chemotools 0.1.11__tar.gz → 0.1.16__tar.gz

chemotools-0.1.16/.gitattributes

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+# make language python
+*.html linguist-language=Python

chemotools-0.1.16/.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    commit-message:
+      prefix: "chore"
+      include: "scope"

chemotools-0.1.16/.github/labels.yml

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+_extends: .github

chemotools-0.1.16/.github/release-drafter.yml

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+_extends: .github

chemotools-0.1.16/.github/workflows/ci.yml

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+name: Python CI
+
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+
+  workflow_dispatch:
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12', '3.13']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Install Task
+        uses: arduino/setup-task@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Print versions
+        run: |
+          python --version
+          uv --version
+          task --version
+
+      # 1. Install dependencies
+      - name: Install dependencies
+        run: task install
+
+      # 2. Format (check-only)
+      - name: Check formatting
+        run: task format-check
+
+      # 3. Lint
+      - name: Run linting
+        run: task lint
+
+      # 4. Type-check
+      - name: Run type checking
+        run: task type-check
+
+      # 5. Tests with coverage
+      - name: Run tests with coverage
+        run: task coverage
+
+      # 6. Upload coverage reports to Codecov
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      # 7. Build package
+      - name: Build package
+        run: task build

chemotools-0.1.16/.github/workflows/python-release.yml

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+name: Publish Python 🐍 distributions 📦 to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+        id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Install Task
+        uses: arduino/setup-task@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Print versions
+        run: |
+          python --version
+          uv --version
+          task --version
+
+      # 1. Install dependencies
+      - name: Install dependencies
+        run: task install
+
+      # 2. Build package
+      - name: Build package
+        run: task build
+
+      # 3. Publish to PyPI
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

chemotools-0.1.16/.github/workflows/release-drafter.yml

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+name: Release Drafter
+
+on:
+  push:
+    # branches to consider in the event; optional, defaults to all
+    branches:
+      - master
+  # pull_request event is required only for autolabeler
+  pull_request:
+    # Only following types are handled by the action, but one can default to all as well
+    types: [opened, reopened, synchronize]
+  # pull_request_target event is required for autolabeler to support PRs from forks
+  # pull_request_target:
+  #   types: [opened, reopened, synchronize]
+
+permissions:
+  contents: read
+
+jobs:
+  update_release_draft:
+    permissions:
+      # write permission is required to create a github release
+      contents: write
+      # write permission is required for autolabeler
+      # otherwise, read permission is required at least
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+      # (Optional) GitHub Enterprise requires GHE_HOST variable set
+      #- name: Set GHE_HOST
+      #  run: |
+      #    echo "GHE_HOST=${GITHUB_SERVER_URL##https:\/\/}" >> $GITHUB_ENV
+
+      # Drafts your next Release notes as Pull Requests are merged into "master"
+      - uses: release-drafter/release-drafter@v5
+        # (Optional) specify config name to use, relative to .github/. Default: release-drafter.yml
+        # with:
+        #   config-name: my-config.yml
+        #   disable-autolabeler: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

chemotools-0.1.16/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv*
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Notebooks
+*.ipynb
+
+# Pyre type checker
+.pyre/
+
+# VScode
+.vscode/
+
+# Task files
+*.task

chemotools-0.1.16/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

chemotools-0.1.16/CONTRIBUTING.md

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+# Contributing to chemotools
+
+Thanks for your interest in contributing to **`chemotools`** 🎉 
+We welcome bug reports, feature ideas, code improvements, and documentation updates. Every contribution helps!
+
+You can also check the [Project Board](https://github.com/users/paucablop/projects/4) to see what’s currently in progress.
+
+---
+
+## Guidelines
+
+`chemotools` is designed for production use, with a focus on **quality and consistency**.  
+When contributing, please keep in mind:
+
+- ✅ **Follow the Scikit-Learn API**  
+  All transformers must implement the [scikit-learn API](https://scikit-learn.org/stable/developers/develop.html) for interoperability.  
+
+- ✅ **Avoid redundancy**  
+  Don’t re-implement functionality already available in other libraries that follow the same API.  
+
+- ✅ **Write tests**  
+  Every new function or fix must include unit tests to ensure reliability.  
+
+- ✅ **Maintain quality**  
+  Use the provided tooling (formatting, linting, typing, tests) to keep the codebase consistent.  
+
+---
+
+## How to Contribute
+
+1. **Report issues**  
+   - For bugs: open an [issue](https://github.com/paucablop/chemotools/issues) with steps to reproduce and sample code/data if possible.  
+   - For enhancements: describe the idea, its benefits, and example usage.  
+
+2. **Propose changes**  
+   - Open an issue first so we can discuss scope.  
+   - Create a new branch for your contribution.  
+   - Make your changes, including tests and documentation updates if needed. 
+   - Branches should be shor-lived with a well defined scope, follwoing a [truck-based development](https://trunkbaseddevelopment.com/) philosophy.
+
+3. **Check your work**  
+   Use the [Taskfile](./Taskfile.yml) for a quick workflow:  
+
+   ```bash
+   task install     # install dependencies
+   task check       # run formatting, linting, typing, tests
+   task coverage    # run tests with coverage
+   task build       # build the package
+   ```
+
+4. **Open a Pull Request (PR)**
+
+   * Explain what the change does and why.
+   * Ensure CI checks pass (formatting, lint, type checks, tests).
+   * Be responsive to feedback.
+
+
+## Code Style
+
+* Code is automatically formatted and linted using [Ruff](https://docs.astral.sh/ruff/).
+* Type checking is done with [MyPy](http://mypy-lang.org/).
+* Follow general Python best practices: descriptive names, no magic numbers, clear docstrings.
+
+
+
+## Testing & Coverage
+
+* Run tests with:
+
+  ```bash
+  task test
+  ```
+
+* Coverage is tracked with [Codecov](https://codecov.io/). PRs should not reduce coverage.
+
+---
+
+## License
+
+By contributing, you agree that your contributions will be licensed under the project’s [MIT License](LICENSE).
+
+

