mirror of
https://github.com/Cian-H/read_aconity_layers.git
synced 2025-12-22 18:31:56 +00:00
Added autogenerated sphinx documentation
This commit is contained in:
1
.gitignore
vendored
1
.gitignore
vendored
@@ -83,6 +83,7 @@ instance/
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.scrapy
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# Sphinx documentation
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docs/rust/crates
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docs/_build/
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# PyBuilder
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@@ -27,6 +27,7 @@ flexbuffers = "25.2.10"
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float-cmp = "0.10.0"
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ndarray = { version = "0.16.1", features = ["rayon", "serde"] }
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serde = "1.0.200"
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sphinx-rustdocgen = "0.8.1"
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tar = "0.4.40"
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tempfile = "3.10.1"
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xz = "0.1.0"
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|
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86
docs/conf.py
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86
docs/conf.py
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@@ -0,0 +1,86 @@
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# Configuration file for the Sphinx documentation builder.
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# For the full list of built-in configuration values, see the documentation:
|
||||
# https://www.sphinx-doc.org/en/master/usage/configuration.html
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|
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# -- Project information -----------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
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project = "read_aconity_layers"
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copyright = "2024, Cian Hughes"
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author = "Cian Hughes"
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release = "0.4.3"
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# -- General configuration ---------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
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extensions = [
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"sphinxcontrib_rust",
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"sphinx.ext.autodoc",
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"sphinx.ext.autosummary",
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"sphinx.ext.napoleon",
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||||
"sphinx.ext.viewcode",
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"sphinx.ext.intersphinx",
|
||||
"sphinx_autodoc_typehints",
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"sphinx_copybutton",
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"myst_parser",
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]
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exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
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|
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# -- Options for HTML output -------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
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html_theme = "sphinx_rtd_theme"
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|
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# -- Extension configuration -------------------------------------------------
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# Napoleon settings
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napoleon_google_style = True
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napoleon_numpy_style = True
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napoleon_include_init_with_doc = False
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napoleon_include_private_with_doc = False
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napoleon_include_special_with_doc = True
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napoleon_use_admonition_for_examples = False
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napoleon_use_admonition_for_notes = False
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napoleon_use_admonition_for_references = False
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napoleon_use_ivar = False
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napoleon_use_param = True
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napoleon_use_rtype = True
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napoleon_preprocess_types = False
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napoleon_type_aliases = None
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napoleon_attr_annotations = True
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|
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# Autodoc settings
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autodoc_typehints = "description"
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autodoc_member_order = "bysource"
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autosummary_generate = True
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|
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# Intersphinx mapping
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intersphinx_mapping = {
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"python": ("https://docs.python.org/3", None),
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"numpy": ("https://numpy.org/doc/stable/", None),
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}
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|
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# Sphinx-rust settings
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rust_crates = {
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"read_aconity_layers": ".",
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}
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rust_doc_dir = "rust/crates"
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rust_rustdoc_fmt = "md"
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|
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# MyST settings
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myst_enable_extensions = [
|
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"deflist",
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"html_image",
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"attrs_block",
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"colon_fence",
|
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"html_admonition",
|
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"replacements",
|
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"smartquotes",
|
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"strikethrough",
|
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"tasklist",
|
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]
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|
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# Copy button settings
|
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copybutton_prompt_text = r">>> |\.\.\. |\$ |In \[\d*\]: | {2,5}\.\.\.: | {5,8}: "
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copybutton_prompt_is_regexp = True
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275
docs/development.rst
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275
docs/development.rst
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@@ -0,0 +1,275 @@
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Development
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||||
===========
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|
||||
This guide covers setting up a development environment and contributing to ``read_aconity_layers``.
