Cleanup from previous PR

.github/workflows/ci.yml

@@ -19,6 +19,7 @@ name: AtChem2 CI
 # ------------------------------ EVENTS ------------------------------ #
 # Controls when the workflow is activated
 on:
+
   # Triggers when a pull request is created or updated (only on the
   # master branch)
   pull_request:
@@ -27,8 +28,7 @@ on:
   # Triggers when a push is made to the master branch (either by
   # merging a pull request, or by direct commit)
   push:
-    branches:
-      - master
+    branches: [ master ]
 
   # Run manually from the Actions tab
   workflow_dispatch:
@@ -54,16 +54,17 @@ jobs:
 
     # -------------------------------------------------------------
     # Sequence of tasks to be executed as part of the `testing` job:
-    # 1. checkout the repository
-    # 2. install gfortran, AtChem2 dependencies
-    # 3. compile AtChem2
-    # 4. run all tests (indent, style, unit, model)
-    # 5. recompile AtChem2, run unit and model tests for Codecov
+    # 1. Checkout the repository
+    # 2. Install gfortran, AtChem2 dependencies
+    # 3. Compile AtChem2
+    # 4. Run all tests (indent, style, unit, model)
+    # 5. Recompile AtChem2, run unit and model tests for Codecov
     steps:
 
       # -------------------------------------------------------------
       # (1) Checkout the repository under $GITHUB_WORKSPACE
-      - uses: actions/checkout@v4
+      - name: Checkout repo
+        uses: actions/checkout@v4
         with:
           fetch-depth: 2
 
@@ -103,7 +104,7 @@ jobs:
           FORT_VERSION: ${{ matrix.fortran }}
         run: |
           cp tools/install/Makefile.skel Makefile
-          ./build/build_atchem2.sh ./model/mechanism.fac
+          ./build/build_atchem2.sh ./model/mechanism.fac ./model/configuration/ .mcm/
 
           # macos only
           if [ $RUNNER_OS != "Linux" ] ; then

build/mech_converter.py

@@ -278,9 +278,6 @@ def convert_to_fortran(input_file, mech_dir, mcm_vers):
     # Check that each of the RO2s from 'Peroxy radicals' are present
     # in the RO2 reference list from the MCM. If not, print a warning
     # at the top of mechanism.f90 for each errant species.
-    #
-    # TODO: This will break the expected format when mechanism.f90 is
-    #       replaced by a parsable format
     print('looping over inputted RO2s')
 
     with open(os.path.join(mech_dir, 'mechanism.f90'), 'w') as mech_rates_file: