Developer Environment

This document explains how to prepare a new development environment and update an existing environment, as necessary, for the development of NiPreps' components. Some components may deviate from these guidelines, in such a case, please follow the guidelines provided in their documentation.

If you plan to contribute back to the community, making your code available via pull-request, please make sure to have read and understood the Community Documents and Contributor Guidelines. If you plan to distribute derived code, please follow our licensing guidelines.

Development in Docker is encouraged, for the sake of consistency and portability. By default, work should be built off of nipreps/fmriprep:unstable, which tracks the master branch, or nipreps/fmriprep:latest, which tracks the latest release version (see BIDS-Apps execution guide for the basic procedure for running).

It will be assumed the developer has a working repository in $HOME/projects/fmriprep, and examples are also given for niworkflows and NiPype.

Patching a working copy into a Docker container¶

In order to test new code without rebuilding the Docker image, it is possible to mount working repositories as source directories within the container. The Docker wrapper script simplifies this for the most common repositories:

    -f PATH, --patch-fmriprep PATH
                          working fmriprep repository (default: None)
    -n PATH, --patch-niworkflows PATH
                          working niworkflows repository (default: None)
    -p PATH, --patch-nipype PATH
                          working nipype repository (default: None)

For instance, if your repositories are contained in $HOME/projects:

$ fmriprep-docker -f $HOME/projects/fmriprep/fmriprep \
                  -n $HOME/projects/niworkflows/niworkflows \
                  -p $HOME/projects/nipype/nipype \
                  -i nipreps/fmriprep:latest \
                  $HOME/fullds005 $HOME/dockerout participant

Note the -i flag allows you to specify an image.

When invoking docker directly, the mount options must be specified with the -v flag:

-v $HOME/projects/fmriprep/fmriprep:/usr/local/miniconda/lib/python3.7/site-packages/fmriprep:ro
-v $HOME/projects/niworkflows/niworkflows:/usr/local/miniconda/lib/python3.7/site-packages/niworkflows:ro
-v $HOME/projects/nipype/nipype:/usr/local/miniconda/lib/python3.7/site-packages/nipype:ro

For example,

$ docker run --rm -v $HOME/ds005:/data:ro -v $HOME/dockerout:/out \
    -v $HOME/projects/fmriprep/fmriprep:/usr/local/miniconda/lib/python3.7/site-packages/fmriprep:ro \
    nipreps/fmriprep:latest /data /out/out participant \
    -w /out/work/

In order to work directly in the container, pass the --shell flag to fmriprep-docker

$ fmriprep-docker --shell $HOME/ds005 $HOME/dockerout participant

This is the equivalent of using --entrypoint=bash and omitting the fMRIPrep arguments in a docker command:

$ docker run --rm -v $HOME/ds005:/data:ro -v $HOME/dockerout:/out \
    -v $HOME/projects/fmriprep/fmriprep:/usr/local/miniconda/lib/python3.7/site-packages/fmriprep:ro --entrypoint=bash \
    nipreps/fmriprep:latest

Patching containers can be achieved in Singularity analogous to docker using the --bind (-B) option:

$ singularity run \
    -B $HOME/projects/fmriprep/fmriprep:/usr/local/miniconda/lib/python3.7/site-packages/fmriprep \
    fmriprep.img \
    /scratch/dataset /scratch/out participant -w /out/work/

Adding dependencies¶

New dependencies to be inserted into the Docker image will either be Python or non-Python dependencies. Python dependencies may be added in three places, depending on whether the package is large or non-release versions are required. The image must be rebuilt after any dependency changes.

Python dependencies should generally be included in the appropriate dependency metadata of the setup.cfg file found at the root of each repository. If some the dependency must be a particular version (or set thereof), it is possible to use version filters in this setup.cfg file.

For large Python dependencies where there will be a benefit to pre-compiled binaries, conda packages may also be added to the conda install line in the Dockerfile.

Non-Python dependencies must also be installed in the Dockerfile, via a RUN command. For example, installing an apt package may be done as follows:

RUN apt-get update && \
    apt-get install -y <PACKAGE>

(Re)Building Docker image¶

If it is necessary to (re)build the Docker image, a local image named fmriprep may be built from within the local repository. Let's assume it is located in ~/projects/fmriprep:

~/projects/fmriprep$ VERSION=$( python get_version.py )
~/projects/fmriprep$ docker build -t fmriprep --build-arg VERSION=$VERSION .

The VERSION build argument is necessary to ensure that help text can be reliably generated. The get_version.py tool constructs the version string from the current repository state.

To work in this image, replace nipreps/fmriprep:latest with just fmriprep in any of the above commands. This image may be accessed by the Docker wrapper via the -i flag, e.g.:

$ fmriprep-docker -i fmriprep --shell

Code-Server Development Environment (Experimental)¶

To get the best of working with containers and having an interactive development environment, we have an experimental setup with code-server.

Important

We have a video walking through the process if you want a visual guide.

1. Build the Docker image. We will use the Dockerfile_devel file to build our development docker image:

$ cd $HOME/projects/fmriprep
$ docker build -t fmriprep_devel -f Dockerfile_devel .

2. Run the Docker image We can start a docker container using the image we built (fmriprep_devel):

$ docker run -it -p 127.0.0.1:8445:8080 -v ${PWD}:/src/fmriprep fmriprep_devel:latest

Windows Users

If you are using windows shell, ${PWD} may not be defined, instead use the absolute path to your repository.

Docker-Toolbox

If you are using Docker-Toolbox, you will need to change your virtualbox settings using these steps as a guide. For step 6, instead of Name = rstudio; Host Port = 8787; Guest Port = 8787, have Name = code-server; Host Port = 8443; Guest Port = 8080. Then in the docker command above, change 127.0.0.1:8445:8080 to 192.168.99.100:8445:8080.

If the container started correctly, you should see the following on your console:

INFO  Server listening on http://localhost:8080
INFO    - No authentication
INFO    - Not serving HTTPS

Now you can switch to your favorite browser and go to: 127.0.0.1:8445 (or 192.168.99.100:8445 for Docker Toolbox).

3. Copy fmriprep.egg-info into your fmriprep/ project directory fmriprep.egg-info makes the package executable inside the docker container. Open a terminal in vscode and type the following:

$ cp -R /src/fmriprep.egg-info /src/fmriprep/

Code-Server Development Environment Features¶

The editor is vscode
There are several preconfigured debugging tests under the debugging icon in the activity bar
see vscode debugging python for details.
The gitlens and python extensions are preinstalled to improve the development experience in vscode.