Fix docker image building + CI improvements

.github/workflows/ci.yaml

@@ -83,7 +83,7 @@ jobs:
         run: |
           pytest -n auto -v --cov=openfe --cov=openfecli --cov-report=xml --durations=10
 
-      - name: codecov
+      - name: codecov-pr
         if: ${{ github.repository == 'OpenFreeEnergy/openfe'
                 && github.event_name == 'pull_request' }}
         uses: codecov/codecov-action@v3
@@ -92,3 +92,19 @@ jobs:
           file: coverage.xml
           fail_ci_if_error: False
           verbose: True
+          flags: fast-tests
+
+      - name: codecov-merge
+        # we only want to upload a slow report if
+        # 1) it isn't a schedule run
+        # 2) it wasn't from a PR (we don't run slow tests on PRs)
+        if: ${{ github.repository == 'OpenFreeEnergy/openfe'  
+                && github.event_name != 'schedule'            
+                && github.event_name != 'pull_request' }}     
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: coverage.xml
+          fail_ci_if_error: False
+          verbose: True
+          flags: slow-tests

.github/workflows/docker-cron.yaml

@@ -90,4 +90,4 @@ jobs:
           docker run --rm ${{ steps.fqirp.outputs.FQIRP }} openfe --version
           docker run --rm ${{ steps.fqirp.outputs.FQIRP }} python -c "import gufe; print(gufe.__version__)"
           docker run --rm ${{ steps.fqirp.outputs.FQIRP }} pytest --pyargs gufe -v
-          docker run --rm ${{ steps.fqirp.outputs.FQIRP }} pytest --pyargs openfecli --pyargs openfe -v
+          docker run --rm ${{ steps.fqirp.outputs.FQIRP }} pytest --pyargs openfe --pyargs openfecli -v