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CSL style: always add space after title #158

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commented Jan 18, 2019

Fix missing space between title and rest of citation when no author present.

Closes #155

@dhimmel dhimmel changed the title fix citation style csl to always add space after title (issue #155) CSL style: always add space after title Jan 18, 2019

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commented Jan 18, 2019

Confirming that c234d49 fixes the issue with the reference mentioned in #155 (comment).

Before

manubot cite --render \
  --csl=https://github.com/greenelab/manubot-rootstock/raw/4103ad39859e2d0e02e72ec204fbd7b80d12aeb4/build/assets/style.csl \
  url:https://blog.dhimmel.com/irreproducible-timestamps/
1. Satoshi Villagehttps://blog.dhimmel.com/irreproducible-timestamps/

After

manubot cite --render \
  --csl=https://github.com/greenelab/manubot-rootstock/raw/c234d496f2d1ac0ce314329edcc1d7be5c6baffb/build/assets/style.csl \
  url:https://blog.dhimmel.com/irreproducible-timestamps/
1. Satoshi Village https://blog.dhimmel.com/irreproducible-timestamps/
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commented Jan 18, 2019

More tests

Before

1. **Opportunities and obstacles for deep learning in biology and medicine**  
Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way, Enrico Ferrero, Paul-Michael Agapow, Michael Zietz, Michael M. Hoffman, … Casey S. Greene  
*Journal of The Royal Society Interface* (2018-04) <https://doi.org/gddkhn>  
DOI: [10.1098/rsif.2017.0387](https://doi.org/10.1098/rsif.2017.0387) · PMID: [29618526](https://www.ncbi.nlm.nih.gov/pubmed/29618526) · PMCID: [PMC5938574](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5938574)

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](https://doi.org/10.7554/elife.32822) · PMID: [29424689](https://www.ncbi.nlm.nih.gov/pubmed/29424689) · PMCID: [PMC5832410](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5832410)

3. **Systematic integration of biomedical knowledge prioritizes drugs for repurposing**  
Daniel Scott Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio E Baranzini  
*eLife* (2017-09-22) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5640425/>  
DOI: [10.7554/elife.26726](https://doi.org/10.7554/eLife.26726) · PMID: [28936969](https://www.ncbi.nlm.nih.gov/pubmed/28936969) · PMCID: [PMC5640425](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5640425)

4. **Generalization of the Fermi Pseudopotential**  
Trang T. Le, Zach Osman, D. K. Watson, Martin Dunn, B. A. McKinney  
*arXiv* (2018-06-14) <https://arxiv.org/abs/1806.05726v1>

After

manubot cite --render --format=markdown \
  --csl=https://github.com/greenelab/manubot-rootstock/raw/c234d496f2d1ac0ce314329edcc1d7be5c6baffb/build/assets/style.csl \
  doi:10.1098/rsif.2017.0387 pmid:29424689 pmcid:PMC5640425 arxiv:1806.05726
1. **Opportunities and obstacles for deep learning in biology and medicine**   
Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way, Enrico Ferrero, Paul-Michael Agapow, Michael Zietz, Michael M. Hoffman, … Casey S. Greene  
*Journal of The Royal Society Interface* (2018-04) <https://doi.org/gddkhn>   
DOI: [10.1098/rsif.2017.0387](https://doi.org/10.1098/rsif.2017.0387) · PMID: [29618526](https://www.ncbi.nlm.nih.gov/pubmed/29618526) · PMCID: [PMC5938574](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5938574)

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](https://doi.org/10.7554/elife.32822) · PMID: [29424689](https://www.ncbi.nlm.nih.gov/pubmed/29424689) · PMCID: [PMC5832410](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5832410)

3. **Systematic integration of biomedical knowledge prioritizes drugs for repurposing**   
Daniel Scott Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio E Baranzini  
*eLife* (2017-09-22) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5640425/>   
DOI: [10.7554/elife.26726](https://doi.org/10.7554/eLife.26726) · PMID: [28936969](https://www.ncbi.nlm.nih.gov/pubmed/28936969) · PMCID: [PMC5640425](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5640425)

4. **Generalization of the Fermi Pseudopotential**   
Trang T. Le, Zach Osman, D. K. Watson, Martin Dunn, B. A. McKinney  
*arXiv* (2018-06-14) <https://arxiv.org/abs/1806.05726v1>

It looks like this change has added an extra trailing space in the markdown output following the title (from 2 to 3 spaces).

