Improve documentation for developers

[WeilerP]

Description

For an easier start of potential contributors, it might be helpful to add a file such as requirements-dev.txt including all packages required to e.g. run unit tests locally. Otherwise, several packages (e.g. leidenalg, louvain, scikit-misc, harmonypy, python-igraph) have to be installed manually which is rather tedious:

-r requirements.txt

harmonypy
leidenalg
louvain
scitkit-misc
python-igraph

The wheels to install python-igraph under Windows can, for example, be found here.

[WeilerP]

Realised this functionality is already available via pip install ".[dev]". May be good to mention somewhere, though.

[fidelram]

This is indeed very valuable information.

Do you mind adding a PR updating https://github.com/theislab/scanpy/blob/master/docs/installation.rst ?

[WeilerP]

Yes, no problem. I'll update it in a bit.

[WeilerP]

I had a look at scanpy's setup file setup.py and realised that running

pip install -e .
pip install ".[dev]"

does neither install all packages used within Scanpy's code base nor packages required for documentation or testing.

IMO, these packages should be installed in a developer installation as they are all part of the development cycle. Adding a file requirements-dev.txt including all needed packages would be an option to allow for an easy developer installation via

pip install -e .
pip install -r requirements-dev.txt

Any thoughts on this?

[WeilerP]

Were there every any thoughts or discussions on adding pre-commit hooks? This would, for example, automatically enforce the black coding style prior to committing new changes.

The .pre-commit-hooks.yaml file could, for example, look as follows:

# .pre-commit-hooks.yaml
repos:
-   repo: https://github.com/ambv/black
    rev: stable
    hooks:
    - id: black

[giovp]

can we follow keep discussing on #1563 ?
@WeilerP not sure if you ever submitted that PR, but otherwise we can close this

[WeilerP]

Sorry, no, I didn't open a PR since I hadn't heard back regarding above comments. Fine to close it in favour of #1563, although it only concerns pre-commit hooks, right? The original idea of this issue was to make the dev installation easier, i.e. installing all required packages to run the full code base, tests etc. This currently doesn't happen when installing through pip install ".[dev]".

[giovp]

that's a very good point yes, I know there is also #1527 underway, can you guys comment on this @flying-sheep @ivirshup cause I'm not sure timing wise how is it going ?

[ivirshup]

I think #1527 is coming along nicely. It seems to mostly work now. It'd be great if some other team members could try it out and see if it works for them!

[WeilerP]

As far as I can tell, #1527 still doesn't install all packages in a dev installation required to run the entire code base and tests.

[ivirshup]

flit install -s by default would install everything, passing --deps=develop actually leads to fewer things being installed. I think this is weird behavior, but it's the way flit works.

[ivirshup]

I think this is has been covered by the "Contributing" section of the docs.