C-PAC Python Package

A Python package that wraps C-PAC, enabling users to install cpac with pip and run from the command line.

Description

cpac Python Package is a lightweight Python package that handles interfacing a user's machine and a C-PAC container through a command line interface.

Dependencies

• Python ≥ 3.10
• pip
• At least one of:
  • Docker
  • Apptainer ≥ 1.0
  • Singularity ≥ 3.0[1]

Usage

cpac --help
usage: cpac [-h] [--version] [-o OPT] [-B CUSTOM_BINDING]
            [--platform {docker,singularity,apptainer}] [--image IMAGE]
            [--tag TAG] [--working_dir PATH] [-v] [-vv]
            {run,utils,version,group,gradients,tsconcat,pull,upgrade,enter,bash,shell,parse-resources,parse_resources,crash}
            ...

cpac: a Python package that simplifies using C-PAC  containerized images. 

This commandline interface package is designed to minimize repetition.
As such, nearly all arguments are optional.

When launching a container, this package will try to bind any paths mentioned in 
 • the command
 • the data configuration

An example minimal run command:
    cpac run /path/to/data /path/for/outputs

An example run command with optional arguments:
    cpac -B /path/to/data/configs:/configs \
        --image fcpindi/c-pac --tag latest \
        run /path/to/data /path/for/outputs \
        --data_config_file /configs/data_config.yml \
        --save_working_dir

Each command can take "--help" to provide additonal usage information, e.g.,

    cpac run --help

Known issues:
- Some Docker containers unexpectedly persist after cpac finishes. To clear them, run
    1. `docker ps` to list the containers
  For each C-PAC conatainer that persists, run
    2. `docker attach `
    3. `exit`
- https://github.com/FCP-INDI/cpac/issues

positional arguments:
  {run,utils,version,group,gradients,tsconcat,pull,upgrade,enter,bash,shell,parse-resources,parse_resources,crash}
    run                 Run C-PAC. See
                        "cpac [--platform {docker,apptainer,singularity}] [--image IMAGE] [--tag TAG] run --help"
                        for more information.
    utils               Run C-PAC commandline utilities. See
                        "cpac [--platform {docker,apptainer,singularity}] [--image IMAGE] [--tag TAG] utils --help"
                        for more information.
    version             Print the version of C-PAC that cpac is using.
    group               Run a group level analysis in C-PAC. See
                        "cpac [--platform {docker,apptainer,singularity}] [--image IMAGE] [--tag TAG] group --help"
                        for more information.
    gradients           Run ba_timeseries_gradients. See
                        "cpac [--platform "{docker,singularity}] gradients --help" 
                        for more information.
    tsconcat            Run ba-tsconcat (<0.2.0,>=0.1.2)
    pull (upgrade)      Upgrade your local C-PAC version to the latest version
                        by pulling from Docker Hub or other repository.
                        Use with "--image" and/or "--tag" to specify an image
                        other than the default "fcpindi/c-pac:latest" to pull.
    enter (bash, shell)
                        Enter a new C-PAC container via BASH.
    parse-resources (parse_resources)
                        .

                        When provided with a `callback.log` file, this utility can sort through
                        the memory `runtime` usage, `estimate`, and associated `efficiency`, to
                        identify the `n` tasks with the `highest` or `lowest` of each of these
                        categories.
                        "parse-resources" is intended to be run outside a C-PAC container.
                        See "cpac parse-resources --help" for more information.
    crash               Convert a crash pickle to plain text (C-PAC < 1.8.0).

options:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  -o OPT, --container_option OPT, --container_options OPT
                        parameters and flags to pass through to Docker or Singularity

                        This flag can take multiple arguments so cannot be
                        the final argument before the command argument (i.e.,
                        run or any other command that does not start with - or --)
  -B CUSTOM_BINDING, --custom_binding CUSTOM_BINDING
                        directories to bind with a different path in
                        the container than the real path of the directory.
                        One or more pairs in the format:
                            real_path:container_path
                        (eg, /home/C-PAC/run5/outputs:/outputs).
                        Use absolute paths for both paths.

                        This flag can take multiple arguments so cannot be
                        the final argument before the command argument (i.e.,
                        run or any other command that does not start with - or --)
  --platform {docker,singularity,apptainer}
                        If neither platform nor image is specified,
                        cpac will try Docker first, then try
                        Apptainer/Singularity if Docker fails.
  --image IMAGE         path to Apptainer/Singularity image file OR name of Docker image (eg, "fcpindi/c-pac").
                        Will attempt to pull from Singularity Hub or Docker Hub if not provided.
                        If image is specified but platform is not, platform is
                        assumed to be Apptainer/Singularity if image is a path or 
                        Docker if image is an image name.
  --tag TAG             tag of the Docker image to use (eg, "latest" or "nightly").
  --working_dir PATH    working directory
  -v, --verbose         set loglevel to INFO
  -vv, --very-verbose   set loglevel to DEBUG

[1] cpac may work with older versions of Singularity, but Singularity Python dropped support for Singularity < 3.0 in version 0.3.0. If you're running an older version of Singularity, you can try maually downgrading Singularity Python (pip install "spython<0.3.0") or try running C-PAC in Singuliarty without this commandline wrapper