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|
||||
Development Setup
|
||||
-----------------
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||||
|
||||
Prerequisites
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
* Rust 1.70+ with Cargo
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* Python 3.11+
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* Poetry
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||||
* Git
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||||
|
||||
Environment Setup
|
||||
~~~~~~~~~~~~~~~~~
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||||
|
||||
1. **Clone and setup the repository:**
|
||||
|
||||
.. code-block:: bash
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||||
|
||||
git clone https://github.com/Cian-H/read_aconity_layers.git
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cd read_aconity_layers
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|
||||
2. **Install dependencies:**
|
||||
|
||||
.. code-block:: bash
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||||
|
||||
poetry install --with dev,docs
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|
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3. **Setup pre-commit hooks:**
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|
||||
.. code-block:: bash
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||||
|
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poetry run pre-commit install
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||||
|
||||
4. **Build the Rust extension:**
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||||
|
||||
.. code-block:: bash
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|
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poetry run maturin develop
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||||
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Code Style and Quality
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||||
----------------------
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This project uses several tools to maintain code quality:
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Python Code
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||||
~~~~~~~~~~~
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||||
|
||||
* **Ruff**: For linting and formatting
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* **MyPy**: For type checking
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||||
* **Pytest**: For testing
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||||
|
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Run quality checks:
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||||
|
||||
.. code-block:: bash
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||||
|
||||
# Format and lint Python code
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||||
poetry run ruff format .
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poetry run ruff check .
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||||
|
||||
# Type checking
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poetry run mypy .
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||||
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# Run tests
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poetry run pytest
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|
||||
Rust Code
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||||
~~~~~~~~~
|
||||
|
||||
* **rustfmt**: For formatting
|
||||
* **clippy**: For linting
|
||||
* **cargo test**: For testing
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||||
|
||||
Run quality checks:
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||||
|
||||
.. code-block:: bash
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||||
|
||||
# Format Rust code
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||||
cargo fmt
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||||
|
||||
# Lint Rust code
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||||
cargo clippy
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||||
|
||||
# Run Rust tests
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||||
cargo test
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||||
|
||||
Testing
|
||||
-------
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||||
|
||||
The project includes comprehensive tests for both Python and Rust components.
|
||||
|
||||
Running Tests
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
.. code-block:: bash
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||||
|
||||
# Run all tests
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||||
poetry run pytest
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||||
|
||||
# Run with coverage
|
||||
poetry run pytest --cov=read_aconity_layers
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||||
|
||||
# Run Rust tests
|
||||
cargo test
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||||
|
||||
Test Structure
|
||||
~~~~~~~~~~~~~~
|
||||
|
||||
* **Python tests**: Located in ``tests/`` directory
|
||||
* **Rust tests**: Integrated into ``src/rust_fn/mod.rs``
|
||||
* **Property-based tests**: Uses ``arbtest`` for Rust property testing
|
||||
* **Regression tests**: Validates against known good outputs
|
||||
|
||||
Adding Tests
|
||||
~~~~~~~~~~~~
|
||||
|
||||
When adding new functionality:
|
||||
|
||||
1. **Add Rust tests** in the appropriate module
|
||||
2. **Add Python integration tests** in ``tests/``
|
||||
3. **Update regression tests** if output format changes
|
||||
4. **Add property tests** for mathematical functions
|
||||
|
||||
Documentation
|
||||
-------------
|
||||
|
||||
Building Documentation
|
||||
~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
**Prerequisites**: You need the Rust toolchain installed for ``sphinxcontrib-rust`` to work.
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
# Install documentation dependencies
|
||||
poetry install --with docs
|
||||
|
||||
# Build documentation
|
||||
cd docs
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||||
make html
|
||||
|
||||
# Or build manually
|
||||
poetry run sphinx-build -b html . _build/html
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||||
|
||||
# Serve locally (optional)
|
||||
make serve
|
||||
|
||||
Documentation Structure
|
||||
~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
* **docs/conf.py**: Sphinx configuration
|
||||
* **docs/index.rst**: Main documentation page
|
||||
* **docs/python/**: Python API documentation
|
||||
* **docs/rust/**: Rust API documentation
|
||||
* **docs/*.rst**: User guides and tutorials
|
||||
|
||||
The documentation automatically generates API references from:
|
||||
|
||||
* Python docstrings and type hints
|
||||
* Rust documentation comments (``///`` and ``//!``)
|
||||
* Type stub files (``*.pyi``)
|
||||
|
||||
**Note**: For Rust API documentation to work properly, you need:
|
||||
|
||||
1. Rust toolchain installed (cargo, rustfmt)
|
||||
2. Proper Rust doc comments in your source code
|
||||
3. The ``sphinxcontrib-rust`` extension configured correctly
|
||||
|
||||
Contributing
|
||||
------------
|
||||
|
||||
Workflow
|
||||
~~~~~~~~
|
||||
|
||||
1. **Fork the repository** on GitHub
|
||||
2. **Create a feature branch** from ``main``
|
||||
3. **Make your changes** following the coding standards
|
||||
4. **Add tests** for new functionality
|
||||
5. **Update documentation** as needed
|
||||
6. **Run the full test suite** to ensure everything works
|
||||
7. **Submit a pull request**
|
||||
|
||||
Pre-commit Checks
|
||||
~~~~~~~~~~~~~~~~~
|
||||
|
||||
The project uses pre-commit hooks that run automatically:
|
||||
|
||||
* Code formatting (Ruff, rustfmt)
|
||||
* Linting (Ruff, Clippy)
|
||||
* Type checking (MyPy)
|
||||
* Version bump validation
|
||||
* Poetry validation
|
||||
|
||||
These checks must pass before commits are accepted.
