using --natbib will generate \cite{} calls, fixes #3

aa/README.md

@@ -3,7 +3,7 @@
 Generate a `tex` file with:
 
 ```
-pandoc demo-structured_abstract.md -s --template aa_template.tex -o demo-structured_abstract.tex -F pandoc-crossref -F pandoc-citeproc --lua-filter=filters/acknowledgments.lua
+pandoc demo-structured_abstract.md -s --template aa_template.tex -o demo-structured_abstract.tex -F pandoc-crossref -F pandoc-citeproc --lua-filter=filters/acknowledgments.lua --natbib
 ```
 
 Go straight to the pdf with:

aastex62/README.md

@@ -3,7 +3,7 @@
 Generate a TeX file with:
 
 ```
-pandoc demo.md -s --template aastex62_template.tex -o demo.tex -F pandoc-crossref -F pandoc-citeproc --lua-filter=filters/acknowledgments.lua --no-highlight
+pandoc demo.md -s --template aastex62_template.tex -o demo.tex -F pandoc-crossref -F pandoc-citeproc --lua-filter=filters/acknowledgments.lua --no-highlight --natbib
 ```
 
 Go straight to the pdf with:

aastex62/demo.md

@@ -224,6 +224,9 @@ These citations take the form of: `[@Astropy2018]`, corresponding to [@Astropy20
 `pandoc-citeproc` uses the Citation Style Language^[<https://citationstyles.org/>] to format citations.
 Presently most of the main astrophysics journals lack entries in the CSL database.
 
+By default, `pandoc-citeproc` will convert the references into text when generating \TeX files.
+In order to convert the citations to `\cite{}` style commands (which are likely preferred for journal submissions) call `pandoc` with the `--natbib` or option.
+
 ## Equations {#sec:equations}
 
 Equations can be specified and labeled in the text using standard \TeX\ macros.

mnras/README.md

@@ -3,7 +3,7 @@
 Generate a `tex` file with:
 
 ```
-pandoc demo.md -s --template mnras_template.tex -o demo.tex -F pandoc-crossref -F pandoc-citeproc --lua-filter=filters/acknowledgments.lua
+pandoc demo.md -s --template mnras_template.tex -o demo.tex -F pandoc-crossref -F pandoc-citeproc --lua-filter=filters/acknowledgments.lua --natbib
 ```
 
 Go straight to the pdf with: