General Guidance for papers, code, and presentations

Zhonghua Zheng (zhonghua.zheng@outlook.com)

Table of Contents

• papers
• code
• presentations

papers

[Click to expand]

1. create and name the private repo paper_xxx_journal (e.g. paper_UHWs_acp) in the MEDAL organization

2. select Add .gitignore:TeX

3. add *.DS_Store and paper_xxx_journal.pdf (paper_UHWs_acp.pdf) to the .gitignore file via webpage

4. import the repo to Overleaf (Menu -> Sync -> GitHub) and create the following folders for different paper versions

   • 0_template (this will help you compare different template versions)
   • 1_draft
   • 2_preprint
   • 2_manuscript
   • 3_reviews_1
     • decision letter (file(s))
   • 3_revised_paper_1
     • response_to_reviews (folder)
     • manuscript (folder)
     • submission_suammry (folder or file)
   • 4_reviews_2
     • decision letter (file(s))
   • 4_revised_paper_2
     • response_to_reviews (folder)
     • manuscript (folder)
     • submission_summary (folder or file)
   • ...
   • final_proofs

5. within each manuscript folder (and the 1_draft and 2_preprint folders)

   • name the latex file the same: paper_xxx_journal.tex (e.g. paper_UHWs_acp.tex)
   • name the bibtex file refs_xxx_journal.bib (e.g. paper_UHWs_acp.bib)
   • make a subdir for graphics called graphics, which includes all figures (we can reuse the the figures in other folders)

6. Share your Overleaf project with your collaborators.

7. Always sync your Overleaf project (Menu -> Sync -> GitHub) whenever you make significant changes (e.g. each time prior to beginning and following completion).

code

[Click to expand]

1. name the repo code_xxx_journal_private, e.g. code_UHWs_acp_private

2. select Add .gitignore:Python (or others)

3. add *.DS_Store to the .gitignore via webpage

4. create the following folders for different paper versions

   • misc
   • model (optional)
   • data (optional, we must deposit data in a FAIR aligned repository)
   • 0_scratch
   • 1_draft
   • 2_submitted (you will copy all the code here to the group repository code_xxx, e.g. code_UHWs)
   • 3_revised_paper_1
   • 4_revised_paper_2
   • ...
   • final_proof

5. create symbolic link

   ln -s ./data ./0_scratch/data
   ln -s ./data ./1_draft/data
   ln -s ./data ./2_submitted/data
   ...
   # to remove the link
   # rm -rf ./0_scratch/data
   # rm -rf ./1_draft/data
   # rm -rf ./2_submitted/data
   ...

6. Before submitting the preprint and manuscript for the first time, using 2_submitted to check the code

presentations

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• PowerPoint templates: (link)

• Beamer: overleaf themes or Mark Kambites’ Beamer theme

  • To make the purple background and white text for Alex's theme (from overleaf) based on the blog:

    \documentclass[11pt,aspectratio=169,ignorenonframetext,t]{beamer}
    AND
    \usetheme[darktitle,dark,framenumber,titleframestart=1]{UoM_alex}
    

References

• http://lagrange.mechse.illinois.edu/latex_quick_ref/