|
||||
|
||||
Release Process
|
||||
~~~~~~~~~~~~~~~
|
||||
|
||||
1. **Update version** in ``Cargo.toml`` (triggers version validation)
|
||||
2. **Update changelog** if applicable
|
||||
3. **Ensure all tests pass**
|
||||
4. **Create a release** on GitHub
|
||||
5. **CI automatically builds and publishes** wheels to PyPI
|
||||
|
||||
Architecture Notes
|
||||
------------------
|
||||
|
||||
The library is structured in two main components:
|
||||
|
||||
Rust Core (``src/rust_fn/``)
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
* **High-performance file I/O** using CSV reader
|
||||
* **Parallel processing** with Rayon
|
||||
* **Memory-efficient array operations** with ndarray
|
||||
* **Coordinate correction algorithms**
|
||||
|
||||
Python Bindings (``src/lib.rs``)
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
* **PyO3 integration** for seamless Python interop
|
||||
* **Error handling** conversion from Rust to Python exceptions
|
||||
* **NumPy integration** for zero-copy array passing
|
||||
* **Type annotations** via stub files
|
||||
|
||||
Performance Considerations
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
* File I/O is the primary bottleneck
|
||||
* Parallel processing scales well with core count
|
||||
* Memory usage is proportional to dataset size
|
||||
* Coordinate corrections use vectorized operations
|
||||
|
||||
Common Development Tasks
|
||||
------------------------
|
||||
|
||||
Adding a New Function
|
||||
~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
1. **Implement in Rust** (``src/rust_fn/mod.rs``)
|
||||
2. **Add Python binding** (``src/lib.rs``)
|
||||
3. **Update type stubs** (``read_layers.pyi``)
|
||||
4. **Add tests** for both Rust and Python
|
||||
5. **Update documentation**
|
||||
|
||||
Debugging Build Issues
|
||||
~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
* **Check Rust version**: Must be 1.70+
|
||||
* **Verify PyO3 compatibility**: Should match Python version
|
||||
* **Clear build cache**: ``cargo clean`` and ``poetry env remove --all``
|
||||
* **Check dependencies**: Ensure all dev dependencies are installed
|
||||
|
||||
Profiling Performance
|
||||
~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
For Rust code:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
# Profile with perf (Linux)
|
||||
cargo build --release
|
||||
perf record --call-graph=dwarf ./target/release/your_binary
|
||||
perf report
|
||||
|
||||
For Python integration:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
# Profile with py-spy
|
||||
pip install py-spy
|
||||
py-spy record -o profile.svg -- python your_script.py
|
||||
52
docs/index.rst
Normal file
52
docs/index.rst
Normal file
@@ -0,0 +1,52 @@
|
||||
read_aconity_layers Documentation
|
||||
==================================
|
||||
|
||||
A utility for fast reading of layer data from the aconity mini powder bed fusion machine.
