Cleanup

[maho3]

Cleanup and refactoring of ltu-ili after many changes over the last months. Addresses #52.

[maho3]

A lot of minor changes have occurred in this PR, resulting in many files changed. The primary functionality remains exactly the same, this PR is just to make everything consistent over the past series of changes. Here's a summary:

• Code has been formatted according to PEP8. All docstrings now use the Google style.
• The readthedocs autodoc functionality has been revitalized. Now, all the modules' docstrings should autocompile into readthedocs html. Instructions for compiling the docs have been given in docs/DOC_README.md.
• All 'examples/sample...' examples have been renamed as 'example/toy...', since 'sample' is confusing.
• Added examples/README.md
• All installation dependencies and examples, for both sbi and pydelfi backends. Everything should now easily run according to INSTALL.md.

For reviewers Since a lot of files changed, it will be difficult to check everything of them. So I recommend you check that at

• [ ] Try installing the sbi and pydelfi version (pydelfi will only work with Python 3.6 on a Linux machine).
• [ ] Try compiling the docs and make sure they have all the information you'd need.
• [ ] Overall, make sure the code structure makes sense and you don't have any qualms of how the main modules work (data/, inference,/ validation/). It will likely be easier to rearrange things here than later on.

Note, SNLE/SNRE support and custom sampling will be added in PR #54 .

[DeaglanBartlett]

Replies to checks:

• Try installing the sbi and pydelfi version (pydelfi will only work with Python 3.6 on a Linux machine).

  Installing pydelfi in a fresh environment led to a few errors. I have updated the setup.cfg file to change the dependencies to remove this

• Try compiling the docs and make sure they have all the information you'd need.

I compiled these without issues locally (some warnings were raised, but did not affect the result).

• Overall, make sure the code structure makes sense and you don't have any qualms of how the main modules work (data/, inference,/ validation/). It will likely be easier to rearrange things here than later on.

I see no issues with the code structure

Other changes I have made:

• Errors were being raised in the sbi example due to the lack of an else statement in https://github.com/maho3/ltu-ili/blob/823faa50c3672096153636d806bb68b164ed38de/ili/validation/runner.py#L111. This has been added
• I have removed using RankStatistics in the pydelfi example as it’s too slow with pydelfi

A request:

• You currently refer the user to the Slack channel if they want the Quijote data (https://github.com/maho3/ltu-ili/blob/823faa50c3672096153636d806bb68b164ed38de/INSTALL.md?plain=1#L53). Please can you move these instructions to this repository so that they are more permanently (and publically) available