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Pin lint tools versions #1429

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Pin lint tools versions #1429

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f0606d5
chore: include missing YAML extension
Midnighter Mar 5, 2025
d8b885b
chore: pin exact lint tools versions
Midnighter Mar 5, 2025
cff59d6
chore: offer pre-commit hooks at same versions
Midnighter Mar 5, 2025
fe34072
style: adjust to latest black version
Midnighter Mar 5, 2025
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2 changes: 1 addition & 1 deletion .editorconfig
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ insert_final_newline = true
trim_trailing_whitespace = true
max_line_length = 88

[*.{json,yml}]
[*.{json,yml,yaml}]
indent_size = 2

[*.{md,rst}]
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20 changes: 20 additions & 0 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
repos:
- repo: https://github.com/pycqa/isort
rev: 6.0.1
hooks:
- id: isort
name: isort (python)
args: [--check-only, --diff, src/cobra, setup.py, tests]
- repo: https://github.com/psf/black
rev: 25.1.0
hooks:
- id: black
args: [--check, --diff, src/cobra, setup.py, tests]
- repo: https://github.com/pycqa/flake8
rev: 7.1.2
hooks:
- id: flake8
args: [src/cobra, setup.py, tests]
additional_dependencies:
- flake8-docstrings
- flake8-bugbear
2 changes: 1 addition & 1 deletion src/cobra/core/gene.py
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Expand Up @@ -680,7 +680,7 @@ def from_symbolic(cls, sympy_gpr: Union[spl.BooleanFunction, Symbol]) -> "GPR":
"""

def _sympy_to_ast(
sympy_expr: Union[spl.BooleanFunction, Symbol]
sympy_expr: Union[spl.BooleanFunction, Symbol],
) -> Union[BoolOp, Name]:
if sympy_expr.func is spl.Or:
return BoolOp(
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2 changes: 1 addition & 1 deletion src/cobra/io/dict.py
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Expand Up @@ -68,7 +68,7 @@


def _fix_type(
value: Union[str, float, bool, Set, Dict]
value: Union[str, float, bool, Set, Dict],
) -> Union[str, float, bool, List, OrderedDict]:
"""Convert possible types to correct Python types.

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2 changes: 1 addition & 1 deletion tests/test_core/test_solution.py
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Expand Up @@ -10,7 +10,7 @@


def test_solution_contains_only_reaction_specific_values(
solved_model: Tuple[Solution, "Model"]
solved_model: Tuple[Solution, "Model"],
) -> None:
"""Test solution contains specific reaction values."""
solution, model = solved_model
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6 changes: 3 additions & 3 deletions tox.ini
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Expand Up @@ -39,21 +39,21 @@ commands =
[testenv:isort]
skip_install = True
deps=
isort
isort ==6.0.1
commands=
isort --check-only --diff {toxinidir}/src/cobra {toxinidir}/setup.py {toxinidir}/tests

[testenv:black]
skip_install = True
deps=
black
black ==25.1.0
commands=
black --check --diff {toxinidir}/src/cobra {toxinidir}/setup.py {toxinidir}/tests

[testenv:flake8]
skip_install = True
deps=
flake8
flake8 ==7.1.2
flake8-docstrings
flake8-bugbear
commands=
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