Code cleaning + add workflows

.github/workflows/tests.yml

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+name: Tests
+
+on:
+  push:
+    branches: [ master, main, develop ]
+  pull_request:
+    branches: [ master, main, develop ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest pytest-cov
+        pip install -e .
+
+    - name: Download knots database
+      run: |
+        python -c "import pyknotid.catalogue; pyknotid.catalogue.download_database()"
+
+    - name: Run tests
+      run: |
+        pytest -v --tb=short --cov=pyknotid --cov-report=xml --cov-report=term
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        file: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+        fail_ci_if_error: false

.gitignore

@@ -1,4 +1,28 @@
 *.pyc
 *.so
 *.c
-*.db
+*.db
+dev/
+
+# Build and distribution
+*.egg-info/
+dist/
+build/
+__pycache__/
+
+# Documentation
+doc/_build/
+doc/_static/
+
+# Testing
+.pytest_cache/
+.coverage
+coverage.xml
+htmlcov/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~

.readthedocs.yaml

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+# Read the Docs configuration file for pyknotid
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
+sphinx:
+  configuration: doc/conf.py
+
+python:
+  install:
+    - requirements: doc/requirements.txt
+    - method: pip
+      path: .

CITATION.bib

@@ -0,0 +1,7 @@
+@Misc{pyknotid,
+  author =    {Alexander J Taylor and other SPOCK contributors},
+  title =     {pyknotid knot identification toolkit},
+  howpublished = {\url{https://github.com/SPOCKnots/pyknotid}},
+  note =      {Accessed YYYY-MM-DD},
+  year = 2017,
+}

CITATION.cff

@@ -0,0 +1,29 @@
+cff-version: 1.2.0
+message: "If you use pyknotid in your research, please cite it as below."
+title: "pyknotid knot identification toolkit"
+version: 0.5.4
+date-released: 2017-01-01
+url: "https://github.com/SPOCKnots/pyknotid"
+repository-code: "https://github.com/SPOCKnots/pyknotid"
+license: MIT
+authors:
+  - family-names: "Taylor"
+    given-names: "Alexander J"
+    email: "alexander.taylor@bristol.ac.uk"
+  - name: "SPOCK contributors"
+keywords:
+  - knot-theory
+  - topology
+  - mathematics
+  - knot-identification
+  - linking
+abstract: "Python modules for detecting and measuring knotting and linking. pyknotid can analyse space-curves, i.e. sets of points in three-dimensions, or can parse standard topological representations of knot diagrams."
+preferred-citation:
+  type: software
+  title: "pyknotid knot identification toolkit"
+  authors:
+    - family-names: "Taylor"
+      given-names: "Alexander J"
+    - name: "other SPOCK contributors"
+  year: 2017
+  url: "https://github.com/SPOCKnots/pyknotid"

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Alexander Taylor and other contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

MANIFEST.in

@@ -0,0 +1,5 @@
+include README.md
+include LICENSE.txt
+include CITATION.cff
+include CITATION.bib
+recursive-include pyknotid *.tmpl *.pov *.py

