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Generate report with phys2bids outputs #407

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@eurunuela eurunuela commented Jun 24, 2021

Closes #131

This is a follow-up of #243 as the branch on that PR got deleted.

Proposed Changes

  • Adds the functionality to generate a report with phys2bids outputs when requested through the CLI interface or the Python function in phys2bids.py.

Change Type

  • bugfix (+0.0.1)
  • minor (+0.1.0)
  • major (+1.0.0)
  • refactoring (no version update)
  • test (no version update)
  • infrastructure (no version update)
  • documentation (no version update)
  • other

Checklist before review

  • I added everything I wanted to add to this PR.
  • [Code or tests only] I wrote/updated the necessary docstrings.
  • [Code or tests only] I ran and passed tests locally.
  • [Documentation only] I built the docs locally.
  • My contribution is harmonious with the rest of the code: I'm not introducing repetitions.
  • My code respects the adopted style, especially linting conventions.
  • The title of this PR is explanatory on its own, enough to be understood as part of a changelog.
  • I added or indicated the right labels.
  • I added information regarding the timeline of completion for this PR.
  • Please, comment on my PR while it's a draft and give me feedback on the development!

@eurunuela eurunuela added Urgent If you don't know where to start, start here! Minormod This PR generally closes an `Enhancement` issue. It increments the minor version (0.+1.0) labels Jun 24, 2021
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codecov bot commented Jun 24, 2021

Codecov Report

Merging #407 (d449661) into master (7369827) will increase coverage by 0.34%.
The diff coverage is 98.78%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #407      +/-   ##
==========================================
+ Coverage   94.81%   95.15%   +0.34%     
==========================================
  Files           8        9       +1     
  Lines         868      950      +82     
==========================================
+ Hits          823      904      +81     
- Misses         45       46       +1     
Impacted Files Coverage Δ
phys2bids/reporting/html_report.py 98.71% <98.71%> (ø)
phys2bids/cli/run.py 96.66% <100.00%> (+0.11%) ⬆️
phys2bids/phys2bids.py 88.33% <100.00%> (+0.19%) ⬆️

@eurunuela
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As of right now, the plots don't get loaded. I checked and tedana is not restricting the Bokeh version and we are doing the same. So, I'd say the issue is not related to the version of Bokeh.

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Minormod This PR generally closes an `Enhancement` issue. It increments the minor version (0.+1.0) Urgent If you don't know where to start, start here!
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Status: BrainHack Vanderbilt 2024
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Generate a report with all the outputs
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