Add snakemake.params to track config updates

[virio-andreyana]

Closes #767

Changes proposed in this Pull Request

Use the params: section in rule definition to keep track of changed settings in config.yaml.

https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules

The goal is that rules for which parameters have changed rerun automatically.

This can currently be done with:

https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-trigger-re-runs-for-rules-with-updated-code-or-parameters

snakemake -n -R `snakemake --list-params-changes`

or

snakemake -R $(snakemake --list-params-changes)

This will be even more convenient, once this snakemake PR is released:

snakemake/snakemake#1107

snakemake --rerun-params-changed

or

snakemake --rerun-changed

(which would also include code changes)

It seems to work very nicely to pass lists/dicts as params, which would help us keep config "blocks".

This PR is not complete yet, but a proof-of-concept for a selection of config settings. We can discuss from here and complete later.

Checklist

• I consent to the release of this PR's code under the AGPLv3 license and non-code contributions under CC0-1.0 and CC-BY-4.0.
• I tested my contribution locally and it seems to work fine.
• Code and workflow changes are sufficiently documented.
• Newly introduced dependencies are added to envs/environment.yaml and doc/requirements.txt.
• Changes in configuration options are added in all of config.default.yaml and config.tutorial.yaml.
• Add a test config or line additions to test/ (note tests are changing the config.tutorial.yaml)
• Changes in configuration options are also documented in doc/configtables/*.csv and line references are adjusted in doc/configuration.rst and doc/tutorial.rst.
• A note for the release notes doc/release_notes.rst is amended in the format of previous release notes, including reference to the requested PR.

[davide-f]

Cool @virio-andreyana ! Thanks for taking care of this issue! :D
Let us know when you need support or a review :)

[virio-andreyana]

You're welcome @davide-f. The addition of the params is almost complete. What's still a bit missing is for the script solve_network.py. This is because it has the function extra_functionalities where the config is defined by the by n.config. But honestly, if any changes happen before this rule, solve_network will always be run.

Other than that, are there any suggestion and naming convention I should follow?

[davide-f]

Really amazing job! :D
This review also let me realize that on a coding perspective some rulues may be improved to trop some params, but that's not for this PR.
Maybe good to open an issue on that.

Added few comments on it :)
Merging this PR is likely to lead to some merge conflicts, so its merging is going to be discussed during the next meetings too. But it is a feature we want! :D

[davide-f]

Awesome job @virio-andreyana !
I think this PR is ready to go :) I would like to discuss on it with the others on thursday to avoid git conflicts and can be merged soon after that :)
Great!

[davide-f]

@virio-andreyana FYI, as #824 and #822 are merged, this PR follows along with the new release v0.2.3 including you as contributor :)
I can take care of the minor conflicts if existing, if major I may ask little support.
Many thanks @virio-andreyana !!!

[davide-f]

Great @virio-andreyana ! The PR is ready to merge :)
Many thanks for the contribution, you are now officially a contributor :D Very useful contribution and looking forward to the next PR that is in the cooking :D