CONTRIBUTING

Docker and singularity

The base recipe was generated using neurodocker from the script create_container_recipe.sh.

If possible do not modify the Dockerfile directly but modify it via this script.

Creating the Dockerfile, building it and testing it can be done with:

make docker_test

The test only run examples 1, 2 and 3 from the examples folder.

The conda-nighres.yml specifies the version of the minimum dependencies.

If you want to freeze all your dependencies you can do so with conda env export > conda-nighres.yml.

Note that if you do this you will need to remove somes lines (for example that concerns nighres as it is a local pacakage.)

make clean_env_file

If you need to update the following packages, do it in the setup.py file:

Then run the following to update conda-nighres.yml

pip install .
conda env export > conda-nighres.yml
make clean_env_file

The following pacakages that are necessary for setting up the environment building nighres JAVA or for running examples can be updated directly.

This can be done with:

conda update -n nighres pip jcc Nilearn dipy gcc_linux-64 gxx_linux-64
pip install .
conda env export > conda-nighres.yml
make clean_env_file

The versions of the Java dependencies for nighres are in dependencies_sha.sh.

They contain the commit id (SHA1) from the cbstools and imcntk repo.

For example.

cbstools_sha=7a34255
imcntk_sha=ea901d8

Those values are then used by the build process (build.sh).

To update those to the latest commit on the master branch simply use make update_dep_shasum.