chemotools-0.1.16/PKG-INFO

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+Metadata-Version: 2.4
+Name: chemotools
+Version: 0.1.16
+Summary: chemotools: A Python Package that Integrates Chemometrics and scikit-learn
+Author: Pau Cabaneros
+License-Expression: MIT
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: numpy<3,>=2.0.0
+Requires-Dist: pandas<3,>=2.0.0
+Requires-Dist: polars<2,>=1.17.0
+Requires-Dist: pyarrow<21,>=18
+Requires-Dist: scikit-learn<2,>=1.4.0
+Provides-Extra: dev
+Requires-Dist: mypy<2,>=1.13.0; extra == 'dev'
+Requires-Dist: pandas-stubs<3,>=2.2.3.241126; extra == 'dev'
+Requires-Dist: pytest-cov>=6.3.0; extra == 'dev'
+Requires-Dist: pytest<9,>=8.3.0; extra == 'dev'
+Requires-Dist: ruff<0.9,>=0.8.0; extra == 'dev'
+Requires-Dist: scipy-stubs<2,>=1.15.1.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+![chemotools](assets/images/banner_dark.png)
+
+# chemotools
+
+
+[![PyPI](https://img.shields.io/pypi/v/chemotools)](https://pypi.org/project/chemotools)
+[![Python Versions](https://img.shields.io/pypi/pyversions/chemotools)](https://pypi.org/project/chemotools)
+[![License](https://img.shields.io/pypi/l/chemotools)](https://github.com/paucablop/chemotools/blob/main/LICENSE)
+[![Coverage](https://codecov.io/github/paucablop/chemotools/branch/main/graph/badge.svg?token=D7JUJM89LN)](https://codecov.io/github/paucablop/chemotools)
+[![Downloads](https://static.pepy.tech/badge/chemotools)](https://pepy.tech/project/chemotools)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.06802/status.svg)](https://doi.org/10.21105/joss.06802)
+
+---
+
+`chemotools` is a Python library that brings **chemometric preprocessing tools** into the [`scikit-learn`](https://scikit-learn.org/) ecosystem.  
+
+It provides modular transformers for spectral data, designed to plug seamlessly into your ML workflows.
+
+## Features
+
+- Preprocessing for spectral data (baseline correction, smoothing, scaling, derivatization, scatter correction).  
+- Fully compatible with `scikit-learn` pipelines and transformers.  
+- Simple, modular API for flexible workflows.  
+- Open-source, actively maintained, and published on [PyPI](https://pypi.org/project/chemotools/) and [Conda](https://anaconda.org/conda-forge/chemotools).  
+
+## Installation
+
+Install from PyPI:
+
+```bash
+pip install chemotools
+````
+
+Install from Conda:
+
+```bash
+conda install -c conda-forge chemotools
+```
+
+## Usage
+
+Example: preprocessing pipeline with 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 = make_pipeline(
+    AirPls(),
+    MultiplicativeScatterCorrection(),
+    StandardScaler(with_std=False),
+)
+
+spectra_transformed = preprocessing.fit_transform(spectra)
+```
+
+➡️ See the [documentation](https://paucablop.github.io/chemotools/) for full details.
+
+## Development
+
+This project uses [uv](https://github.com/astral-sh/uv) for dependency management and [Task](https://taskfile.dev) to simplify common development workflows.
+You can get started quickly by using the predefined [Taskfile](./Taskfile.yml), which provides handy shortcuts such as:
+
+```bash
+task install     # install all dependencies
+task check       # run formatting, linting, typing, and tests
+task coverage    # run tests with coverage reporting
+task build       # build the package for distribution
+```
+
+## Contributing
+
+Contributions are welcome!
+Check out the [contributing guide](CONTRIBUTING.md) and the [project board](https://github.com/users/paucablop/projects/4).
+
+## License
+
+Released under the [MIT License](LICENSE).
+