What did I learn from failed experiments
If I create a markdown block and push it through git, it may work.
Perhaps create a structure with html or insert text first. Then pull and push from github?
If I create a new html file and add to layout.md and upload will it work?
Create a table and push it with a new file
This is a table. Now convert thoughts.md to thoughts.html and add to layout.md Then git it to authorea. Works?
Yes it did work. Figure will work likewise. All other text elements will work likewise.
How about citations?
Create folder bibliography and then within it biblio.bib and put in root folder Then populate the file with a reference from Google scholar, say the Git article by Karthik Ram and instead of using pandoc to process the citation, I add the cite command \cite{ram2013} and continue with it to process the html.
Changed the cite command. Did it work?
How does this work?
\cite{ram2013}
To put the above I had to click cite then search and then cite.
So, I changed the file on Authorea and added citations. Now I want to bring in the file to my local repo (git pull?), create a thoughts2.md and append those few lines to the html file
So, I changed the file on Authorea and added citations. Now I want to bring in the file to my local repo (git pull?), create a thoughts2.md and append those few lines to the html file.
Now if I went ahead and placed another reference and then modified the thoughts2.html using the cite class equals ltx_cite raw v1 within quote marks, would this work?
Say we cite Leonard's work \cite{leonard2016} then went ahead and modified this document on thoughts2.html, appended as before and tested. Would it work?
What did I learn from failed experiments
If I create a markdown block and push it through git, it may work.
Perhaps create a structure with html or insert text first. Then pull and push from github?
If I create a new html file and add to layout.md and upload will it work?
Create a table and push it with a new file
This is a table. Now convert thoughts.md to thoughts.html and add to layout.md Then git it to authorea. Works?
Yes it did work. Figure will work likewise. All other text elements will work likewise.
How about citations?
Create folder bibliography and then within it biblio.bib and put in root folder Then populate the file with a reference from Google scholar, say the Git article by Karthik Ram and instead of using pandoc to process the citation, I add the cite command \cite{ram2013} and continue with it to process the html.
Changed the cite command. Did it work?
How does this work?
\cite{ram2013}
To put the above I had to click cite then search and then cite.
So, I changed the file on Authorea and added citations. Now I want to bring in the file to my local repo (git pull?), create a thoughts2.md and append those few lines to the html file
So, I changed the file on Authorea and added citations. Now I want to bring in the file to my local repo (git pull?), create a thoughts2.md and append those few lines to the html file.
Now if I went ahead and placed another reference and then modified the thoughts2.html using the cite class equals ltx_cite raw v1 within quote marks, would this work?
Say we cite Leonard's work \cite{leonard2016} then went ahead and modified this document on thoughts2.html, appended as before and tested. Would it work?
So far I am enjoying the workflow in Authorea and Atom with git and pandoc. It can be frustrating at times, but if it can be made to work, nothing like it. We are not going to use markdown or latex on Authorea's editor, just plain html. We will work on the backend at the local machine. So, we make changes here, then import them or pull them into our folder, convert the document to markdown, preserve the citation tags, and perhaps table tags as well as these are not well translated by pandoc, and work on the markdown document some more and then add references and citations from the markdownified local document and push it back. This forward and backward pushing is needed to test that markdown at the machine level and html at Authorea level should work. The only non-pleb level changes that need to be done should be at the html level with citations where we need to add the cite tag with class equals ltx_cite raw v1 within quotes and close the tag but that can be done using an edit find and replace kind of automated script or step for large number of citations. Hopefully, pandoc will preserve all cite tags during parse raw unless I am too ambitious. Let's put it to test.
What did I learn from failed experiments
If I create a markdown block and push it through git, it may work.
Perhaps create a structure with html or insert text first. Then pull and push from github?
If I create a new html file and add to layout.md and upload will it work?
Create a table and push it with a new file
This is a table. Now convert thoughts.md to thoughts.html and add to layout.md Then git it to authorea. Works?
Yes it did work. Figure will work likewise. All other text elements will work likewise.
