switch from clone to checkout to try and get fpaths right

.github/workflows/CI.yml

@@ -33,6 +33,9 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+env:
+  # update this to run tests with un merged rmg-py branches
+  RMG_PY_BRANCH: main
 
 jobs:
   build-osx:
@@ -43,16 +46,11 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - name: Checkout RMG-database
-        uses: actions/checkout@v3
-        with:
-          path: ../
-
       - name: Checkout RMG-Py
         uses: actions/checkout@v3
         with:
           repository: ReactionMechanismGenerator/RMG-Py
-          ref: main
+          ref: ${{ env.RMG_PY_BRANCH }}
 
       # configures the mamba environment manager and builds the environment
       - name: Setup Mambaforge Python 3.7
@@ -71,6 +69,10 @@ jobs:
           mamba info
           mamba list
 
+      # Clone RMG-database
+      - name: Clone RMG-database
+        uses: actions/checkout@v3
+
       # modify env variables as directed in the RMG installation instructions
       - name: Set Environment Variables
         run: |
@@ -95,17 +97,11 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - name: Checkout RMG-database
-        uses: actions/checkout@v3
-        with:
-          path: ../
-
       - name: Checkout RMG-Py
         uses: actions/checkout@v3
         with:
-          # change this if working on a different fork or branch
           repository: ReactionMechanismGenerator/RMG-Py
-          ref: main
+          ref: ${{ env.RMG_PY_BRANCH }}
 
       # configures the mamba environment manager and builds the environment
       - name: Setup Mambaforge Python 3.7
@@ -124,6 +120,10 @@ jobs:
           mamba info
           mamba list
 
+      # Clone RMG-database
+      - name: Clone RMG-database
+        uses: actions/checkout@v3
+
       # modify env variables as directed in the RMG installation instructions
       - name: Set Environment Variables
         run: |