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Merge pull request #10 from biosustain/cdci update
🚧 start with GitHub Actions to ensure tests pass before larger refactor
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‎.github/workflows/README.md‎

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# Workflows
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## cicd
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Basic continuous integration and deployment (CI/CD) workflow for Python packages.
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- checks formatting (black, isort)
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- checks linting (ruff)
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- run unit tests (pytest)
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- optional: add c extensions to a package
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- if all checks pass, build and deploy to PyPI if `tag` triggered the workflow

‎.github/workflows/cicd.yml‎

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# This workflow will install Python dependencies, run tests and lint with a single version of Python
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# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
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name: CI/CD
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on:
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push:
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pull_request:
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branches: ["main"]
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schedule:
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- cron: "0 2 * * 3"
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permissions:
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contents: read
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jobs:
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format:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: psf/black@stable
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- uses: isort/isort-action@v1
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lint:
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name: Lint with ruff
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: "3.12"
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- name: Install ruff
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run: |
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pip install ruff
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- name: Lint with ruff
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run: |
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# stop the build if there are Python syntax errors or undefined names
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ruff check .
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test:
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name: Test
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runs-on: macos-latest
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strategy:
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matrix:
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python-version: ["3.11", "3.12", "3.13"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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cache: "pip" # caching pip dependencies
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cache-dependency-path: "**/pyproject.toml"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install pytest
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pip install -e .
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- name: Run tests
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run: python -m pytest tests
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build_source_dist:
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name: Build source distribution
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if: startsWith(github.ref, 'refs/heads/main') || startsWith(github.ref, 'refs/tags')
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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- name: Install build
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run: python -m pip install build
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- name: Run build
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run: python -m build --sdist
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- uses: actions/upload-artifact@v4
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with:
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path: ./dist/*.tar.gz
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# Needed in case of building packages with external binaries (e.g. Cython, RUst-extensions, etc.)
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# build_wheels:
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# name: Build wheels on ${{ matrix.os }}
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# if: startsWith(github.ref, 'refs/heads/main') || startsWith(github.ref, 'refs/tags')
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# runs-on: ${{ matrix.os }}
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# strategy:
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# matrix:
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# os: [ubuntu-20.04, windows-2019, macOS-10.15]
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# steps:
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# - uses: actions/checkout@v4
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# - uses: actions/setup-python@v5
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# with:
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# python-version: "3.10"
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# - name: Install cibuildwheel
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# run: python -m pip install cibuildwheel==2.3.1
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# - name: Build wheels
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# run: python -m cibuildwheel --output-dir wheels
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# - uses: actions/upload-artifact@v4
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# with:
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# path: ./wheels/*.whl
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publish:
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name: Publish package
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if: startsWith(github.ref, 'refs/tags')
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permissions:
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id-token: write
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needs:
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- format
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- lint
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- test
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- build_source_dist
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# - build_wheels
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runs-on: ubuntu-latest
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steps:
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- uses: actions/download-artifact@v4
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with:
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name: artifact
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path: ./dist
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# register PyPI integration:
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# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
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- uses: pypa/gh-action-pypi-publish@release/v1
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with:
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# remove repository key to set the default to pypi (not test.pypi.org)
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repository-url: https://test.pypi.org/legacy/

‎.gitignore‎

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.vscode
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# Test output
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test.*.pdf
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test.*.pdf
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# find more examples here:
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# https://github.com/github/gitignore/blob/main/Python.gitignore
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# Binaries (object files) produced by a compiler
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*.so
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*.o
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# Python/Jupyter uses these cache directories
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__pycache__
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.ipynb_checkpoints
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# Produced when measuring code coverage
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.coverage
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# These files are produced during the Python build process
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build/
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.eggs
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dist/
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**.egg-info
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# Sphinx documenter creates these
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_build
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_static
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_templates
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/docs/reference
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/docs/jupyter_execute
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# MacOS automatically creates these files
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.DS_Store
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# VSCode may create a config file with this name
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**.vscode
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# Ruff stuff:
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.ruff_cache/
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# Environments
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.env
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.envrc
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.venv
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env/
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venv/
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py.cover
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.hypothesis/
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.pytest_cache/
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cover/

‎.travis.yml‎

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‎croissance/__init__.py‎

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import pandas
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import croissance.figures.plot
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from croissance.estimation import (
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AnnotatedGrowthCurve,
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GrowthEstimationParameters,
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estimate_growth,
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)
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from croissance.estimation.util import normalize_time_unit
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__all__ = [
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"plot_processed_curve",
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"process_curve",

‎croissance/estimation/__init__.py‎

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import logging
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from collections import namedtuple
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from operator import attrgetter
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from croissance.estimation.ranking import rank_phases
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from croissance.estimation.regression import fit_exponential
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from croissance.estimation.smoothing.segments import segment_spline_smoothing
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from croissance.estimation.util import savitzky_golay, points_per_hour
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from croissance.estimation.util import points_per_hour, savitzky_golay
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class RawGrowthPhase(namedtuple("RawGrowthPhase", ("start", "end"))):
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}
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growth_estimation_defaults = GrowthEstimationParameters()
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def estimate_growth(
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curve: pandas.Series,
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*,
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params=GrowthEstimationParameters(),
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name: str = "untitled curve"
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params=growth_estimation_defaults,
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name: str = "untitled curve",
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) -> AnnotatedGrowthCurve:
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log = logging.getLogger(__name__)
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series = curve.dropna()

‎croissance/estimation/regression.py‎

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series.values,
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p0=p0,
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maxfev=10000,
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bounds=([0.0, 0.0, 0.0], numpy.inf)
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if n0 is None
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else ([0.0, 0.0], numpy.inf),
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bounds=(
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([0.0, 0.0, 0.0], numpy.inf) if n0 is None else ([0.0, 0.0], numpy.inf)
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),
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)
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if n0 is not None:
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series.values,
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p0=p0,
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maxfev=10000,
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bounds=([0.0, 0.0, 0.0], numpy.inf)
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if n0 is None
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else ([0.0, 0.0], numpy.inf),
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bounds=(
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([0.0, 0.0, 0.0], numpy.inf) if n0 is None else ([0.0, 0.0], numpy.inf)
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),
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)
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if n0 is not None:

‎croissance/estimation/smoothing/segments.py‎

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import numpy
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import pandas
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from scipy.signal import detrend
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from scipy.interpolate import InterpolatedUnivariateSpline
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from scipy.signal import detrend
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def segment_by_std_dev(series, increment=2, maximum=20):

‎croissance/figures/plot.py‎

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a = 1 / numpy.exp(phase.intercept * phase.slope)
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def gf(x):
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def gf(x, phase=phase, a=a):
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return a * numpy.exp(phase.slope * x) + phase.n0
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phase_series = curve.series[phase.start : phase.end]

‎croissance/figures/writer.py‎

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import matplotlib.pyplot as plt
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from matplotlib.backends.backend_pdf import PdfPages
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from croissance.estimation import AnnotatedGrowthCurve

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