diff --git a/analysis/2026-10-07_report-design-review.md b/analysis/2026-10-07_report-design-review.md index c15c1b1..99bb3f6 100644 --- a/analysis/2026-10-07_report-design-review.md +++ b/analysis/2026-10-07_report-design-review.md @@ -1,5 +1,5 @@ # Per-genome HTML/PDF report (`matpredict report genome`): build and design review -Status: open (implemented on branch `report-genome`; awaiting curator review) +Status: decided (PR #48; design questions 1-3 settled 2026-10-07) ## Question Can one `detect` run be turned into a report that a biologist reads in five seconds and a curator can audit, that @@ -81,7 +81,8 @@ What the report now does: ## Curator decisions Decided 2026-10-07: (1) `detect` writes report.html by default, opt out with `--no-html` / `MATPREDICT_HTML=0` (set in the batch scripts). (2) PDF engine: WeasyPrint in the pixi environment and image (25 packages, 10.3 MB -download, against about 300 MB for chrome-headless-shell 154 and its libraries); revisit if insufficient. Open: (3) Withheld loci collapsed (current) or hidden by default? +download, against about 300 MB for chrome-headless-shell 154 and its libraries); revisit if insufficient. (3) Withheld loci: kept as now (curator 2026-10-07): an always-visible section with count, explanation and +reasons; the table collapsed on screen and expanded in print/PDF. ## Files - Code: `src/MATPredict/report/`, `src/MATPredict/detect/provenance.py`; tests `tests/report/`, diff --git a/analysis/INDEX.md b/analysis/INDEX.md index c5a20ea..d103ea5 100644 --- a/analysis/INDEX.md +++ b/analysis/INDEX.md @@ -71,6 +71,10 @@ in yet; superseded = replaced by a later study. `results/` = main checkout. ## Reads-only typing | Date | Report | Status | Key numbers | |---|---|---|---| -| 10-07 | [Per-genome HTML/PDF report: design review](2026-10-07_report-design-review.md) | open | 3 review rounds; round 1 6 P0, round 2 1 P0; Chrome and WeasyPrint PDFs; 30 tests | | 10-06 | [Fola reads-type](2026-10-06_fola-reads-type.md) | open | 147/148 agree with samtools breadth using a Fola-derived panel (145/148 with GenBank); 50a locus assembled (MAT1-2) | | 10-07 | [A. fumigatus reads and assembly](2026-10-07_afum-reads-and-assembly.md) | open | reads 293/296 vs assembly BLAST truth; `detect` 288/297, one idiomorph reported for all 8 assemblies holding both | + +## Reports and tooling +| Date | Report | Status | Key numbers | +|---|---|---|---| +| 10-07 | [Per-genome HTML/PDF report: design review](2026-10-07_report-design-review.md) | decided; PR #48 | 3 review rounds; round 1 6 P0, round 2 1 P0; Chrome and WeasyPrint PDFs; 30 tests | diff --git a/docs/superpowers/specs/2026-10-07-genome-report-and-reads-intake-design.md b/docs/superpowers/specs/2026-10-07-genome-report-and-reads-intake-design.md index 78f0beb..a6a846b 100644 --- a/docs/superpowers/specs/2026-10-07-genome-report-and-reads-intake-design.md +++ b/docs/superpowers/specs/2026-10-07-genome-report-and-reads-intake-design.md @@ -276,8 +276,8 @@ and the possible causes (heterokaryon, diploid, mixed or contaminated library). 1. ~~`detect --html` default~~: decided 2026-10-07, on by default everywhere, opt out. 2. ~~PDF engine~~: decided 2026-10-07, WeasyPrint in the pixi environment (10.3 MB download against about 300 MB for Chromium); revisit if its output proves insufficient. -3. Show withheld loci in the default report, or only in an "expert" section - (proposed: collapsed section, always present)? +3. ~~Withheld loci~~: decided 2026-10-07, always-present section, table collapsed on screen and expanded in + print. 4. Genus-level panels: offer them at all in the service, or species-level only until a divergence test exists? 5. Assembly route in the service: offer it (hours of compute per sample) or