Merge pull request #2 from ReactionMechanismGenerator/debug_settings_2

Add new files and comment out imports irrelevant to chemkin

Author: mjohnson541

.conda/meta.yaml

@@ -18,7 +18,7 @@ requirements:
     - numpy
     - openbabel >=3
     - pyrdl
-    - python {{ python }}
+    - python==3.7
     - quantities
     - rdkit >=2018
     - scipy
@@ -37,7 +37,7 @@ requirements:
     - openbabel >=3
     - pydot
     - pyrdl
-    - python {{ python }}
+    - python==3.7
     - quantities
     - rdkit >=2018
     - scikit-learn

.gitignore

@@ -0,0 +1,98 @@
+################################################################################
+#
+#   Files for git to ignore
+#
+################################################################################
+
+# MacOS files
+.DS_Store
+
+# Compiled Python modules
+*.pyc
+*.so
+*.pyd
+
+# Image files generated by RMG
+*.png
+*.svg
+*.pdf
+
+# Temporary build files
+build/*
+
+# Compiled documentation
+documentation/build/*
+
+# Compilation helper files
+# (These will be unique to each developer's setup)
+make.inc
+
+# Example output files
+examples/*
+!examples/*/input.py
+!examples/**/*.ipynb
+
+# NetBeans project files
+nbproject/*
+
+# Eclipse project files
+.project
+.pydevproject
+.settings/*
+
+# PyCharm project files
+*/.idea/*
+.idea/*
+
+# VS Code settings
+*/.vscode/*
+.vscode/*
+
+# Unit test files
+.coverage
+testing/*
+htmlcov/*
+
+# Quantum Mechanics temporary, cache, and result files
+QMfiles/*
+QMscratch/*
+
+# Solver settings file
+molecule/solver/settings.pxi
+
+# bin/symmetry
+bin/symmetry
+
+# ipython checkpoints
+**/.ipynb_checkpoints/**
+
+# cantera files
+*.cti
+
+# csv files
+*.csv
+
+# ipython folder except for notebooks
+ipython/*
+!ipython/*.ipynb
+
+# Q2DTor
+external/Q2DTor
+
+# egg files (pip install -e)
+RMG_Py.egg-info/*
+
+# deleted files
+**/.fuse_hidden*
+
+# RMG configuration file
+molecule/rmgrc
+
+scripts/treegen.log
+
+scripts/treegen_backup.log
+
+# regression testing files - ignore everything but input and regression input
+test/regression/*
+!test/regression/*/input.py
+!test/regression/*/regression_input.py

molecule/data/kinetics/family.py

@@ -45,7 +45,7 @@
 from sklearn.model_selection import KFold
 
 from molecule import settings
-from molecule.constraints import fails_species_constraints
+# from molecule.constraints import fails_species_constraints
 from molecule.data.base import Database, Entry, LogicNode, LogicOr, ForbiddenStructures, get_all_combinations
 from molecule.data.kinetics.common import save_entry, find_degenerate_reactions, generate_molecule_combos, \
                                        ensure_independent_atom_ids
@@ -61,7 +61,7 @@
 from molecule.molecule.atomtype import ATOMTYPES
 from molecule.reaction import Reaction, same_species_lists
 from molecule.species import Species
-from molecule.tools.uncertainty import KineticParameterUncertainty
+# from molecule.tools.uncertainty import KineticParameterUncertainty
 from molecule.molecule.fragment import Fragment
 
 ################################################################################

molecule/pdep/__init__.py

@@ -0,0 +1,33 @@
+#!/usr/bin/env python3
+
+###############################################################################
+#                                                                             #
+# RMG - Reaction Mechanism Generator                                          #
+#                                                                             #
+# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu),           #
+# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)   #
+#                                                                             #
+# Permission is hereby granted, free of charge, to any person obtaining a     #
+# copy of this software and associated documentation files (the 'Software'),  #
+# to deal in the Software without restriction, including without limitation   #
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,    #
+# and/or sell copies of the Software, and to permit persons to whom the       #
+# Software is furnished to do so, subject to the following conditions:        #
+#                                                                             #
+# The above copyright notice and this permission notice shall be included in  #
+# all copies or substantial portions of the Software.                         #
+#                                                                             #
+# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR  #
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,    #
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE #
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER      #
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING     #
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER         #
+# DEALINGS IN THE SOFTWARE.                                                   #
+#                                                                             #
+###############################################################################
+
+# from molecule.pdep.collision import SingleExponentialDown
+# from molecule.pdep.configuration import Configuration
+from molecule.pdep.network import Network
+# from molecule.pdep.draw import NetworkDrawer