refactor: use pathlib in tests

fgpyo/fasta/tests/test_builder.py

@@ -4,7 +4,6 @@
 from tempfile import NamedTemporaryFile as NamedTemp
 
 import pytest
-from py._path.local import LocalPath as TmpDir
 from pytest import raises
 
 from fgpyo.fasta.builder import FastaBuilder
@@ -64,14 +63,14 @@ def test_bases_string_from_ContigBuilder_add(
  bases: str,
  times: int,
  expected: str,
- tmpdir: TmpDir,
+ tmp_path: Path,
 ) -> None:
  """
  Reads bases back from fasta and checks that extra spaces are removed and bases are uppercase
  """
  builder = FastaBuilder()
  builder.add(name).add(bases, times)
- with NamedTemp(suffix=".fa", dir=tmpdir, mode="w", delete=True) as fp:
+ with NamedTemp(suffix=".fa", dir=tmp_path, mode="w", delete=True) as fp:
  builder.to_file(Path(fp.name))
  with open(fp.name, "r") as read_fp:
  for line in read_fp.readlines():

fgpyo/sam/tests/test_sam.py

@@ -10,7 +10,6 @@
 
 import pysam
 import pytest
-from py._path.local import LocalPath as TmpDir
 from pysam import AlignmentHeader
 
 import fgpyo.sam as sam
@@ -141,10 +140,10 @@ def test_sam_file_open_writing(
  file_type: SamFileType,
  expected_records: List[pysam.AlignedSegment],
  header_dict: AlignmentHeader,
- tmpdir: TmpDir,
+ tmp_path: Path,
 ) -> None:
  # use header as a keyword argument
- with NamedTemp(suffix=file_type.extension, dir=tmpdir, mode="w", delete=False) as fp:
+ with NamedTemp(suffix=file_type.extension, dir=tmp_path, mode="w", delete=False) as fp:
  kwargs = {"header": header_dict}
  with sam._pysam_open(
  path=fp.file, open_for_reading=False, file_type=file_type, **kwargs # type: ignore
@@ -155,11 +154,13 @@ def test_sam_file_open_writing(
 
 
 def test_sam_file_open_writing_header_keyword(
- expected_records: List[pysam.AlignedSegment], header_dict: AlignmentHeader, tmpdir: TmpDir
+ expected_records: List[pysam.AlignedSegment],
+ header_dict: AlignmentHeader,
+ tmp_path: Path,
 ) -> None:
  # Use SamWriter
  # use header as a keyword argument
- with NamedTemp(suffix=".sam", dir=tmpdir, mode="w", delete=False) as fp:
+ with NamedTemp(suffix=".sam", dir=tmp_path, mode="w", delete=False) as fp:
  with sam.writer(path=fp.name, header=header_dict, file_type=SamFileType.SAM) as sam_writer:
  for r in expected_records:
  sam_writer.write(r)

fgpyo/util/tests/test_metric.py

@@ -11,7 +11,6 @@
 
 import attr
 import pytest
-from py._path.local import LocalPath as TmpDir
 
 from fgpyo.util.metric import Metric
 
@@ -139,8 +138,11 @@ class PersonDefault(Metric["PersonDefault"]):
 
 
 @pytest.mark.parametrize("metric", DUMMY_METRICS)
-def test_metric_roundtrip(tmpdir: TmpDir, metric: DummyMetric) -> None:
- path: Path = Path(tmpdir) / "metrics.txt"
+def test_metric_roundtrip(
+ tmp_path: Path,
+ metric: DummyMetric,
+) -> None:
+ path: Path = tmp_path / "metrics.txt"
 
  DummyMetric.write(path, metric)
  metrics: List[DummyMetric] = list(DummyMetric.read(path=path))
@@ -149,8 +151,8 @@ def test_metric_roundtrip(tmpdir: TmpDir, metric: DummyMetric) -> None:
  assert metrics[0] == metric
 
 
-def test_metrics_roundtrip(tmpdir: TmpDir) -> None:
- path: Path = Path(tmpdir) / "metrics.txt"
+def test_metrics_roundtrip(tmp_path: Path) -> None:
+ path: Path = tmp_path / "metrics.txt"
 
  DummyMetric.write(path, *DUMMY_METRICS)
  metrics: List[DummyMetric] = list(DummyMetric.read(path=path))
@@ -173,9 +175,9 @@ def test_metrics_roundtrip_gzip(tmp_path: Path) -> None:
  assert metrics == DUMMY_METRICS
 
 
-def test_metrics_read_extra_columns(tmpdir: TmpDir) -> None:
+def test_metrics_read_extra_columns(tmp_path: Path) -> None:
  person = Person(name="Max", age=42)
- path = Path(tmpdir) / "metrics.txt"
+ path = tmp_path / "metrics.txt"
  with path.open("w") as writer:
  header = Person.header()
  header.append("foo")
@@ -188,9 +190,9 @@ def test_metrics_read_extra_columns(tmpdir: TmpDir) -> None:
  list(Person.read(path=path, ignore_extra_fields=False))
 
 
-def test_metrics_read_missing_optional_columns(tmpdir: TmpDir) -> None:
+def test_metrics_read_missing_optional_columns(tmp_path: Path) -> None:
  person = PersonMaybeAge(name="Max", age=None)
- path = Path(tmpdir) / "metrics.txt"
+ path = tmp_path / "metrics.txt"
 
  # The "age" column is optional, and not in the file, but that's ok
  with path.open("w") as writer:
@@ -204,9 +206,9 @@ def test_metrics_read_missing_optional_columns(tmpdir: TmpDir) -> None:
  list(PersonMaybeAge.read(path=path))
 
 
-def test_metric_read_missing_column_with_default(tmpdir: TmpDir) -> None:
+def test_metric_read_missing_column_with_default(tmp_path: Path) -> None:
  person = PersonDefault(name="Max")
- path = Path(tmpdir) / "metrics.txt"
+ path = tmp_path / "metrics.txt"
 
  # The "age" column hs a default, and not in the file, but that's ok
  with path.open("w") as writer: