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: "0.3.15"
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 your python:
from clophfit import prtecan, binding
Installation
pipx install clophfit
You can get the library directly from PyPI:
pip install clophfit
Development
You need the following requirements:
noxfor test automation. If you don't have nox, you can usepipx run noxto run it without installing, orpipx install nox. To use, runnox. This will lint and test using every installed version of Python on your system, skipping ones that are not installed. You can also run specific jobs:nox -l # list available tests nox -s lint # Lint only nox -s tests-3.9 # Python 3.9 tests only nox -s docs -- serve # Build and serve the docs nox -s build # Make an SDist and wheel
Nox handles everything for you, including setting up an temporary virtual environment for each run.pdmfor package dependency managements;pre-commitfor all style and consistency checking. While you can run it with nox, this is such an important tool that it deserves to be installed on its own. Install pre-commit and run:pre-commit install --hook-type commit-msg --hook-type pre-push pre-commit run -a
to check all files. If pre-commit fails during pushing upstream then stage changes, Commit Extend (into previous commit), and repeat pushing.
pip, nox, pdm and pre-commit are pinned in
.github/workflows/constraints.txt for consistency with CI/CD.
Setting up a development environment manually
You can set up a development environment by running:
python3 -m venv .venv
source ./.venv/bin/activate
pip install -v -e .[dev,tests,docs]
For using Jupyter during development:
pdm run jupiter notebook
And only in case you need a system wide easy accessible kernel:
pdm run python -m ipykernel install --user --name="cloph-310"
Testing and coverage
Use pytest to run the unit checks:
pytest
Use coverage to generate coverage reports:
coverage run --parallel -m pytest
Or use nox:
nox -rs tests typeguard xdoctest
Building docs
You can build the docs using:
nox -s docs
You can see a preview with:
nox -s docs -- serve
When needed (e.g. API updates):
sphinx-apidoc -f -o docs/api/ src/clophfit/
Bump and releasing
I can bump and upload build to test.pypi using:
nox -rs bump
I can test new dist in local venv using:
python -m pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ clophfit
- Revise changelog, stage files, commit and push
- gh pr create (wait for test completion)
- git co main
- pr merge --squash --delete-branch -t "fix| refactor| ci: msg" #number
- gh release create ”v0.3.12”
- git pull --tags
Basically use commitizen and github-cli to release:
pipx run --spec commitizen cz bump --changelog-to-stdout --files-only (--prerelease alpha) --increment MINOR
gh release create (--target devel) v0.3.0a0
Configuration files
Manually updated pinned dependencies for CI/CD:
- docs/requirements.txt
- .github/workflows/constraints.txt
Configuration files:
- pre-commit configured in .pre-commit-config.yaml;
- flake8 configured in .flake8 (pinned in pre-commit);
- black configured in pyproject.toml (pinned in pre-commit);
- isort configured in pyproject.toml (pinned in pre-commit);
- darglint configured in .darglint (pinned in pre-commit);
- coverage configured in pyproject.toml (tests deps);
- mypy configured in pyproject.toml (tests deps);
- commitizen in pyproject.toml (after
cz init) (both pinned in pre-commit and test deps).
pre-commit ensures up-to-date constraints.txt pin/freeze all packages in “.[dev,docs,tests]”.
TODO
-
mypy into lint?
-
clean all commented leftover
-
release drafter; maybe useful when merging pr into main.
-
readthedocs or ghpages? https://www.docslikecode.com/articles/github-pages-python-sphinx/
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