adds venv activation step, removes wheel path usage

.github/workflows/ci.yml

@@ -26,9 +26,9 @@ concurrency:
 jobs:
   prepare:
     runs-on: ubuntu-latest
-    outputs:
-      wheel-path: ${{ steps.distribution-paths.outputs.wheel }}
-      tarball-path: ${{ steps.distribution-paths.outputs.tarball }}
+    # outputs:
+    #   wheel-path: ${{ steps.distribution-paths.outputs.wheel }}
+    #   tarball-path: ${{ steps.distribution-paths.outputs.tarball }}
     steps:
       - uses: actions/checkout@v3
         with: {fetch-depth: 0}  # deep clone for setuptools-scm
@@ -38,22 +38,22 @@ jobs:
         run: pipx run pre-commit run --all-files --show-diff-on-failure
       - name: Install tox-gh plugin
         run: python -m pip install tox-gh>=1.2
-      - name: Build package distribution files
-        run: tox -e clean,build
-      - name: Record the paths of wheel and source tarball distributions
-        id: distribution-paths
-        run: |
-          echo "wheel=$(ls dist/*.whl)" >> $GITHUB_OUTPUT
-          echo "tarball=$(ls dist/*.tar.gz)" >> $GITHUB_OUTPUT
-      - name: Store the distribution files for use in other stages
-        # `tests`, `pypi-publish`, and `docker-publish` will use the same
-        # pre-built distributions, so we make sure to release the exact
-        # same package that was tested
-        uses: actions/upload-artifact@v3
-        with:
-          name: python-distribution-files
-          path: dist/
-          retention-days: 1
+      # - name: Build package distribution files
+      #   run: tox -e clean,build
+      # - name: Record the paths of wheel and source tarball distributions
+      #   id: distribution-paths
+      #   run: |
+      #     echo "wheel=$(ls dist/*.whl)" >> $GITHUB_OUTPUT
+      #     echo "tarball=$(ls dist/*.tar.gz)" >> $GITHUB_OUTPUT
+      # - name: Store the distribution files for use in other stages
+      #   # `tests`, `pypi-publish`, and `docker-publish` will use the same
+      #   # pre-built distributions, so we make sure to release the exact
+      #   # same package that was tested
+      #   uses: actions/upload-artifact@v3
+      #   with:
+      #     name: python-distribution-files
+      #     path: dist/
+      #     retention-days: 1
         # Prevent scheduled workflow from ever being paused
       - name: Keepalive Workflow
         uses: gautamkrishnar/[email protected]
@@ -88,15 +88,16 @@ jobs:
         run: tox -vv --notest
       - name: Install dependencies
         run: ./dev_setup.sh ${{ matrix.python }}
+      - name: activate venv
+        run: source py-orca-venv-${{ matrix.python }}/bin/activate
       - name: Run tests
         env:
           # New variables should match a `passenv` pattern under `[testenv]` in tox.ini
           SEVENBRIDGES_CONNECTION_URI: ${{ secrets.SEVENBRIDGES_CONNECTION_URI }}
           NEXTFLOWTOWER_CONNECTION_URI: ${{ secrets.NEXTFLOWTOWER_CONNECTION_URI }}
           SYNAPSE_CONNECTION_URI: ${{ secrets.SYNAPSE_CONNECTION_URI }}
         run: >-
-            tox --installpkg '${{ needs.prepare.outputs.wheel-path }}'
-            -- -rFEx --durations 10 --color yes
+            tox -- -rFEx --durations 10 --color yes
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3
         with: