Formatted docs with rstfmt

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Installation
============
##############
Installation
##############
Requirements
------------
**************
Requirements
**************
* Python 3.11 or higher
* NumPy 2.0.0 or higher
- Python 3.11 or higher
- NumPy 2.0.0 or higher
From PyPI (Recommended)
-----------------------
*************************
From PyPI (Recommended)
*************************
.. code-block:: bash
.. code:: bash
pip install read-aconity-layers
From Source
-----------
*************
From Source
*************
If you want to build from source or contribute to the project:
Prerequisites
~~~~~~~~~~~~~
=============
* Rust 1.70 or higher
* Python 3.11 or higher
* Poetry (for development)
- Rust 1.70 or higher
- Python 3.11 or higher
- Poetry (for development)
Build Steps
~~~~~~~~~~~
===========
1. Clone the repository:
#. Clone the repository:
.. code-block:: bash
.. code:: bash
git clone https://github.com/Cian-H/read_aconity_layers.git
cd read_aconity_layers
2. Install Python dependencies:
#. Install Python dependencies:
.. code-block:: bash
.. code:: bash
poetry install
3. Build the Rust extension:
#. Build the Rust extension:
.. code-block:: bash
.. code:: bash
poetry run maturin develop
4. Run tests to verify installation:
#. Run tests to verify installation:
.. code-block:: bash
.. code:: bash
poetry run pytest
Development Installation
------------------------
**************************
Development Installation
**************************
For development work, you'll also want the development dependencies:
.. code-block:: bash
.. code:: bash
poetry install --with dev,docs
This installs additional tools for:
* Code formatting (ruff)
* Type checking (mypy)
* Testing (pytest)
* Documentation building (sphinx)
- Code formatting (ruff)
- Type checking (mypy)
- Testing (pytest)
- Documentation building (sphinx)
Troubleshooting
---------------
*****************
Troubleshooting
*****************
Common Issues
~~~~~~~~~~~~~
=============
**Import Error**: If you get import errors, make sure you've run ``maturin develop``
to build the Rust extension.
**Import Error**: If you get import errors, make sure you've run
``maturin develop`` to build the Rust extension.
**Performance Issues**: The library uses parallel processing by default. If you
encounter memory issues with very large datasets, consider processing files in
smaller batches.
**Performance Issues**: The library uses parallel processing by default.
If you encounter memory issues with very large datasets, consider
processing files in smaller batches.
**Rust Compilation Errors**: Make sure you have a recent version of Rust installed.
The minimum supported version is 1.70.
**Rust Compilation Errors**: Make sure you have a recent version of Rust
installed. The minimum supported version is 1.70.
Platform Notes
~~~~~~~~~~~~~~
==============
**Windows**: You may need to install the Microsoft C++ Build Tools if you don't
already have them.
**Windows**: You may need to install the Microsoft C++ Build Tools if
you don't already have them.
**macOS**: Xcode command line tools are required for Rust compilation.
**Linux**: Most distributions should work out of the box. You may need to install
``build-essential`` on Debian/Ubuntu systems.
**Linux**: Most distributions should work out of the box. You may need
to install ``build-essential`` on Debian/Ubuntu systems.