Loading bib file also from github

[lsaravia]

You can load the manuscript from github but you may need also the bib file that should be on github too. Also can be assumed that the bib file has the same name as the manuscript with bib extension.

[yoavram]

Well, that's the assumption I made for saving files (pushing them). Have you tried it?

As far as loading bib files I'm not so sure and would appreciate the discussion.

There are two BibTeX objects in Markx right now - the reference library and the citation list. The reference library contains the references loaded from a file using the menu. The citation list contains references copied from the reference library during and update citations event - these were copied because their citation keys appeared in the editor text.

Pushing a bib file is easy - you just create a file from the citations in the citation list and push it. Pulling is more complicated - do I pull it to the citation lis or to the reference library? The only way out I see is to merge the pulled bib file into the reference library. Does this make sense?

Also putting a reference to #7 and #13 where this feature was handled before.

[lsaravia]

I was thinking that you don't want to clone the repo locally, this is why you included the github button I thought. So you pull the manuscript and start to work but you can't load the bibliography because you don't have it locally but it is in the remote repo. What I was thinking is that markx could automatically pull it when you pull the manuscript, but only if you don't have another bib file loaded. The other way maybe better is that after pulling the manuscript if you pull a bib file taking it as the bibliography.

The other point is that you surely will want to modify the bib file so what is the most easy way to handle this?. Save it, edit it with an external editor and then load it again to markx and also push it to the repo, is not very straight.

On Tue, Feb 26, 2013 at 3:48 AM, Yoav Ram notifications@github.com wrote:

Well, that's the assumption I madbe for saving files (pushing them). Have you tried it?b

As far as loading bib files I'm not so sure and would appreciate the discussion.

There are two BibTeX objects in Markx right now - the reference library and the citation list. The reference library contains the references loaded from a file using the menu. The citation list contains references copied from the reference library during and update citations event - these were copied because their citation keys appeared in the editor text.

Pushing a bib file is easy - you just create a file from the citations in the citation list and push it. Pulling is more complicated - do I pull it to the citation lis or to the reference library? The only way out I see is to merge the pulled bib file into the reference library. Does this make sense?

Also putting a reference to #7 https://github.com/yoavram/markx/issues/7and

13 https://github.com/yoavram/markx/issues/13 where this feature was

handled before.

— Reply to this email directly or view it on GitHubhttps://github.com/yoavram/markx/issues/36#issuecomment-14098125 .

Dr. Leonardo A. Saravia Área Biología y Bioinformática Instituto de Ciencias Universidad Nacional de General Sarmiento J.M. Gutierrez 1159 (1613) Los Polvorines Buenos Aires Argentina Tel: 54 11 4469-7533 http://waterthinking.blogspot.com/

[yoavram]

Hey, @lsaravia , check the latest commit, I added a button that loads .bib files directly to the references library and adds them, without removing older references. Also, reading from file doesn't erase loaded references, so you can load more and more references from multiple files on user side computer and on GitHub. I will probably add that when you load a .md file, if there is a .bib file with the same name, just different extension, it will load it, but I'd like to see if this work flow isn't flawed first.

[lsaravia]

Yes bib loading it's working!!

In the pandoc converted pdf the references are added as footnotes.

In the conversion to pdf in hosted markx (both pandoc o docverter), the pdf is opened inside the browser you can view it fine or save it if you like, but when you go back to the document (with the browser back button), the help file is loaded and your work is lost.

I didn't test it locally.

On Tue, Feb 26, 2013 at 3:54 PM, Yoav Ram notifications@github.com wrote:

Hey, @lsaravia https://github.com/lsaravia , check the latest commit, I added a button that loads .bib files directly to the references library and adds them, without removing older references. Also, reading from file doesn't erase loaded references, so you can load more and more references from multiple files on user side computer and on GitHub. I will probably add that when you load a .md file, if there is a .bibfile with the same name, just different extension, it will load it, but I'd like to see if this work flow isn't flawed first.

— Reply to this email directly or view it on GitHubhttps://github.com/yoavram/markx/issues/36#issuecomment-14132464 .

Dr. Leonardo A. Saravia Área Biología y Bioinformática Instituto de Ciencias Universidad Nacional de General Sarmiento J.M. Gutierrez 1159 (1613) Los Polvorines Buenos Aires Argentina Tel: 54 11 4469-7533 http://waterthinking.blogspot.com/

[yoavram]

1. References and footnotes - I played around and I if I change the CSL from chicago-full to chicago it doesn't happen - I'll remove chicago-full and commit and in the future we will deal with choosing CSLs.
2. PDF opens in the same window - I tested in Chrome 25 and Firefox 18 and it doesn't happen , does it happen with another browser?

[yoavram]

I see the problem - on heroku, the PDF opens in the same tab instead of opening a new tab. Will fix.

[lsaravia]

1. It's a new behavior of firefox 19.0 I didn't installed a pdf plugin but it's there.. all pdf are opened in the same browser window that you were navigating.

On Wed, Feb 27, 2013 at 4:37 AM, Yoav Ram notifications@github.com wrote:

1. References and footnotes - I see it too, not sure why. I'll investigate.
2. PDF opens in the same window - I tested in Chrome 25 and Firefox 18 and it doesn't happen , does it happen with another browser?

— Reply to this email directly or view it on GitHubhttps://github.com/yoavram/markx/issues/36#issuecomment-14160864 .

[yoavram]

Yeah, they started using pdf.js. Try it now, I deliberately told it to open in a new window when converting with Pandoc, if it works I'll do the same with Docverter.