pirl-unc / hitlist / 25003665076
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coverage: 60.714% (+0.05%) from 60.667%
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v1.22.0: response_measured field in binding-assay schema (#135) (#162)

* v1.22.0: Add response_measured to binding-assay schema (#135)

Issue #135 asked for the IEDB/CEDAR "Assay | Response measured" field
to be preserved alongside the existing quantitative fields (#148) so
consumers can disambiguate IC50 (qualitative binding + competitive
fluorescence) from Kd (dissociation constant KD + direct fluorescence)
from t_half (half life + direct fluorescence) without re-scanning the
raw IEDB exports.

Changes:
- scanner.py: add response_measured to _COLUMN_NAMES + _FALLBACK_INDICES
  (IEDB column index 91), capture in record dict alongside assay_method.
- supplement.py: pass-through empty string for schema parity.
- export.py: generate_binding_table gains response_measured kwarg
  (case-insensitive exact match, list-or-scalar) and a docstring
  explaining how to compose response_measured + assay_method +
  measurement_units to identify a measurement type.
- cli.py: --response-measured flag on `hitlist export binding`.
- tests/test_scanner.py: extend the quantitative-fields test with Kd
  + t_half rows and assert response_measured round-trips.
- tests/test_export.py: new
  test_generate_binding_table_response_measured_filter covering
  scalar / multi-value / case-insensitive variants.

Schema-additive only — existing rows have empty response_measured;
existing filters (assay_method, measurement_units, quantitative_value
bounds) are unchanged.

* Address PR #161 review: ground-truth IEDB vocabulary + supp schema test

- export.generate_binding_table docstring: replace the speculative
  "dissociation constant KD" example with the actual IEDB vocabulary
  surveyed across the full mhc_ligand_full.csv (4M+ rows): 'ligand
  presentation', 'MHC binding', 'qualitative binding', 'dissociation
  constant KD (~IC50)', 'half maximal inhibitory concentration (IC50)',
  'half life', etc., in descending row count.  Document the
  exact-vs-substring asymmetry between resp... (continued)

2550 of 4200 relevant lines covered (60.71%)

0.61 hits per line

Coverage Regressions

Lines Coverage ∆ File
91
17.34
 -0.04% cli.py
82
81.1
 0.32% export.py
26
78.92
 0.0% scanner.py
2
87.5
 0.0% supplement.py
Jobs
ID Job ID Ran Files Coverage
1 25003665076.1 23
60.71
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