Enh/read the doc

[Slowblitz]

This is the new documentation for read the doc

[pep8speaks]

Hello @Slowblitz! Thanks for updating this PR.

There are currently no PEP 8 issues detected in this Pull Request. Cheers! :beers:

Comment last updated at 2021-04-06 09:35:36 UTC

[coveralls]

Pull Request Test Coverage Report for Build 722043534

• 0 of 0 changed or added relevant lines in 0 files are covered.
• 14 unchanged lines in 2 files lost coverage.
• Overall coverage increased (+8.1%) to 40.123%

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Files with Coverage Reduction	New Missed Lines	%
ando/tests/test_AnDOChecker.py	2	98.15%
ando/AnDOChecker.py	12	71.79%
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Totals
Change from base Build 679700768:	8.1%
Covered Lines:	195
Relevant Lines:	486

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💛 - Coveralls

[Slowblitz]

Hi @SylvainTakerkart can you check the content of introduction in the docs/source/ando.rst file it needs to be updated, and also can you give us to @JuliaSprenger or me the admin right that we can do the configuration on read the doc pls .

[SylvainTakerkart]

Hi @SylvainTakerkart can you check the content of introduction in the docs/source/ando.rst file it needs to be updated, and also can you give us to @JuliaSprenger or me the admin right that we can do the configuration on read the doc pls .

I've upgraded both of you from Maintainer to Administrator of the AnDO project... I'm now gonna check the content of the ando.rst file ;)

[SylvainTakerkart]

Just pushed an update of index.rst ... I completily changed its content... I'm not sure whether it's worth adding other things... We could also wonder whether it's really worth having a readthedoc site... WDYT?

[SylvainTakerkart]

We should probably discuss before moving further...

[JuliaSprenger]

I think it would still be good to have version controlled documentation of the AnDO package out there, as we discussed a couple of weeks ago. This way we can keep the documentation / specifications of AnDO linked to specific versions of the code and still have all of them accessible via the different doc versions on readthedocs. Also having a reduced more user friendly version of the specifications as developed on docs.google could help not scaring potential users by the complexity of the complete documentation.

[Slowblitz]

Also It's maybe a good idea to have it , for the INCF talk .

[SylvainTakerkart]

ok, fair points ;)

so, what we need, besides the intro is:

• a list of the tools with a very short description of what they do (checker, generator, nnw2bids converter under dev)
• a simplified version of the specs (importantly: with a snapshot view of a dataset, for example the reach2grasp dataset, similarly to what is on the BIDS homepage, with the right part only: https://bids.neuroimaging.io/assets/img/dicom-reorganization-transparent-white_1000x477.png)

anything else? WDYT?

[SylvainTakerkart]

Hi @Slowblitz ! The image you just uploaded contains several errors with respect to the specs:

• the exp-XXX directory is not required anymore (it's the top level directory = what you show as "dataset")...
• there are underscores in the session name, they are forbidden!
• maybe others...

Also, I would put real names from a real dataset! Can you take a look at https://gin.g-node.org/sprenger/multielectrode_grasp/src/bep_animalephys? this is our example dataset! (but some files at the root directory are forbidden there... just keep the sub-XX directories!). To make sure your example on the image is ok, you can create it on disk and run the AnDOChecker on it ;)

[JuliaSprenger]

@Slowblitz can you add the link to the latest compilation of the docs here, so it is easier to compare the code changes to the output?

[Slowblitz]

Here's the link https://ando.readthedocs.io/en/enh-read_the_doc/

[SylvainTakerkart]

Hi @Slowblitz ! For the image: could you put all the files at the top of the image, and the two directories sub-i ad sub-l at the bottom? that will make the image more readable I think!

Other than this, it looks good! I'll just make some small final adjustments to the text later (or more probably tuesday morning)...

Thanks ;)

[Slowblitz]

So I manage to sort it, but the other way around so WDYT?

[SylvainTakerkart]

So I manage to sort it, but the other way around so WDYT?

the last version you pushed looks perfect ;)

[SylvainTakerkart]

Hi @JuliaSprenger @Slowblitz . Can you both proofread before I merge? https://ando.readthedocs.io/en/enh-read_the_doc/ (you probably need to refresh or else the changes don't show up...)

(and yes, @Slowblitz , I finished my sentence ;) )

[SylvainTakerkart]

@Slowblitz oooops, no, there's a mistage on the image: the sub-XX_sessions files (tsv and json) should be in the sub-XX directory, not in the ses-YY directory (they describe the different sessions, so they cannot be inside a specific session directory)... can you please update the image?

[Slowblitz]

@SylvainTakerkart like this :

[SylvainTakerkart]

@SylvainTakerkart like this :

yep!

do you have this dataset on disk? just run the AnDOChecker to validate ;) ; and then commit and I'll merge!

[Slowblitz]

@SylvainTakerkart so the data set does not validate , so let me correct it and push it after

[Slowblitz]

@SylvainTakerkart @JuliaSprenger WDYT ?

[SylvainTakerkart]

@SylvainTakerkart @JuliaSprenger WDYT ?

what's the difference with the previous one (I don't see it, hehe :dark_sunglasses: )? what was the reason from the non-validation?

[SylvainTakerkart]

@SylvainTakerkart @JuliaSprenger WDYT ?

what's the difference with the previous one (I don't see it, hehe dark_sunglasses )? what was the reason from the non-validation?

ps: at this point, I don't think anymore, coz it looks good and it is easily readable!!! so if you tell me it's validated, it's good to go ;)

[Slowblitz]

@SylvainTakerkart so there were no "_ephys" at the end of the data file, and the structured rules did not include the 'task' and 'run' options for data file see #78 I've fixed it I will push it after merging the doc

[JuliaSprenger]

Nice, the first version is merged! @Slowblitz So the next step is setting up the readthedocs page and the correct triggers of the doc build.