From 6ab7a729359ff9d772c16a955274f2ebbe926cc0 Mon Sep 17 00:00:00 2001 From: Kemal Yaylali Date: Wed, 30 Sep 2026 08:10:57 +0100 Subject: [PATCH] Keep Claude Code files local: untrack CLAUDE.md, ignore CLAUDE.md, CLAUDE.local.md and .claude/ --- .gitignore | 4 ++++ CLAUDE.md | 19 ------------------- SIMURGARRAY_MASTER_PLAN.md | 2 +- 3 files changed, 5 insertions(+), 20 deletions(-) delete mode 100644 CLAUDE.md diff --git a/.gitignore b/.gitignore index cc5051d..9943a88 100644 --- a/.gitignore +++ b/.gitignore @@ -20,3 +20,7 @@ target/ results/ # editor lock files .~lock.*# +# Claude Code files (kept local only) +CLAUDE.md +CLAUDE.local.md +.claude/ diff --git a/CLAUDE.md b/CLAUDE.md deleted file mode 100644 index 30dc343..0000000 --- a/CLAUDE.md +++ /dev/null @@ -1,19 +0,0 @@ -# SimurgArray -Personal research toolkit for Illumina Infinium genotyping arrays (IDAT→GTC→VCF, QC, CN, PGx). -The full spec and roadmap is SIMURGARRAY_MASTER_PLAN.md — read the relevant section before changing code. -Externally visible behaviour (CLI options, file schemas, QC semantics, messages, edge cases) is defined item-by-item -in SIMURGARRAY_FUNCTIONAL_SPEC.md (IDs like CLI-021, OUT-031); cite item IDs in commits and tests. - -## Rules -- Work phase by phase (§18). Don't start a phase until the previous gate passes. -- Science modules (signal/, genotype/, cn/, qc/, pgx/) are pure functions; no I/O inside them. -- Every algorithm cites its source (§7 tags) in its docstring. -- MIT/BSD/Apache/Unlicense code may be ported with attribution in THIRD_PARTY_NOTICES.md. - GPL tools (plink2, illuminaio, verifyIDintensity) = subprocess oracles only; never copy their code. -- Never commit vendor data (BPM/CSV/EGT/IDAT) — only tests/fixtures/ (Artistic-2.0 Bioconductor files, synthetic data). -- Never hide oracle discrepancies; record them in docs/known_unknowns.md. -- Default mode is bit-exact vs Illumina-produced GTCs; keep a clean-math mode too. - -## Commands -- uv sync ; uv run pytest -q ; uv run ruff check . ; uv run mypy src -- bash scripts/fetch_data.sh p0|p1|p2 ; bash scripts/bootstrap_refs.sh diff --git a/SIMURGARRAY_MASTER_PLAN.md b/SIMURGARRAY_MASTER_PLAN.md index 7c03699..94e80fa 100644 --- a/SIMURGARRAY_MASTER_PLAN.md +++ b/SIMURGARRAY_MASTER_PLAN.md @@ -189,7 +189,7 @@ bash scripts/bootstrap_refs.sh && bash scripts/fetch_data.sh p0 ``` simurg/ ├── pyproject.toml # uv/hatch; package "simurg"; entry point `simurg` -├── CLAUDE.md # Appendix A +├── CLAUDE.md # Appendix A (local only, git-ignored) ├── SIMURGARRAY_MASTER_PLAN.md # this file ├── THIRD_PARTY_NOTICES.md ├── scripts/