ENH: Automatic generation of template citations

[mgxd]

This is a proof of concept of #33

This requires a few changes to existing template descriptions:

• Change ReferencesAndLinks type from list to dictionary to facilitate extraction

"ReferencesAndLinks": {
    "1": "https://doi.org/10.1093/cercor/bhr291",
    "2": "https://github.com/Washington-University/HCPpipelines/tree/master/global/templates"
  }

• Standardizing HowToAcknowledge fields to include curly brackets with Reference IDs

"HowToAcknowledge": "Reference the following entries in ReferencesAndLinks: {1, 2}"

[oesteban]

Sounds like a reasonable extra to me

…

On Thu, Feb 27, 2020, 08:44 Mathias Goncalves ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In setup.cfg <#35 (comment)> : > @@ -23,6 +23,7 @@ install_requires = pybids >= 0.9.2 requests tqdm + doi2bib Do we want to have this in the base installation or as an extra? — You are receiving this because your review was requested. Reply to this email directly, view it on GitHub <#35?email_source=notifications&email_token=AAESDRQOQWPPSO5RP3ASC5TRE7UWBA5CNFSM4K46WYE2YY3PNVWWK3TUL52HS4DFWFIHK3DMKJSXC5LFON2FEZLWNFSXPKTDN5WW2ZLOORPWSZGOCXG7J5I#pullrequestreview-365819125>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAESDRUOFYETPFZTSEDQKULRE7UWBANCNFSM4K46WYEQ> .

[codecov]

Codecov Report

Merging #35 into master will increase coverage by 17.55%.
The diff coverage is 81.81%.

@@             Coverage Diff             @@
##           master      #35       +/-   ##
===========================================
+ Coverage   67.88%   85.44%   +17.55%     
===========================================
  Files           5        5               
  Lines         137      158       +21     
===========================================
+ Hits           93      135       +42     
+ Misses         44       23       -21     

Flag	Coverage Δ
#api	85.44% <81.81%> (+17.55%)	⬆️
#config	43.03% <0.00%> (?)
#datalad	73.41% <81.81%> (+22.32%)	⬆️
#dls3	48.73% <22.72%> (-4.56%)	⬇️
#s3	53.16% <22.72%> (-5.23%)	⬇️

Impacted Files	Coverage Δ
templateflow/api.py	77.90% <81.81%> (+0.98%)	⬆️
templateflow/conf/bids.py	100.00% <0.00%> (+28.57%)	⬆️
templateflow/conf/__init__.py	92.72% <0.00%> (+41.81%)	⬆️

---

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[mgxd]

Okay - this is ready for review

[oesteban]

This is a very solid starting point to nontrivial problem - thanks much!

[mgxd]

Once we drop 3.5 fully (#36), things should be working.

[mgxd]

@oesteban did the skeleton change between the last 2 commits?

[oesteban]

I was testing, so that's possible.

[oesteban]

I would get #39 merged first to avoid this kind of problems