add docker compose file

[benmalef]

Fixes #875

Proposed Changes

• Add compose.yaml file. It is another way to manage and run commands in the docker.

You can check ref

you can run

docker compose up

to build and run your container

Checklist

• [ ] CONTRIBUTING guide has been followed.
• [ ] PR is based on the current GaNDLF master .
• [ ] Non-breaking change (does not break existing functionality): provide as many details as possible for any breaking change.
• [ ] Function/class source code documentation added/updated (ensure typing is used to provide type hints, including and not limited to using Optional if a variable has a pre-defined value).
• [ ] Code has been blacked for style consistency and linting.
• [ ] If applicable, version information has been updated in GANDLF/version.py.
• [ ] If adding a git submodule, add to list of exceptions for black styling in pyproject.toml file.
• [ ] Usage documentation has been updated, if appropriate.
• [ ] Tests added or modified to cover the changes; if coverage is reduced, please give explanation.
• [ ] If customized dependency installation is required (i.e., a separate pip install step is needed for PR to be functional), please ensure it is reflected in all the files that control the CI, namely: python-test.yml, and all docker files [1,2,3].
• [ ] The logging library is being used and no print statements are left.

[github-actions[bot]]

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[sarthakpati]

Looks good, but should we not be using this for all Docker builds?

[benmalef]

Looks good, but should we not be using this for all Docker builds?

It's the same with this, IMO but in an easier way. You can modify the compose.yaml. You can choose the dockerfile, the volume, the commands that you want to execute.

[sarthakpati]

Looks good, but should we not be using this for all Docker builds?

It's the same with this, IMO but in an easier way. You can modify the compose.yaml. You can choose the dockerfile, the volume, the commands that you want to execute.

Okay, then please provide clear examples of how this improves the existing docker workflow.

[benmalef]

I have created an example to demonstrate how to use it, but I have noticed that extra effort is required from the user to modify the compose.yaml file.

Using the docker command line

docker run -it --rm --name dataprep \
  --volume /home/researcher/gandlf_input:/input:ro \ # input data is mounted as read-only
  --volume /home/researcher/gandlf_output:/output \ # output data is mounted as read-write
  cbica/gandlf:latest-cpu \ # change to appropriate docker image tag
  construct-csv \ # standard construct CSV API starts
  --input-dir /input/data \
  --output-file /output/data.csv \
  --channels-id _t1.nii.gz \
  --label-id _seg.nii.gz

Using the docker compose file.

version: '1'

services:
  gandlf:
    build:
      context: .
      dockerfile: Dockerfile-CPU #choose the dockerfile
#    volumes: 
#     - /home/researcher/gandlf_input:/input:to
       - /home/researcher/gandlf_output:/output
    entrypoint: ["gandlf"]
    command: ["construct-csv",
"--input-dir ","/input/data",
"--output-file ","/output/data.csv",
" --channels-id"," _t1.nii.gz ",
" --label-id", "_seg.nii.gz" ] 

You can run docker compose up to run the container and execute the command.

[sarthakpati]

@hasan7n since you are far more familiar with docker than I am, what are you views on this?