Skip to content

Latest commit

 

History

History
50 lines (37 loc) · 1.76 KB

README.md

File metadata and controls

50 lines (37 loc) · 1.76 KB
Raw

Docs

This repo is a submodule of bioimageloader for documentation. Compile docs using make and sphinx. Find HTML inside _build/html/index.html.

Main repo: https://github.com/LaboratoryOpticsBiosciences/bioimageloader

Notes

  • [IMPORTANT] Separate environment for compiling docs. Follow below instruction.
  • Allow only HTML compilation
  • Post compilation
    • modify_table_html.py: Add necessary tags to table_maskdataset.html
    • add_images_table_html.py: Add samples images to table_maskdataset.html

Steps

  1. Install requirements from bioimageloader package. pip intall bioimageloader[dev]

  2. (optional) Execute notebook first and save outputs

  3. Switch to env for docs

  4. Compile docs

    make html
  • (anytime) Clean docs 
    make clean

How to update table overview

Table is stored in _static/table_maskdataset.md as a Markdown format. Once you added a new dataset, please update this table accordingly. After that go to https://www.tablesgenerator.com/ and copy and paste the table to convert it into HTML format. Download and save it in _static/table_maskdataset.html.orig.

Make exactly two sample images in PNG format and save them in _static/sample_images. Set filenames following other examples "{acronym}_{n_sample}_{ind_sample}.png". Normally, it should be enough to write acronym in the filename.

This HTML file will be processed before sphinx-build by scripts/add_images_table_html.py and scripts/modify_table_html.py.

Troubleshooting

  • pandoc missing

    nbsphinx requires pandoc. If you are using conda, install it by executing conda install -c conda-forge pandoc. Otherwise, follow the official documentation (https://pandoc.org/installing.html).