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Add clinical trials figure #480

Merged
merged 18 commits into from
Jul 20, 2020
Merged

Add clinical trials figure #480

merged 18 commits into from
Jul 20, 2020

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agitter
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@agitter agitter commented Jul 7, 2020

Description of the proposed additions or changes

Adds the clinical trials figure and expands the scheduled workflow that re-generates the figure

Related issues

#406 #465

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Checklist

  • Text is formatted so that each sentence is on its own line.
  • Pre-prints cited in this pull request have a GitHub issue opened so that they can be reviewed.

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AppVeyor build 1.0.1528 for commit 87f75a4 is now complete.

Found 2 potential spelling error(s). Preview:content/20.treatments.md:15:ebm
content/20.treatments.md:20:ebm...
The rendered manuscript from this build is temporarily available for download at:

@rando2 rando2 added the in progress text still being developed label Jul 7, 2020
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AppVeyor build 1.0.1530 for commit 790d541 is now complete.

Found 2 potential spelling error(s). Preview:content/20.treatments.md:15:ebm
content/20.treatments.md:20:ebm...
The rendered manuscript from this build is temporarily available for download at:

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agitter commented Jul 7, 2020

I ran into the pandoc-fignos numbering bug described in tomduck/pandoc-fignos#76 Fortunately, the workaround in tomduck/pandoc-fignos#76 (comment) worked.

We'll have to add secno=1 after all figure ids until the bug is fixed.

@agitter agitter mentioned this pull request Jul 10, 2020
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@agitter agitter marked this pull request as ready for review July 16, 2020 22:35
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agitter commented Jul 16, 2020

I added a basic description of the figure, so this is now ready for review. There are more ideas for clinical trials data in #406. However, I'd like to work on merging this before implementing any of those so that the updated nightly clinical trials data update added here starts to run.

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AppVeyor build 1.0.1681 for commit 1bc1fca is now complete.

Found 1 potential spelling error(s). Preview:content/20.treatments.md:22:TrialsTracker...
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AppVeyor build 1.0.1687 for commit f2b5aeb is now complete.

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@agitter agitter added Text for Review Feedback on this text is welcome! and removed in progress text still being developed labels Jul 17, 2020
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agitter commented Jul 17, 2020

I updated the nightly workflow to support versioned figures. This pull request is now linked to #512. They should be merged on the same day.

There may be errors because I can't fully test to new external resources scripts until they run in the nightly GitHub Actions workflow. After we merge, I'll watch the CI logs to see whether this worked.

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AppVeyor build 1.0.1695 for commit 4a11b52 is now complete.

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@agitter agitter mentioned this pull request Jul 17, 2020
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AppVeyor build 1.0.1707 for commit ad1453a is now complete.

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rando2
rando2 approved these changes Jul 20, 2020
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Feel like I learned a lot about CI and manubot reading through this -- so likely not the most critical review ever, but it all looks very reasonable!

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rando2 commented Jul 20, 2020

#512 just merged so will merge this ASAP

@rando2 rando2 added Merge Pending Checks and removed Text for Review Feedback on this text is welcome! labels Jul 20, 2020
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rando2 commented Jul 20, 2020

Manubot approved and I want this to merge as close to #512 as possible, so going ahead!

@rando2 rando2 merged commit b197337 into greenelab:master Jul 20, 2020
github-actions bot pushed a commit that referenced this pull request Jul 20, 2020
Merge pull request #480 from agitter/add-trials-figure
480dff7 
[ci skip]

This build is based on
b197337.

This commit was created by the following CI build and job:
https://github.com/greenelab/covid19-review/commit/b197337b9410f00ed0586c1bc51837a1e5791fb2/checks
https://github.com/greenelab/covid19-review/runs/176235487
github-actions bot pushed a commit that referenced this pull request Jul 20, 2020
Merge pull request #480 from agitter/add-trials-figure
5afb6cd 
[ci skip]

This build is based on
b197337.

This commit was created by the following CI build and job:
https://github.com/greenelab/covid19-review/commit/b197337b9410f00ed0586c1bc51837a1e5791fb2/checks
https://github.com/greenelab/covid19-review/runs/176235487
@agitter agitter deleted the add-trials-figure branch July 20, 2020 22:18
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agitter commented Jul 20, 2020

Thanks @rando2. I made a note to check what happens with the nightly external resources update tonight so I can fix any errors that arise.

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