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Refactor code for use within interactive environments #1051

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ewels opened this issue Nov 11, 2019 · 3 comments
Closed
7 tasks done

Refactor code for use within interactive environments #1051

ewels opened this issue Nov 11, 2019 · 3 comments

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@ewels
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ewels commented Nov 11, 2019

Now that #1042 is merged, I think that we should be able to import MultiQC into a Jupyter Notebook and use sort of interactively. It would be nice to refactor the code so that it can be used for specific plots rather than only generating a big report, though I don't know how easy this will be.

  • Make a new repository for an example notebook
  • Get a basic notebook that imports MultiQC and just runs it on some data to generate a report
  • Look into whether we can access results in the multiqc.report object
  • Figure out whether we can print individual plots and result tables
  • Refactor the code to make the above more intuitive
  • Interactively add and remove sections using custom data (Jupyter Notebooks: Iterative running with custom content #2452)
  • Write documentation

This could be quite a bit task with all of that, but would be good to get at least a basic run working.

@ewels ewels modified the milestones: MultiQC v1.8, MultiQC v1.9 Nov 13, 2019
@ewels ewels modified the milestones: MultiQC v1.9, MultiQC v1.10 May 30, 2020
@ewels
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ewels commented Aug 12, 2021

This needs fixing for good Jupyter usage: #1141

@ewels ewels changed the title MultiQC Jupyter Notebook Example Refactor code for use within interactive environments Oct 30, 2022
@ewels ewels modified the milestones: MultiQC v1.10, MultiQC v2.0 Oct 30, 2022
@ewels ewels mentioned this issue Oct 30, 2022
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@ewels
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ewels commented Oct 30, 2022

Tightly linked to the refactoring described in #1790

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ewels commented Mar 25, 2023

Maybe related, just stumbled across https://github.com/olkuka/multiqc_jupyterlab/ - may be useful.

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