kmhelpers 0.7.0__py3-none-any.whl

kmhelpers-0.7.0.dist-info/METADATA

@@ -0,0 +1,197 @@
+Metadata-Version: 2.4
+Name: kmhelpers
+Version: 0.7.0
+Summary: A Python toolkit for managing, compressing, and querying indexes with kmindex
+Author-email: Sébastien BELLENOUS <kmhelpers@groupes.renater.fr>
+License: GPL-3.0-only
+Project-URL: Repository, https://github.com/sebllns/kmhelpers
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: psutil>=5.8.0
+Requires-Dist: pyyaml>=5.4
+Requires-Dist: click>=8.1
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: zstandard>=0.19
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=3.0; extra == "dev"
+Requires-Dist: black>=22.0; extra == "dev"
+Requires-Dist: flake8>=4.0; extra == "dev"
+Requires-Dist: mypy>=0.950; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.0; extra == "docs"
+Requires-Dist: mkdocstrings[python]>=0.25; extra == "docs"
+Requires-Dist: mike>=2.0; extra == "docs"
+Requires-Dist: termynal>=0.12; extra == "docs"
+Dynamic: license-file
+
+# kmhelpers
+
+---
+
+<img src="assets/kmhelpers-logo-v1.png" alt="Kmhelpers Logo" width="64" height="64">
+
+A Python toolkit for managing, compressing, and querying [kmindex](https://github.com/tlemane/kmindex) indices efficiently.
+
+**Documentation:** <https://sebllns.github.io/kmhelpers/>
+
+---
+
+## Table of Contents
+
+- [Disclaimers](#disclaimers)
+- [Getting Started](#getting-started)
+- [Documentation](#documentation)
+- [License](#license)
+- [Contact](#contact)
+- [Changelog](#changelog)
+- [Acknowledgements](#acknowledgements)
+
+## Disclaimers
+
+`kmhelpers` is provided "as is", without warranty (see [LICENSE](LICENSE)). Operations that build, update, or compress indices modify data in place, so it might be useful to back up important data beforehand, and if you are not sure of something, [ask here](https://github.com/sebllns/kmhelpers/discussions) before running it.
+
+## Getting started
+
+### Clone the repository and navigate to it
+
+```bash
+git clone https://github.com/sebllns/kmhelpers
+cd kmhelpers
+```
+
+To clone a [released version](https://github.com/sebllns/kmhelpers/releases) directly:
+
+```bash
+git clone --branch vX.Y.Z https://github.com/sebllns/kmhelpers
+cd kmhelpers
+```
+
+### Quick Install with Conda 
+
+This will automatically:
+- Install `kmhelpers` Python package
+- Install `kmindex` and `ntcard`
+
+**Prerequisites:** Conda (Miniconda or Anaconda) must be installed. If you don't have it, see [Installation Instructions](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html).
+
+```bash
+# Create environment with kmindex pre-installed
+conda env create -f conda/environment.yml -p ./.env
+
+# Activate the environment
+# Run this each time you open a new terminal session before using kmhelpers
+conda activate ./.env
+```
+
+> **Note:** Once per terminal session, activate the environment before using `kmhelpers`:
+> ```bash
+> conda activate /path/to/kmhelpers/.env
+> ```
+> `.env` can be replaced by any path, for example a shared or permanent location like `~/.kmhelpers`:
+> ```bash
+> conda env create -f conda/environment.yml -p ~/.kmhelpers
+> conda activate ~/.kmhelpers
+> ```
+
+### Verify Installation
+
+Once the environment has been activated:
+
+```bash
+# Check the installed version
+kmhelpers --version
+
+# View available commands
+kmhelpers --help
+```
+
+> **Tip:** `kh` is available as a short alias for `kmhelpers` (e.g. `kh --help`).
+
+```bash
+
+# Check ntcard
+ntcard --version
+
+# Check kmtricks
+kmtricks --version
+
+# Check kmindex
+kmindex --version
+```
+
+### Update
+
+To pull the latest changes from the default branch (`main`):
+
+```bash
+git pull origin main
+```
+
+To check out a [released version](https://github.com/sebllns/kmhelpers/releases) instead:
+
+```bash
+git fetch --tags
+git checkout vX.Y.Z
+```
+
+If your local branch is already tracking a remote branch, you can simply run:
+
+```bash
+git pull
+```
+
+Check the installed version:
+
+```bash
+kmhelpers --version
+```
+
+## Documentation
+
+<https://sebllns.github.io/kmhelpers/>
+
+Covers installation, a full tutorial, command reference, core concepts, and the API reference.
+
+## License
+
+This project is licensed under the GNU General Public License - see the [LICENSE](LICENSE) file for details.
+
+Copyright (c) 2026 Sébastien Bellenous, Genscale, INRIA
+
+## Contact
+
+For questions, bug reports, or contributions, please contact:
+
+- **Author**: [Sébastien BELLENOUS](https://github.com/sebllns)
+- **Email**: kmhelpers@groupes.renater.fr
+- **Repository**: [GitHub](https://github.com/sebllns/kmhelpers)
+- **Supervisor**: [Pierre Peterlongo](https://github.com/pierrepeterlongo)
+
+---
+
+**Version**: 0.7.0
+**Status**: Development
+
+## Changelog
+
+See [CHANGELOG.md](CHANGELOG.md) for detailed version history.
+
+
+## Acknowledgements
+
+The authors thank Téo Lemane for developing `kmindex` and for his
+responsiveness in addressing feature requests and issues raised during the
+development of `kmhelpers`. We acknowledge the GenOuest core facility
+(<https://www.genouest.org>) for providing the computing infrastructure.
+The work was funded by the Inria Challenge "OmicFinder"
+(<https://project.inria.fr/omicfinder/>), and by the state funding managed by the French National Research Agency under the France 2030 program [ANR-22-PEAE-0005].

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kmhelpers-0.7.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (84.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

kmhelpers-0.7.0.dist-info/entry_points.txt

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+[console_scripts]
+kh = pykmhelpers.cli.kmhelpers:cli
+kmhelpers = pykmhelpers.cli.kmhelpers:cli