Genovisio reporting

Creating PDF/HTML reports from predictions.

Installation

In python3.12 you can simply use pip to install:

pip install git+https://github.com/cuspuk/genovisio_reporting.git

Without python3.12, you can install using mamba:

mamba env create -f conda_example.yaml

This gives you the following entrypoint command: genovisio-report.

Running

To create a report, you need outputs from genovisio tools. There are some example outputs provided in tests/ directory, so you can run:

genovisio-report --annot tests/isv_annot.json --isv tests/isv.json --marcnv tests/marcnv.json --hybrid tests/hybrid.json --out_html report.html

This will generate report.html from the inputs.

Development

There are some changes whether you develop on machines with Python 3.12 and on machines without Python 3.12. If you cannot install python3.12 and are limited to conda environments, skip to the next guide.

Development with Python 3.12

Install poetry using pipx:

pipx install poetry

Now in the cloned repository, install the package:

poetry install

Activate the virtual environment where dependencies are installed:

poetry shell

All dependencies are now installed and you can run entrypoint command genovisio-report {ARGS} or by using python:

python genovisio_report/main.py {ARGS}

Development without python 3.12

Install custom conda environment with python3.12.

Then, install poetry (python packaging management library):

curl -sSL https://install.python-poetry.org | python3 -

Now in the cloned repository, install the package:

poetry install

All dependencies are now installed and you can run entrypoint command genovisio-report {ARGS} or by using python:

python genovisio_report/main.py {ARGS}

Adding/removing dependencies

When adding or removing dependencies, you need to define them in pyproject.toml.

Then, locked versions need to be redefined:

poetry lock

Install again:

poetry install

Conventional PRs

When committing, you must follow the Conventional Commits spec. Each PR is automatically validated by the GH action. This means that there the PR title must be like feat: XY or fix: XY and so on, and the PR should contain at least one commit named like this.

Further, any push (i.e. after merged PR) to the main branch creates in a new PR:

• a new release following the Semantic Versioning
• an automatic changelog as parsed from the commit history