fix(plate-reader): clarify response-window diagnostics by e-south · Pull Request #33 · e-south/reader

e-south · 2026-08-12T13:47:42Z

Summary

clarify dashed reference traces without competing with candidate treatment encoding
remove event-timing sensitivity and 90% resampling-interval entries from the scientific legend
construct diagnostic figures without accumulating pyplot-managed figures during cohort rendering

Verification

22 focused diagnostic/domain tests passed
full suite: 1224 passed, 4 skipped
Ruff check and format check passed
full 34-subject OPAL cohort rebuilt and Reader verification passed (6 records checked, 0 failed)

e-south · 2026-08-12T13:47:54Z

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codecov · 2026-08-12T13:50:03Z

Codecov Report

❌ Patch coverage is 85.15008% with 94 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/reader_workbench/plugins/transform/overflow.py	76.11%	9 Missing and 7 partials ⚠️
...nalysis/four_state_event_window/contract_fields.py	66.66%	5 Missing and 5 partials ⚠️
...sis/four_state_event_window/design_dispositions.py	74.19%	4 Missing and 4 partials ⚠️
...ur_state_event_window/well_exclusion_validation.py	77.14%	4 Missing and 4 partials ⚠️
...kbench/domains/plate_reader/plots/distributions.py	86.44%	2 Missing and 6 partials ⚠️
...bench/domains/plate_reader/analysis/fold_change.py	86.04%	2 Missing and 4 partials ⚠️
...sis/four_state_event_window/disposition_records.py	84.61%	3 Missing and 3 partials ⚠️
...nalysis/four_state_event_window/well_exclusions.py	81.25%	3 Missing and 3 partials ⚠️
...er_workbench/plugins/validator/to_tidy_plus_map.py	66.66%	3 Missing and 3 partials ⚠️
...domains/plate_reader/plots/ts_and_snap/__init__.py	85.18%	2 Missing and 2 partials ⚠️
... and 8 more

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e-south · 2026-08-15T16:10:03Z

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e-south · 2026-08-15T16:21:56Z

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e-south · 2026-08-15T16:34:48Z

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e-south · 2026-08-15T16:43:51Z

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e-south · 2026-08-15T16:53:27Z

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e-south · 2026-08-15T17:04:31Z

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e-south · 2026-08-15T17:14:48Z

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e-south · 2026-08-15T17:27:43Z

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reader/src/reader_workbench/domains/plate_reader/plots/distributions.py

Lines 121 to 123 in 7dc6198

    
           fig_groups = _figure_groups( 
        
               df=(work if not gcol else work.rename(columns={gcol: str(gcol)})), 
        
               group_on=(str(gcol) if gcol else None),

Retain groups whose distributions are entirely bounded

When group_on partitions the growth distribution by design and one design has only overflow or otherwise bounded observations, filtering into work removes every row for that design before _figure_groups() builds the roster. If another design has exact data, the step succeeds but silently emits no artifact or omission description for the fully bounded design, hiding an entire experimental cohort. Build the figure roster from selected_work and render an explicit withheld-data artifact for groups with no exact observations.

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e-south · 2026-08-15T17:38:10Z

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Codex Review: Didn't find any major issues. Keep them coming!

Reviewed commit: d868831aab

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e-south · 2026-08-15T17:46:31Z

Terminal release review for exact head d868831aab5521567eb83e861d27343bfa437b5e:

all nine GitHub checks pass;
the full local gate passes (1,299 tests, 4 documented optional skips);
the exact-head Codex review reported no major issues;
every P1 finding is addressed and covered by causal regression tests.

