Update Readme

Readme.md

@@ -46,50 +46,71 @@ efficiency and simplicity (both in terms of implementation and
 comprehensibility). Plus, it's my favorite and I'm doing active research with
 it.
 
-* Numerical python extensions written in Rust
-* Seamless integration via [PyO3](https://pyo3.rs/v0.16.1/) and [rust-numpy](https://docs.rs/numpy/0.7.0/numpy/)
-* High-performance via [ndarray](https://github.com/rust-ndarray/ndarray)/[rayon](https://docs.rs/ndarray/0.13.1/ndarray/parallel/index.html), [tch-rs](https://github.com/LaurentMazare/tch-rs) ([PyTorch](https://pytorch.org/) bindings)
-* Dependency management / publishing with [Poetry](https://python-poetry.org/docs/) and [Maturin](https://github.com/PyO3/maturin)
-* [Monorepo](https://en.wikipedia.org/wiki/Monorepo) with [Cargo workspaces][(](<https://doc.rust-lang.org/book/ch14-03-cargo-workspaces.html>))
-* Technical documentation / GitHub page with [Sphinx](https://www.sphinx-doc.org/en/master/) and [MyST](https://myst-parser.readthedocs.io/en/latest/sphinx/intro.html)
-* Eventually, distributed computation (e.g., [actor model](https://en.wikipedia.org/wiki/Actor_model) or [timely
-  dataflow](https://timelydataflow.github.io/timely-dataflow/))
-* Hopefully, GUI application using [Tauri](https://tauri.studio/), [Angular](https://angular.io/) and [ThreeJS](https://threejs.org/)
-
-Feel free use as a basis for your own projects (MIT licensed).
+The development explores:
 
-## Development
-
-For the monorepo, there is a top-level python project defined using poetry. This project is
-mainly for dependency locking, integration testing and the overall project's documentation.
-The python module
-build with Maturin is in a nested folder and it's project file is also created with poetry.
-This is necessary as the top-level project can only add local packages that are either
-created with Poetry or contain a `setup.py` file.
+* Numerical python extensions written in Rust: Seamless integration via [PyO3](https://pyo3.rs/v0.16.1/) and [rust-numpy](https://docs.rs/numpy/0.7.0/numpy/). Dependency management / publishing with [Poetry](https://python-poetry.org/docs/) and [Maturin](https://github.com/PyO3/maturin)
+* High-performance via [ndarray](https://github.com/rust-ndarray/ndarray)/[rayon](https://docs.rs/ndarray/0.13.1/ndarray/parallel/index.html).
 
-While this setup supports a monorepo setup (and should support integration
-testing on the imported local packages), there is another caveat. Building the python extension with
-`pip` creates a temp directory which does not copy the local rust dependencies. Newer versions of `pip`
-build within the tree, so this limitation can be avoided easily. Use the following commands to
-setup the environment.
+## The cerebral and potpourri Python packages
 
-> :warning: We want to avoid creating a virtual environment for the nested packages. Work in
-> a top-level shell instead.
+The`potpourri` and `citrate` sub folders contain the Python bindings for
+the two crates in `potpourri-rs` and `citrate-rs`. You can build them in a
+similar fashion.
 
 ```sh
-cd self-organization
-pyenv shell 3.10.2
-poetry env use 3.10.2
-poetry run pip install -U pip # only required until pip>=22.0 becomes the default
+cd citrate
+# skip the next line if you are not using pyenv
+pyenv shell 3.10.2 # replace with desired/installed version
+# skip if you only have one version of python installed
+poetry env use 3.10.2 # replace with desired/installed version
+# Install dependencies
 poetry install
-# to debug / develop the extension
+# Or optionally, with jupyter
+poetry install --with jupyter
+# activate the virtual environment
 poetry shell
-cd pysom
+# install into the current environment
 maturin develop
+# with optimizations (recommended)
+maturin develop --release
+# build an installable package
+maturin build --release
 ```
 
 To install the virtual environment as a kernel for jupyter:
 
 ```sh
-python -m ipykernel install --user --name py310_selforganization --display-name "Python3.10 (self-organization)"
+poetry add ipykernel
+# Adjust names as suitable
+python -m ipykernel install --user --name py320_citrate --display-name "Python3.10 (Citrate)"
 ```
+
+## Development
+
+* Bulding documentation. We need extra headers to have formulas in the rustdoc
+
+  ```sh
+  RUSTDOCFLAGS="--html-in-header ./static/header.html" cargo doc  -p cerebral --no-deps
+  RUSTDOCFLAGS="--html-in-header ./static/header.html" cargo doc -F ndarray -p potpourri  --no-deps
+  # Open (e.g. with Firefox)
+  firefox target/doc/citrate/index.html
+  firefox target/doc/potpourri/index.html
+  ```
+
+* Benchmarks (currently only in Potpourri)
+
+  ```sh
+  cd potpourri-rs
+  cargo bench -F ndarray
+  ```
+
+* Running individual tests
+
+  ```sh
+  cd potpourri-rs
+  cargo test -F ndarray -p potpourri  test_multi_pass
+  ```
+
+## License
+
+Published under the MIT license.