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more hacks for pytest compat, remove deprecated methods
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RWest removed black formatting of:
-  rmgpy/tools/loader.py
-  arkane/encorr/isodesmic.py
-  rmgpy/data/kinetics/rules.py
-  rmgpy/molecule/inchi.py
-  rmgpy/molecule/adjlist.py
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@JacksonBurns @rwest
JacksonBurns authored and rwest committed Aug 9, 2023
1 parent b0be3b6 commit 9f293be
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Showing 21 changed files with 281 additions and 1,792 deletions.
4 changes: 4 additions & 0 deletions arkane/encorr/isodesmic.py
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Original file line number Diff line number Diff line change
Expand Up @@ -379,6 +379,10 @@ def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
except ValueError:
# This is not being run in the main thread, so we cannot reset signal
pass
except TypeError:
print(
"Failed to reset signal handling in LPSolve - are you running pytest?"
)

# Return the solution if a valid reaction is found. Otherwise continue to next solver
if status == 0:
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150 changes: 15 additions & 135 deletions rmgpy/chemkin.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -1367,25 +1367,6 @@ def read_reactions_block(f, species_dict, read_comments=True):
energy_units = unit
else:
raise ChemkinError('Unknown unit type "{0}"'.format(unit))

elif len(tokens) > 0 and tokens[0].lower() == 'unit:':
# RMG-Java kinetics library file
warnings.warn("The RMG-Java kinetic library files are"
" no longer supported and may be"
" removed in version 2.3.", DeprecationWarning)
found = True
while 'reactions:' not in line.lower():
line = f.readline()
line = remove_comment_from_line(line)[0]
line = line.strip()

if 'A:' in line or 'E:' in line:
units = line.split()[1]
if 'A:' in line:
molecule_units, volume_units, time_units = units.lower().split(
'/') # Assume this is a 3-tuple: moles or molecules, volume, time
elif 'E:' in line:
energy_units = units.lower()
else:
line = f.readline()

Expand Down Expand Up @@ -1480,12 +1461,6 @@ def read_reactions_block(f, species_dict, read_comments=True):
# True for Chemkin files generated from RMG-Py
kinetics_list.pop(0)
comments_list.pop(-1)
elif kinetics_list[0] == '' and comments_list[0] == '':
# True for Chemkin files generated from RMG-Java
warnings.warn("RMG-Java loading is no longer supported and may be"
" removed in version 2.3.", DeprecationWarning)
kinetics_list.pop(0)
comments_list.pop(0)
else:
# In reality, comments can occur anywhere in the Chemkin
# file (e.g. either or both of before and after the
Expand Down Expand Up @@ -1515,30 +1490,6 @@ def read_reactions_block(f, species_dict, read_comments=True):

return reaction_list

################################################################################


def save_html_file(path, read_comments=True):
"""
Save an output HTML file from the contents of a RMG-Java output folder
"""
warnings.warn("RMG-Java loading is no longer supported and may be"
" removed in version 2.3.", DeprecationWarning)
from rmgpy.rmg.model import CoreEdgeReactionModel
from rmgpy.rmg.output import save_output_html
chemkin_path = os.path.join(path, 'chemkin', 'chem.inp')
dictionary_path = os.path.join(path, 'RMG_Dictionary.txt')
model = CoreEdgeReactionModel()
model.core.species, model.core.reactions = load_chemkin_file(chemkin_path, dictionary_path,
read_comments=read_comments)
output_path = os.path.join(path, 'output.html')
species_path = os.path.join(path, 'species')
if not os.path.isdir(species_path):
os.makedirs(species_path)
save_output_html(output_path, model)

################################################################################


def get_species_identifier(species):
"""
Expand Down Expand Up @@ -1738,45 +1689,22 @@ def write_reaction_string(reaction, java_library=False):
'that support different reaction orders for the Low and High pressures limits. '
'You should revise reaction {0}'.format(reaction.label))

if java_library:
warnings.warn("Writing RMG-Java format is no longer supported and may be"
" removed in version 2.3.", DeprecationWarning)
third_body = ''
if kinetics.is_pressure_dependent():
if (isinstance(kinetics, _kinetics.ThirdBody) and
not isinstance(kinetics, (_kinetics.Lindemann, _kinetics.Troe))):
third_body = ' + M'
elif isinstance(kinetics, _kinetics.PDepArrhenius):
third_body = ''
elif isinstance(kinetics, _kinetics.Chebyshev):
third_body = ''
else:
third_body = ' (+{0})'.format(
get_species_identifier(reaction.specific_collider)) if reaction.specific_collider else ' (+M)'

reaction_string = ' + '.join([get_species_identifier(reactant) for reactant in reaction.reactants])
reaction_string += third_body
reaction_string += ' = ' if reaction.reversible else ' => '
reaction_string += ' + '.join([get_species_identifier(product) for product in reaction.products])
reaction_string += third_body

else:
third_body = ''
if kinetics.is_pressure_dependent():
if (isinstance(kinetics, _kinetics.ThirdBody) and
not isinstance(kinetics, (_kinetics.Lindemann, _kinetics.Troe))):
third_body = '+M'
elif isinstance(kinetics, (_kinetics.PDepArrhenius, _kinetics.MultiPDepArrhenius)):
third_body = ''
else:
third_body = '(+{0})'.format(
get_species_identifier(reaction.specific_collider)) if reaction.specific_collider else '(+M)'
third_body = ''
if kinetics.is_pressure_dependent():
if (isinstance(kinetics, _kinetics.ThirdBody) and
not isinstance(kinetics, (_kinetics.Lindemann, _kinetics.Troe))):
third_body = '+M'
elif isinstance(kinetics, (_kinetics.PDepArrhenius, _kinetics.MultiPDepArrhenius)):
third_body = ''
else:
third_body = '(+{0})'.format(
get_species_identifier(reaction.specific_collider)) if reaction.specific_collider else '(+M)'

reaction_string = '+'.join([get_species_identifier(reactant) for reactant in reaction.reactants])
reaction_string += third_body
reaction_string += '<=>' if reaction.reversible else '=>'
reaction_string += '+'.join([get_species_identifier(product) for product in reaction.products])
reaction_string += third_body
reaction_string = '+'.join([get_species_identifier(reactant) for reactant in reaction.reactants])
reaction_string += third_body
reaction_string += '<=>' if reaction.reversible else '=>'
reaction_string += '+'.join([get_species_identifier(product) for product in reaction.products])
reaction_string += third_body

if len(reaction_string) > 52:
logging.debug("Chemkin reaction string '%s' is too long for Chemkin 2!", reaction_string)
Expand Down Expand Up @@ -1933,12 +1861,6 @@ def write_kinetics_entry(reaction, species_list, verbose=True, java_library=Fals
# Print dummy values that Chemkin parses but ignores
string += '{0:<9.3e} {1:<9.3f} {2:<9.3f}'.format(1, 0, 0)

if java_library:
warnings.warn("RMG-Java libraries are no longer supported and may be"
" removed in version 2.3.", DeprecationWarning)
# Assume uncertainties are zero (when parsing from chemkin), may need to adapt later
string += '{0:<9.1f} {1:<9.1f} {2:<9.1f}'.format(0, 0, 0)

string += '\n'

if getattr(kinetics, 'coverage_dependence', None):
Expand Down Expand Up @@ -2291,48 +2213,6 @@ def save_chemkin_surface_file(path, species, reactions, verbose=True, check_for_
_chemkin_reaction_count = None


def save_java_kinetics_library(path, species, reactions):
"""
Save the reaction files for a RMG-Java kinetics library: pdepreactions.txt
and reactions.txt given a list of reactions, with species.txt containing the
RMG-Java formatted dictionary.
"""
warnings.warn("Java kinetics libararies are no longer supported and may be" \
"removed in version 2.3.", DeprecationWarning)
# Check for duplicate
mark_duplicate_reactions(reactions)

f = open(os.path.join(path, 'reactions.txt'), 'w')
f2 = open(os.path.join(path, 'pdepreactions.txt'), 'w')

# Headers
f.write('Unit:\n')
f.write('A: mol/cm3/s\n')
f.write('E: kcal/mol\n')
f.write('\n')
f.write('Reactions:\n')
f.write('\n')

f2.write('Unit:\n')
f2.write('A: mol/cm3/s\n')
f2.write('E: kcal/mol\n')
f2.write('\n')
f2.write('Reactions:\n')
f2.write('\n')

for rxn in reactions:
if rxn.kinetics.is_pressure_dependent():
f2.write(write_kinetics_entry(rxn, species_list=species, verbose=False, java_library=True))
f2.write('\n')
else:
f.write(write_kinetics_entry(rxn, species_list=species, verbose=False, java_library=True))
f.write('\n')
f.close()
f2.close()

save_species_dictionary(os.path.join(path, 'species.txt'), species, old_style=True)


def save_chemkin(reaction_model, path, verbose_path, dictionary_path=None, transport_path=None,
save_edge_species=False):
"""
Expand Down
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