Allows configurable RMG environment and database path

Enables users to specify the RMG environment name and database path.
This makes it easier to use different RMG installations and databases.

The environment variables RMG_ENV_NAME and RMG_DB_PATH are now respected.

Author: calvinp0

arc/processor.py

@@ -8,6 +8,7 @@
 
 import arc.plotter as plotter
 from arc.common import ARC_PATH, get_logger, read_yaml_file, save_yaml_file
+from arc.imports import settings
 from arc.level import Level
 from arc.job.local import execute_command
 from arc.statmech.factory import statmech_factory
@@ -246,11 +247,15 @@ def compare_thermo(species_for_thermo_lib: list,
     species_thermo_path = os.path.join(output_directory, 'RMG_thermo.yml')
     save_yaml_file(path=species_thermo_path,
                    content=[{'label': spc.label, 'adjlist': spc.mol.copy(deep=True).to_adjacency_list()} for spc in species_for_thermo_lib])
+    env_name = settings.get('RMG_ENV_NAME', 'rmg_env')
+    rmg_db_path = settings.get('RMG_DB_PATH') or ""
     commands = ['bash -lc "set -euo pipefail; '
+                f'export RMG_DB_PATH=\\"{rmg_db_path}\\"; '
+                f'export RMG_DATABASE=\\"{rmg_db_path}\\"; '
                 'if command -v micromamba >/dev/null 2>&1; then '
-                f'    micromamba run -n rmg_env python {THERMO_SCRIPT_PATH} {species_thermo_path}; '
+                f'    micromamba run -n {env_name} python {THERMO_SCRIPT_PATH} {species_thermo_path}; '
                 'elif command -v conda >/dev/null 2>&1 || command -v mamba >/dev/null 2>&1; then '
-                f'    conda run -n rmg_env python {THERMO_SCRIPT_PATH} {species_thermo_path}; '
+                f'    conda run -n {env_name} python {THERMO_SCRIPT_PATH} {species_thermo_path}; '
                 'else '
                 '    echo \'❌ Micromamba/Mamba/Conda required\' >&2; exit 1; '
                 'fi"',
@@ -300,7 +305,8 @@ def compare_rates(rxns_for_kinetics_lib: list,
                              'family': rxn.family,
                              } for rxn in rxns_for_kinetics_lib],
                    )
-    env_name = 'rmg_env'
+    env_name = settings.get('RMG_ENV_NAME', 'rmg_env')
+    rmg_db_path = settings.get('RMG_DB_PATH') or ""
     shell_script = f"""if command -v micromamba &> /dev/null; then
     eval "$(micromamba shell hook --shell=bash)"
     micromamba activate {env_name}
@@ -313,6 +319,8 @@ def compare_rates(rxns_for_kinetics_lib: list,
 else
     exit 1
 fi
+export RMG_DB_PATH="{rmg_db_path}"
+export RMG_DATABASE="{rmg_db_path}"
 python {KINETICS_SCRIPT_PATH} {reactions_kinetics_path}   > >(tee -a stdout.log) 2> >(tee -a stderr.log >&2)
 """
     o, e = execute_command(command=shell_script,