Create folder bibliography and then within it biblio.bib and put in root folder Then populate the file with a reference from Google scholar, say the Git article by Karthik Ram and instead of using pandoc to process the citation, I add the cite command \cite{ram2013} and continue with it to process the html.
Changed the cite command. Did it work?
To put the above I had to click cite then search and then cite.
So, I changed the file on Authorea and added citations. Now I want to bring in the file to my local repo (git pull?), create a thoughts2.md and append those few lines to the html file
So, I changed the file on Authorea and added citations. Now I want to bring in the file to my local repo (git pull?), create a thoughts2.md and append those few lines to the html file.
Now if I went ahead and placed another reference and then modified the thoughts2.html using the cite class equals ltx_cite raw v1 within quote marks, would this work?
Say we cite Leonard's work \cite{leonard2016} then went ahead and modified this document on thoughts2.html, appended as before and tested. Would it work?
What did I learn from failed experiments
If I create a markdown block and push it through git, it may work.
Perhaps create a structure with html or insert text first. Then pull and push from github?
If I create a new html file and add to layout.md and upload will it work?
Create a table and push it with a new file
This is a table. Now convert thoughts.md to thoughts.html and add to layout.md Then git it to authorea. Works?
Yes it did work. Figure will work likewise. All other text elements will work likewise.
Create folder bibliography and then within it biblio.bib and put in root folder Then populate the file with a reference from Google scholar, say the Git article by Karthik Ram and instead of using pandoc to process the citation, I add the cite command \cite{ram2013} and continue with it to process the html.
Changed the cite command. Did it work?
To put the above I had to click cite then search and then cite.
So, I changed the file on Authorea and added citations. Now I want to bring in the file to my local repo (git pull?), create a thoughts2.md and append those few lines to the html file
So, I changed the file on Authorea and added citations. Now I want to bring in the file to my local repo (git pull?), create a thoughts2.md and append those few lines to the html file.
Now if I went ahead and placed another reference and then modified the thoughts2.html using the cite class equals ltx_cite raw v1 within quote marks, would this work?
Say we cite Leonard's work \cite{leonard2016} then went ahead and modified this document on thoughts2.html, appended as before and tested. Would it work?
So far I am enjoying the workflow in Authorea and Atom with git and pandoc. It can be frustrating at times, but if it can be made to work, nothing like it. We are not going to use markdown or latex on Authorea's editor, just plain html. We will work on the backend at the local machine. So, we make changes here, then import them or pull them into our folder, convert the document to markdown, preserve the citation tags, and perhaps table tags as well as these are not well translated by pandoc, and work on the markdown document some more and then add references and citations from the markdownified local document and push it back. This forward and backward pushing is needed to test that markdown at the machine level and html at Authorea level should work. The only non-pleb level changes that need to be done should be at the html level with citations where we need to add the cite tag with class equals ltx_cite raw v1 within quotes and close the tag but that can be done using an edit find and replace kind of automated script or step for large number of citations. Hopefully, pandoc will preserve all cite tags during parse raw unless I am too ambitious. Let's put it to test.
then we continue to work some more
Now add a table and image and that kind of thing and it should work. Just make sure that two backslashes not one backslash in markdown and use --parse-raw as option. Add a citation here, \cite{sauermaking} to make things easy.
Bottomline
After much trial and error:
- Start a document in Authorea
- Establish the git bridge and pull the document in your machine
- You can add the bibliography from your local drive
- Populate the document in Authorea form your local drive by concatenating rather than adding your own html files (is this correct? I am still not sure why only this works!)
- Markdown is just fine, make sure for citation use the tag cite class equals ltx underscore cite within quote marks and close the tag
- For both inbound and outbound conversions in pandoc, use the flag parse raw; you do not need to use the pandoc-citeproc option.
- Use the citation ID in the biblio.bib file and remember to include the biblio.bib file
- To keep things simple, just use the Authorea document and the necessary files in git add and then push/pull/commit from there. Stage only these files.