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adds csv data for consortium contributors collected via tripetto #61

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Merged
merged 18 commits into from
Mar 18, 2021
Merged

adds csv data for consortium contributors collected via tripetto #61

merged 18 commits into from
Mar 18, 2021

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@jsheunis
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@jsheunis jsheunis commented Mar 5, 2021

Requested by @Remi-Gau to add the data collected via tripetto to the jupyter book repo

@htwangtw
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htwangtw commented Mar 5, 2021

Thank you @jsheunis! Just a heads up: we are expecting one or two people to fill this in and might ask you to update this PR on Monday the latest.

@SNeuroble
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SNeuroble commented Mar 8, 2021

Thanks @jsheunis !

Just took a look and I think these will be the next steps updating the authors + affiliations list. Not sure who is interested in doing this but I'm willing to help where I can! Albeit a little busy atm.

  1. extract columns "First and Last Name" (2) and "Affiliation" (4)
  2. split column "First and Last Name" into 3 columns: "First", "Middle", and "Last"
  3. rename "Affiliation" to "Department" (no need to split unless people feel inspired)
  4. manual curation of names and affiliations (mainly: some lack city/state 😕 )
  5. merge columns with the existing table
    (5.5. To automate co-first stars, we can add an "Other" field + stars to the original table. This is parsed by Author Arranger)
  6. sort consortium names alphabetically
  7. Author Arranger!

SNeuroble
SNeuroble approved these changes Mar 8, 2021
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By the way, I'm fine with this being merged but we can wait for any updates if need be.

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htwangtw commented Mar 8, 2021

@SNeuroble I am on this - just waiting for the call 😎

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SNeuroble commented Mar 8, 2021

@htwangtw As usual, thank you for being amazing ❤️

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htwangtw commented Mar 8, 2021 •
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The input for Author Arranger is ready.
Once the trippetto input doesn't get any new updates, we can merge the tmp files marked in the new tripetto script.
@jsheunis if there's any new entry please append them to the existing file as I already deleted a few duplicates.

Edit: Extra notes -
If the trippetto data need some manual check, update affiliation_consent_and_contributions_for_the_brainhack_consortium_tripetto.csv
Any framaform curation, please update
affiliations_curated.tsv

Run scripts in the following order:

python scripts/trippetto_to_curated.py 
python scripts/neuroview_author_ranking.py
bash scripts/neuroview_affiliations_organizer.sh

@jsheunis
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jsheunis commented Mar 8, 2021

@htwangtw I've added the new data. hope I didn't screw things up...

@htwangtw
ADD All entry
801c9bc 
We are not accepting any more things.
I don't think we need to proof read the affiliation super hard. Can just
give the editor the `data/authors_affiliations.tsv` for copy-editing.
@htwangtw htwangtw self-requested a review March 8, 2021 23:00
@htwangtw
ADD interim file
14a6136 
not an important file but better keep things consistent.
htwangtw
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We are not accepting any more entry for the paper, I hope.

I am not going to proofread this too hard. We can send data/authors_affiliations.tsv to the copy editor when it is time.

@SNeuroble
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SNeuroble commented Mar 9, 2021

Re waiting to send super-finalized affiliations to copy editor: sounds like a good plan to me :)

Remi-Gau
Remi-Gau reviewed Mar 15, 2021
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htwangtw added 7 commits March 16, 2021 22:09
@htwangtw
Squashed commit of the following:
5e1802f 
commit e9b36d2
Author: Hao-Ting Wang <htwangtw@gmail.com>
Date:   Tue Mar 16 22:03:54 2021 +0000

    ADD/FIX file name consistency for neuroview data

    * Tidy up the data dir and added a README
    * Separated Jupyter Book and Manuscript related data
    * Improve naming consistency

commit 5af605c
Author: Hao-Ting Wang <htwangtw@gmail.com>
Date:   Tue Mar 16 21:25:16 2021 +0000

    ENH tidy up the data directory

    move contributor related files to new subdir and all path in relevant
    scripts

    still need to add README

commit 59bdfd7
Author: Hao-Ting Wang <htwangtw@gmail.com>
Date:   Tue Mar 16 21:02:46 2021 +0000

    ENH add a switch for email related lines

    we worked on a internal version with emails attached
    email should not appear in the public version

commit 6695962
Author: Hao-Ting Wang <htwangtw@gmail.com>
Date:   Tue Mar 16 20:59:16 2021 +0000

    FIX names and affiliations

commit 497bb63
Author: Hao-Ting Wang <htwangtw@gmail.com>
Date:   Fri Mar 12 10:28:50 2021 +0000

    FIX duplicated rows

commit bee43d0
Author: Hao-Ting Wang <htwangtw@gmail.com>
Date:   Fri Mar 12 10:17:54 2021 +0000

    ENH modified for generating the submission sheet with emails
@htwangtw
FIX update deploy workflow
850beec 
`contributor` removed from `Makefile as we no longer need it
@htwangtw
FIX contributor files path in Makefile
19d2103
@htwangtw
FIX contributor table for jupyterbook
afea0a7 
Since we are separating the manuscript affilation and the book
contributor, I would clean up and remove the special contributor flag in
the md table generator.

This is just a quick fix
@htwangtw
ADD social media link to JB contibutor info
94ddcc2
@htwangtw
FIX reduntant dependecy in make brainhack_book/contributors.md
9cb4089
@htwangtw
BK Brainbox URL insecure
ab4108b 
Insecure URL break the test.
Address with separated issue
@htwangtw htwangtw mentioned this pull request Mar 16, 2021
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htwangtw commented Mar 16, 2021 •
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The Jupyter Book data is now updated with the manuscript.
I also cleaned the data directory and a drafted readme to address issue #63.
I would recommend a separate PR for completing the draft I started here.

The test is failing because of the Brainbox URL security. This is likely an external issue so we might want to manually deploy the book and ignore this failed test. (see #64)

@htwangtw htwangtw requested a review from Remi-Gau March 18, 2021 16:34
Remi-Gau
Remi-Gau approved these changes Mar 18, 2021
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Cool.

LGTM.

Will use that to generate the final list of authors and update (manually) all the stuff downstream.

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Remi-Gau commented Mar 18, 2021

Everyone stand back! we are MERGING !!!!

🚀

@Remi-Gau Remi-Gau merged commit 13b8465 into brainhackorg:main Mar 18, 2021
@htwangtw htwangtw mentioned this pull request Apr 16, 2021
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@htwangtw htwangtw htwangtw approved these changes

@Remi-Gau Remi-Gau Remi-Gau approved these changes

@SNeuroble SNeuroble SNeuroble approved these changes

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@jsheunis @htwangtw @SNeuroble @Remi-Gau