clophfit 0.3.4

Cli for fitting macromolecule pH titration or binding assays data e.g. fluorescence spectra.

ClopHfit

Cli for fitting macromolecule pH titration or binding assay data, e.g. fluorescence spectra.

• Version: “0.3.4”

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 --help

  For example:

  clop prtecan list.pH -k ph --scheme ../scheme.txt --dil additions.pH --norm \
    --out prova2 --Klim 6.8,8.4 --sel 7.6,20

  To reproduce older pr.tecan add –no-weight 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 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

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-quickstart

  Edit 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.yml

  Remember 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.