capfinder 0.3.1

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

Installing Capfinder

1. Installing and activate new Python Environment

Please make a fresh conda/micromamba env with required supported Python versions like so:

micromamba create -n capfinder_env python=3.12

Next, activate the newly created conda env:

micromamba activate capfinder_env

2. Installing Capfinder package

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

Capfinder depends on JAX internally for using GPUS. Jax requires CUDA to work. So the CUDA requierments for capfinder are the same as the CUDA requirements for JAX. For more information here on the required CUDA version for JAX.

TPU installation

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

3. Updating Capfinder

If you are using an older version of Capfinder, and would like to upgrade to the latest version, then please do the following in your activate Python enviorment:

Updating Capfinder on CPU-based system

pip install capfinder[cpu]

Updating Capfinder on GPU-based system

pip install capfinder[gpu]

Updating Capfinder on TPU-based system

pip install capfinder[tpu]

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