Add the transport tutorial

[danielhuppmann]

This PR copies over the transport tutorial (with linopy) from #101 in a more streamlined manner. Most importantly, the term "tutorial" is now used for the entire thing consisting of three notebooks:

0. set up the database
1. implement the base version of the transport problem
2. do a scenario/variation

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 87.1%. Comparing base (d69ff7c) to head (4cc277d).

Additional details and impacted files

@@              Coverage Diff              @@
##           enh/run-clone    #146   +/-   ##
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  Coverage           87.1%   87.1%           
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  Files                231     231           
  Lines               8216    8216           
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  Hits                7160    7160           
  Misses              1056    1056           

[glatterf42]

Thanks for starting this work and outlining the structure you envision :)

I have cleaned up the notebook files, made formatting consistent, added some content where I thought it was needed, updated the syntax to fit our current API, and made the code comply with the mypy config.
This last step includes adding linopy to the dependencies. Unfortunately, linopy still doesn't support numpy 2.0, see PyPSA/linopy#386 and PyPSA/linopy#332, so this brings with it an effective numpy pin to < 2.0. I would like to avoid that, so I would not merge this PR right away.
Even more so since Volker previously indicated that linopy might not be the tool of choice for us since it doesn't support non-linear programming. I've opened PyPSA/linopy#384 to ask their maintainers about plans for that, but haven't received a reply yet.

On top of all this, I'm not sure why the codecov report says that all coverable lines are covered. It seems to me that this PR so far copies over the utility code for running the tutorials, but not the tests for the same, which should be a TODO:

• Add tests for the tutorials and their utility code

[glatterf42]

Not sure why mypy is still failing here. I bumped the version locally, which removed the linopy/numpy pin. So this latest commit might also break the usability of linopy, but poetry allowed this.

[glatterf42]

Thanks for your updates here, @danielhuppmann! I have reworked some of them, mainly in terms of formatting: we seem to have different preferences how to highlight things. I differentiate between names of tools and software, which I write like this, and vocabulary of our tool in particular, including function names and code object names, which I write like this. I think this helps newcomers to spot the difference and they will need to learn the vocabulary, anyway. I also apply the same highlighting always to indicate that Run still means Run and not "run". The only exception to this rule is when I think we're talking about "real world" units, for examples, as opposed to the Unit objects we have in ixmp4.

[glatterf42]

Just noting here that this might change soon if the "Normalize Parameter DB storage" PR gets finished and accepted.

[glatterf42]

Maybe by having this cell here, we can remove the almost identical ones in Notebook 0.

[danielhuppmann]

Well, my thinking for having it twice is to show users that do something stupid during setup how to quickly restart - and then show how clean up at the end of the tutorial.

[glatterf42]

Sure, we can also have it twice :)