Add mkdocs documentation

[johnbradley]

Simplifies the README and adds a mkdocs-based documentation website. Pulls changes from the wiki. After this change the wiki will not be used. Adds logic to pull in python API.

To build/view the documentation run:

pip install mkdocs mkdocs-material mkdocstrings-python mkdocs-material-extensions
mkdocs serve

Fixes #65

[thompsonmj]

Can we add the following to pyproject.toml:

[project.optional-dependencies]
docs = [
    "mkdocs",
    "mkdocs-material",
    "mkdocs-material-extensions",
    "mkdocstrings-python"
]

Then for local testing, pip install .[docs] will let you mkdocs serve it.

[egrace479]

This looks great! A few stylistic suggestions and I think a couple pages are missing.

[egrace479]

Last two suggestions and I think it's good!

I'd just add a note on the homepage of the wiki that the docs have moved to the site in case anyone's looking there for now.

[egrace479]

Since this is going to supplant #61, wanted to recall this change suggestion. It probably requires an updated test too, so a bit out-of-scope here, but it's related and don't want it getting lost.

EDIT: I realize this is resolved in #63.

[egrace479]

LGTM!

[thompsonmj]

Two inline points.

Also optionally, we could add a link to the PyPI package in the footer of the site by placing:

extra:
  social:
    - icon: simple/pypi
      link: https://pypi.org/project/pybioclip/

into mkdocs.yml.

another option would be for the Docker image with:

    - icon: simple/docker
      link: https://github.com/Imageomics/pybioclip/pkgs/container/pybioclip

To do the same for the Apptainer image, it would need a custom icon because I couldn't find the Apptainer logo in the default sources.

This only looks any good with 2 or more icons down there in my opinion

[johnbradley]

Using social for pypi and docker seems incorrect to me. PyPi and docker aren't social media.

[thompsonmj]

One optional comment, otherwise looks good!

[hlapp]

See inline edits and comments.

[hlapp]

Suggested change

	In order to access your images the docker container requires you to [mount a volume](https://docs.docker.com/engine/storage/volumes). To avoid redownloading various bioclip files mounting a volume to hold a `.cache` directory to is recommended. By default the working and home directories for this container are both set to `/home/bcuser`.
	In order to access your images the docker container requires you to [mount a volume](https://docs.docker.com/engine/storage/volumes). To avoid redownloading various bioclip files mounting a volume to hold a `.cache` directory is recommended. By default the working and home directories for this container are both set to `/home/bcuser`.

The .cache directory needs to be in the home directory, i.e., /home/bcuser, right? Should we therefore say ~/.cache, or how is this best clarified as instruction?

[johnbradley]

The examples below show OS specific ways of mounting in a directory (eg. -v $(pwd):/home/bcuser).

[johnbradley]

The cache directory could be any directory. For example lab members might share a single directory. Users just need to mount a directory to hold .cache.

[johnbradley]

I'll create an issue for this so we can proceed with this PR.

[hlapp]

This is an acknowledgment statement, not a copyright or license statement. But I suppose this is the only way to place this as a footer or something?

I'd argue that (1) this doesn't have to be a footer on every page, and (2) is perhaps best kept on an acknowledgments page.

[johnbradley]

This is the same content from the imageomics guide footer.
Added here #66 (comment).

I'll move this to an Acknowledgments page so we can see how that looks.

[johnbradley]

[hlapp]

Acknowledgment page looks great 👍