::virtualenv_create(
-                envname = env_name,
-                version = python_version,
-                packages = "pip",
-                system_site_packages = TRUE
-              )
-            }
-            
-            # Activate the environment
-            reticulate::use_virtualenv(env_name, required = TRUE)
-            return(TRUE)
-          }, error = function(e) {
-            warning(sprintf("Failed to create/activate Python environment: %s", e$message))
-            return(FALSE)
-          })
+          # Test imports
+          reticulate::py_run_string("
+          import numpy
+          import pandas
+          import matplotlib
+          import pyEpiabm
+          print('All required Python packages successfully imported')
+          ")
 
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          RETICULATE_PYTHON: ${{ env.pythonLocation }}/python
         run: |
           options(crayon.enabled = TRUE)
           rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
         shell: Rscript {0}
 
       - name: Show testthat output
         if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true