Collection of scripts used in the Bone Imaging Laboratory.

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• Python All source code is Python, no C++, ergo no compilation
• Examples Please do upload individual, one-off project scripts to the /examples directory!
• Open source The whole world can see your code, and the whole world can contribute back
• Testing Automatically runs tests on a server. So, please write your tests!

# Clone the repository onto your computer and change into the directory.
# ... with SSH authentication
git clone git@github.com:Bonelab/Bonelab.git
# ... or straight HTTPS
git clone https://github.com/Bonelab/Bonelab.git

# It is recommended to use anaconda and install from the environment file
conda env create -f environment.yml

# ... alternatively, you can setup the environment directly
conda create -n bl -c numerics88 -c simpleitk -c conda-forge python=3.7 n88tools pbr nose six simpleitk pydicom gdcm

# ... or start fresh
conda create -n bl -c numerics88 -c conda-forge python=3.7 n88tools pbr nose

# Activate the environemnt
conda activate bl

# change directory into the Bonelab repo
cd Bonelab

# Install in an 'editable' format
pip install -e .

Installing in an 'editable' format allows changes to the code to be immediately reflected in your programs. This removes the need to run pip install with each change. However, changing entry points in setup.cfg will require re-runing pip install.

# Be at the root
cd Bonelab

# Run tests
nosetests tests/

A collection of example data is provided by the Bone Imaging Laboratory.

These data can be fetched by executing the command blDownloadData in your terminal. Currently, the data is downloaded into the user's directory under the directory ~/.bldata. Please see blDownloadData -h for additional information.

If you're going to contribute to the repository, it is suggested you create a branch:

$ git checkout master
$ git pull
$ git checkout -b <BRANCH_NAME>

Merge the branch once you're certain your changes won't break other code.

To add a new application, do the following:

• Add entry point in setup.cfg
• Add file with main function in bonelab.cli
• Rerun pip install -e .
• Add tests to tests.cli. test_cli_setup.py and, if appropriate, add other tests.