A Python package that wraps C-PAC, enabling users to install cpac with pip and run from the command line.
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.
Note about cpac versioning
This package's versioning scheme changed in version 1.8.5 to match C-PAC's versioning. From cpac v1.8.5 forward, the version of cpac indicates the newest supported version of C-PAC.
| [*] | 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 |
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 <http://fcp-indi.github.io> 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 <container_name>`
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