README.md

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+# Pyknotid
+
+[![PyPI version](https://img.shields.io/pypi/v/pyknotid.svg)](https://pypi.org/project/pyknotid/)
+[![Documentation Status](https://readthedocs.org/projects/pyknotid/badge/?version=latest)](https://pyknotid.readthedocs.io/en/latest/?badge=latest)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+Python modules for detecting and measuring knotting and linking. pyknotid can analyse space-curves (sets of points in three dimensions) or parse standard topological representations of knot diagrams.
+
+<p align="center">
+  <img src="doc/k10_92_ideal_small.png" alt="The knot 10_92, visualised by pyknotid" width="300"/>
+</p>
+
+## Features
+
+- **Knot identification** from space curves or topological representations
+- **Polynomial invariants** (Alexander, Jones, HOMFLY-PT, Kauffman)
+- **Vassiliev invariants** computation
+- **Knot simplification** using octree algorithms
+- **Visualization** of knots in 3D
+- **Database** of known knots for identification
+- **High performance** with optional Numba JIT compilation (2-3x faster)
+
+## Installation
+
+pyknotid requires Python 3.8 or later. Install it with:
+
+```bash
+pip install pyknotid
+```
+
+**For best performance**, install with Numba support:
+
+```bash
+pip install pyknotid[performance]
+```
+
+This enables JIT-compiled high-performance numerical computations (2-3x faster). Without Numba, pyknotid will work but use slower pure Python fallbacks.
+
+### Development Installation
+
+To try the latest development version, clone this repository and run:
+
+```bash
+git clone https://github.com/SPOCKnots/pyknotid.git
+cd pyknotid
+pip install -e .
+```
+
+For development with all optional dependencies:
+
+```bash
+pip install -e ".[dev]"
+```
+
+## Quick Start
+
+```python
+import pyknotid.spacecurves as sp
+import pyknotid.make as mk
+
+# Create a figure-eight knot
+k = sp.Knot(mk.figure_eight(num_points=100))
+
+# Visualize it
+k.plot()
+
+# Calculate the Alexander polynomial at t=-1
+k.alexander_polynomial(-1)
+# Output: 6.9999999999999991
+
+# Calculate the symbolic Alexander polynomial
+import sympy as sym
+t = sym.var('t')
+k.alexander_polynomial(t)
+# Output: 2/t - 3/t**2 + 2/t**3
+
+# Simplify the knot representation
+k.octree_simplify(5)
+# Run 0 of 5, 100 points remain
+# Run 1 of 5, 98 points remain
+# ...
+# Reduced to 77 points
+
+k.plot()
+```
+
+## Documentation
+
+Full documentation is available at [pyknotid.readthedocs.io](http://pyknotid.readthedocs.io).
+
+## Requirements
+
+The following dependencies are automatically installed:
+
+- numpy >= 1.19
+- networkx >= 2.5
+- planarity >= 0.4
+- peewee >= 3.14
+- vispy >= 0.6
+- sympy >= 1.8
+- appdirs >= 1.4
+- requests >= 2.25
+- tqdm >= 4.60
+
+### Optional Dependencies
+
+- **numba >= 0.55** (recommended for performance): Install with `pip install pyknotid[performance]`
+- **pytest, pytest-cov, black, flake8, mypy** (for development): Install with `pip install pyknotid[dev]`
+- **sphinx, sphinx-rtd-theme** (for documentation): Install with `pip install pyknotid[docs]`
+
+## About
+
+pyknotid was originally developed as part of the Leverhulme Trust Research Programme Grant RP2013-K-009: Scientific Properties of Complex Knots (SPOCK), a collaboration between the University of Bristol and Durham University in the UK.
+
+For more information, see the [SPOCK homepage](http://www.maths.dur.ac.uk/spock/index.html/).
+
+## Citation
+
+If you use pyknotid in your research, please cite it. See [CITATION.cff](CITATION.cff) for citation information, or use:
+
+```bibtex
+@Misc{pyknotid,
+  author = {Alexander J Taylor and other SPOCK contributors},
+  title = {pyknotid knot identification toolkit},
+  howpublished = {\url{https://github.com/SPOCKnots/pyknotid}},
+  year = 2017,
+}
+```
+
+For more details, see our [citation guidelines](http://pyknotid.readthedocs.io/en/latest/sources/about.html#cite-us).
+
+## License
+
+pyknotid is released under the [MIT License](LICENSE.txt).
+
+## Contributing
+
+Contributions are welcome! Please feel free to:
+
+- Report bugs or request features via [GitHub Issues](https://github.com/SPOCKnots/pyknotid/issues)
+- Submit pull requests
+- Improve documentation
+
+## Contact
+
+Questions or comments are welcome. Please do not hesitate to open an issue or pull request on GitHub.
+
+## Links
+
+- **Homepage**: https://github.com/SPOCKnots/pyknotid
+- **Documentation**: http://pyknotid.readthedocs.io
+- **PyPI**: https://pypi.org/project/pyknotid/
+- **Bug Tracker**: https://github.com/SPOCKnots/pyknotid/issues