RNA Biology Package

This package contains Python tools for RNA Biology, frequently used at the Panagiotis Alexiou's group at CEITEC (Brno, Czechia).

For lab members

• We use Python3 (ideally 3.7.4)
• For testing, we use pytest. (For automated testing, we use Travis CI.)
• To make your life easier, get GitHub account, ask to be added to ML-Bioinfo-CEITEC organization and set up GitHub SSH keys (if you have never done that, let me help you).
• Please, use virtualenv / pyenv / conda environments for everybody's sake.
• Ask for forgiveness, not for permission. We are currently all admins, you are allowed to push to the master branch.

Install

From GitHub:

• Clone this repository
  • git clone git@github.com:ML-Bioinfo-CEITEC/rbp.git
• Cd into the folder and install rbp package with make/setuptools
  • cd rbp
  • make develop

From PyPi (do not use for development):

• pip install rbp

Structure of the package

We describe just high-level structure of package. Details related to particular modules etc. find in dedicated READMEs.

• examples - Examples should be kept up to date. They demonstrate package functionalities.
• notebooks - Notebooks are excluded from tests, showcasing best practices and interesting experiments. Those notebooks can become obsolete during the time. Notebooks may use packages not included in requirements.txt.
• src/rbp - Contains the package itself.
  • encoding - functions to encode/decode genomic sequences into numeric vectors
  • preprocessing - conversion between formats (bed -> fasta, bed -> conservation)
  • random - random genomic coordinates, permutations (shuffling) of genomic sequences
  • utils - system utilities (file i/o, parsing arguments, ...)
• tests - Test coverage of rbp package.
• tutorials - Tutorials for newcomers to the lab.

Development

• Update master: git checkout master, git pull
• Modify the code (e.g. add a new module).
• Always write tests.
• Run tests as make test to check everything works, you can also test a specific file or tests in a specific folder with pytest -v ./tests/test_specific_file.py.
• If you added a new dependence, update setup.py and requirements.txt (ask for help if you need it).
• Commit the changes to git and push them to GitHub: git push (Never push --force to master!)
• Consider adding an example or a notebook (be nice to future self and the others).
• Ask somebody else from the lab to discuss the changes you made. Document what have you done.

How to rock

If you develop something big or refactor the whole package, create a new branch git checkout -b my_huge_feature and pull request. Ask for review before merging to master. (Are pull requests a new concept to you? Read this friendly guide to help you write/review the first one.)

If you have a problem, probably everyone has a similar problem. Ask for help, add more documentation, fix it globally and for everyone.

If you have an idea how to improve the package, put it as an Issue. If you have time, check the issues and fix/implement something.

Codestyle

Linters are your friends. For Visual Studio, I recommend PEP-8 and FLAKE8 with minor relaxations (e.g. allow longer lines).

Pushing to Python Package Index

I am following this guide. To push a new version to PyPI, first check that all tests are passing (make test), then increase the version of rbp in setup.py and finally run the following:

  python setup.py sdist
  twine upload dist/*

You need to have an account at PyPI and be registered as the package's maintainer.

GitLab Mirror

This repository has a mirror on GitLab RBP_Bioinformatics/rbp. Push to this repository using git push --mirror gitlab. Create a new mirror from an empty repository by git remote add NAME_OF_MIRROR git@gitlab.com:USER_NAME/rbp.git.