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 2
|
||||
:caption: Contents:
|
||||
|
||||
installation
|
||||
quickstart
|
||||
python/index
|
||||
rust/index
|
||||
development
|
||||
|
||||
Overview
|
||||
--------
|
||||
|
||||
``read_aconity_layers`` is a high-performance Python library for reading and processing layer data from Aconity mini powder bed fusion machines. It's built with Rust for maximum performance and uses PyO3 for seamless Python integration.
|
||||
|
||||
Features
|
||||
--------
|
||||
|
||||
* **Fast**: Built with Rust for high-performance data processing
|
||||
* **Simple**: Easy-to-use Python API
|
||||
* **Parallel**: Leverages Rayon for parallel processing of multiple files
|
||||
* **Type-safe**: Full type annotations and stub files included
|
||||
|
||||
Quick Example
|
||||
-------------
|
||||
|
||||
.. code-block:: python
|
||||
|
||||
import read_aconity_layers as ral
|
||||
import numpy as np
|
||||
|
||||
# Read all layers from a directory
|
||||
data = ral.read_layers("/path/to/layer/files/")
|
||||
|
||||
# Read specific layer files
|
||||
files = ["/path/to/layer1.pcd", "/path/to/layer2.pcd"]
|
||||
data = ral.read_selected_layers(files)
|
||||
|
||||
# Read a single layer
|
||||
layer = ral.read_layer("/path/to/layer.pcd")
|
||||
|
||||
Indices and tables
|
||||
==================
|
||||
|
||||
* :ref:`genindex`
|
||||
* :ref:`modindex`
|
||||
* :ref:`search`
|
||||
98
docs/installation.rst
Normal file
98
docs/installation.rst
Normal file
@@ -0,0 +1,98 @@
|
||||
Installation
|
||||
============
|
||||
|
||||
Requirements
|
||||
------------
|
||||
|
||||
* Python 3.11 or higher
|
||||
* NumPy 2.0.0 or higher
|
||||
|
||||
From PyPI (Recommended)
|
||||
-----------------------
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
pip install read-aconity-layers
|
||||
|
||||
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)
|
||||
|
||||
Build Steps
|
||||
~~~~~~~~~~~
|
||||
|
||||
1. Clone the repository:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
git clone https://github.com/Cian-H/read_aconity_layers.git
|
||||
cd read_aconity_layers
|
||||
|
||||
2. Install Python dependencies:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
poetry install
|
||||
|
||||
3. Build the Rust extension:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
poetry run maturin develop
|
||||
|
||||
4. Run tests to verify installation:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
poetry run pytest
|
||||
|
||||
Development Installation
|
||||
------------------------
|
||||
|
||||
For development work, you'll also want the development dependencies:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
poetry install --with dev,docs
|
||||
|
||||
This installs additional tools for:
|
||||
|
||||
* Code formatting (ruff)
|
||||
* Type checking (mypy)
|
||||
* Testing (pytest)
|
||||
* Documentation building (sphinx)
|
||||
|
||||
Troubleshooting
|
||||
---------------
|
||||
|
||||
Common Issues
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
**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.
|
||||
|
||||
**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.
|
||||
|
||||
**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.
|
||||
50
docs/justfile
Normal file
50
docs/justfile
Normal file
@@ -0,0 +1,50 @@
|
||||
# Justfile for Sphinx documentation
|
||||
|
||||
sphinxopts := ""
|
||||
sphinxbuild := "poetry run sphinx-build"
|
||||
sourcedir := "."
|
||||
builddir := "./_build"
|
||||
|
||||
# Default recipe - equivalent to "just" without arguments
|
||||
default: help
|
||||
|
||||
# Show help
|
||||
help:
|
||||
@{{sphinxbuild}} -M help "{{sourcedir}}" "{{builddir}}" {{sphinxopts}}
|
||||
|
||||
# Build the Rust extension first (required for autodoc)
|
||||
build-extension:
|
||||
@echo "Checking Rust toolchain..."
|
||||
@which cargo > /dev/null || (echo "Error: Rust/Cargo not found. Please install Rust toolchain." && exit 1)
|
||||
cd .. && poetry run maturin develop
|
||||
|
||||
# Clean build directory
|
||||
clean:
|
||||
rm -rf {{builddir}}/*
|
||||
|
||||
# Build HTML documentation
|
||||
html: build-extension
|
||||
{{sphinxbuild}} -b html "{{sourcedir}}" "{{builddir}}/html" {{sphinxopts}}
|
||||
@echo
|
||||
@echo "Build finished. The HTML pages are in {{builddir}}/html."
