chemotools
chemotools: A Python Package that Integrates Chemometrics and scikit-learn - Published in JOSS (2024)
Science Score: 93.0%
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Published in Journal of Open Source Software
Keywords
Keywords from Contributors
Repository
Integrate your chemometric tools with the scikit-learn API 🧪 🤖
Basic Info
- Host: GitHub
- Owner: paucablop
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://paucablop.github.io/chemotools/
- Size: 30.3 MB
Statistics
- Stars: 61
- Watchers: 4
- Forks: 7
- Open Issues: 17
- Releases: 41
Topics
Metadata Files
README.md
chemotools
Welcome to Chemotools, a Python package that integrates chemometrics with Scikit-learn.
Note
Since I released Chemotools, I have received a fantastic response from the community. I am really happy for the interest in the project 🤗. This also means that I have received a lot of good feedback and suggestions for improvements. I have been intensively working on releasing new versions of Chemotools to address the feedback and suggestions. If you use Chemotools, make sure you are using the latest version (see installation), which will be aligned with the documentation.
👉👉 Check the latest version and make sure you don't miss out on cool new features.
👉👉 Check the documentation for a full description on how to use chemotools.
Description
Chemotools is a Python package that provides a collection of preprocessing tools and utilities for working with spectral data. It is built on top of popular scientific libraries and is designed to be highly modular, easy to use, and compatible with Scikit-learn transformers.
If you are interested in learning more about chemotools, please visit the documentation page.
Benefits: - Provides a collection of preprocessing tools and utilities for working with spectral data - Highly modular and compatible with Scikit-learn transformers - Can perform popular preprocessing tasks such as baseline correction, smoothing, scaling, derivatization, and scattering correction - Open source and available on PyPI
Applications: - Analyzing and processing spectral data in chemistry, biology, and other fields - Developing machine learning models for predicting properties or classifying samples based on spectral data - Teaching and learning about chemometrics and data preprocessing in Python
Installation
Chemotools is distributed via PyPI and can be easily installed using pip:
bash
pip install chemotools
Upgrading to the latest version is as simple as:
bash
pip install chemotools --upgrade
Usage
Chemotools is designed to be used in conjunction with Scikit-learn. It follows the same API as other Scikit-learn transformers, so you can easily integrate it into your existing workflow. For example, you can use chemotools to build pipelines that include transformers from chemotools and Scikit-learn:
```python from sklearn.preprocessing import StandardScaler from sklearn.pipeline import make_pipeline
from chemotools.baseline import AirPls from chemotools.scatter import MultiplicativeScatterCorrection
preprocessing = makepipeline(AirPls(), MultiplicativeScatterCorrection(), StandardScaler(withstd=False)) spectratransformed = preprocessing.fittransform(spectra) ```
Check the documentation for more information on how to use chemotools.
Development
To install/update the package and its development dependencies, the following command can be used:
bash
python -m pip install --upgrade . -r requirements.txt -r requirements-dev.txt
chemotools also comes with a Makefile that provides shortcuts for common development tasks. The equivalent command to the one above would be:
bash
make install-dev
Other useful commands include:
building the package: ```bash python -m build
or using the Makefile
make build ```
checking the linting of the package: ```bash flake8 ./chemotools ./tests --count --select=E9,F63,F7,F82 --show-source --statistics flake8 ./chemotools ./tests --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
or using the Makefile
make lint-flake8 ```
parallelized testing the package with a coverage report: ```bash pytest --cov=chemotools .\tests -n="auto" --cov-report=html -x # for an HTML report pytest --cov=chemotools .\tests -n="auto" --cov-report=xml -x # for an XML report
or using the Makefile
make test-htmlcov make test-xmlcov ```
Contributing
We welcome contributions to Chemotools from anyone interested in improving the package. Whether you have ideas for new features, bug reports, or just want to help improve the code, we appreciate your contributions! You are also welcome to see the Project Board to see what we are currently working on.
To contribute to Chemotools, please follow the contributing guidelines.
License
This package is distributed under the MIT license. See the LICENSE file for more information.
Credits
AirPLS baseline correction is based on the implementation by Zhang et al.. The current implementation is based on the Python implementation by zmzhang.
Owner
- Name: Pau Cabaneros
- Login: paucablop
- Kind: user
- Location: Denmark
- Company: Specshell ApS
- Repositories: 6
- Profile: https://github.com/paucablop
JOSS Publication
chemotools: A Python Package that Integrates Chemometrics and scikit-learn
Authors
Novo Nordisk A/S, Bagsvaerd, Denmark
Editor
Brian McFee
Tags
Chemometrics Spectroscopy Machine Learning scikit-learnGitHub Events
Total
- Create event: 36
- Issues event: 3
- Release event: 6
- Watch event: 9
- Delete event: 27
- Issue comment event: 20
- Push event: 56
- Pull request review comment event: 12
- Pull request review event: 18
- Pull request event: 55
- Fork event: 2
Last Year
- Create event: 36
- Issues event: 3
- Release event: 6
- Watch event: 9
- Delete event: 27
- Issue comment event: 20
- Push event: 56
- Pull request review comment event: 12
- Pull request review event: 18
- Pull request event: 55
- Fork event: 2
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| paucablop | p****s@g****m | 467 |
| dependabot[bot] | 4****] | 15 |
| Niklas Z | n****e@w****e | 1 |
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 50
- Total pull requests: 142
- Average time to close issues: 3 months
- Average time to close pull requests: about 1 month
- Total issue authors: 6
- Total pull request authors: 3
- Average comments per issue: 0.94
- Average comments per pull request: 0.6
- Merged pull requests: 45
- Bot issues: 0
- Bot pull requests: 110
Past Year
- Issues: 1
- Pull requests: 63
- Average time to close issues: N/A
- Average time to close pull requests: 11 days
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.54
- Merged pull requests: 17
- Bot issues: 0
- Bot pull requests: 48
Top Authors
Issue Authors
- paucablop (38)
- MothNik (5)
- mdarmstr (1)
- ssuwelack (1)
- jguenther504 (1)
- acmoudleysa (1)
Pull Request Authors
- dependabot[bot] (158)
- paucablop (28)
- MothNik (4)
Top Labels
Issue Labels
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Packages
- Total packages: 1
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Total downloads:
- pypi 589 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 36
- Total maintainers: 1
pypi.org: chemotools
chemotools: A Python Package that Integrates Chemometrics and scikit-learn
- Documentation: https://chemotools.readthedocs.io/
- License: MIT
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Latest release: 0.1.11
published 7 months ago