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Apply 2024 black style
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@JanCBrammer
JanCBrammer committed Jan 29, 2024
1 parent dcce3ae commit 4688536
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Showing 7 changed files with 133 additions and 95 deletions.
176 changes: 98 additions & 78 deletions tests/io/test_molfile_v3000_reader.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -236,21 +236,25 @@ def test_graph_from_file_with_multi_attachment():
[
# missing "BEGIN ATOM"
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 1 1\n"
"M V30 1 H 0 0 0 0\n",
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 1 1\n"
"M V30 1 H 0 0 0 0\n"
),
'Expected "BEGIN ATOM" on line 7, found "1 H 0 0 0 0"',
),
# missing "END ATOM"
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 2 0\n"
"M V30 BEGIN ATOM\n"
"M V30 1 H 0 0 0 0\n"
"M V30 2 H 0 0 0 0\n"
"M V30 3 H 0 0 0 0\n",
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 2 0\n"
"M V30 BEGIN ATOM\n"
"M V30 1 H 0 0 0 0\n"
"M V30 2 H 0 0 0 0\n"
"M V30 3 H 0 0 0 0\n"
),
'Expected "END ATOM" on line 10, found "3 H 0 0 0 0"',
),
],
Expand Down Expand Up @@ -293,29 +297,33 @@ def test_parsing_bond_block():
[
# missing "BEGIN BOND"
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 2 1\n"
"M V30 BEGIN ATOM\n"
"M V30 1 H 0 0 0 0\n"
"M V30 2 H 0 0 0 0\n"
"M V30 END ATOM\n"
"M V30 1 1 1 2",
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 2 1\n"
"M V30 BEGIN ATOM\n"
"M V30 1 H 0 0 0 0\n"
"M V30 2 H 0 0 0 0\n"
"M V30 END ATOM\n"
"M V30 1 1 1 2"
),
'Expected "BEGIN BOND" on line 11, found "1 1 1 2"',
),
# missing "END BOND"
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 2 2\n"
"M V30 BEGIN ATOM\n"
"M V30 1 H 0 0 0 0\n"
"M V30 2 H 0 0 0 0\n"
"M V30 END ATOM\n"
"M V30 BEGIN BOND\n"
"M V30 1 1 1 2\n"
"M V30 1 1 2 1\n"
"M V30 1 1 1 1",
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 2 2\n"
"M V30 BEGIN ATOM\n"
"M V30 1 H 0 0 0 0\n"
"M V30 2 H 0 0 0 0\n"
"M V30 END ATOM\n"
"M V30 BEGIN BOND\n"
"M V30 1 1 1 2\n"
"M V30 1 1 2 1\n"
"M V30 1 1 1 1"
),
'Expected "END BOND" on line 14, found "1 1 1 1"',
),
],
Expand Down Expand Up @@ -420,16 +428,20 @@ def test_concat_lines_with_dash_raises_exception(lines, expected_error_msg):
[
# missing COUNTS line
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 BEGIN ATOM",
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 BEGIN ATOM"
),
'Bad counts line: "M V30 BEGIN ATOM"',
),
# number of bonds missing
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 1",
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 1"
),
'Bad counts line: "M V30 COUNTS 1"',
),
],
Expand All @@ -446,29 +458,33 @@ def test_molfile_with_invalid_counts_line_raises_exception(molfile, expected_err
"molfile, expected_error_msg",
[
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 2 1\n"
"M V30 BEGIN ATOM\n"
"M V30 1 H 0 0 0 0\n"
"M V30 2 H 0 0 0 0\n"
"M V30 END ATOM\n"
"M V30 BEGIN BOND\n"
"M V30 1 1 3 1\n"
"M V30 END BOND",
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 2 1\n"
"M V30 BEGIN ATOM\n"
"M V30 1 H 0 0 0 0\n"
"M V30 2 H 0 0 0 0\n"
"M V30 END ATOM\n"
"M V30 BEGIN BOND\n"
"M V30 1 1 3 1\n"
"M V30 END BOND"