|
||||
|
||||
# Build and serve documentation locally
|
||||
serve: html
|
||||
@echo "Serving documentation at http://localhost:8000"
|
||||
cd {{builddir}}/html && python -m http.server 8000
|
||||
|
||||
# Build documentation with live reload (requires sphinx-autobuild)
|
||||
livehtml: build-extension
|
||||
poetry run sphinx-autobuild "{{sourcedir}}" "{{builddir}}/html" {{sphinxopts}}
|
||||
|
||||
# Check for broken links
|
||||
linkcheck:
|
||||
{{sphinxbuild}} -b linkcheck "{{sourcedir}}" "{{builddir}}/linkcheck" {{sphinxopts}}
|
||||
|
||||
# Build all formats
|
||||
all: html
|
||||
|
||||
# Catch-all recipe for Sphinx targets (equivalent to Make's % target)
|
||||
# Usage: just sphinx <target> [options]
|
||||
sphinx target *options="":
|
||||
@{{sphinxbuild}} -M {{target}} "{{sourcedir}}" "{{builddir}}" {{sphinxopts}} {{options}}
|
||||
25
docs/python/index.rst
Normal file
25
docs/python/index.rst
Normal file
@@ -0,0 +1,25 @@
|
||||
Python API Reference
|
||||
====================
|
||||
|
||||
This section contains the complete Python API reference for ``read_aconity_layers``.
|
||||
|
||||
Module
|
||||
-----------
|
||||
|
||||
.. automodule:: read_aconity_layers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Return Type Information
|
||||
-----------------------
|
||||
|
||||
The library includes comprehensive type stubs for full IDE support and type checking.
|
||||
|
||||
All functions return NumPy arrays with the following structure:
|
||||
|
||||
* **Column 0**: X coordinates (corrected)
|
||||
* **Column 1**: Y coordinates (corrected)
|
||||
* **Column 2**: Z coordinates (layer height)
|
||||
* **Column 3**: Pyrometer 1 readings
|
||||
* **Column 4**: Pyrometer 2 readings
|
||||
190
docs/quickstart.rst
Normal file
190
docs/quickstart.rst
Normal file
@@ -0,0 +1,190 @@
|
||||
Quickstart Guide
|
||||
================
|
||||
|
||||
This guide will get you up and running with ``read_aconity_layers`` in just a few minutes.
|
||||
|
||||
Basic Usage
|
||||
-----------
|
||||
|
||||
Reading All Layers from a Directory
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
The most common use case is reading all layer files from a directory:
|
||||
|
||||
.. code-block:: python
|
||||
|
||||
import read_aconity_layers as ral
|
||||
import numpy as np
|
||||
|
||||
# Read all .pcd files from a directory
|
||||
data = ral.read_layers("/path/to/your/layer/files/")
|
||||
|
||||
print(f"Loaded {data.shape[0]} data points")
|
||||
print(f"Data shape: {data.shape}")
|
||||
print(f"Columns: [x, y, z, data1, data2]")
|
||||
|
||||
Reading Specific Files
|
||||
~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
If you want to read only specific layer files:
|
||||
|
||||
.. code-block:: python
|
||||
|
||||
import read_aconity_layers as ral
|
||||
|
||||
# List of specific files to read
|
||||
files = [
|
||||
"/path/to/0.1.pcd",
|
||||
"/path/to/0.2.pcd",
|
||||
"/path/to/0.3.pcd"
|
||||
]
|
||||
|
||||
data = ral.read_selected_layers(files)
|
||||
|
||||
Reading a Single Layer
|
||||
~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
For processing individual layers:
|
||||
|
||||
.. code-block:: python
|
||||
|
||||
import read_aconity_layers as ral
|
||||
|
||||
# Read just one layer file
|
||||
layer_data = ral.read_layer("/path/to/single_layer.pcd")
|
||||
|
||||
# Extract coordinates
|
||||
x_coords = layer_data[:, 0]
|
||||
y_coords = layer_data[:, 1]
|
||||
z_coords = layer_data[:, 2]
|
||||
|
||||
Working with the Data
|
||||
---------------------
|
||||
|
||||
Understanding the Data Format
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
All functions return NumPy arrays with 5 columns:
|
||||
|
||||
* **Column 0**: X coordinates (corrected)
|
||||
* **Column 1**: Y coordinates (corrected)
|
||||
* **Column 2**: Z coordinates (layer height)
|
||||
* **Column 3**: Original data column 3
|
||||
* **Column 4**: Original data column 4
|
||||
|
||||
The X and Y coordinates are automatically corrected using the calibration
|
||||
formulas built into the library.
