Fix install and test (#71)

* Fix failing unit test
* Bump pysam version to fix install problems

fgpyo/fasta/builder.py

@@ -43,6 +43,7 @@ def samtools_dict(*args: Any) -> None:
  def samtools_faidx(*args: Any) -> None:
  pass
 
+
 else:
  from pysam import dict as samtools_dict
  from pysam import faidx as samtools_faidx

fgpyo/util/tests/test_metric.py

@@ -321,12 +321,13 @@ def test_metric_list_parse_with_none() -> None:
  )
 
 
-def test_metrics_fast_concat(tmpdir: TmpDir) -> None:
- path_input = []
- path_input.append(Path(tmpdir) / "metrics_1.txt")
- path_input.append(Path(tmpdir) / "metrics_2.txt")
- path_input.append(Path(tmpdir) / "metrics_3.txt")
- path_output: Path = Path(tmpdir) / "metrics_concat.txt"
+def test_metrics_fast_concat(tmp_path: Path) -> None:
+ path_input = [
+ tmp_path / "metrics_1.txt",
+ tmp_path / "metrics_2.txt",
+ tmp_path / "metrics_3.txt",
+ ]
+ path_output: Path = tmp_path / "metrics_concat.txt"
 
  DummyMetric.write(path_input[0], DUMMY_METRICS[0])
  DummyMetric.write(path_input[1], DUMMY_METRICS[1])

pyproject.toml

@@ -30,8 +30,8 @@ attrs = ">=19.3.0"
 typing_extensions = { version = ">=3.7.4", python = "<3.8" } # Literal support
 typing_inspect = { version = ">=0.3.1", python = "<3.8" } # inspecting types
 sphinx = {version = "4.3.1", optional = true}
-pysam = ">=0.20.0"
 sphinx_rtd_theme = {version = "^1.3.0", optional = true}
+pysam = ">=0.22.0"
 
 [tool.poetry.extras]
 docs = ["sphinx", "sphinx_rtd_theme"]