Merge pull request #29 from molssi-seamm/dev

Added ability to run in containers.

HISTORY.rst

@@ -1,7 +1,9 @@
 =======
 History
 =======
-
+2024.1.16 -- Adding support for containers
+    * Added the ability to work in Docker containers.
+
 2023.9.6 -- Using fractional coordinates for periodic systems.
     * By convention, SEAMM is using fractional coordinates for periodic systems. The
       PACKMOL step was creating periodic structures with Cartesian coordinates, which

devtools/conda-envs/test_env.yaml

@@ -29,6 +29,9 @@ dependencies:
 
   # Pip-only installs
   - pip:
+    # SEAMM
+    - seamm-exec
+
     # Documentation
     - sphinx-copybutton
 

packmol_step/packmol.py

@@ -2,9 +2,10 @@
 
 """A step for building fluids with Packmol in a SEAMM flowchart"""
 
+import configparser
 import logging
 import math
-import os.path
+from pathlib import Path
 import pprint
 import textwrap
 
@@ -69,14 +70,6 @@ def create_parser(self):
         if parser_exists:
             return result
 
-        # Options for Packmol
-        parser.add_argument(
-            self.step_type,
-            "--packmol-path",
-            default="",
-            help="the path to the Packmol executables",
-        )
-
         return result
 
     def description_text(self, P=None):
@@ -185,12 +178,8 @@ def run(self):
         # Get the system database
         system_db = self.get_variable("_system_db")
 
-        # The options from command line, config file ...
-        path = self.options["packmol_path"]
-
-        # and the executable
-        packmol_exe = os.path.join(path, "packmol")
-        seamm_util.check_executable(packmol_exe)
+        # Access the options
+        seamm_options = self.global_options
 
         P = self.parameters.current_values_to_dict(
             context=seamm.flowchart_variables._data
@@ -221,32 +210,35 @@ def run(self):
 
         self.logger.log(0, pprint.pformat(files))
 
-        # Save the files to disk.
-        os.makedirs(self.directory, exist_ok=True)
-        for filename in files:
-            with open(os.path.join(self.directory, filename), mode="w") as fd:
-                fd.write(files[filename])
+        executor = self.flowchart.executor
+
+        # Read configuration file for MOPAC
+        ini_dir = Path(seamm_options["root"]).expanduser()
+        full_config = configparser.ConfigParser()
+        full_config.read(ini_dir / "packmol.ini")
+        executor_type = executor.name
+        if executor_type not in full_config:
+            raise RuntimeError(
+                f"No section for '{executor_type}' in PACKMOL ini file "
+                f"({ini_dir / 'packmol.ini'})"
+            )
+        config = dict(full_config.items(executor_type))
 
-        local = seamm.ExecLocal()
-        result = local.run(
-            cmd=(packmol_exe + " < input.inp"),
-            shell=True,
+        result = executor.run(
+            cmd=["{code}", "<", "input.inp", ">", "packmol.out"],
+            config=config,
+            directory=self.directory,
             files=files,
             return_files=["packmol.pdb"],
+            in_situ=True,
+            shell=True,
         )
 
-        self.logger.debug(pprint.pformat(result))
-
-        # And write the output files out.
-        with open(os.path.join(self.directory, "packmol.out"), "w") as fd:
-            fd.write(result["stdout"])
+        if not result:
+            self.logger.error("There was an error running PACKMOL")
+            return None
 
-        for filename in result["files"]:
-            with open(os.path.join(self.directory, filename), mode="w") as fd:
-                if result[filename]["data"] is not None:
-                    fd.write(result[filename]["data"])
-                else:
-                    fd.write(result[filename]["exception"])
+        self.logger.debug(pprint.pformat(result))
 
         # Get the bond orders and extra parameters like ff atom types
         bond_orders = []
@@ -271,7 +263,7 @@ def run(self):
         tmp_db.close()
 
         # Get the system to fill and make sure it is empty
-        system, configuration = self.get_system_configuration(P)
+        system, configuration = self.get_system_configuration(P, same_as=None)
         configuration.clear()
         configuration.charge = total_q
 

requirements.txt

@@ -1,2 +1,3 @@
-seamm==2021.2.2
+seamm
+seamm_exec
 tabulate

tests/test_flowcharts.py

@@ -4,7 +4,7 @@
 """Tests for `packmol_step` running full flowcharts."""
 from pathlib import Path
 import pytest
-from seamm import run_flowchart
+from seamm_exec import run
 
 test_dir = Path(__file__).resolve().parent
 
@@ -30,7 +30,7 @@ def test_ideal_gas(monkeypatch, tmp_path, flowchart):
         ],
     )
 
-    run_flowchart(wdir=str(tmp_path))
+    run(wdir=str(tmp_path))
 
 
 @pytest.mark.unit
@@ -46,4 +46,4 @@ def test_unit(monkeypatch, tmp_path, flowchart):
         ],
     )
 
-    run_flowchart(wdir=str(tmp_path))
+    run(wdir=str(tmp_path))