Tests fail when running the full testing suite

[HarmonicReflux]

Description

This pull request refactors the way muse --model -default is executed to ensure that all tests pass.

Specifically, the Results/MCACapacity.csv file is now placed within the docs folder, which is where the test expects to find MCACapacity.csv. The necessary file is created during the test run by the notebook itself and subsequently picked up by it. This change resolves the error that causes pytest to fail, and as a result, all tests now pass by default.

Fixes #261

Type of change

Please add a line in the relevant section of CHANGELOG.md to document the change (include PR #) - note reverse order of PR #s.

• [ ] New feature (non-breaking change which adds functionality)
• [ ] Optimization (non-breaking, back-end change that speeds up the code)
• [x] Bug fix (non-breaking change which fixes an issue)
• [ ] Breaking change (whatever its nature)

Key checklist

• [x] All tests pass: $ python -m pytest
• [ ] The documentation builds and looks OK: $ python -m sphinx -b html docs docs/build

Further checks

• [ ] Code is commented, particularly in hard-to-understand areas
• [ ] Tests added that prove fix is effective or that feature works

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 71.39%. Comparing base (2e8e1b5) to head (297e8db).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #365 +/- ## =========================================== + Coverage 71.36% 71.39% +0.03% =========================================== Files 44 44 Lines 5915 5915 Branches 1162 1162 =========================================== + Hits 4221 4223 +2 + Misses 1371 1370 -1 + Partials 323 322 -1 ```

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[HarmonicReflux]

Well, for "Results/MCACapacity.csv" to be visible, one has to create it first, and the most simple way of creating it is by running a model, say the default model via muse --model default. Hence, I included invocation of this command in the documentation. If users then run the test suite, the failure will not occur.

As @dalonsoa pointed out: If my suggestion is not the one to go for, I can think of either: i) Include the file into the codebase (still feels a bit hacky to me) ii) Defining to tun the default model in the setup file such that it is created while running python -m pip install -e .[dev,doc] iii) Any other suggestions?

[dalonsoa]

I think the main issue here is:

1. to figure out what notebook needs the Results folder in the root folder
2. then take the steps such that the data it looks for is within the docs directory - like any other of the notebooks - and put the data in the right place.
3. And yes, committing the data as well, as it is done with the other notebooks that need data, like those of the tutorials.

What makes no sense is to have a notebook in the docs requiring data in the root directory.

There's a discussion going on on how to avoid committing data to the repository, but that's a longer term discussion and we do not have an answer for it, yet.

[dalonsoa]

And remember to update the branch and, ideally, add a PR description - not essential, but serve as reference for the future.

[alexdewar]

Did you want me to review this @HarmonicReflux?

[HarmonicReflux]

Did you want me to review this @HarmonicReflux?

Yes, please take a look, so we are all on the same page. Thks.

[HarmonicReflux]

Appreciated comments of the reviewers.

[HarmonicReflux]

@alexdewar please take a look at this reworked pull request.

[tsmbland]

I'm still a bit unsure about this, because we specifically need a results folder in the docs folder, so running muse --model default in the root folder won't be enough. The link that Alex created in the docs workflow will only exist if the user runs the documentation build locally (right?) which we're not asking people to do before running the tests, so I'm not sure how this fixes the problem. Am I missing something?

[HarmonicReflux]

Running a model will create a "Results" folder in the directory MUSE is installed. The results folder itself then contains subfolder that of which one contains the file the one testing the notebooks needs to have access in order to run successfully. To my knowledge, building the documentation is a separate process unrelated to the tests themselves.

[tsmbland]

I get that, but the notebook in question (running-muse-example.ipynb) points to a Results folder contained in the docs folder, not the root folder

[HarmonicReflux]

@dalonsoa and @tsmbland, please review this pull-request.

@alexdewar is out of office until later this week.