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@jan-petr jan-petr commented May 3, 2022

Linked issue

Close #1075

@jan-petr jan-petr requested a review from HenkMutsaerts May 3, 2022 14:39
@jan-petr jan-petr self-assigned this May 3, 2022
@jan-petr jan-petr linked an issue May 3, 2022 that may be closed by this pull request
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@jan-petr jan-petr force-pushed the doc-#1075_DocuUpdate branch from 8037425 to 5434c49 Compare May 3, 2022 15:09
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jan-petr commented May 3, 2022

  • With start of ExploreASL - link to documentation.
  • When starting processing, show links to Processing parameter Examples and full manual.
  • Rename DataParTemplate.md to Processing parameters (dataPar.json)
  • Some commits don't have numbers
  • in ExploreASL code - remove examples and put them to docu
  • in Docu - remove mention of the examples
  • Import - reference import manual, have studyPar and sourcestructure example there

All solved in 5434c49

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  • HENK : 4161489 7607878 . Not clear where the deleted code went to
    JAN: This went to CustomsScripts - ExploreASLLegacy and StudyConfigFiles. As agreed previously.

  • HENK: Also, README.md will conflict with other changes that I recently did on the CFF (that you merged already I believe)
    JAN: I know about these. That's why I push to do this ASAP.

  • HENK: 94e2b4c Can you please next time add the filename in the commit ;)
    JAN: Yes, sure. Though note that this goes against the good practice of keeping it short under 50 chars. Because then it's cutted when displayed in this GUI.
    HENK: Good point, but still I think we're faster when having the overview with the filename first in the commit title :) What would you prefer?

  • HENK: 57349ae Are you sure the contributors should go to another file, and everyone can then still easily find it? This contributors thingy is updated automatically with a separate plugin.
    JAN: I moved these to Docu, to avoid having them on two places. But if this is updated automatically, then I can leave a copy here and also in Docu. Up to you.
    HENK: I think this should stay in README.md indeed, as this is crawled automatically by third-party tools/others.

  • HENK: baa0243 I would remove the whole templates folder, move these source and study templates to the docu online, and add a link to them when starting the import (like we did with datapar for processing).
    JAN: Done as discussed. 93e0092

  • HENK: 1a99be5 Are you sure development should be a subfolder of Functions? That means that they will be added to the path by default. I thought the whole idea of having the development separately from the functions folder, was not to have them automatically added to the Matlab path.
    JAN: We still have the ExploreASL/Development folder there that contains things that are still being developed. And you are right about this one. But I haven't changed that one. This folder ExploreASL/Functions/Development contain functions that are mature enough to be included in the real code, but are seldom used by the user but rather by the core development team. These are things like compilation, docu deployment etc. We've discussed this previously and the consensus was to create this new subfolder and prefix dev to separate these from the often used adm functions. So I would keep as it as following our previous decision ;)
    HENK: OK but that would be confusing, as the code is not in development (who uses what code is not the reason for the categorization). Cannot remember this decision :( Do you think the user actually looks into these folders? I would vote for a folder with docu and a folder with deploy rather than putting all the functions in a general dev folder. Otherwise, it defies the purpose of having a clear prefix (soon many stuff can have the prefix dev; same for adm. Best to keep more categories?).
    JAN: Consensus Functions/Development stays. ExploreASL/Development is renamed to WorkInProgress.

  • https://exploreasl.github.io/Documentation/latest/ProcessingParameters is not compiled properly:

image

  • The order of xASL_init_DataLoading is incorrectly managed, only inside this function we check if data should be loaded, this should be done before the function, for proper modularity and readability. I've done this in ae07cba and 5bbab41.

  • Remove all commits related to initLoading to a new issue.

@jan-petr jan-petr requested a review from HenkMutsaerts May 3, 2022 16:32
@jan-petr jan-petr force-pushed the doc-#1075_DocuUpdate branch 3 times, most recently from ccb4103 to c59af0f Compare May 4, 2022 11:20
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You can put the ExploreASL team back to the docu, only the contributors part is crawled.

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Why don't we add genpath(fullfile(x.opts.MyPath, 'Functions')) ?That's much shorter than that long list of folders

@jan-petr jan-petr force-pushed the doc-#1075_DocuUpdate branch from 984dc04 to ddbb7f8 Compare May 4, 2022 13:01
@jan-petr jan-petr merged commit ddbb7f8 into develop May 4, 2022
@jan-petr jan-petr deleted the doc-#1075_DocuUpdate branch May 4, 2022 13:03
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Update documentation functions to a new structure

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