معرفی شرکت ها
clophfit-0.4.9
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشترتوضیحات
Cli for fitting macromolecule pH titration or binding assays data e.g. fluorescence spectra.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | clophfit-0.4.9 |
| نام | clophfit |
| نسخه کتابخانه | 0.4.9 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | - |
| ایمیل نویسنده | daniele arosio <daniele.arosio@cnr.it> |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/clophfit/ |
| مجوز | - |
# ClopHfit
[](https://pypi.org/project/ClopHfit/)
[](https://github.com/darosio/ClopHfit/actions/workflows/ci.yml)
[](https://codecov.io/gh/darosio/ClopHfit)
[](https://clophfit.readthedocs.io/)
[](https://doi.org/10.5281/zenodo.6354112)
Cli for fitting macromolecule pH titration or binding assay data, e.g.
fluorescence spectra.
- Version: "0.4.10"
## 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 your python:
from clophfit import prtecan, binding
## Installation
pipx install clophfit
You can get the library directly from
[PyPI](https://pypi.org/project/ClopHfit/):
pip install clophfit
## Development
You need the following requirements:
- `hatch` for test automation and package dependency managements. If you don't
have hatch, you can use `pipx run hatch` to run it without installing, or
`pipx install hatch`. Dependencies are locked thanks to
[pip-deepfreeze](https://pypi.org/project/pip-deepfreeze/). You can run
`hatch env show` to list available environments and scripts.
hatch run init # init repo with pre-commit hooks
hatch run sync # sync venv with deepfreeze
hatch run lint:run
hatch run tests.py3.10:all
Hatch handles everything for you, including setting up an temporary virtual
environment for each run.
- `pre-commit` for 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. If pre-commit fails during pushing upstream then stage changes, Commit
Extend (into previous commit), and repeat pushing.
`pip`, `pip-deepfreeze` and `hatch` are pinned in
.github/workflows/constraints.txt for consistency with CI/CD.
pipx install pre-commit
pipx install hatch
pipx runpip hatch install hatch-pip-deepfreeze
### Setting up a development with direnv
echo "layout hatch" > .envrc
hatch run init
### 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]
With direnv for using [Jupyter](https://jupyter.org/) during development:
jupiter notebook
And only in case you need a system wide easy accessible kernel:
python -m ipykernel install --user --name="clop"
### Testing and coverage
Use pytest to run the unit checks:
pytest
Use `coverage` to generate coverage reports:
coverage run --parallel -m pytest
Or use hatch:
hatch run tests:all
hatch run coverage:combine
hatch run coverage:report
### Building docs
You can build the docs using:
hatch run docs:sync
hatch run docs:build
You can see a preview with:
hatch run docs:serve
When needed (e.g. API updates):
sphinx-apidoc -f -o docs/api/ src/clophfit/
### Bump and releasing
To bump version and upload build to test.pypi using:
hatch run bump
hatch run bump "--increment PATCH" "--files-only" \
["--no-verify" to bypass pre-commit and commit-msg hooks]
while to update only the CHANGELOG.md file:
hatch run ch
Release will automatically occur after pushing.
(Otherwise)
pipx run --spec commitizen cz bump --changelog-to-stdout --files-only \
(--prerelease alpha) --increment MINOR
To keep clean development history use branches and pr:
gh pr create --fill
gh pr merge --squash --delete-branch [-t “fix|ci|feat: msg”]
### Configuration files
Manually updated pinned dependencies for CI/CD:
- .github/workflows/constraints.txt (testing dependabot)
Configuration files:
- pre-commit configured in .pre-commit-config.yaml;
- flake8 (for rst-docstrings and bandit) configured in .flake8 (pinned in
pre-commit);
- black configured in pyproject.toml (pinned in pre-commit);
- ruff configured in pyproject.toml (pinned in pre-commit);
- darglint configured in .darglint (pinned in pre-commit);
- codespell configured in .codespellrc (pinned in pre-commit);
- coverage configured in pyproject.toml (tests deps);
- mypy configured in pyproject.toml (tests deps);
- commitizen in pyproject.toml (dev deps and pinned in pre-commit).
pip-df generates requirements[-dev,docs,tests].txt.
Other manual actions:
pylint src/ tests/
bandit -r src/
نیازمندی
| مقدار | نام |
|---|---|
| - | click<8.1.4 |
| - | corner<2.2.3 |
| - | emcee<3.1.5 |
| - | lmfit<1.2.2 |
| - | matplotlib<3.7.2 |
| - | numpy<1.24.4 |
| - | openpyxl<3.1.3 |
| - | pandas<2.0.2 |
| - | rpy2<3.5.12 |
| - | scipy<1.10.2 |
| - | seaborn<0.12.3 |
| - | sympy<1.11.2 |
| - | tqdm<4.65.1 |
| - | xlrd<2.0.2 |
| xtr | commitizen<3.2.1; |
| xtr | ipykernel; |
| xtr | jupyter; |
| xtr | pylsp-mypy; |
| xtr | python-lsp-ruff; |
| xtr | ruff==0.0.264; |
| xtr | autodocsumm==0.2.11; |
| xtr | myst-parser==1.0.0; |
| xtr | nbsphinx==0.9.1; |
| xtr | pydata-sphinx-theme==0.13.3; |
| xtr | sphinx-autodoc-typehints==1.23.0; |
| xtr | sphinx-click==4.4.0; |
| xtr | sphinx==6.2.1; |
| xtr | sphinxcontrib-plantuml==0.25; |
| xtr | coverage[toml]<7.2.6; |
| xtr | mypy<1.3; |
| xtr | pandas-stubs==2.0.1.230501; |
| xtr | pygments<2.15.2; |
| xtr | pytest<7.3.2; |
| xtr | typeguard==4.0.0rc5; |
| xtr | xdoctest<1.1.2; |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| <3.12,>=3.8 | Python |
نحوه نصب
نصب پکیج whl clophfit-0.4.9:
pip install clophfit-0.4.9.whl
نصب پکیج tar.gz clophfit-0.4.9:
pip install clophfit-0.4.9.tar.gz