MucOneUp/mypy.ini at main · berntpopp/MucOneUp · GitHub

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[mypy]
# Python version
python_version = 3.10

# Import discovery
mypy_path = .
namespace_packages = True
explicit_package_bases = True
follow_imports = normal

# Strictness (gradual typing approach)
warn_return_any = True
warn_unused_configs = True
warn_unused_ignores = True
warn_redundant_casts = True
warn_no_return = True
warn_unreachable = True

# Start with lenient settings, tighten over time
# disallow_untyped_defs: Start False, migrate to True per module
disallow_untyped_defs = False
disallow_incomplete_defs = False
check_untyped_defs = True
disallow_untyped_calls = False

# Error display
show_error_codes = True
show_column_numbers = True
pretty = True

# Strict settings for new modules with complete type hints
[mypy-muc_one_up.exceptions]
disallow_untyped_defs = True
disallow_incomplete_defs = True

[mypy-muc_one_up.type_defs]
disallow_untyped_defs = True
disallow_incomplete_defs = True

[mypy-muc_one_up.config]
disallow_untyped_defs = True
disallow_incomplete_defs = True

[mypy-muc_one_up.validation]
disallow_untyped_defs = True
disallow_incomplete_defs = True

[mypy-muc_one_up.bioinformatics.validation]
disallow_untyped_defs = True
disallow_incomplete_defs = True

[mypy-muc_one_up.bioinformatics.reference_validation]
disallow_untyped_defs = True
disallow_incomplete_defs = True

[mypy-muc_one_up.probabilities]
disallow_untyped_defs = True
disallow_incomplete_defs = True

[mypy-muc_one_up.distribution]
disallow_untyped_defs = True
disallow_incomplete_defs = True

# Gradually enable for modules with type hints
[mypy-muc_one_up.simulate]
disallow_untyped_defs = False
disallow_incomplete_defs = False

[mypy-muc_one_up.mutate]
disallow_untyped_defs = False
disallow_incomplete_defs = False

# Ignore third-party libraries without type stubs
[mypy-orfipy.*]
ignore_missing_imports = True

[mypy-orfipy_core.*]
ignore_missing_imports = True

[mypy-jsonschema.*]
ignore_missing_imports = True

[mypy-pysam.*]
ignore_missing_imports = True

[mypy-Bio.*]
ignore_missing_imports = True

[mypy-muc_one_up.read_simulator.stages.source_manifest]
# pysam has stubs on this machine but is declared optional; the ImportError
# fallback branch holds a `type: ignore[assignment]` that is unreachable when
# pysam is installed, triggering warn_unused_ignores.  Suppress for this file.
warn_unused_ignores = False