Tools for a scientific research

Table of Contents

• How to setup simple markdown converter to pdf in Sublime:
• How to check grammar in your text:
• SVG draw tool for papers and posters:
• How to keep order of papers:
• How to use jupyter notebooks efficiently:
• Create and Maintain python package:

How to setup simple markdown converter to pdf in Sublime:

1. Install pandoc and pdflatex

   sudo apt-get install texlive-latex-base texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra
   

2. Start Sublime go to menu: Tools -> Build System -> New Build System
3. In the New window pandoc.sublime-build put the following:

   {
    "shell_cmd": "pandoc --toc --toc-depth=5 $file_base_name.md -o  $file_base_name.pdf"
   }
   

   • --toc --toc-depth=5 is responsible for generating Table of content and takes into account depth of #####
4. In order to modify pandoc.sublime-build:
   • In menu: Preferences -> Browse Packages -> User -> pandoc.sublime-build
5. In order to execute the pandoc press Cmnd+B

How to check grammar in your text:

• Language Tool with the DB of n-gramms in 5 different languages(works not worth than Grammarly, can be connected to the IDE).

SVG draw tool for papers and posters:

• Inkscape

How to keep order of papers:

• There is a tool called Mendeley which helps to keep order of all papers in one place. There is a posibility to connect it with cloud as well as to use extension in a browser.
• Tutorial how to use it efficiently is here

How to use jupyter notebooks efficiently:

• Represent ipynb, md as a webpage hosted by GitHub
• How to use Jupyter Notebooks in 2020.
  • version control of jupyter notebooks
  • version control of data with DVC
  • deployment
• How to run an MLflow tracking server on AWS EC2
• Jupyter notebook to PDF extension

Create and Maintain python package:

• https://package-helper.readthedocs.io/en/latest/readme.html
• https://antonz.org/python-packaging/