[MAINT] Add affiliations #3956

Remi-Gau · 2023-09-08T19:26:14Z

Closes Updating contributors affiliations #3808

Changes proposed in this pull request:

get contributors infor from google spreadsheet set during OHBM hackathon
get extra info from ORCID or github
add affiliation to authors.rst

github-actions · 2023-09-08T19:26:32Z

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codecov · 2023-09-08T19:38:15Z

Codecov Report

Merging #3956 (ddfa0d9) into main (45065b5) will not change coverage.
Report is 5 commits behind head on main.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main    #3956   +/-   ##
=======================================
  Coverage   91.79%   91.79%           
=======================================
  Files         134      134           
  Lines       15772    15772           
  Branches     3284     3284           
=======================================
  Hits        14478    14478           
  Misses        751      751           
  Partials      543      543

Flag	Coverage Δ
macos-latest_3.10	`91.70% <ø> (ø)`
macos-latest_3.11	`91.70% <ø> (ø)`
macos-latest_3.8	`91.67% <ø> (ø)`
macos-latest_3.9	`91.67% <ø> (ø)`
ubuntu-latest_3.10	`91.70% <ø> (ø)`
ubuntu-latest_3.11	`91.70% <ø> (ø)`
ubuntu-latest_3.8	`91.67% <ø> (ø)`
ubuntu-latest_3.9	`91.67% <ø> (ø)`
windows-latest_3.10	`91.64% <ø> (ø)`
windows-latest_3.11	`91.64% <ø> (ø)`
windows-latest_3.8	`91.61% <ø> (ø)`
windows-latest_3.9	`91.61% <ø> (ø)`

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Remi-Gau · 2023-09-08T19:52:52Z

AUTHORS.rst

+* `Ahmad Chamma`_: INRIA, Saclay, France
 * `Aina Frau-Pascual`_
-* `Alex Rothberg`_
-* `Alexandre Abadie`_
+* `Alex Rothberg`_: Free Agency, New York, USA
+* `Alexandre Abadie`_: Inria, Paris
 * `Alexandre Abraham`_
-* `Alexandre Gramfort`_
+* `Alexandre Gramfort`_: Meta, France
 * `Alexandre Savio`_
-* `Alexis Thual`_
-* `Alisha Kodibagkar`_
+* `Alexis Thual`_: INRIA, Saclay, France
+* `Alisha Kodibagkar`_: MIT McGovern Institute, Cambridge, Massachusetts, United States


Could turn this into a table if we think it would look better.

Remi-Gau · 2023-09-08T20:49:33Z

If anyone feels like I can try to add map of the location of our contributors in the authors.rst file.

bthirion

Thx for doing that !

AUTHORS.rst

CITATION.cff

Co-authored-by: bthirion <bertrand.thirion@inria.fr>

Remi-Gau · 2023-09-11T14:32:37Z

Will try to tackle the people with no affiliation or with just a country as affiliation but I think we should not aim to be 100% completionist on this one.

Remi-Gau · 2023-09-12T02:08:54Z

Will most likely move this to another PR but here is a little script that should help us consolidate the ORCID of some of our contributors

"""list authors with no orcid id

ping the ORCID API to see what match we get
and only print when there are less than 5 results 
"""
import pandas as pd
import requests
from rich import print

from citation_cff_maint import read_citation_cff

citation = read_citation_cff()

author_list = []
orcid_list = []

for author in citation["authors"]:
    if "orcid" not in author:
        print(f"{author['given-names']} {author['family-names']}")

        url = f"https://pub.orcid.org/v3.0/search/?q=family-name:{author['family-names']}+AND+given-names:{author['given-names']}"

        response = requests.get(
            url,
            headers={
                "Accept": "application/json",
            },
        )

        if response.status_code == 200:
            resp = response.json()
            if resp["num-found"] > 0 and resp["num-found"] < 6:
                author_list.append(
                    f"{author['given-names']} {author['family-names']}"
                )
                orcid = [x["orcid-identifier"]["uri"] for x in resp["result"]]
                orcid_list.append(", ".join(orcid))

df = pd.DataFrame({"author": author_list, "orcid": orcid_list})
df.to_csv("orcid.tsv", index=False, sep="\t")

Remi-Gau · 2023-09-12T12:00:57Z

Will merge this one and move the ORCID update to another issue.

Remi-Gau · 2023-09-12T12:39:40Z

For the record.

Note that Alexis has multiple affiliations (INSERM, College de France)

Citation.cff do not yet support multiple affiliations but this is the discussion thread about it.

citation-file-format/citation-file-format#268

Remi-Gau added 3 commits September 8, 2023 13:57

update citation.cff

3d1500c

get affiliations from github

87a049b

manual claeaning

c90dfc0

Remi-Gau added 2 commits September 8, 2023 15:26

update citation.cff

8cdf9c8

rm tsv

5dce1b3

Remi-Gau added 2 commits September 8, 2023 15:43

add affiliations to AUTHORS.rst

fa86aa2

rm utility scripts

682ab90

Remi-Gau marked this pull request as ready for review September 8, 2023 19:45

Remi-Gau commented Sep 8, 2023

View reviewed changes

update affiliations after manual lookup

f4ff1d4

bthirion reviewed Sep 10, 2023

View reviewed changes

Remi-Gau and others added 4 commits September 10, 2023 23:48

Apply suggestions from code review

bd3d0bb

Co-authored-by: bthirion <bertrand.thirion@inria.fr>

Apply suggestions from code review

2fe0bb2

Co-authored-by: bthirion <bertrand.thirion@inria.fr>

uniformize changes into citation.cff

9db79bd

update affiliations

168ea95

bthirion approved these changes Sep 11, 2023

View reviewed changes

Remi-Gau added 2 commits September 11, 2023 18:59

update some affiliations that only had countries

4471858

update some orcid

d53c619

update more orcid and affiliations

ddfa0d9

Remi-Gau merged commit 18fae8e into nilearn:main Sep 12, 2023
29 checks passed

Remi-Gau deleted the affiliations branch September 12, 2023 12:01

Remi-Gau mentioned this pull request Sep 12, 2023

Update ORCID of contributors #3966

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[MAINT] Add affiliations #3956

[MAINT] Add affiliations #3956

Remi-Gau commented Sep 8, 2023 •

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[MAINT] Add affiliations #3956

[MAINT] Add affiliations #3956

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