Streamlines RMG installation in CI and docs build

Removes redundant RMG-Py and RMG-database checkouts and caching from CI and documentation build workflows.

This change simplifies the setup by utilizing micromamba to manage the RMG environment, ensuring consistent and efficient installation of necessary dependencies.
It now directly installs RMG via `conda` and sets the correct path for the RMG database.

Author: calvinp0

.github/workflows/ci.yml

@@ -71,23 +71,6 @@ jobs:
           echo "::endgroup::"
           julia --version # Check that Julia is installed correctly
 
-      - name: Set RMG-Py + database in PATH and PYTHONPATH
-        shell: micromamba-shell {0}
-        working-directory: ARC
-        run: |
-          # bash devtools/install_rmg.sh
-          echo "RMG_PY_PATH=$(realpath ../RMG-Py)"       >> $GITHUB_ENV
-          echo "RMG_DB_PATH=$(realpath ../RMG-database)" >> $GITHUB_ENV
-          echo "PATH=$(realpath ../RMG-Py):$PATH"        >> $GITHUB_ENV
-          echo "PYTHONPATH=$(realpath ../RMG-Py):$PYTHONPATH" >> $GITHUB_ENV
-
-      - name: Cache RMG-Py source
-        uses: actions/cache@v4
-        with:
-          path: RMG-Py
-          key: ${{ runner.os }}-rmgpy-${{ hashFiles('ARC/devtools/install_rmg.sh') }}
-          restore-keys: ${{ runner.os }}-rmgpy-
-
       - name: Install all extras - CI
         shell: micromamba-shell {0}
         working-directory: ARC

.github/workflows/gh-pages.yml

@@ -20,34 +20,17 @@ jobs:
           path: ARC
           fetch-depth: 1
 
-      # ── pull RMG sources ────────────────────────────────────────
-      - name: Checkout RMG‑Py
-        uses: actions/checkout@v4
-        with:
-          repository: ReactionMechanismGenerator/RMG-Py
-          path: RMG-Py
-          fetch-depth: 1
-
-      - name: Checkout RMG‑database
-        uses: actions/checkout@v4
-        with:
-          repository: ReactionMechanismGenerator/RMG-database
-          path: RMG-database
-          fetch-depth: 1
-
-      # ── build‑only env ───────────────────────────────────────────
+      # ── rmg_env for Arkane/database availability ───────────────
       - name: Set up micromamba (rmg_env)
         uses: mamba-org/setup-micromamba@v2
         with:
           environment-name: rmg_env
-          environment-file: RMG-Py/environment.yml
+          create-args: >-
+            -c rmg -c conda-forge python=3.9 numpy<2 rmg=3.3.0 connie::symmetry
           cache-environment: true
           cache-downloads: true
           generate-run-shell: false
 
-      - name: Build RMG‑Py in rmg_env
-        run: micromamba run -n rmg_env make -C RMG-Py -j"$(nproc)"
-
       # ── docs env (wrapper shell) ────────────────────────────────
       - name: Set up micromamba (arc_env)
         uses: mamba-org/setup-micromamba@v2
@@ -77,9 +60,8 @@ jobs:
       # ── build HTML docs ─────────────────────────────────────────
       - name: Set env vars & Build docs
         run: |
-          export RMG_PATH="$GITHUB_WORKSPACE/RMG-Py"
-          export RMG_DB_PATH="$GITHUB_WORKSPACE/RMG-database"
-          export PYTHONPATH="$GITHUB_WORKSPACE/RMG-Py:$GITHUB_WORKSPACE/ARC:$PYTHONPATH"
+          export RMG_DB_PATH="$MAMBA_ROOT_PREFIX/envs/rmg_env/share/RMG-database"
+          export PYTHONPATH="$GITHUB_WORKSPACE/ARC:$PYTHONPATH"
           export PATH="$GITHUB_WORKSPACE/ARC:$PATH"
           make -C ARC/docs html
         shell: micromamba-shell {0}

.github/workflows/update-cache.yml

@@ -21,42 +21,6 @@ jobs:
       - name: Checkout ARC
         uses: actions/checkout@v4
 
-      # ────────── RMG‑Py ──────────
-      - name: Cache RMG
-        id: cache-rmg
-        uses: actions/cache@v4
-        with:
-          path: RMG-Py
-          key: ${{ runner.os }}-rmg-main
-          restore-keys: |
-            ${{ runner.os }}-rmg-
-      - name: Checkout RMG-Py
-        if: steps.cache-rmg.outputs.cache-hit != 'true'
-        uses: actions/checkout@v4
-        with:
-          repository: ReactionMechanismGenerator/RMG-Py
-          path: RMG-Py
-          ref: 55464c54d1fa61b531e865682df598d33718597d
-          fetch-depth: 1
-
-      # ────────── RMG‑database ──────────
-      - name: Cache RMG-database
-        id: cache-rmg-db
-        uses: actions/cache@v4
-        with:
-          path: RMG-database
-          key: ${{ runner.os }}-rmgdb-main
-          restore-keys: |
-            ${{ runner.os }}-rmgdb-
-      - name: Checkout RMG-database
-        if: steps.cache-rmg-db.outputs.cache-hit != 'true'
-        uses: actions/checkout@v4
-        with:
-          repository: ReactionMechanismGenerator/RMG-database
-          path: RMG-database
-          ref: main
-          fetch-depth: 1
-
       # ────────── AutoTST ──────────
       - name: Cache AutoTST
         id: cache-autotst

.gitignore

@@ -67,3 +67,6 @@ build/*
 
 *.log
 *.xml
+
+# AI Agent files
+AGENTS.md

devtools/install_rmg.sh

@@ -129,6 +129,7 @@ if [[ "$MODE" == "source" ]]; then
     else
       echo ">>> Creating new environment: $ENV_NAME"
         $COMMAND_PKG env create -n "$ENV_NAME" -f environment.yml -y --strict-channel-priority
+    fi
 
     ###############################################################################
     # COMPILE RMG