Refactor installation scripts to improve environment setup and streamline installation process

Author: calvinp0

.github/workflows/ci.yml

@@ -65,10 +65,10 @@ jobs:
           key: ${{ runner.os }}-rmgpy-${{ hashFiles('ARC/devtools/install_rmg.sh') }}
           restore-keys: ${{ runner.os }}-rmgpy-
 
-      - name: Build ARC (make install)
+      - name: Install all extras
         shell: micromamba-shell {0}
         working-directory: ARC
-        run: make install
+        run: bash devtools/install_all.sh --no-clean
 
       - name: Run Unit Tests
         shell: micromamba-shell {0}

devtools/install_all.sh

@@ -1,6 +1,13 @@
-#!/bin/bash -l
+#!/usr/bin/env bash
 set -euo pipefail
 
+###################################################################################
+# Flag for cleaning
+#################################################################################
+SKIP_CLEAN=false
+[[ "${1:-}" == --no-clean ]] && SKIP_CLEAN=true
+
+
 # -----------------------------------------------------------------------------
 # Helper: aggressively clean conda/micromamba caches & remove any known build
 # directories in our workspace.  Ignores any permission errors.
@@ -41,56 +48,56 @@ pushd . >/dev/null
 # 1) RMG
 echo "=== Installing RMG ==="
 bash devtools/install_rmg.sh
-cleanup_disk
+! $SKIP_CLEAN && cleanup_disk
 
 # 2) PyRDL
 echo "=== Installing PyRDL ==="
 bash devtools/install_pyrdl.sh
-cleanup_disk
+! $SKIP_CLEAN && cleanup_disk
 
 # 3) ARC itself (skip env creation in CI)
 if [[ -z "${CI:-}" ]]; then
     echo "=== Installing ARC ==="
     bash devtools/install_arc.sh
-    cleanup_disk
+    ! $SKIP_CLEAN && cleanup_disk
 else
     echo "ℹ️ CI detected, skipping arc_env creation."
 fi
 
 # 4) GCN (CPU)
 echo "=== Installing GCN CPU ==="
 bash devtools/install_gcn_cpu.sh
-cleanup_disk
+! $SKIP_CLEAN && cleanup_disk
 
 # 5) AutoTST
 echo "=== Installing AutoTST ==="
 bash devtools/install_autotst.sh
-cleanup_disk
+! $SKIP_CLEAN && cleanup_disk
 
 # 6) KinBot
 echo "=== Installing KinBot ==="
 bash devtools/install_kinbot.sh
-cleanup_disk
+! $SKIP_CLEAN && cleanup_disk
 
 # 7) Open Babel
 echo "=== Installing OpenBabel ==="
 bash devtools/install_ob.sh
-cleanup_disk
+! $SKIP_CLEAN && cleanup_disk
 
 # 8) xtb
 echo "=== Installing xtb ==="
 bash devtools/install_xtb.sh
-cleanup_disk
+! $SKIP_CLEAN && cleanup_disk
 
 # 9) Sella
 echo "=== Installing Sella ==="
 bash devtools/install_sella.sh
-cleanup_disk
+! $SKIP_CLEAN && cleanup_disk
 
 # 10) TorchANI
 echo "=== Installing TorchANI ==="
 bash devtools/install_torchani.sh
-cleanup_disk
+! $SKIP_CLEAN && cleanup_disk
 
 popd >/dev/null
 

devtools/install_rmg.sh

@@ -68,7 +68,11 @@ cd "$RMG_PY_PATH"
 echo "📚 Creating conda env: $ENV_NAME"
 $COMMAND env create -n "$ENV_NAME" -f environment.yml || {
     echo "⚠️ Environment likely exists; trying update..."
-    $COMMAND env update -n "$ENV_NAME" -f environment.yml
+    if [[ "$COMMAND" == micromamba ]]; then
+        micromamba env update -n "$ENV_NAME" --file environment.yml
+    else
+        $COMMAND env update -n "$ENV_NAME" -f environment.yml
+    fi
 }
 
 ###############################################################################