capfinder 0.2.0

A package for decoding RNA cap types

capfinder

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Documentation: https://adnaniazi.github.io/capfinder

Source Code: https://github.com/adnaniazi/capfinder

PyPI: https://pypi.org/project/capfinder/

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A package for decoding RNA cap types

Installation

CPU installation

pip install capfinder[cpu]

GPU installation (CUDA 12)

pip install capfinder[gpu] "jax[cuda12]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

TPU installation

pip install capfinder[tpu] "jax[tpu]" -f https://storage.googleapis.com/jax-releases/libtpu_releases.html

Development

• Clone this repository
• Requirements:
  • Poetry
  • Python 3.7+
• Create a virtual environment and install the dependencies

CPU installation

poetry install --extras cpu

GPU installation (CUDA 12)

poetry install --extras gpu
poetry run pip install "jax[cuda12]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

TPU installation

poetry install --extras tpu
poetry run pip install "jax[tpu]" -f https://storage.googleapis.com/jax-releases/libtpu_releases.html

• Activate the virtual environment

poetry shell

Testing

pytest

Documentation

The documentation is automatically generated from the content of the docs directory and from the docstrings of the public signatures of the source code. The documentation is updated and published as a Github project page automatically as part each release.

Releasing

Trigger the Draft release workflow (press Run workflow). This will update the changelog & version and create a GitHub release which is in Draft state.

Find the draft release from the GitHub releases and publish it. When a release is published, it'll trigger release workflow which creates PyPI release and deploys updated documentation.

Pre-commit

Pre-commit hooks run all the auto-formatters (e.g. black, isort), linters (e.g. mypy, flake8), and other quality checks to make sure the changeset is in good shape before a commit/push happens.

You can install the hooks with (runs for each commit):

pre-commit install

Or if you want them to run only for each push:

pre-commit install -t pre-push

Or if you want e.g. want to run all checks manually for all files:

pre-commit run --all-files