Package: tmkit
tags:bioinformatics,protein-protein interfacesOverview_____ __  __ _  ___ _
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  |_| |_|  |_|_|\_\_|\__|TMKit is a scalable Python programming interface holding a bundle of function modules to allow a variety of transmembrane protein studies.DocumentationWebsite:https://tmkit-guide.herokuapp.com/doc/overviewSource:https://github.com/2003100127/tmkit-guideWe also provided a jupyter notebook (examples.ipynb) to demonstrate the usage of TMKit.InstallationUsing pip (recommended)# create a conda environmentcondacreate--nametmkitpython=3.10# activate the conda environmentcondaactivatetmkit# a stable version 0.0.5 (recommended)pipinstalltmkit==0.0.5Using condaIf you want to install TMKit with some optional packages, including hh-suite, pymol, and hmmer, you can select the conda option. You should haveminicondainstalled first. Please run the following commands to create a new conda environment and install TMKit.# create a conda environmentcondacreate--nametmkitpython=3.10# activate the conda environmentcondaactivatetmkit

condainstall-c2003100127-cconda-forge-cbiocondatmkitUsing dockerYou can also use docker to run TMKit. You should havedockerinstalled first. Then run the following commands to pull the docker image.dockerpull2003100127/tmkit:latestFor developersIf you want to contribute to TMKit, be sure to review thecontribution guidelines. Please fork the repository and create a new branch for development. We provided adocker imageand aMakefileto help you get started quickly. After cloned the repo and connected to the docker container, you can run the following commands to get started.# install poetrymakepoetry-download# create a virtual environmentmakecreate-venv# install dependenciesmakeinstall# install pre-commit hooksmakepre-commit-install# happy coding :)# ...# after coding, run the following commands to check your code before making a pull requestmaketestThe development environment is managed byPoetry.pre-commitis used to manage the git hooks, which include code formatting, linting, security check, etc, and is configured in the.pre-commit-config.yamlfile. Usingpre-commitis highly recommended to ensure the code quality.Makefile usageMakefilecontains a lot of functions for faster development.1. Download and remove PoetryTo download and install Poetry run:makepoetry-downloadTo uninstallmakepoetry-remove2. Install all dependencies and pre-commit hooksInstall requirements:makeinstallPre-commit hooks coulb be installed aftergit initviamakepre-commit-install3. CodestyleAutomatic formatting usespyupgrade,isortandblack.makecodestyle# or use synonymmakeformattingCodestyle checks only, without rewriting files:makecheck-codestyleNote:check-codestyleusesisort,blackanddarglintlibraryUpdate all dev libraries to the latest version using one comandmakeupdate-dev-deps4. Code securitymakecheck-safetyThis command launchesPoetryintegrity checks as well as identifies security issues withSafetyandBandit.makecheck-safety5. Type checksRunmypystatic type checkermakemypy6. Tests with coverage badgesRunpytestmaketest7. All lintersOf course there is a command torulerun all linters in one:makelintthe same as:maketest&&makecheck-codestyle&&makemypy&&makecheck-safety8. Dockermakedocker-buildwhich is equivalent to:makedocker-buildVERSION=latestRemove docker image withmakedocker-removeMore informationabout docker.9. CleanupDelete pycache filesmakepycache-removeRemove package buildmakebuild-removeDelete .DS_STORE filesmakedsstore-removeRemove .mypycachemakemypycache-removeOr to remove all above run:makecleanupCitationPlease cite our work if you use TMKit in your research.ContactPlease report any questions onissuepages.