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).