),
"Unknown atom index 3 in bond",
),
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 2 1\n"
"M V30 BEGIN ATOM\n"
"M V30 1 H 0 0 0 0\n"
"M V30 2 H 0 0 0 0\n"
"M V30 END ATOM\n"
"M V30 BEGIN BOND\n"
"M V30 1 1 2 5\n"
"M V30 END BOND",
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 2 1\n"
"M V30 BEGIN ATOM\n"
"M V30 1 H 0 0 0 0\n"
"M V30 2 H 0 0 0 0\n"
"M V30 END ATOM\n"
"M V30 BEGIN BOND\n"
"M V30 1 1 2 5\n"
"M V30 END BOND"
),
"Unknown atom index 5 in bond",
),
],
Expand All @@ -485,31 +501,35 @@ def test_molfile_with_invalid_bond_index_raises_exception(molfile, expected_erro
"molfile, expected_error_msg",
[
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 2 1\n"
"M V30 BEGIN ATOM\n"
"M V30 1 * 0 0 0 0\n"
"M V30 2 * 0 0 0 0\n"
"M V30 END ATOM\n"
"M V30 BEGIN BOND\n"
"M V30 1 1 1 2\n"
"M V30 END BOND",
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 2 1\n"
"M V30 BEGIN ATOM\n"
"M V30 1 * 0 0 0 0\n"
"M V30 2 * 0 0 0 0\n"
"M V30 END ATOM\n"
"M V30 BEGIN BOND\n"
"M V30 1 1 1 2\n"
"M V30 END BOND"
),
re.escape('Two "star" atoms (index 1 and 2) may not be connected'),
),
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 4 1\n"
"M V30 BEGIN ATOM\n"
"M V30 1 * 0 0 0 0\n"
"M V30 2 H 0 0 0 0\n"
"M V30 3 H 0 0 0 0\n"
"M V30 4 H 0 0 0 0\n"
"M V30 END ATOM\n"
"M V30 BEGIN BOND\n"
"M V30 1 1 1 2 ENDPTS=(1 3 4)\n"
"M V30 END BOND",
(
"\n\n\n 0 0 0 0 0 999 V3000\n"
"M V30 BEGIN CTAB\n"
"M V30 COUNTS 4 1\n"
"M V30 BEGIN ATOM\n"
"M V30 1 * 0 0 0 0\n"
"M V30 2 H 0 0 0 0\n"
"M V30 3 H 0 0 0 0\n"
"M V30 4 H 0 0 0 0\n"
"M V30 END ATOM\n"
"M V30 BEGIN BOND\n"
"M V30 1 1 1 2 ENDPTS=(1 3 4)\n"
"M V30 END BOND"
),
re.escape('Error in "ENDPTS=(1 3 4)": Expected 1 endpoints, found 2'),
),
],
Expand Down
9 changes: 6 additions & 3 deletions tests/parser/test_exception.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,15 @@
(
"CH4/(1-2)/(1:=14)",
re.escape(
"line 1:13 missing {'mass', 'rad'} at '='\nCH4/(1-2)/(1:=14)\n ^"
"line 1:13 missing {'mass', 'rad'} at '='\nCH4/(1-2)/(1:=14)\n "
" ^"
),
),
(
"CH4/(1-2)/(1:massmass=14)",
re.escape(
"line 1:17 extraneous input 'mass' expecting '='\nCH4/(1-2)/(1:massmass=14)\n ^^^^"
"line 1:17 extraneous input 'mass' expecting"
" '='\nCH4/(1-2)/(1:massmass=14)\n ^^^^"
),
),
(
Expand All @@ -31,7 +33,8 @@
(
"CH4/(1-)",
re.escape(
"line 1:7 mismatched input ')' expecting {'1', '2', '3', '4', '5', '6', '7', '8', '9', GREATER_THAN_NINE}\nCH4/(1-)\n ^"
"line 1:7 mismatched input ')' expecting {'1', '2', '3', '4', '5', '6',"
" '7', '8', '9', GREATER_THAN_NINE}\nCH4/(1-)\n ^"
),
),
],
Expand Down
5 changes: 4 additions & 1 deletion tests/parser/test_parser.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -128,7 +128,10 @@ def test_node_attributes(node_attributes, expected_node_attributes):
def test_overriding_node_attribute_raises_exception(
node_attributes, offending_node_index, offending_key
):
expected_error_msg = f'^Atom {offending_node_index}: Attribute "{offending_key}" was already defined.$'
expected_error_msg = (
f'^Atom {offending_node_index}: Attribute "{offending_key}" was already'
" defined.$"
)
with pytest.raises(TucanParserException, match=expected_error_msg):
_extract_node_attributes(node_attributes)

