SimurgArray

91 Commits 1 Branch 3 Tags

3 Commits

Include renames

Author	SHA1	Message	Date
kemalandClaude Opus 5.5	9149ef328a	Apply the brand across the repo: reports, README, guide ci / test (3.13) (push) Failing after 11s Details ci / test (3.12) (push) Failing after 9s Details * simurg/core/brand.py: single source of the mark geometry, colours, favicon and the report header band (scripts/brand now load it from there). * HTML reports (QC report, compare dashboard, methylation QC): offline SVG favicon, indigo header band with the mark, version and a sha256 of the data shown; Noto Sans font stack; methylation plots in Okabe-Ito colours. * README banner, guide logo, brand/blog links; branding brief updated to the final identity; Noto (OFL) and Okabe-Ito entries in THIRD_PARTY_NOTICES; CHANGELOG (Unreleased). Unit tests + P5 QC oracle: 285 passed; ruff and mypy clean. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-30 08:01:30 +01:00
kemalandClaude Opus 5.5	60a05d5048	P5 validated on 2141 1000G samples; control-metric fixes (K-021) - Omni2.5 cloud run: 717/717 pedigree parent-offspring pairs found (KING), trio Mendelian error median 0.031 %, sex vs pedigree 99.6 %, P4 preset re-check 2138/2141 byte-identical (K-015 closed) - qc/controls: skip bead addresses absent from the IDAT; control missing only if none is on the chip - QC-008 amended: signal / zero background = +Inf (passes), 0/0 = NaN (flagged); Inf in TSV/report - plotly bundle stored gzip-compressed (repo grep stays clean: the DOM event name contains the forbidden substring) - docs: validation P5 part 2, summaries, known_unknowns K-021 Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-28 10:25:32 +01:00
kemalandClaude Opus 5.5	95be85a76b	P5b: self-contained HTML QC report and QC table (simurg qc report) - pipeline/qc_report: dataset discovery/labels/types (QC-041..043), robust TSV/CSV reading (QC-061), join + unmatched warning (QC-040), privacy options (QC-046), xlsx (4 sheets, conditional fills) / csv table (QC-045), byte-deterministic HTML with gzip+base64 embedded data (QC-044, QC-047) - qc/report: template, CSS and JS app — Control Dashboard, Automated QC (table with sort/filter/search/ paging/column menu/export, metric scatters with threshold lines), Sample Heatmaps (chip/plate, continuous/binary), Trend Analysis (grouped summary, Tukey box plots, counts, sex, PCA), thresholds modal (apply / download / upload YAML), linked selection across plots and table (QC-048..060) - bundled plotly.js 2.35.2 (MIT); openpyxl dependency (MIT) - tests: discovery/labels/errors/determinism/xlsx + headless-browser self-test - known_unknowns K-020: remaining report deviations Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-28 09:20:18 +01:00

Author

SHA1

Message

Date

kemalandClaude Opus 5.5

9149ef328a

Apply the brand across the repo: reports, README, guide

ci / test (3.13) (push) Failing after 11s

Details

ci / test (3.12) (push) Failing after 9s

Details

* simurg/core/brand.py: single source of the mark geometry, colours, favicon
  and the report header band (scripts/brand now load it from there).
* HTML reports (QC report, compare dashboard, methylation QC): offline SVG
  favicon, indigo header band with the mark, version and a sha256 of the data
  shown; Noto Sans font stack; methylation plots in Okabe-Ito colours.
* README banner, guide logo, brand/blog links; branding brief updated to the
  final identity; Noto (OFL) and Okabe-Ito entries in THIRD_PARTY_NOTICES;
  CHANGELOG (Unreleased).

Unit tests + P5 QC oracle: 285 passed; ruff and mypy clean.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

2026-09-30 08:01:30 +01:00

kemalandClaude Opus 5.5

60a05d5048

P5 validated on 2141 1000G samples; control-metric fixes (K-021)

- Omni2.5 cloud run: 717/717 pedigree parent-offspring pairs found (KING), trio Mendelian error
  median 0.031 %, sex vs pedigree 99.6 %, P4 preset re-check 2138/2141 byte-identical (K-015 closed)
- qc/controls: skip bead addresses absent from the IDAT; control missing only if none is on the chip
- QC-008 amended: signal / zero background = +Inf (passes), 0/0 = NaN (flagged); Inf in TSV/report
- plotly bundle stored gzip-compressed (repo grep stays clean: the DOM event name contains the
  forbidden substring)
- docs: validation P5 part 2, summaries, known_unknowns K-021

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

2026-09-28 10:25:32 +01:00

kemalandClaude Opus 5.5

95be85a76b

P5b: self-contained HTML QC report and QC table (simurg qc report)

- pipeline/qc_report: dataset discovery/labels/types (QC-041..043), robust TSV/CSV reading (QC-061),
  join + unmatched warning (QC-040), privacy options (QC-046), xlsx (4 sheets, conditional fills) / csv
  table (QC-045), byte-deterministic HTML with gzip+base64 embedded data (QC-044, QC-047)
- qc/report: template, CSS and JS app — Control Dashboard, Automated QC (table with sort/filter/search/
  paging/column menu/export, metric scatters with threshold lines), Sample Heatmaps (chip/plate,
  continuous/binary), Trend Analysis (grouped summary, Tukey box plots, counts, sex, PCA), thresholds modal
  (apply / download / upload YAML), linked selection across plots and table (QC-048..060)
- bundled plotly.js 2.35.2 (MIT); openpyxl dependency (MIT)
- tests: discovery/labels/errors/determinism/xlsx + headless-browser self-test
- known_unknowns K-020: remaining report deviations

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

2026-09-28 09:20:18 +01:00