maslongbow 0.4.4

Annotation and segmentation of MAS-seq data

# Longbow Annotation and segmentation of MAS-seq data

Current version: 0.4.4

## Documentation

[Longbow documentation.](https://broadinstitute.github.io/longbow/)

## Installation

pip install .

## Usage

TBW

## Development

To do development in this codebase, the python3 development package must be installed.

After installation the development environment can be set up by the following commands:

python3 -mvenv venv . venv/bin/activate pip install –upgrade pip pip install -r dev-requirements.txt pip install -e .

### Linting files

# run all linting commands tox -e lint

# reformat all project files black src tests setup.py

# sort imports in project files isort -rc src tests setup.py

# check pep8 against all project files flake8 src tests setup.py

# lint python code for common errors and codestyle issues pylint src

### Tests

# run all linting and test tox

# run only (fast) unit tests tox -e unit

# run only integration tests tox -e integration

# run only linting tox -e lint

Note: If you run into “module not found” errors when running tox for testing, verify the modules are listed in test-requirements.txt and delete the .tox folder to force tox to refresh dependencies.

## Versioning

We use bumpversion to maintain version numbers. It will automatically create a new tag every time you run it. DO NOT MANUALLY EDIT ANY VERSION NUMBERS.

Our versions are specified by a 3 number semantic version system (https://semver.org/):

major.minor.patch

To update the version with bumpversion do the following:

bumpversion PART where PART is one of: - major - minor - patch

This will increase the corresponding version number by 1.

You should always bump the version from the main branch _after_ merging in any PRs for that version. Then you will have to push both the bumpversion code update AND the tag that was created:

` git push && git push --tags `

## Releasing

The release process is as follows:

1. Bump the version by the appropriate PART (see Versioning for details).

2. Build and push the docker container (See Docker). NOTE: The version will have already been updated by using bumpversion in step 1.

## Docker

This repository includes a docker folder that contains a Dockerfile and a Makefile. DO NOT manually modify the Makefile or the Dockerfile (unless you have to add dependencies). The version is automatically updated by bumpversion.

### Building

To build the docker image and push it to the release location do the following from the root of this repository:

` cd docker make build && make push `