Welcome to bioengineering-toolbox’s documentation!

Contents:

• Code development
  • Git FAQ
    • General
    • GitHub
    • CLI (command line interface)
  • Github FAQ
    • Adding badges to repositories
    • Renaming repositories and updating remote paths of clones
  • Pycharm FAQ
    • How to open interactive python console by default?
• Documentation
  • Creating documentation
    • Getting started
    • Example repositories
    • Markdown
    • Building documentation
    • Additional features
    • restructuredText
  • Sphinx FAQ
    • Force rebuild of html, including autodoc
    • Adding a sphinx build configuration to pycharm
    • Table width fix for Read the Docs Sphinx theme
    • Sphinx and Jupyter notebooks
    • Updating logo for sphinx_rtd_theme
    • Updating sphinx_rtd_theme colours
    • Graphs in Sphinx/RestructuredText
  • Markdown FAQ
    • Best practices
    • Cheatsheet
    • Table generator
    • Escape characters
    • Create note
  • Restructured text FAQ
    • Examples of well documented code repositories
    • Commenting restructuredText files
    • Hyperlinks and cross-referencing
    • Showing example code
    • Add images
    • Creating tables
    • Notes and warnings
  • ReadTheDocs FAQ
    • Adding Github organisation repos to readthedocs
    • Troubleshooting
• Documentation
  • Docker FAQ
    • Common commands
    • Activating a Conda environment in your Dockerfile
    • Tips to Reduce Docker Image Sizes
    • Create Docker Images for Docker Hub
    • Debugging applications with totalview in dockers
• FEM
  • OpenCMISS FAQ
    • Building OpenCMISS
    • Using python bindings on hpc3
    • Debugging OpenCMISS examples
    • Hydrostatic pressure export
  • CMGUI FAQ
    • Replicating cmgui 3.01 visualisation using gfx commands
• File formats
  • JSON FAQ
    • JSON examples
    • Schema
• Linux
  • Linux FAQ
    • Find files in a terminal
    • Change file permissions
    • tar/untar or zip/unzip
    • Search for files in directory
    • Find size of directory
    • Print all environmental variables
    • Download file from the internet
    • Restart network manager (Ubuntu 16.04)
    • GUI utility to mount remote filesystems over SSH
  • Screen FAQ
  • Photo and video FAQ
    • Video software
    • Create gifs from images (commandline)
• Python
  • Python FAQ
    • Python virtual environments
    • Strings
    • Displaying docstrings to see function arguments and info
    • Comparisons
    • Objects
    • Dictionaries
    • Path and IO functions
    • Load/save json
    • Understanding decorators
    • Manually throw/raise an exception
  • Python bindings
    • Manually building h5py bindings with local version of hdf5
  • Virtualenv FAQ
    • Create virtual environments for python with conda
  • Pandas FAQ
    • Create empty dataframe
    • Creating & editing entries
    • Concatenating dataframes
    • Renaming headers
    • Concatenating
    • Find number of rows in dataframe
    • Indexing data
  • Jupyter notebook FAQ
    • Guide
  • Matplotlib FAQ
    • Plotting tutorials
  • Morphic FAQ
    • Using groups
    • Build wxPython on Ubuntu 16.04 (required by mayavi2, which is used by morphic)
  • Mayavi FAQ
    • Speed up mayavi rendering
  • Goolge API FAQs
    • First steps
• University of Auckland
  • UoA eResearch Virtual machine FAQ
    • Add user on eReserach VM
• Web
  • Best practices
  • Javascript FAQ
    • var vs let vs const
    • Comparisons
    • Strings
    • Arrays
    • Converting between data types
    • Conditional operator (if and ?)
    • Classes
    • Objects
    • Looping
    • TypedArray
    • ES6 Modules
    • Mastering javascript callbacks/bind/apply/call
    • Fetching
    • Adding and removing event listeners with access to ‘this’
    • Alerts
    • Disable right-click context menu
  • Dat.Gui FAQ
    • Accessing object methods and attributes inside an event callback.
  • Three.js FAQ
    • Tips and tricks
    • Vector to array conversion
    • View axes
    • Find absolute position of a vertex
    • View point cloud
    • View vertices of an existing geometry
    • Create BufferGeometry
    • Dynamic visualisations using BufferGeometry
    • Copying attributes for a buffer geometry
    • Duplicating objects using THREE.InstancedMesh
    • Add stats.js
    • Get camera world coordinates
    • Enable or disable orbit controls
  • Webpack 4 FAQ
    • Getting started
• Visualisations
  • Graphviz FAQ
    • Examples

Indices and tables

• Index
• Module Index
• Search Page