25531306553
77%

Ran 08 May 2026 01:25AM UTC

Jobs 4

Files 23

Run time 1min

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Committed 08 May 2026 01:23AM UTC coverage: 70.561%. Remained the same

Build # 25531306553

Build Type

push

github

Committed by

web-flow

Commit Message

Serialize uns['sample_sheet'] as JSON to fix h5ad write (#7)

`combined.uns["sample_sheet"] = sample_sheet.to_dataframe().to_dict()`
produced `{col: {row_idx: val}}`; the int row-index keys aren't
h5ad-serializable, blocking `tcrsift run` from completing. Same shape
as the obs-column issues fixed in #4 (#3) and #6 (#5).

Tried two structured alternatives first — they each hit a different
anndata/h5py limitation:
  - `to_dict(orient="list")`: dict-of-lists with None values produces
    object arrays h5py can't convert.
  - DataFrame in uns directly: object columns containing only None
    fail with the same "Can't implicitly convert non-string objects to
    strings" error; coercing to pandas StringDtype requires the
    `allow_write_nullable_strings` opt-in not enabled by default in
    anndata < 0.11.

JSON-encoding the records side-steps every mixed-None edge case: the
sheet becomes a single string in uns, which serializes trivially.
Read back with `pd.read_json(io.StringIO(adata.uns["sample_sheet"]),
orient="records")` or `json.loads(...)`.

Adds a regression test that round-trips a sparsely-populated sample
sheet through write_h5ad / read_h5ad.

Bumps version to 0.2.9.

Coverage Stats

4065 of 5761 relevant lines covered (70.56%)

2.82 hits per line

Jobs

ID	Job ID	Ran	Files	Coverage
1	python-3.11 - 25531306553.1	08 May 2026 01:25AM UTC	23	70.55	GitHub Action Run
2	python-3.12 - 25531306553.2	08 May 2026 01:25AM UTC	23	70.55	GitHub Action Run
3	python-3.9 - 25531306553.3	08 May 2026 01:25AM UTC	23	70.52	GitHub Action Run
4	python-3.10 - 25531306553.4	08 May 2026 01:25AM UTC	23	70.55	GitHub Action Run

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