feat: offer GZIP support for Metric IO

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 +154,11 @@ 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/metric.py

@@ -115,6 +115,7 @@
 
 import attr
 
+from fgpyo import io
 from fgpyo.util import inspect
 
 MetricType = TypeVar("MetricType")
@@ -161,7 +162,7 @@ def read(cls, path: Path, ignore_extra_fields: bool = True) -> Iterator[Any]:
             ignore_extra_fields: True to ignore any extra columns, False to raise an exception.
         """
         parsers = cls._parsers()
-        with path.open("r") as reader:
+        with io.to_reader(path) as reader:
             header: List[str] = reader.readline().rstrip("\r\n").split("\t")
             # check the header
             class_fields = set(cls.header())
@@ -234,7 +235,7 @@ def write(cls, path: Path, *values: MetricType) -> None:
             path: path to the output file
             values: zero or more metrics.
         """
-        with path.open("w") as writer:
+        with io.to_writer(path) as writer:
             writer.write("\t".join(cls.header()))
             writer.write("\n")
             for value in values:

fgpyo/util/tests/test_metric.py

@@ -1,4 +1,5 @@
 import enum
+import gzip
 from pathlib import Path
 from typing import Any
 from typing import Callable
@@ -10,7 +11,6 @@
 
 import attr
 import pytest
-from py._path.local import LocalPath as TmpDir
 
 from fgpyo.util.metric import Metric
 
@@ -138,8 +138,8 @@ 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 = Path(tmp_path) / "metrics.txt"
 
     DummyMetric.write(path, metric)
     metrics: List[DummyMetric] = list(DummyMetric.read(path=path))
@@ -148,8 +148,8 @@ 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 = Path(tmp_path) / "metrics.txt"
 
     DummyMetric.write(path, *DUMMY_METRICS)
     metrics: List[DummyMetric] = list(DummyMetric.read(path=path))
@@ -158,9 +158,23 @@ def test_metrics_roundtrip(tmpdir: TmpDir) -> None:
     assert metrics == DUMMY_METRICS
 
 
-def test_metrics_read_extra_columns(tmpdir: TmpDir) -> None:
+def test_metric_roundtrip_gzip(tmp_path: Path) -> None:
+    path: Path = Path(tmp_path) / "metrics.txt.gz"
+
+    DummyMetric.write(path, *DUMMY_METRICS)
+
+    with gzip.open(path, "r") as handle:
+        handle.read(1)  # Will raise an exception if not a GZIP file.
+
+    metrics: List[DummyMetric] = list(DummyMetric.read(path=path))
+
+    assert len(metrics) == len(DUMMY_METRICS)
+    assert metrics == DUMMY_METRICS
+
+
+def test_metrics_read_extra_columns(tmp_path: Path) -> None:
     person = Person(name="Max", age=42)
-    path = Path(tmpdir) / "metrics.txt"
+    path = Path(tmp_path) / "metrics.txt"
     with path.open("w") as writer:
         header = Person.header()
         header.append("foo")
@@ -173,9 +187,9 @@ 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 = 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:
@@ -189,9 +203,9 @@ 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 = 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: