Cleanups

mispr/lammps/database.py

@@ -1,6 +1,4 @@
-# coding: utf-8
-
-# Defines classes for handling mongodb interactions.
+"""Define classes for handling mongodb interactions."""
 
 import sys
 import logging

mispr/lammps/firetasks/parse_outputs.py

@@ -1,7 +1,4 @@
-# coding: utf-8
-
-
-# Defines firetasks for reading output of Ambertools programs and LAMMPS.
+"""Define firetasks for reading output of Ambertools programs and LAMMPS."""
 
 import os
 import json

mispr/lammps/firetasks/run.py

@@ -1,7 +1,4 @@
-# coding: utf-8
-
-
-# Defines firetasks for running LAMMPS simulations and AmberTools.
+"""Define firetasks for running LAMMPS simulations and AmberTools."""
 
 import os
 import re

mispr/lammps/firetasks/write_inputs.py

@@ -1,7 +1,4 @@
-# coding: utf-8
-
-
-# Defines firetasks for writing LAMMPS input files.
+"""Define firetasks for writing LAMMPS input files."""
 
 import os
 import json

mispr/lammps/fireworks/core.py

@@ -1,7 +1,4 @@
-# coding: utf-8
-
-
-# Defines core fireworks for ambertools and lammps.
+"""Define core fireworks for ambertools and lammps."""
 
 import os
 import logging

mispr/lammps/utilities/opls.py

@@ -1,8 +1,5 @@
-# coding: utf-8
-
-
-# Implements a core class MaestroRunner for assigning force field
-# parameters on a molecule using Maestro software.
+"""Implements a core class MaestroRunner for assigning force field parameters on a
+molecule using Maestro software."""
 
 import os
 import re

mispr/lammps/utilities/utilities.py

@@ -1,7 +1,4 @@
-# coding: utf-8
-
-
-# Defines lammps utility functions.
+"""Define lammps utility functions."""
 
 import os
 import json

mispr/lammps/workflows/base.py

@@ -1,7 +1,4 @@
-# coding: utf-8
-
-
-# Defines standard lammps workflows.
+"""Define standard lammps workflows."""
 
 import os
 

setup.py

@@ -14,17 +14,20 @@
     url="https://github.com/molmd/mispr",
     install_requires=[
         "numpy >= 1.21.1",
+        # "pymongo >= 3.11.0",
+        # "pymongo <= 3.12.0",
         "pymongo>=3.3.0,<=3.12.0",
         "matplotlib >= 3.3.1",
         "networkx >= 2.5",
-        "fireworks >= 1.9.6",
-        "monty >= 4.0.0",
+        "FireWorks >= 2.0.3",
+        # "monty >= 4.0.0",
         "scipy >= 1.5.2",
         "pandas >= 1.1.2",
         "pubchempy",
         "parmed",
         "mdproptools",
-        "dnspython"
+        "dnspython",
+        "ruamel.yaml>=0.15.35,<=0.17.40",  # should be removed in the future, but is needed since FireWorks has not updated their function calls to match newer versions of ruamel.yaml
     ],
     packages=setuptools.find_packages(),
     classifiers=[