chore: Require error codes on type: ignore pragmas (#190)

This PR adds the mypy config introduced into our template in
fulcrumgenomics/python-template#28.

Error codes are now required on any `type: ignore` pragmas. This PR also
adds error codes to any existing `ignore`s without a code.

fgpyo/sam/__init__.py

@@ -266,7 +266,7 @@ def _pysam_open(
  else:
  file_type = file_type or SamFileType.from_path(path)
  path = str(path)
- elif not isinstance(path, _IOClasses): # type: ignore
+ elif not isinstance(path, _IOClasses): # type: ignore[unreachable]
  open_type = "reading" if open_for_reading else "writing"
  raise TypeError(f"Cannot open '{type(path)}' for {open_type}.")
 

fgpyo/sam/builder.py

@@ -596,12 +596,12 @@ def to_path(
  file_handle.close()
  if self._sort_order == SamOrder.QueryName:
  # Ignore type hints for now until we have wrappers to use here.
- pysam.sort("-n", *samtools_sort_args) # type: ignore
+ pysam.sort("-n", *samtools_sort_args) # type: ignore[attr-defined]
  elif self._sort_order == SamOrder.Coordinate:
  # Ignore type hints for now until we have wrappers to use here.
  if index:
  samtools_sort_args.insert(0, "--write-index")
- pysam.sort(*samtools_sort_args) # type: ignore
+ pysam.sort(*samtools_sort_args) # type: ignore[attr-defined]
 
  return path
 

fgpyo/vcf/__init__.py

@@ -83,7 +83,7 @@ def reader(path: VcfPath) -> Generator[VcfReader, None, None]:
  with fgpyo.io.suppress_stderr():
  # to avoid spamming log about index older than vcf, redirect stderr to /dev/null: only
  # when first opening the file
- _reader = VariantFile(path, mode="r") # type: ignore
+ _reader = VariantFile(path, mode="r") # type: ignore[arg-type]
  # now stderr is back, so any later stderr messages will go through
  yield _reader
  _reader.close()

pyproject.toml

@@ -87,3 +87,4 @@ warn_return_any = true
 warn_unreachable = true
 warn_unused_configs = true
 warn_unused_ignores = true
+enable_error_code = "ignore-without-code"

tests/fgpyo/sam/test_sam.py

@@ -149,7 +149,7 @@ def test_sam_file_open_writing(
  path=fp.file,
  open_for_reading=False,
  file_type=file_type,
- **kwargs, # type: ignore
+ **kwargs, # type: ignore[arg-type]
  ) as sam_writer:
  for r in expected_records:
  sam_writer.write(r)

tests/fgpyo/util/test_inspect.py

@@ -126,10 +126,10 @@ class NonDataClass:
  x: int
 
  with pytest.raises(TypeError):
- get_fields_dict(NonDataClass) # type: ignore
+ get_fields_dict(NonDataClass) # type: ignore[arg-type]
 
  with pytest.raises(TypeError):
- get_fields(NonDataClass) # type: ignore
+ get_fields(NonDataClass) # type: ignore[arg-type]
 
  with pytest.raises(TypeError):
  attr_from(cls=NonDataClass, kwargs={"x": "1"}, parsers={int: int})