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README_devel.md

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README for developers of this package

We currently develop this package using Python 3.8.9, venv, pylint, flake8, pytest, pytest-cov, Black, isort, and other tools. This document should guide you to install and set up the devel environment on a new machine. It is not set in stone and is likely to evolve with the package.

Basics

Install Python 3.8.9, create a new virtual environment and activate it. Clone this repository and do editable pip installation. Finally, install TensorFlow and PyTorch.

   git clone [email protected]:ML-Bioinfo-CEITEC/genomic_benchmarks.git
   cd genomic_benchmarks
   pip install --editable .

   pip install jupyter>=1.0.0
   pip install papermill>=2.3.0

   pip install tensorflow>=2.6.0
   pip install tensorflow-addons
   pip install typing-extensions --upgrade  # fixing TF installation issue

   pip install torch>=1.10.0
   pip install torchtext

Pushing to PyPI

The package is distributed through The Python Package Index (PyPI): https://pypi.org/project/genomic-benchmarks/

Instruction to upload a new version of the package to PyPI:

  1. You mush have PyPI and be registered as admin of the package (ask the owner - currently Petr - to add you)
  2. Always push the new version to GitHub and run tests before pushing to PyPI. Make sure to increase the version number in setup.py.
  3. Remove dist subfolder if it exists and run the following
    python setup.py sdist
    twine upload dist/*

VS Code Settings

Python

Install VS Code Python Extension: use Ctrl-Shift-x to open MarketPlace, search for Python Extension, and install it.

To select Python interpreter, activate Command Palette (Cmd-Shift-P or View -> Command Palette) and select Python: Select Interpreter. You should see a virtual environment you created in previous step.

Linters

We use pylint (PEP8) and flake8. VS Code setting is provided in settings.json file.

If pylint and flake8 were not yet installed in your Python environment, after restarting VS Code and opening any Python file, you should see the following dialog in the bottom right corner:

Linters Missing

After clicking on Install buttons, linters will be automatically installed. To check that you have multiple linters selected, go to Command Palette (Cmd-Shift-P or View -> Command Palette), select Python: Select Linter and you should get current: multiple selected as below

Linters Selection

Formatters

We use black and isort to auto-format on Save. VS Code setting is provided in settings.json file. (You will need to install those two packages.)

Docstrings

We use Python Docstring Generator extension to help us with writing useful and well formated documentation. Install this extension from VS Code Extensions Marketplace (Ctrl-Shift-x). VS Code settings are already provided in settings.json file. For now, we use numpydoc docstring format. Keyboard shortcut: Ctrl+Shift+2.