|
||||
|
||||
Example: Basic Data Analysis
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
.. code-block:: python
|
||||
|
||||
import read_aconity_layers as ral
|
||||
import numpy as np
|
||||
import matplotlib.pyplot as plt
|
||||
|
||||
# Load data
|
||||
data = ral.read_layers("/path/to/layers/")
|
||||
|
||||
# Basic statistics
|
||||
print(f"X range: {data[:, 0].min():.2f} to {data[:, 0].max():.2f}")
|
||||
print(f"Y range: {data[:, 1].min():.2f} to {data[:, 1].max():.2f}")
|
||||
print(f"Z range: {data[:, 2].min():.2f} to {data[:, 2].max():.2f}")
|
||||
|
||||
# Plot layer distribution
|
||||
unique_z = np.unique(data[:, 2])
|
||||
layer_counts = [np.sum(data[:, 2] == z) for z in unique_z]
|
||||
|
||||
plt.figure(figsize=(10, 6))
|
||||
plt.plot(unique_z, layer_counts)
|
||||
plt.xlabel('Layer Height (Z)')
|
||||
plt.ylabel('Number of Points')
|
||||
plt.title('Points per Layer')
|
||||
plt.show()
|
||||
|
||||
Example: Processing by Layer
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
.. code-block:: python
|
||||
|
||||
import read_aconity_layers as ral
|
||||
import numpy as np
|
||||
|
||||
# Read data
|
||||
data = ral.read_layers("/path/to/layers/")
|
||||
|
||||
# Group by Z coordinate (layer)
|
||||
unique_z = np.unique(data[:, 2])
|
||||
|
||||
layer_stats = []
|
||||
for z in unique_z:
|
||||
layer_mask = data[:, 2] == z
|
||||
layer_points = data[layer_mask]
|
||||
|
||||
stats = {
|
||||
'z': z,
|
||||
'point_count': len(layer_points),
|
||||
'x_mean': layer_points[:, 0].mean(),
|
||||
'y_mean': layer_points[:, 1].mean(),
|
||||
'data1_mean': layer_points[:, 3].mean(),
|
||||
'data2_mean': layer_points[:, 4].mean(),
|
||||
}
|
||||
layer_stats.append(stats)
|
||||
|
||||
# Convert to structured array for easier analysis
|
||||
layer_stats = np.array(layer_stats)
|
||||
|
||||
Performance Tips
|
||||
----------------
|
||||
|
||||
Parallel Processing
|
||||
~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
The library automatically uses parallel processing for multiple files.
|
||||
For best performance:
|
||||
|
||||
* Use ``read_layers()`` for directories with many files
|
||||
* The library will automatically use all available CPU cores
|
||||
* Larger numbers of files will see better speedup
|
||||
|
||||
Memory Usage
|
||||
~~~~~~~~~~~~
|
||||
|
||||
For very large datasets:
|
||||
|
||||
* Consider processing files in batches if memory is limited
|
||||
* Use ``read_selected_layers()`` to process subsets
|
||||
* The library streams data efficiently, but the final arrays are held in memory
|
||||
|
||||
File Organization
|
||||
~~~~~~~~~~~~~~~~~
|
||||
|
||||
For optimal performance:
|
||||
|
||||
* Keep layer files in a single directory when using ``read_layers()``
|
||||
* Use consistent naming (the Z coordinate is extracted from the filename)
|
||||
* Ensure files are properly formatted space-delimited text
|
||||
|
||||
Error Handling
|
||||
--------------
|
||||
|
||||
The library provides detailed error messages for common issues:
|
||||
|
||||
.. code-block:: python
|
||||
|
||||
import read_aconity_layers as ral
|
||||
|
||||
try:
|
||||
data = ral.read_layers("/path/to/layers/")
|
||||
except IOError as e:
|
||||
print(f"File read error: {e}")
|
||||
except RuntimeError as e:
|
||||
print(f"Processing error: {e}")
|
||||
|
||||
Next Steps
|
||||
----------
|
||||
|
||||
* Check out the full :doc:`python/index` for detailed function documentation
|
||||
* See :doc:`development` if you want to contribute to the project
|
||||
* For performance-critical applications, review the :doc:`rust/index`
|
||||
57
docs/rust/index.rst
Normal file
57
docs/rust/index.rst
Normal file
@@ -0,0 +1,57 @@
|
||||
Rust API Reference
|
||||
==================
|
||||
|
||||
This section documents the internal Rust implementation of ``read_aconity_layers``.
|
||||
|
||||
.. note::
|
||||
This documentation is primarily intended for contributors and developers
|
||||
who want to understand the internal implementation. Most users should
|
||||
refer to the :doc:`../python/index` instead.
|
||||
|
||||
.. toctree::
|
||||
:glob:
|
||||
:caption: Rust API:
|
||||
|
||||
crates/read_aconity_layers/lib
|
||||
|
||||
Overview
|
||||
--------
|
||||
|
||||
The Rust implementation provides the high-performance core of ``read_aconity_layers``.
|
||||
Key characteristics include:
|
||||
|
||||
Performance Features
|
||||
~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
* **Parallel Processing**: Uses Rayon for parallel file reading across all CPU cores
|
||||
* **Memory Efficiency**: Streams data rather than loading everything into memory at once
|
||||
* **SIMD Operations**: Leverages vectorized operations for coordinate corrections
|
||||
* **Zero-Copy**: Minimizes data copying between Rust and Python using PyO3
|
||||
|
||||
Architecture
|
||||
~~~~~~~~~~~~
|
||||
|
||||
The crate is organized into two main components:
|
||||
|
||||
* **Public API** (``src/lib.rs``): PyO3 bindings that expose Rust functions to Python
|
||||
* **Core Logic** (``src/rust_fn/``): Pure Rust implementation of file reading and processing
|
||||
|
||||
Error Handling
|
||||
~~~~~~~~~~~~~~
|
||||
|
||||
The Rust code uses a comprehensive ``ReadError`` enum that covers all possible
|
||||
failure modes, from I/O errors to parsing failures. These are automatically
|
||||
converted to appropriate Python exceptions through the PyO3 integration.
|
||||
|
||||
Dependencies
|
||||
~~~~~~~~~~~~
|
||||
|
||||
Key Rust dependencies that power the performance:
|
||||
|
||||
* ``ndarray`` - N-dimensional arrays with BLAS integration
|
||||
* ``rayon`` - Data parallelism library
|
||||
* ``csv`` - Fast CSV parsing
|
||||
* ``pyo3`` - Python bindings
|
||||
* ``numpy`` - NumPy integration for PyO3
|
||||
* ``glob`` - File path pattern matching
|
||||
* ``indicatif`` - Progress bars for long operations
|
||||
7
justfile
Normal file
7
justfile
Normal file
@@ -0,0 +1,7 @@
|
||||
# Lists available just commands
|
||||
default:
|
||||
@just --list
|
||||
|
||||
# Documentation commands - delegates to docs/justfile
|
||||
docs command *args:
|
||||
cd docs && just {{command}} {{args}}
|
||||
975
poetry.lock
generated
975
poetry.lock
generated
File diff suppressed because it is too large
Load Diff
@@ -34,6 +34,15 @@ mypy = "^1.15.0"
|
||||
pytest = "^8.3.5"
|
||||
loguru = "^0.7.3"
|
||||
|
||||
[tool.poetry.group.docs.dependencies]
|
||||
sphinx = "^8.2.3"
|
||||
sphinx-autodoc-typehints = "^3.2.0"
|
||||
sphinx-copybutton = "^0.5.2"
|
||||
sphinx-rtd-theme = "^3.0.2"
|
||||
sphinxcontrib-rust = "^0.8.1"
|
||||
myst-parser = "^4.0.1"
|
||||
sphinx-autobuild = "^2024.10.3"
|
||||
|
||||
[build-system]
|
||||
requires = ["maturin>=1.7,<2.0"]
|
||||
build-backend = "maturin"
|
||||
|
||||
Reference in New Issue
Block a user