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Fix install and test #71

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merged 1 commit into from
Nov 7, 2023
Merged

Fix install and test #71

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1 change: 1 addition & 0 deletions fgpyo/fasta/builder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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13 changes: 7 additions & 6 deletions fgpyo/util/tests/test_metric.py
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Expand Up @@ -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])
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56 changes: 31 additions & 25 deletions poetry.lock
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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"]
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