Upgrade manubot & environment on 2018-08-22

[dhimmel]

Work in progress.

[dhimmel]

Running the following which uses the CSL style from 2a4a44a:

manubot cite --render \
  --csl=https://github.com/greenelab/manubot-rootstock/raw/2a4a44a5088e587aa25b9655f93842a264362038/build/assets/style.csl \
  doi:10.7554/eLife.32822 pmid:29424689 pmcid:PMC5832410 url:https://greenelab.github.io/meta-review/ 

Produced the following:

1. Sci-Hub provides access to nearly all scholarly literature
   Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas
   Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey
   S Greene
   eLife (2018-03-01) https://doi.org/ckcj
   DOI: 10.7554/elife.32822 · PMID: 29424689 · PMCID: PMC5832410

2. Sci-Hub provides access to nearly all scholarly literature.
   Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas
   Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey
   S Greene
   eLife (2018-03-01) https://www.ncbi.nlm.nih.gov/pubmed/29424689
   DOI: 10.7554/elife.32822 · PMID: 29424689 · PMCID: PMC5832410

3. Sci-Hub provides access to nearly all scholarly literature
   Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas
   Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey
   S Greene
   eLife (2018) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5832410/
   DOI: 10.7554/elife.32822 · PMID: 29424689 · PMCID: PMC5832410

4. Open collaborative writing with Manubot
   Daniel S. Himmelstein, David R. Slochower, Venkat S. Malladi, Casey S.
   Greene, Anthony Gitter
   (2018-08-03) https://greenelab.github.io/meta-review/

Relates to discussion in manubot/manubot#45 and manubot/manubot#49 (comment)

[dhimmel]

As long as you are editing the style, is it easy to add a default value when there is no author? I'll open a separate issue if it is out of scope.

@agitter you possibly could try manubot.csl.txt... I added a conditional statement if author is not present, but I don't think it necessarily will work.

Anyways, I am moving and shutting down my systems... so you'll have to proceed without me.

[dhimmel]

Not going to get a chance to do more CSL work before returning. @agitter consider merging this. Perhaps would be good to have a bit more testing of the CSL changes, perhaps with the meta-review bibliography. Up to you whether to wait or proceed

[agitter]

@dhimmel I'll review this once more and squash merge once I approve. I'll create a new issue regarding CSL, or add to our existing issue.

Can you please remind me what I need to do for the squash commit message so that the issue doesn't appear in other downstream repositories? Do I include the full URL https://github.com/greenelab/manubot-rootstock/pull/132?

[dhimmel]

Just make sure not to have any relative github references... So yes use the full PR url in the message. The problem we want to avoid is this commit incorrectly linking to another PR in another repository