Prepare for public release on Gitea: simurgarray package names, community files, Gitea templates, pseudonymised P6 probe names

README.md

@@ -40,6 +40,7 @@ It runs on anything from a Raspberry Pi to a cloud server.
 * [Development](#development)
 * [Repository layout](#repository-layout)
 * [Documentation](#documentation)
+* [Citing](#citing)
 * [Licence, data and trademarks](#licence-data-and-trademarks)
 
 ## Features
@@ -76,6 +77,7 @@ Each phase has its own report in `docs/validation/`.
 * **Python 3.12 or 3.13** on 64 bit Linux (x86_64 or aarch64). Tested on Ubuntu 24.04 and Raspberry Pi OS.
 * **Memory:** about 2 to 3 GB per worker process for GSA or Omni sized arrays. 8 GB is enough for a Pi with two workers.
 * **Optional:** Rust and a C compiler for the compiled kernels; Docker or conda for those installs.
+* The Python package is called `simurgarray`; the command and the import name are `simurg`.
 * Only pure Python dependencies are needed (numpy, pyarrow, typer, rich, pyyaml, openpyxl). bcftools and plink2
   are **not** required; SimurgArray writes VCF, BCF, indexes and PLINK files itself. They are used only as test oracles.
 
@@ -118,8 +120,8 @@ aarch64 (glibc 2.28 or newer) to `dist/`:
 
 ```bash
 python3 -m venv simurg-env
-simurg-env/bin/pip install simurg-2.0.0-py3-none-any.whl \
-    simurg_core-1.1.0-cp312-abi3-manylinux_2_28_$(uname -m).whl    # the kernel wheel is optional
+simurg-env/bin/pip install simurgarray-2.0.0-py3-none-any.whl \
+    simurgarray_core-1.1.0-cp312-abi3-manylinux_2_28_$(uname -m).whl    # the kernel wheel is optional
 ```
 
 ### Docker
@@ -136,7 +138,7 @@ docker run --rm --user "$(id -u):$(id -g)" -v "$PWD":/work simurg:2.0.0 \
 
 ```bash
 conda build -c conda-forge --output-folder conda-bld packaging/conda/simurg-core packaging/conda/simurg
-conda create -n simurg -c ./conda-bld -c conda-forge simurg simurg-core
+conda create -n simurgarray -c ./conda-bld -c conda-forge simurgarray simurgarray-core
 ```
 
 All installs give identical results on x86_64 and aarch64 (`docs/validation/P10.md`).
@@ -340,6 +342,7 @@ examples/          end to end demo
 branding/          logo, icons, templates and the brand guide
 blog/              five posts about the project, with featured images
 packaging/         conda recipes (plus Dockerfile at the root)
+.gitea/            CI workflow, issue and pull request templates
 ```
 
 ## Documentation
@@ -350,8 +353,13 @@ packaging/         conda recipes (plus Dockerfile at the root)
 * [`docs/validation/`](docs/validation/): one report per phase and module
 * [`docs/known_unknowns.md`](docs/known_unknowns.md): every difference from reference tools, with dates and explanations
 * [`docs/messages.md`](docs/messages.md): all error and warning codes
+* [`CONTRIBUTING.md`](CONTRIBUTING.md), [`SECURITY.md`](SECURITY.md), [`CODE_OF_CONDUCT.md`](CODE_OF_CONDUCT.md)
 * [`branding/README.md`](branding/README.md) and [`blog/`](blog/)
 
+## Citing
+
+If SimurgArray helps your research, please cite it using [`CITATION.cff`](CITATION.cff) (version 2.0.0, 2026).
+
 ## Licence, data and trademarks
 
 SimurgArray is released under the [MIT licence](LICENSE). Code adapted from MIT, BSD and Apache licensed projects