Rename submodules in rmgpy.tools

ipython/mechanism_analyzer.ipynb

@@ -92,7 +92,7 @@
    "source": [
     "import networkx as nx\n",
     "import matplotlib.pyplot as plt\n",
-    "from rmgpy.tools.extractInfoFromckcsv import get_concentration_dict_from_ckcsv, get_rop_from_ckcsv, get_flux_graph_edges_dict\n",
+    "from rmgpy.tools.ckcsvparser import get_concentration_dict_from_ckcsv, get_rop_from_ckcsv, get_flux_graph_edges_dict\n",
     "from rmgpy.chemkin import get_species_identifier\n",
     "from IPython.display import display\n",
     "import numpy as np\n",

rmgpy/rmg/main.py

@@ -1036,7 +1036,7 @@ def run_uncertainty_analysis(self):
             else:
                 import re
                 import random
-                from rmgpy.tools.canteraModel import Cantera
+                from rmgpy.tools.canteramodel import Cantera
                 from rmgpy.tools.muq import ReactorPCEFactory
 
         if self.uncertainty is not None and self.uncertainty['local']:

rmgpy/tools/canteraTest.py → rmgpy/tools/canteramodelTest.py

@@ -34,7 +34,7 @@
 
 import rmgpy
 from rmgpy.quantity import Quantity
-from rmgpy.tools.canteraModel import find_ignition_delay, CanteraCondition, Cantera
+from rmgpy.tools.canteramodel import find_ignition_delay, CanteraCondition, Cantera
 
 
 class CanteraTest(unittest.TestCase):
@@ -115,14 +115,14 @@ def test_species_conversion(self):
         """
         Test that species objects convert properly
         """
-        from rmgpy.tools.canteraModel import check_equivalent_cantera_species
+        from rmgpy.tools.canteramodel import check_equivalent_cantera_species
         for i in range(len(self.ctSpecies)):
             self.assertTrue(check_equivalent_cantera_species(self.ctSpecies[i], self.rmg_ctSpecies[i]))
 
     def test_reaction_conversion(self):
         """
         Test that species objects convert properly
         """
-        from rmgpy.tools.canteraModel import check_equivalent_cantera_reaction
+        from rmgpy.tools.canteramodel import check_equivalent_cantera_reaction
         for i in range(len(self.ctReactions)):
             self.assertTrue(check_equivalent_cantera_reaction(self.ctReactions[i], self.rmg_ctReactions[i]))

rmgpy/tools/diff_modelsTest.py → rmgpy/tools/diffmodelsTest.py

@@ -31,7 +31,7 @@
 import shutil
 import unittest
 
-from rmgpy.tools.diff_models import execute
+from rmgpy.tools.diffmodels import execute
 
 
 class DiffModelsTest(unittest.TestCase):

rmgpy/tools/testGenerateReactions.py → rmgpy/tools/generatereactionsTest.py

@@ -35,7 +35,7 @@
 
 import rmgpy
 from rmgpy.rmg.main import RMG
-from rmgpy.tools.generate_reactions import execute
+from rmgpy.tools.generatereactions import execute
 
 
 @attr('functional')

rmgpy/tools/merge_modelsTest.py → rmgpy/tools/mergemodelsTest.py

@@ -31,7 +31,7 @@
 import os.path
 import unittest
 
-from rmgpy.tools.merge_models import get_models_to_merge, combine_models
+from rmgpy.tools.mergemodels import get_models_to_merge, combine_models
 
 
 class MergeModelsTest(unittest.TestCase):

rmgpy/tools/observablesRegression.py → rmgpy/tools/observablesregression.py

@@ -32,7 +32,7 @@
 import numpy as np
 
 from rmgpy.chemkin import load_chemkin_file
-from rmgpy.tools.canteraModel import Cantera, generate_cantera_conditions, get_rmg_species_from_user_species
+from rmgpy.tools.canteramodel import Cantera, generate_cantera_conditions, get_rmg_species_from_user_species
 from rmgpy.tools.plot import GenericPlot, SimulationPlot, find_nearest
 
 

rmgpy/tools/regression.py

@@ -39,8 +39,8 @@
 from rmgpy.molecule import Molecule
 from rmgpy.quantity import Quantity
 from rmgpy.species import Species
-from rmgpy.tools.observablesRegression import ObservablesTestCase
-from rmgpy.tools.canteraModel import CanteraCondition
+from rmgpy.tools.observablesregression import ObservablesTestCase
+from rmgpy.tools.canteramodel import CanteraCondition
 
 observables = []
 setups = None

scripts/checkModels.py

@@ -31,7 +31,7 @@
 import logging
 import math
 
-from rmgpy.tools.diff_models import execute
+from rmgpy.tools.diffmodels import execute
 
 logger = logging.getLogger('checkModels')
 

scripts/diffModels.py

@@ -51,7 +51,7 @@
 --commonDiffOnly        Only show species and reactions present in BOTH models which have different values
 ======================= ==================================================================================== 
 """
-import rmgpy.tools.diff_models as diff_models
+import rmgpy.tools.diffmodels as diff_models
 
 
 ################################################################################

scripts/generateReactions.py

@@ -34,14 +34,14 @@
 
 The input file is a subset of that used with regular RMG jobs. 
 """
-import rmgpy.tools.generate_reactions as generate_reactions
+import rmgpy.tools.generatereactions
 
 
 ################################################################################
 
 
 def main():
-    generate_reactions.main()
+    rmgpy.tools.generatereactions.main()
 
 
 if __name__ == '__main__':

scripts/mergeModels.py

@@ -39,7 +39,7 @@
 ``species_dictionary.txt`` in the execution directory.
 """
 
-import rmgpy.tools.merge_models as merge_models
+import rmgpy.tools.mergemodels as merge_models
 
 
 ################################################################################

scripts/rmg2to3.py

@@ -82,6 +82,21 @@
 from tqdm import tqdm
 
 
+# Module names
+MODULES = {
+    'canteraModel': 'canteramodel',
+    'canteraTest': 'canteramodelTest',
+    'extractInfoFromckcsv': 'ckcsvparser',
+    'diff_models': 'diffmodels',
+    'diff_modelsTest': 'diffmodelsTest',
+    'fluxtest': 'fluxdiagramTest',
+    'generate_reactions': 'generatereactions',
+    'testGenerateReactions': 'generatereactionsTest',
+    'merge_models': 'mergemodels',
+    'merge_modelsTest': 'mergemodelsTest',
+    'observablesRegression': 'observablesregression',
+}
+
 # Global variables and functions
 GLOBALS1 = {
     # Arkane
@@ -1818,6 +1833,7 @@
     'terminationTime': 'termination_time',
 }
 
+# Names which are risky to replace using regex
 DANGEROUS = ['SMILES', 'InChI', 'R', 'Run', 'atomTypes', 'format', 'F']
 
 
@@ -1947,6 +1963,7 @@ def find_name_in_line(pattern, line, replacement=None):
 
     replacements = []
     if arguments.both_stages or arguments.stage1:
+        replacements.extend(compile_regex(MODULES, args=False, attr=False, words=words, avoid_danger=avoid_danger))
         replacements.extend(compile_regex(GLOBALS1, args=False, attr=False, words=words, avoid_danger=avoid_danger))
         replacements.extend(compile_regex(METHODS1, args=False, attr=attr, words=words, avoid_danger=avoid_danger))
         replacements.extend(compile_regex(ATTRIBUTES1, args=False, attr=attr, words=words, avoid_danger=avoid_danger))