Metadata-Version: 2.1
Name: cpac
Version: 0.2.5
Summary: C-PAC Python Package
Home-page: https://github.com/FCP-INDI/cpac-python-package
Author: C-PAC developers
Author-email: cpac@cnl.childmind.org
License: mit
Description: ========================================================================
        C-PAC Python Package |build-status| |github-version| |upload| |coverage|
        ========================================================================
        
        
        A Python package that wraps `C-PAC <http://fcp-indi.github.io>`_, enabling users to install cpac with `pip <https://pip.pypa.io>`_ and run from the command line.
        
        
        Description
        ===========
        
        C-PAC 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 <https://www.python.org>`_ ≥3.6
        * `pip <https://pip.pypa.io>`_
        * At least one of:
        
          * `Docker <https://www.docker.com>`_
          * `Singularity <https://sylabs.io/singularity>`_ ≥2.5&≤3.0
        
        Usage
        =====
        
        .. BEGIN USAGE
        
        .. code-block:: shell
        
            cpac --help
            usage: cpac [-h] [--version] [-o [OPT [OPT ...]]]
                        [-B [CUSTOM_BINDING [CUSTOM_BINDING ...]]]
                        [--platform {docker,singularity}] [--image IMAGE] [--tag TAG]
                        [--working_dir PATH] [--temp_dir PATH] [-v] [-vv]
                        {run,group,utils,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
            
            positional arguments:
              {run,group,utils,crash}
            
            optional arguments:
              -h, --help            show this help message and exit
              --version             show program's version number and exit
              -o [OPT [OPT ...]], --container_option [OPT [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 [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}
                                    If neither platform nor image is specified,
                                    cpac will try Docker first, then try
                                    Singularity if Docker fails.
              --image IMAGE         path to 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 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
              --temp_dir PATH       directory for temporary files
              -v, --verbose         set loglevel to INFO
              -vv, --very-verbose   set loglevel to DEBUG
        
        .. END USAGE
        
        .. |github-version| image:: https://img.shields.io/github/tag/shnizzedy/cpac-python-package.svg
            :target: https://github.com/shnizzedy/cpac-python-package/releases
            :alt: GitHub version
        .. |build-status| image:: https://travis-ci.org/shnizzedy/cpac-python-package.svg?branch=trunk
            :target: https://travis-ci.org/shnizzedy/cpac-python-package
            :alt: Travis CI build status
        .. |coverage| image:: https://coveralls.io/repos/github/shnizzedy/cpac-python-package/badge.svg?branch=trunk
            :target: https://coveralls.io/github/shnizzedy/cpac-python-package?branch=trunk
            :alt: coverage badge
        .. |upload| image:: https://github.com/shnizzedy/cpac-python-package/workflows/Upload%20Python%20Package/badge.svg
            :target: https://pypi.org/project/cpac-py/
            :alt: upload Python package
        
        
Platform: any
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/x-rst
Provides-Extra: testing
