Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Asterisk is already used for excited state in photochemistry #231

Merged
merged 2 commits into from Apr 23, 2024
Merged

Asterisk is already used for excited state in photochemistry #231

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
da3f3ef
Asterisk is already used for excited state in photochemistry
bjodah Apr 23, 2024
51557e4
tidy up
bjodah Apr 23, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
18 changes: 7 additions & 11 deletions chempy/util/parsing.py
View file
Open in desktop
Expand Up @@ -96,7 +96,7 @@ def _get_formula_parser():
| '{' formula '}'
| '[' formula ']' ) count prime charge?
formula :: term+
hydrate :: ( '.' | '\u00B7' | '*' ) count? formula
hydrate :: ( '..' | '\u00B7' | '.' ) count? formula
state :: '(' ( 's' | 'l' | 'g' | 'aq' | 'cr' ) ')'
compound :: count formula hydrate? state?

Expand All @@ -115,7 +115,7 @@ def _get_formula_parser():
| '{' formula '}'
| '[' formula ']' ) count prime charge?
formula :: term+
hydrate :: ( '..' | '\u00B7' | '*' ) count? formula
hydrate :: ( '..' | '\u00B7' | '.' ) count? formula
state :: '(' ( 's' | 'l' | 'g' | 'aq' | 'cr' ) ')'
compound :: count formula hydrate? state?
"""
Expand Down Expand Up @@ -378,7 +378,7 @@ def formula_to_composition(
True
>>> formula_to_composition('.NHO-(aq)') == {0: -1, 1: 1, 7: 1, 8: 1}
True
>>> formula_to_composition('Na2CO3*7H2O') == {11: 2, 6: 1, 8: 10, 1: 14}
>>> formula_to_composition('Na2CO3..7H2O') == {11: 2, 6: 1, 8: 10, 1: 14}
True

"""
Expand All @@ -387,10 +387,10 @@ def formula_to_composition(

stoich_tok, chg_tok = _formula_to_parts(formula, prefixes, suffixes)[:2]
tot_comp = {}
if ".." in stoich_tok:
parts = stoich_tok.split("..")
elif "\u00b7" in stoich_tok:
if "\u00b7" in stoich_tok:
parts = stoich_tok.split('\u00b7')
elif '..' in stoich_tok:
parts = stoich_tok.split("..")
elif '.' in stoich_tok:
warnings.warn(
("dot is ambiguous in chempy-0.8.x, prefer '*' or '\u00b7' for complexes."
Expand All @@ -399,7 +399,7 @@ def formula_to_composition(
)
parts = stoich_tok.split('.')
else:
parts = list(filter(len, internal_asterisk.split(stoich_tok)))
parts = [stoich_tok]

for idx, stoich in enumerate(parts):
if idx == 0:
Expand Down Expand Up @@ -536,9 +536,6 @@ def to_reaction(line, substance_keys, token, Cls, globals_=None, **kwargs):
)


internal_asterisk = re.compile(r"([^\s\*]+)\*([a-zA-Z0-9]+)")


def _formula_to_format(
sub,
sup,
Expand All @@ -549,7 +546,6 @@ def _formula_to_format(
):
parts = _formula_to_parts(formula, prefixes.keys(), suffixes)
parts0 = parts[0].replace("..", "\u00B7")
parts0 = internal_asterisk.sub("\u00B7", parts0)
if '.' in parts0:
warnings.warn(
("dot is ambiguous in chempy-0.8.x, prefer '*' or '' for complexes."
Expand Down
2 changes: 1 addition & 1 deletion chempy/util/tests/test_parsing.py
View file
Open in desktop
Expand Up @@ -724,7 +724,7 @@ def test_composition_dot_as_crystal_water_chempy08x():
as floating point delimiter in fractional stoichiometric coefficients."""
ref = {30: 1, 7: 2, 8: 12, 1: 12}
assert formula_to_composition('Zn(NO3)2{}6H2O'.format('\u00B7')) == ref
assert formula_to_composition('Zn(NO3)2*6H2O') == ref
assert formula_to_composition('Zn(NO3)2..6H2O') == ref
# https://docs.pytest.org/en/7.1.x/how-to/capture-warnings.html#ensuring-code-triggers-a-deprecation-warning
with pytest.deprecated_call():
assert formula_to_composition('Zn(NO3)2.6H2O') == ref