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kemalandClaude Opus 5.5 b2e0c09f2a
ci / test (3.12) (push) Failing after 10s
Details
ci / test (3.13) (push) Failing after 11s
Details
Track the packaged CN data files (the data/ ignore rule matched src/simurg/cn/data) 
Found by the CN cloud validation: mask_GRCh3{7,8}.bed and cytoBand_GRCh3{7,8}.txt.gz were
never committed nor shipped in the wheel. The ignore rule now covers only the top-level data/.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
2026-09-29 07:06:47 +01:00
..
cli
v2 CN: cn annotate (JSON report, ISCN 2020, cytobands, genes) and the annotation bundle builder
2026-09-29 01:37:56 +01:00
cn
Track the packaged CN data files (the data/ ignore rule matched src/simurg/cn/data)
2026-09-29 07:06:47 +01:00
compare
P7: differential-testing harness (simurg compare) and nightly run on the Pi
2026-09-28 17:00:37 +01:00
core
v2 CN/LOH (WIP): cn build-model and cn call
2026-09-29 01:13:51 +01:00
formats
v2 methylation control QC (WIP): simurg methyl qc|convert-manifest (MET-001..018)
2026-09-29 00:13:22 +01:00
genotype
P9 (WIP): compiled kernels (rust/simurg-core, PyO3) with bit-identical pure-Python fallback
2026-09-28 21:28:55 +01:00
harmonize
P6 complete: optional VCF fields, SNV+indel merging, auxiliary MNV loci, PLINK 2 .pgen
2026-09-28 14:29:42 +01:00
pgx
P1: file parsers, sample sheet, discovery, CLI inspect
2026-09-27 16:56:39 +01:00
pipeline
v2 CN: cn annotate (JSON report, ISCN 2020, cytobands, genes) and the annotation bundle builder
2026-09-29 01:37:56 +01:00
qc
v2 methylation control QC (WIP): simurg methyl qc|convert-manifest (MET-001..018)
2026-09-29 00:13:22 +01:00
signal
methylation: combine_neg option; oracle compares both background variants and logs sesame's negative controls
2026-09-29 00:36:44 +01:00
synth
P1: file parsers, sample sheet, discovery, CLI inspect
2026-09-27 16:56:39 +01:00
__init__.py
Release 1.1.0: compiled kernels (P9) and packaging (P10)
2026-09-28 23:56:39 +01:00
_core.py
P9 (WIP): compiled kernels (rust/simurg-core, PyO3) with bit-identical pure-Python fallback
2026-09-28 21:28:55 +01:00