One nonblocking P2 advisory remains documented: the optional growth overflow.action="nan" path does not emit the promoted provenance schema. The stress-promoter workflow uses the validated action="none" path, so this advisory does not affect the current scientific pipeline. Under the agreed terminal threshold, it does not reopen this release.

e-south added 2 commits August 12, 2026 08:29

fix(plate-reader): clarify reference traces

d058de9

fix(plate-reader): simplify diagnostic legend

0734503

chatgpt-codex-connector Bot reviewed Aug 12, 2026

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Comment thread src/reader_workbench/domains/plate_reader/plots/four_state_event_window/diagnostic_render.py

fix(plate-reader): simplify component diagnostics

a5df893

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Comment thread ...reader_workbench/domains/plate_reader/plots/four_state_event_window/diagnostic_components.py Outdated

e-south added 2 commits August 12, 2026 10:04

fix(plate-reader): align quality notes with visible data

f803df0

fix(plate-reader): restore captioned component intervals

c1fa154

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Comment thread ...reader_workbench/domains/plate_reader/plots/four_state_event_window/diagnostic_components.py

fix(plate-reader): summarize replicate spread

51e08cb

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Comment thread src/reader_workbench/domains/plate_reader/plots/four_state_event_window/diagnostic_render.py Outdated

feat: preserve plate-reader cohort evidence

1f7c318

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Comment thread src/reader_workbench/protocols/compilers/plate_reader_pipeline.py

Comment thread ...workbench/domains/plate_reader/analysis/four_state_event_window/well_exclusion_validation.py

chore: align the Reader uv runtime

506c192

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Comment thread src/reader_workbench/domains/plate_reader/analysis/fold_change.py

e-south added 4 commits August 15, 2026 12:09

fix: preserve classified growth overflow evidence

ddb9e3f

fix: validate pre-event exclusion support

af1045a

fix: reject absent fold-change cohorts

a355a1b

fix: label diagnostic uncertainty encodings

fc9f691

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Comment thread src/reader_workbench/protocols/compilers/plate_reader.py

Comment thread src/reader_workbench/domains/plate_reader/analysis/fold_change.py

e-south added 2 commits August 15, 2026 12:21

fix: withhold bounded snapshot observations

f6147f4

fix: enforce expected fold-change target

d6d26a9

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Comment thread src/reader_workbench/protocols/compilers/plate_reader.py Outdated

fix: enforce exact growth plot summaries

fa4f537

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Comment thread src/reader_workbench/plugins/transform/overflow.py Outdated

Comment thread src/reader_workbench/protocols/compilers/plate_reader.py Outdated

fix: retain shared overflow capping default

2cb3e00

fix: route growth plots through sample cohort

2a5fbd2

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Comment thread src/reader_workbench/plugins/transform/overflow.py Outdated

Comment thread src/reader_workbench/domains/plate_reader/plots/distributions.py Outdated

e-south added 2 commits August 15, 2026 12:53

fix: preserve overflow provenance on no-op

71d8d35

fix: count distribution sources independently

ffbfbe2

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Comment thread src/reader_workbench/domains/plate_reader/analysis/fold_change.py Outdated

Comment thread src/reader_workbench/domains/plate_reader/plots/ts_and_snap/__init__.py Outdated

e-south added 2 commits August 15, 2026 13:04

fix: scope fold change bounds to report cohorts

50428d1

fix: deduplicate composite observation counts

1708092

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Comment thread src/reader_workbench/protocols/compilers/plate_reader_pipeline.py

fix: emit exact provenance for drop policy

bcd6157

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Comment thread src/reader_workbench/protocols/compilers/plate_reader_pipeline.py

Comment thread src/reader_workbench/domains/plate_reader/plots/four_state_event_window/diagnostic_render.py Outdated

fix: preserve diagnostic trace cohort continuity

7dc6198

chatgpt-codex-connector Bot reviewed Aug 15, 2026

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fix: retain bounded distribution cohorts

d868831

e-south merged commit e8bddec into main Aug 15, 2026
9 checks passed

e-south deleted the codex/20260812-reference-trace-video-cohort branch August 15, 2026 17:47

	fig_groups = _figure_groups(
	df=(work if not gcol else work.rename(columns={gcol: str(gcol)})),
	group_on=(str(gcol) if gcol else None),

Conversation

e-south commented Aug 12, 2026

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