Pandoc can be installed in anaconda by

conda install pandoc

or in brew.

brew install pandoc

I strongly recommand to use brew version. For brew, switch to the brew environment first.

swt_brew # custom command in .bash_profile

Then go to the folder where you have .tex files to convert. Run the following command:

pandoc  --citeproc -f latex -s FeSH-JGR.tex -o FeSH-JGR.docx --bibliography=FeSH.bib

Change the file names appropriately.

• The command works only with brew version of pandoc for me.
• Note that the order betweeen pandoc-crossref and citeproc should not change.
• Run multiples of time (unconfirmed).
• Pandoc knows how to deal with bibunits and \input{}.
• Note that line number referencing and citing do not work with pandoc.
• Do not place both -F pandoc-crossref and --citeproc at the same time, it will repeat the figure and table caption titles.
• Note that renumbering for figures and tables (for example S1 for supplementary contents) are all ignored. So be careful if this is important.

pandoc  --citeproc -f latex -s Nature-main\ text.tex --csl=../ieee.csl -o main.docx --bibliography=B30.bib

Source: https://tex.stackexchange.com/questions/268196/how-to-convert-latex-to-word-using-pandoc-and-keep-citations-as-numeral

ieee.csl can be donwloaded from: https://github.com/citation-style-language/styles

If you have track change commands from the TrackChanges package (not the changes package), the commands can be removed by:

python ../acceptchanges.py -c -n --infile=0-main.tex --outfile=0-main-no-track.tex

• Note that acceptchanges.py works only with python v2.7.
• The acceptchanges.py can be found under TrackChanges folder or it comes with the latex package.
• acceptchanges.py does not automatically deal with \input{} or \include{} files. So I have to process with acceptchanges.py all associated files individually.
• For the command above to work, copy entire latex folder under /trackchanges-0.7.0/PythonPackage/ folder.

For latex changes package was used for track change, use pyMergeChanges.py.

python ../pyMargeChanges.py -a input.tex output.tex # python 3

Under the base environment of anaconda, I installed arxiv_latex_cleaner (https://github.com/google-research/arxiv-latex-cleaner).

arxiv_latex_cleaner Hydrogen_FeS_paper/ --im_size 500

• This will create organized package in a new folder, Hydrogen_FeS_paper_arXiv.
• arxiv_latex_cleaner seems to know how to deal with \include{} and \input{}. It also deals well with bibunits.

pandoc -t latex -f docx in.docx -o out.tex

pandoc -F pandoc-crossref  --citeproc --mathjax -f latex -t html -s FeSH-JGR.tex -o FeSH-JGR.html --bibliography=FeSH.bib

For better outcome to html:

• convert all pdf figures to png figures
• \multicolumn is not compatible with pandoc
• Figure labelings are properly done, but not for table labeling. I try everything but so far the line above is the best. If you remove any of -F pandoc-crossref and --citeproc from the line above, it will mess up the citations.