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commented Jan 18, 2019

BTW I fixed the citation metadata on my Satoshi Village blog, so the URL https://blog.dhimmel.com/irreproducible-timestamps/ will no longer return such scant metadata. Now getting:

1. The most interesting case of scientific irreproducibility?
Daniel Himmelstein
Satoshi Village (2017-03-08) https://blog.dhimmel.com/irreproducible-timestamps/

So no longer a good test case for #155

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commented Jan 22, 2019

I just peeked at the latest PDF @vincerubinetti posted in #159 and realized there's an ellipsis in the Deep Review citation. Checking back here, I see it must have been around for a little while. Was there a particular reason you chose an ellipsis over "et al." and to include the final author? I don't have a specific issue, but I do think it's an unusual style choice. For web consumption, I don't mind listing all authors for a given citation. Of course this is easy to override with another CSL style file.

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commented Jan 22, 2019

Was there a particular reason you chose an ellipsis over "et al." and to include the final author?

I thought that the et-al-use-last=true option of CSL was useful since oftentimes the last author(s) play a large role in the study. Obviously, this varies by field and study. Here's the full CSL configuration related to this currently:

https://github.com/greenelab/manubot-rootstock/blob/eb4cb3efef46af8bfff1e391853006777cef373c/build/assets/style.csl#L17-L19

Some studies have 100s or 1000s of authors, so I do like setting a max. Let's move additional discussion to #53 or a new issue.

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commented Apr 12, 2019

Possibly related is dhimmel@12b4783

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commented Apr 12, 2019

What was the reason for wanting to do more tests on this? It seems pretty straightforward.

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dhimmel added a commit that referenced this pull request May 14, 2019

CSL author macro: substitute editor/venue
Merges #219

Ensures there is a newline between the title and venue,
when authors are missing.
Closes #218
Supersedes #158

Substitutes editors for authors when authors are missing.
Editors are labeled like "Sönke Bartling, Sascha Friesike (editors)".
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commented May 14, 2019

The issue of a missing newline after title when no author is present should be fixed by #219.

@dhimmel dhimmel closed this May 14, 2019

dhimmel added a commit that referenced this pull request May 14, 2019

CSL author macro: substitute editor/venue
This build is based on
5da1d32.

This commit was created by the following Travis CI build and job:
https://travis-ci.com/manubot/rootstock/builds/111763307
https://travis-ci.com/manubot/rootstock/jobs/200071500

[ci skip]

The full commit message that triggered this build is copied below:

CSL author macro: substitute editor/venue

Merges #219

Ensures there is a newline between the title and venue,
when authors are missing.
Closes #218
Supersedes #158

Substitutes editors for authors when authors are missing.
Editors are labeled like "Sönke Bartling, Sascha Friesike (editors)".

dhimmel added a commit that referenced this pull request May 14, 2019

CSL author macro: substitute editor/venue
This build is based on
5da1d32.

This commit was created by the following Travis CI build and job:
https://travis-ci.com/manubot/rootstock/builds/111763307
https://travis-ci.com/manubot/rootstock/jobs/200071500

[ci skip]

The full commit message that triggered this build is copied below:

CSL author macro: substitute editor/venue

Merges #219

Ensures there is a newline between the title and venue,
when authors are missing.
Closes #218
Supersedes #158

Substitutes editors for authors when authors are missing.
Editors are labeled like "Sönke Bartling, Sascha Friesike (editors)".

slochower added a commit to slochower/smirnoff-host-guest-manuscript that referenced this pull request May 15, 2019

Rootstock 2019 05 15 (#36)
* webpage.py: note to ignore error in versions checkout

Merges manubot/rootstock#211
Closes manubot/rootstock#183

* Use Athena to build PDF, if Docker installed

Merges manubot/rootstock#210
Closes manubot/rootstock#170

More information about Athena is available at
https://github.com/arachnys/athenapdf

Based on meta-review commit:
greenelab/meta-review@cffcfea

* Add meta review link to readme

Merges manubot/rootstock#217
Closes manubot/rootstock#216

* Increase shared memory of athenapdf container

Merges manubot/rootstock#220
Closes arachnys/athenapdf#195

Increase --shm-size from the default value of 64m to 1g when
running the athenapdf Docker image. Resolves athena issue:
`The renderer process has crashed`

Switch to using equal sign to separate Docker arguments
and values for consistency.
https://stackoverflow.com/q/50319060/4651668

* CSL author macro: substitute editor/venue

Merges manubot/rootstock#219

Ensures there is a newline between the title and venue,
when authors are missing.
Closes manubot/rootstock#218
Supersedes manubot/rootstock#158

Substitutes editors for authors when authors are missing.
Editors are labeled like "Sönke Bartling, Sascha Friesike (editors)".

slochower added a commit to slochower/smirnoff-host-guest-manuscript that referenced this pull request May 15, 2019

Rootstock 2019 05 15 (#36)
This build is based on
d62afc4.

This commit was created by the following Travis CI build and job:
https://travis-ci.com/slochower/smirnoff-host-guest-manuscript/builds/532938787
https://travis-ci.com/slochower/smirnoff-host-guest-manuscript/jobs/532938788

[ci skip]

The full commit message that triggered this build is copied below:

Rootstock 2019 05 15 (#36)

* webpage.py: note to ignore error in versions checkout

Merges manubot/rootstock#211
Closes manubot/rootstock#183

* Use Athena to build PDF, if Docker installed

Merges manubot/rootstock#210
Closes manubot/rootstock#170

More information about Athena is available at
https://github.com/arachnys/athenapdf

Based on meta-review commit:
greenelab/meta-review@cffcfea

* Add meta review link to readme

Merges manubot/rootstock#217
Closes manubot/rootstock#216

* Increase shared memory of athenapdf container

Merges manubot/rootstock#220
Closes arachnys/athenapdf#195

Increase --shm-size from the default value of 64m to 1g when
running the athenapdf Docker image. Resolves athena issue:
`The renderer process has crashed`

Switch to using equal sign to separate Docker arguments
and values for consistency.
https://stackoverflow.com/q/50319060/4651668

* CSL author macro: substitute editor/venue

Merges manubot/rootstock#219

Ensures there is a newline between the title and venue,
when authors are missing.
Closes manubot/rootstock#218
Supersedes manubot/rootstock#158

Substitutes editors for authors when authors are missing.
Editors are labeled like "Sönke Bartling, Sascha Friesike (editors)".

slochower added a commit to slochower/smirnoff-host-guest-manuscript that referenced this pull request May 15, 2019

Rootstock 2019 05 15 (#36)
This build is based on
d62afc4.

This commit was created by the following Travis CI build and job:
https://travis-ci.com/slochower/smirnoff-host-guest-manuscript/builds/532938787
https://travis-ci.com/slochower/smirnoff-host-guest-manuscript/jobs/532938788

[ci skip]

The full commit message that triggered this build is copied below:

Rootstock 2019 05 15 (#36)

* webpage.py: note to ignore error in versions checkout

Merges manubot/rootstock#211
Closes manubot/rootstock#183

* Use Athena to build PDF, if Docker installed

Merges manubot/rootstock#210
Closes manubot/rootstock#170

More information about Athena is available at
https://github.com/arachnys/athenapdf

Based on meta-review commit:
greenelab/meta-review@cffcfea

* Add meta review link to readme

Merges manubot/rootstock#217
Closes manubot/rootstock#216

* Increase shared memory of athenapdf container

Merges manubot/rootstock#220
Closes arachnys/athenapdf#195

Increase --shm-size from the default value of 64m to 1g when
running the athenapdf Docker image. Resolves athena issue:
`The renderer process has crashed`

Switch to using equal sign to separate Docker arguments
and values for consistency.
https://stackoverflow.com/q/50319060/4651668

* CSL author macro: substitute editor/venue

Merges manubot/rootstock#219

Ensures there is a newline between the title and venue,
when authors are missing.
Closes manubot/rootstock#218
Supersedes manubot/rootstock#158

Substitutes editors for authors when authors are missing.
Editors are labeled like "Sönke Bartling, Sascha Friesike (editors)".
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