Cli for fitting macromolecule pH titration or binding assays data e.g. fluorescence spectra.
Project description
ClopHfit
Cli for fitting macromolecule pH titration or binding assay data, e.g. fluorescence spectra.
- Version: "0.3.8"
Features
- Plate Reader data Parser.
- Perform non-linear least square fitting.
- Extract and fit pH and chloride titrations of GFP libraries.
- For 2 labelblocks (e.g. 400, 485 nm) fit data separately and globally.
- Estimate uncertainty using bootstrap.
- Subtract buffer for each titration point.
- Report controls e.g. S202N, E2 and V224Q.
- Correct for dilution of titration additions.
- Plot data when fitting fails and save txt file anyway.
Usage
-
Extract and fit titrations from a list of tecan files collected at various pH or chloride concentrations:
clop prtecan --helpFor example:
clop prtecan list.pH -k ph --scheme ../scheme.txt --dil additions.pH --norm \ --out prova2 --Klim 6.8,8.4 --sel 7.6,20To reproduce older pr.tecan add [--no-weight]{.title-ref} option:
clop prtecan list.pH -k ph --scheme ../scheme.txt --no-bg --no-weight \ --out 4old --Klim 6.8,8.4 --sel 7.6,20 -
Predict chloride dissociation constant [K_d]{.title-ref} at given pH:
clop eq1 --help
To use clophfit in a project:
from clophfit import prtecan, binding
Installation
You can get the library directly from
pip install clophfit
Development
Prepare a virtual development environment and test first installation:
pyenv install 3.10.2
poetry env use 3.10
poetry install
poetry run pytest -v
Make sure:
pre-commit install
pre-commit install --hook-type commit-msg
For Jupyter:
poetry run python -m ipykernel install --user --name="cloph-310"
To generate docs:
poetry run nox -rs docs
When needed (e.g. API updates):
sphinx-apidoc -f -o docs/api/ src/clophfit/
Use commitizen and github-cli to release:
poetry run cz bump --changelog-to-stdout --files-only (--prerelease alpha) --increment MINOR
gh release create (--target devel) v0.3.0a0
Remember!!! Update::
- ClopHfit/docs/requirements.txt
- ClopHfit/.github/workflows/constraints.txt
Development environment
-
Test automation requires nox and nox-poetry.
-
Formatting with black[jupyter] configured in pyproject.
-
Linters are configured in .flake8 .darglint and .isort.cfg and include:
- flake8-isort - flake8-bugbear - flake8-docstrings - darglint - flake8-eradicate - flake8-comprehensions - flake8-pytest-style - flake8-annotations (see mypy) - flake8-rst-docstrings- rst-lint
-
pre-commit configured in .pre-commit-config.yaml activated with:
- pre-commit install - commitizen install --hook-type commit-msg -
Tests coverage (pytest-cov) configured in .coveragerc.
-
Type annotation configured in mypy.ini.
-
Commitizen also used to bump version:
cz bump --changelog-to-stdout --files-only --prerelease alpha --increment MINOR-
need one-time initialization:
(cz init)
-
-
xdoctest
-
sphinx with pydata-sphinx-theme and sphinx-autodoc-typehints. (nbsphinx, sphinxcontrib-plantuml):
mkdir docs; cd docs sphinx-quickstartEdit conf.py ["sphinx.ext.autodoc"] and index.rst [e.g. api/modules]:
sphinx-apidoc -f -o docs/api/ src/clophfit/ -
CI/CD configured in .github/workflows:
tests.yml release.ymlRemember to update tools version e.g. nox_poetry==0.9.
What is missing to modernize:
- coveralls/Codecov
- release drafter; maybe useful when merging pr into main.
- readthedocs or ghpages? https://www.docslikecode.com/articles/github-pages-python-sphinx/
Code of Conduct
Everyone interacting in the readme_renderer project's codebases, issue trackers, chat rooms, and mailing lists is expected to follow the PSF Code of Conduct.
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