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FIx tests + update coverage
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@jvivian
jvivian committed Jun 6, 2024
1 parent 8c16dd9 commit 1df008e
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87 changes: 47 additions & 40 deletions coverage.xml
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<?xml version="1.0" ?>
<coverage version="7.4.3" timestamp="1711594976212" lines-valid="308" lines-covered="297" line-rate="0.9643" branches-valid="92" branches-covered="80" branch-rate="0.8696" complexity="0">
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<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.4.3 -->
<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
<sources>
<source>/Users/jvivian/git/covid19-drDFM/covid19_drdfm</source>
<source>/home/jvivian/covid19-drDFM/covid19_drdfm</source>
</sources>
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<methods/>
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2 changes: 1 addition & 1 deletion covid19_drdfm/dfm.py
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Expand Up @@ -90,7 +90,7 @@ def run(self, maxiter=10_000, global_multiplier=1, columns: Optional[list[str]]
- Exception: If an error occurs during model fitting.
"""
self.outdir.mkdir(exist_ok=True)
self.ad.obs = self.ad.obs.drop(columns="Time")
# self.ad.obs = self.ad.obs.drop(columns="Time")
print(f"{len(self.batches)} batches to run")
for batch_name, batch in track(list(self.batches.items())):
data = DataProcessor(batch, global_multiplier, maxiter).process(columns)
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2 changes: 1 addition & 1 deletion tests/test_processing.py
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Expand Up @@ -28,7 +28,7 @@ def test_write(data, tmpdir):
data.write(outdir)
assert (outdir / "df.csv").exists()
assert (outdir / "raw.csv").exists()
assert (outdir / "run-info.json").exists()
assert (outdir / "run-info.yaml").exists()


def test_get_factors(data):
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4 changes: 2 additions & 2 deletions tests/test_results.py
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Expand Up @@ -12,7 +12,7 @@ def runs_dir() -> pd.DataFrame:

@pytest.fixture
def run_path(runs_dir) -> pd.DataFrame:
return runs_dir / "test-all-global-1_2019"
return runs_dir / "pandemic-only"


@pytest.fixture
Expand All @@ -37,4 +37,4 @@ def test_parse_run_results(run_path):

def test_parse_multiple_runs(runs_dir):
df = parse_multiple_runs(runs_dir)
assert df.shape == (87, 5)
assert df.shape == (196, 5)

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