WIP: Clone external repositories

[dominikburri]

Zarp-cli relies on other github repositories, such as zarp. Those need to be available for successful execution. This PR includes a new class in the module zarp.config.init that clones repos as submodules. See also the more comprehensive documentation of git submodules.

Fixes #22

A simple test was added, but the functionality of downloading and preparing new repos is not yet tested. I manually ran the code and successfully cloned zarp into a directory of my choice submodules/zarp. However, addition as test was more complicated, as some files and directories need to be deleted and use of temporary directory does not work with submodules. In particular, .gitmodules, .git/modules/ and the repo itself should be torn down after test.

Remaining issues:

• [x] error handling
• [ ] Mock cloning (or actual cloning with proper teardown)
• [ ] installation of submodules dependencies (e.g. pandas for zarp execution)

Type of change

Please delete options that are not relevant.

• [x] New feature (non-breaking change which adds functionality)
• [x] Documentation update

Checklist

Please carefully read these items and tick them off if the statements are true or do not apply.

• [x] I have performed a self-review of my own code
• [ ] My code follows the existing coding style, lints and generates no new warnings
• [x] I have added type annotations to all function/method signatures, and I have added type annotations for any local variables that are non-trivial, potentially ambiguous or might otherwise benefit from explicit typing.
• [x] I have commented my code in hard-to-understand areas
• [x] I have added ["Google-style docstrings"] to all new modules, classes, methods/functions or updated previously existing ones
• [ ] I have added tests that prove my fix is effective or that my feature works
• [ ] New and existing unit tests pass locally with my changes and I have not reduced the code coverage relative to the previous state
• [ ] I have updated any sections of the app's documentation that are affected by the proposed changes

If for some reason you are unable to tick off all boxes, please leave a comment explaining the issue you are facing so that we can work on it together.

[uniqueg]

This seems like quite a lot of work still and and we don't this to block. For now I will just require that ZARP and dependencies are installed and that the root path is passed during ZARP-cli init.

Closing for now but may be revisited in due time.

Some additional issues to consider when designing this:

• Upgrading ZARP and ZARP-cli from within ZARP-cli, e.g., via zarp upgrade ...
• Package ZARP-cli as Conda package and install via ZARP, then set ZARP dir automatically
• Write installers for ZARP w/ and w/o cli, Singularity, dev deps