Release 1.1.0: compiled kernels (P9) and packaging (P10)

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

CHANGELOG.md

@@ -1,6 +1,6 @@
 # Changelog
 
-## Unreleased (P9, P10)
+## 1.1.0 — 2026-09-28 (P9, P10)
 
 **Packaging (P10).** `scripts/build_dist.sh` (sdist, pure wheel, manylinux_2_28 kernel wheels for x86_64 and
 aarch64), `Dockerfile`, conda recipes (`packaging/conda/`). Verified on fresh x86_64 and aarch64 VMs: pip, Docker

Dockerfile

@@ -1,6 +1,6 @@
 # SimurgArray container: the `simurg` CLI with the compiled kernels.
-#   docker build -t simurg:1.0.0 .
+#   docker build -t simurg:1.1.0 .
-#   docker run --rm -v "$PWD":/work simurg:1.0.0 genotype --bpm M.bpm --egt C.egt --idats idats --out run/gtc
+#   docker run --rm -v "$PWD":/work simurg:1.1.0 genotype --bpm M.bpm --egt C.egt --idats idats --out run/gtc
 # Inputs and outputs live in the mounted /work folder; the image holds no data.
 ARG PYTHON=3.12
 

README.md

@@ -9,7 +9,7 @@ Personal research toolkit for Illumina Infinium genotyping BeadChip data
 
 ## Status
 
-**v1.0.0** (2026-09-28) — see `CHANGELOG.md`. IDAT → normalization → GenCall-equivalent genotype calling → GTC v5 →
+**v1.1.0** (2026-09-28) — see `CHANGELOG.md`. IDAT → normalization → GenCall-equivalent genotype calling → GTC v5 →
 sample/control QC with an HTML report → plus-strand VCF/BCF → PLINK 1/2, bedGraph, final report; plus a
 differential-testing harness. Validation (`docs/validation/`):
 

docs/user_guide.md

@@ -1,4 +1,4 @@
-# SimurgArray user guide (v1.0)
+# SimurgArray user guide (v1.1)
 
 SimurgArray turns Illumina Infinium genotyping BeadChip scans (IDAT files) into genotype calls, QC tables and
 reports, VCF/BCF and PLINK files. It is a personal, non-commercial **research** tool — not for clinical or
@@ -24,7 +24,7 @@ uv venv && uv pip install -e .          # add ".[dev]" for tests and linters
 ```bash
 curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y --profile minimal   # Rust (needs a C linker, e.g. gcc)
 uv pip install ./rust/simurg-core
-.venv/bin/python -c "from simurg._core import backend; print(backend())"                   # rust 1.0.0
+.venv/bin/python -c "from simurg._core import backend; print(backend())"                   # rust 1.1.0
 ```
 
 Without them the same code runs in pure Python/NumPy; `SIMURG_PURE_PYTHON=1` forces that path.
@@ -33,15 +33,15 @@ Without them the same code runs in pure Python/NumPy; `SIMURG_PURE_PYTHON=1` for
 `manylinux_2_28` kernel wheels for x86_64 and aarch64, glibc ≥ 2.28):
 
 ```bash
-python3 -m venv simurg-env && simurg-env/bin/pip install simurg-1.0.0-py3-none-any.whl \
+python3 -m venv simurg-env && simurg-env/bin/pip install simurg-1.1.0-py3-none-any.whl \
-    simurg_core-1.0.0-cp312-abi3-manylinux_2_28_$(uname -m).whl        # the second wheel is optional
+    simurg_core-1.1.0-cp312-abi3-manylinux_2_28_$(uname -m).whl        # the second wheel is optional
 ```
 
 **Docker** (image ≈ 550 MB, kernels included, runs as a non-root user; data stay in the mounted folder):
 
 ```bash
-docker build -t simurg:1.0.0 .
+docker build -t simurg:1.1.0 .
-docker run --rm --user "$(id -u):$(id -g)" -v "$PWD":/work simurg:1.0.0 \
+docker run --rm --user "$(id -u):$(id -g)" -v "$PWD":/work simurg:1.1.0 \
     genotype --bpm M.bpm --egt C.egt --idats idats --out run/gtc
 ```
 

rust/simurg-core/Cargo.lock

@@ -198,7 +198,7 @@ checksum = "6b1e7f9a428571be2dc5bc0505c13fb6bf936822b894ec87abf8a08a4e51742d"
 
 [[package]]
 name = "simurg-core"
-version = "1.0.0"
+version = "1.1.0"
 dependencies = [
  "numpy",
  "pyo3",

rust/simurg-core/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "simurg-core"
-version = "1.0.0"
+version = "1.1.0"
 edition = "2021"
 license = "MIT"
 description = "Compiled kernels for SimurgArray (plan §18 P9)"

src/simurg/__init__.py

@@ -4,5 +4,5 @@ Specification: SIMURGARRAY_MASTER_PLAN.md (algorithms, roadmap) and
 SIMURGARRAY_FUNCTIONAL_SPEC.md (externally visible behaviour, item IDs such as CLI-021).
 """
 
-__version__ = "1.0.0"
+__version__ = "1.1.0"
 PRODUCT_NAME = "SimurgArray"