Expand Down
1 change: 1 addition & 0 deletions tucan/element_attributes.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
which was set to lightgrey for better visibility. Colors beyond meitnerium are
not officially assigned so far and were thus set to the same value as for Mt.
"""

from __future__ import annotations
from typing import Final

Expand Down
8 changes: 5 additions & 3 deletions tucan/graph_utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -42,9 +42,11 @@ def _add_invariant_code(
) -> None:
for atom, attrs in atom_attrs.items():
invariant_code = tuple(
attrs[icd.key]
if (default_value := icd.default_value) is None
else attrs.get(icd.key, default_value)
(
attrs[icd.key]
if (default_value := icd.default_value) is None
else attrs.get(icd.key, default_value)
)
for icd in invariant_code_definitions
)
atom_attrs[atom].update({INVARIANT_CODE: invariant_code})
Expand Down
26 changes: 17 additions & 9 deletions tucan/io/molfile_v3000_reader.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -78,13 +78,15 @@ def _parse_atom_block(

if (begin_atom_str := " ".join(lines[atom_block_offset - 1][2:])) != "BEGIN ATOM":
raise MolfileParserException(
f'Expected "BEGIN ATOM" on line {atom_block_offset}, found "{begin_atom_str}"'
f'Expected "BEGIN ATOM" on line {atom_block_offset}, found'
f' "{begin_atom_str}"'
)
if (
end_atom_str := " ".join(lines[atom_block_offset + atom_count][2:])
) != "END ATOM":
raise MolfileParserException(
f'Expected "END ATOM" on line {atom_block_offset + atom_count + 1}, found "{end_atom_str}"'
f'Expected "END ATOM" on line {atom_block_offset + atom_count + 1}, found'
f' "{end_atom_str}"'
)

atom_attrs = {}
Expand Down Expand Up @@ -120,9 +122,11 @@ def _parse_atom_attributes(

optional_attrs = {
CHG: [int(i.split("=")[1]) for i in line if "CHG" in i],
MASS: [int(i.split("=")[1]) for i in line if "MASS" in i]
if not isotope_mass
else [isotope_mass],
MASS: (
[int(i.split("=")[1]) for i in line if "MASS" in i]
if not isotope_mass
else [isotope_mass]
),
RAD: [int(i.split("=")[1]) for i in line if "RAD" in i],
}
for key, val in optional_attrs.items():
Expand All @@ -147,13 +151,15 @@ def _parse_bond_block(

if (begin_bond_str := " ".join(lines[bond_block_offset - 1][2:])) != "BEGIN BOND":
raise MolfileParserException(
f'Expected "BEGIN BOND" on line {bond_block_offset}, found "{begin_bond_str}"'
f'Expected "BEGIN BOND" on line {bond_block_offset}, found'
f' "{begin_bond_str}"'
)
if (
end_bond_str := " ".join(lines[bond_block_offset + bond_count][2:])
) != "END BOND":
raise MolfileParserException(
f'Expected "END BOND" on line {bond_block_offset + bond_count + 1}, found "{end_bond_str}"'
f'Expected "END BOND" on line {bond_block_offset + bond_count + 1}, found'
f' "{end_bond_str}"'
)

bonds = {}
Expand All @@ -166,7 +172,8 @@ def _parse_bond_block(
atom2_is_star = atom2_index in star_atoms
if atom1_is_star and atom2_is_star:
raise MolfileParserException(
f'Two "star" atoms (index {atom1_index + 1} and {atom2_index + 1}) may not be connected'
f'Two "star" atoms (index {atom1_index + 1} and {atom2_index + 1}) may'
" not be connected"
)
elif atom1_is_star:
bond_tuples = _parse_bond_line_with_star_atom(line, atom2_index)
Expand Down Expand Up @@ -197,7 +204,8 @@ def _parse_bond_line_with_star_atom(
numbers = [int(num) for num in endpts_token[8:-1].split()]
if (expected_n_endpts := numbers[0]) != (n_endpts := len(numbers) - 1):
raise MolfileParserException(
f'Error in "{endpts_token}": Expected {expected_n_endpts} endpoints, found {n_endpts}'
f'Error in "{endpts_token}": Expected {expected_n_endpts} endpoints, found'
f" {n_endpts}"
)

return [(start_atom_index, end_atom_index - 1) for end_atom_index in numbers[1:]]
Expand Down
3 changes: 2 additions & 1 deletion tucan/visualization.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,8 @@ def draw_molecules(
"""
if highlight not in [ATOMIC_NUMBER, PARTITION]:
print(
f"Please select one of {{'{PARTITION}', '{ATOMIC_NUMBER}'}} for `highlight`."
f"Please select one of {{'{PARTITION}', '{ATOMIC_NUMBER}'}} for"
" `highlight`."
)
return
n_molecules = len(m_list)
Expand Down

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