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docs/contributing.md

@@ -1,105 +0,0 @@
-# Contributing
-
-Here you will find all the information and steps necessary to contribute
-to UnCoVar.
-
-## Snakemake
-
-We use [`snakemake`](https://snakemake.readthedocs.io/en/stable/) as the
-backbone of this project. Have a look at the [official documentation](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html).
-
-If you already have [`conda`](https://docs.conda.io/en/latest/) installed, run:
-
-```bash
-conda create -c conda-forge -c bioconda -n snakemake snakemake
-```
-
-For faster installation, you can use [`mamba`](https://github.com/mamba-org/mamba),
-a reimplementation of the conda package manager in C++.
-
-```bash
-mamba create -c conda-forge -c bioconda -n snakemake snakemake
-```
-
-Once installed, activate your [`snakemake`](https://snakemake.readthedocs.io/en/stable/)
-environment by running
-
-`conda activate snakemake`.
-
-## Pre-Commit
-
-Git hook scripts help identify simple issues before submission to code review. We
-run our hooks on every commit to automatically point out problems in code such
-as missing semicolons, trailing whitespace, and debug statements. Pointing these
-issues out before code review allows a code reviewer to focus on the architecture
-of a change while not wasting time with trivial style nitpicks.
-
-Before you can run hooks, you need to have the
-[`pre-commit`](https://pre-commit.com/) package manager installed.
-
-Using pip:
-
-```bash
-pip install pre-commit
-```
-
-Using homebrew:
-
-```bash
-brew install pre-commit
-```
-
-Using conda (via conda-forge):
-
-```bash
-conda install -c conda-forge pre-commit
-```
-
-Finally, set up the git hook scripts:
-
-```bash
-pre-commit install
-```
-
-Now, [`pre-commit`](https://pre-commit.com/) will run automatically on `git commit`.
-If you want to manually run all pre-commit hooks on a repository, run
-
-```bash
-pre-commit run --all-files
-```
-
-To run individual hooks use `pre-commit run <hook_id>`.
-
-## Get a Copy of the Workflow
-
-Follow the following steps to acquire a local copy of UnCoVar:
-
-1. [Fork](https://help.github.com/en/articles/fork-a-repo) the original repo
-   to a personal or lab account.
-1. [Clone](https://help.github.com/en/articles/cloning-a-repository) the
-   fork to your local system (to a different place than where you would run analysis).
-1. Implement your changes.
-
-## Before Submitting
-
-Before submitting your code, please do the following:
-
-1. Add tests, if possible, for the new changes.
-1. Edit documentation if you have changed something significant.
-1. Make sure the [`pre-commit`](https://pre-commit.com/)
-   hooks had run (e.g. by `precommit run --all`).
-1. [Commit](https://git-scm.com/docs/git-commit)and [push](https://git-scm.com/docs/git-push)
-   your changes to your fork.
-1. Create a [pull request](https://help.github.com/en/articles/creating-a-pull-request)
-   against the original repository.
-
-## Testing
-
-Test cases are in the subfolder `.tests`. They are automatically executed via continuous
-integration with [Github Actions](https://github.com/features/actions).
-
-## Other Help
-
-You can contribute by spreading the word about this project.
-Writing a short article on using this project would also be a considerable contribution.
-You can also share your best practices with us.

docs/license.md

@@ -1,25 +0,0 @@
-# BSD 2-Clause License
-
-Copyright (c) 2024, Thomas Battenfeld, Johannes Köster, Folker Meyer, Alexander Thomas
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.