25584084210
71%

Ran 08 May 2026 11:14PM UTC

Jobs 4

Files 24

Run time 1min

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Committed 08 May 2026 11:13PM UTC coverage: 71.139% (+0.2%) from 70.984%

Build # 25584084210

Build Type

push

github

Committed by

web-flow

Commit Message

Add timepoint/APC filter knobs (#9 chunk 3) (#21)

Third slice of #9. Surfaces the per-axis aggregations from chunk 2
(v0.7.0) as filter knobs, mirroring the donor/method knobs from
#15 chunk 3.

New knobs on filter_clonotypes_threshold + filter_clonotypes:
  - min_timepoints              (reads n_timepoints)
  - min_timepoints_per_donor    (reads max_timepoints_per_donor)
  - min_apcs                    (reads n_apcs)
  - min_apcs_per_donor          (reads max_apcs_per_donor)

Each is a no-op when its source column isn't on the table. Composes
multiplicatively with the existing donor/method knobs — e.g.
"selected across >=2 donors AND >=2 timepoints within at least one
donor" is just `min_donors=2 min_timepoints_per_donor=2`.

CLI: same flags wired into both `tcrsift filter` and `tcrsift run`.
FilterConfig gains the four fields with the same `--min-*-per-donor`
naming convention.

Tests: per-knob behavior on a synthetic clone table with known
timepoint/APC profiles; composition with the existing min_donors
knob; no-op when axis columns absent.

Bumps version to 0.7.1 — additive CLI/API surface, no breaking
change.

Next chunk: TIL-overlap knob (--require-til-overlap-per-donor) and
per-axis report breakdowns. After that, #9 fully addressed.

Coverage Stats

4252 of 5977 relevant lines covered (71.14%)

2.85 hits per line

Coverage Regressions

Lines	Coverage	∆	File
186	56.11	0.43%	cli.py
20	92.06	0.68%	filter.py
16	89.88	0.25%	config.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	python-3.9 - 25584084210.1	08 May 2026 11:14PM UTC	24	71.1	GitHub Action Run
2	python-3.10 - 25584084210.2	08 May 2026 11:14PM UTC	24	71.13	GitHub Action Run
3	python-3.11 - 25584084210.3	08 May 2026 11:14PM UTC	24	71.13	GitHub Action Run
4	python-3.12 - 25584084210.4	08 May 2026 11:14PM UTC	24	71.13	GitHub Action Run

pirl-unc / tcrsift / 25584084210
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pirl-unc / tcrsift / 25584084210 71%

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pirl-unc / tcrsift / 25584084210
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