🔖 v0.2.5 (#47)

.travis.yml

@@ -43,14 +43,15 @@ before_install:
 install:
   - source tests/travis_install.sh
   - pip install -r requirements.txt
+  - pip install -r requirements-dev.txt
   - pip install twine
-  - pip install .
+  - pip install -e .
 before_script:
   - git config --global user.email "[email protected]"
   - git config --global user.name "Travis"
   - singularity pull shub://FCP-INDI/C-PAC || singularity pull docker://fcpindi/c-pac:latest
 script:
-  - coverage run -m pytest
+  - coverage run --append -m pytest
   - coverage report -m
 after_success:
   - if [[ "$COVERAGE" == "true" ]]; then coveralls || echo "failed"; fi

CHANGELOG.rst

@@ -2,9 +2,15 @@
 Changelog
 =========
 `Version 0.2.5 <https://github.com/shnizzedy/cpac-python-package/releases/tag/v0.2.5>`_
-=======================================================================================
+========================================================================================
+* 📚 Update the main usage string to better articulate functionality
 * 📢🐳 Provide a clearer error message if package cannot connect to Docker.
 * 🐳 Fix a bug introduced in `v0.2.4 <https://github.com/shnizzedy/cpac-python-package/releases/tag/v0.2.4>` where some crashfiles would print for ``cpac --platform singularity crash`` but not for ``cpac --platform docker crash`` 
+* 🚑 Fix some installation issues: 
+   * All required packages are now installed with ``pip install cpac-py``
+   * Version is now set correctly
+* 🐳 Fix a bug introduced in `v0.2.4 <https://github.com/shnizzedy/cpac-python-package/releases/tag/v0.2.4>`_ where some crashfiles would print for ``cpac --platform singularity crash`` but not for ``cpac --platform docker crash`` 
+* 🔬 Set `coverage reports <http://coveralls.io/github/shnizzedy/cpac-python-package>`_ to report local paths
 
 `Version 0.2.4 <https://github.com/shnizzedy/cpac-python-package/releases/tag/v0.2.4>`_
 =======================================================================================

README.rst

@@ -1,6 +1,7 @@
-===============================================================
-C-PAC Python Package |github-version| |build-status| |coverage|
-===============================================================
+========================================================================
+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.
 
@@ -28,42 +29,72 @@ Usage
 .. code-block:: shell
 
     cpac --help
-    usage: cpac [-h] [--platform {docker,singularity}] [--image IMAGE] [--tag TAG]
-                [--version] [-v] [-vv] [--working_dir PATH] [--temp_dir PATH]
-                [--output_dir PATH] [-o OPT [OPT ...]]
-                [-B CUSTOM_BINDING [CUSTOM_BINDING ...]]
+    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. If no platform nor image is specified, cpac will try
-    Docker first, then try Singularity if Docker fails.
+    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
-      --platform {docker,singularity}
-      --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.
-      --tag TAG             tag of the Docker image to use (eg, "latest" or
-                            "nightly").
       --version             show program's version number and exit
-      -v, --verbose         set loglevel to INFO
-      -vv, --very-verbose   set loglevel to DEBUG
+      -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
-      --output_dir PATH     directory where output files should be stored
-      -o OPT [OPT ...], --container_option OPT [OPT ...]
-                            parameters and flags to pass through to Docker or
-                            Singularity
-      -B CUSTOM_BINDING [CUSTOM_BINDING ...], --custom_binding CUSTOM_BINDING [CUSTOM_BINDING ...]
-                            directory to bind to container with a different path
-                            than the real path in the format
-                            real_path:container_path (eg,
-                            /home/C-PAC/run5/outputs:/outputs). Use absolute paths
-                            for both paths
+      -v, --verbose         set loglevel to INFO
+      -vv, --very-verbose   set loglevel to DEBUG
 
 .. END USAGE
 
@@ -76,3 +107,7 @@ Usage
 .. |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
+

requirements-dev.txt

@@ -0,0 +1,5 @@
+coveralls
+pytest
+pytest-remotedata >= 0.3.2
+pytest-runner
+sphinx

requirements.txt

@@ -1,15 +1,10 @@
-coveralls
 docker >= 4.2.1
 docker-pycreds
 nipype
 pandas >= 0.23.4
-pytest
-pytest-remotedata>=0.3.2
-pytest-runner
 pyyaml
 setuptools
-sphinx
 spython >= 0.0.81
 tabulate >= 0.8.6
 tornado
-websocket-client
+websocket-client

setup.cfg

@@ -3,7 +3,7 @@
 # http://setuptools.readthedocs.io/en/latest/setuptools.html#configuring-setup-using-setup-cfg-files
 
 [metadata]
-name = cpac_py
+name = cpac
 description = C-PAC Python Package
 author = C-PAC developers
 author-email = [email protected]
@@ -41,6 +41,7 @@ install_requires =
     nipype
     pandas >= 0.23.4
     spython >= 0.0.81
+    pyyaml
     tabulate >= 0.8.6
     tornado
     websocket-client

src/cpac/__main__.py

@@ -33,30 +33,86 @@ def parse_args(args):
 
     parser = argparse.ArgumentParser(
         description='cpac: a Python package that simplifies using C-PAC '
-                    '<http://fcp-indi.github.io> containerized images. If no '
-                    'platform nor image is specified, cpac will try Docker '
-                    'first, then try Singularity if Docker fails.',
-        conflict_handler='resolve'
+                    '<http://fcp-indi.github.io> containerized images. \n\n'
+                    'This commandline interface package is designed to ' 'minimize repetition.\nAs such, nearly all arguments are '
+                    'optional.\n\nWhen launching a container, this package '
+                    'will try to bind any paths mentioned in \n • the command'
+                    '\n • the data configuration\n\nAn example minimal run '
+                    'command:\n\tcpac run /path/to/data /path/for/outputs'
+                    '\n\nAn example run command with optional arguments:\n\t'
+                    'cpac -B /path/to/data/configs:/configs \\\n\t\t'
+                    '--image fcpindi/c-pac --tag latest \\\n\t\t'
+                    'run /path/to/data /path/for/outputs \\\n\t\t'
+                    '--data_config_file /configs/data_config.yml \\\n\t\t'
+                    '--save_working_dir\n\n'
+                    'Each command can take "--help" to provide additonal '
+                    'usage information, e.g.,\n\n\tcpac run --help',
+        conflict_handler='resolve',
+        formatter_class=argparse.RawTextHelpFormatter
+    )
+
+    parser.add_argument(
+        '--version',
+        action='version',
+        version='cpac {ver}'.format(ver=__version__)
+    )
+
+    parser.add_argument(
+        '-o', '--container_option',
+        dest='container_option',
+        nargs='*',
+        help='parameters and flags to pass through to Docker or Singularity\n'
+             '\nThis flag can take multiple arguments so cannot '
+             'be\nthe final argument before the command argument (i.e.,\nrun '
+             'or any other command that does not start with - or --)\n',
+        metavar='OPT'
     )
 
-    parser.add_argument('--platform', choices=['docker', 'singularity'])
+    parser.add_argument(
+        '-B', '--custom_binding',
+        dest='custom_binding',
+        nargs='*',
+        help='directories to bind with a different path in\nthe container '
+             'than the real path of the directory.\nOne or more pairs in the ' 'format:\n\treal_path:container_path\n(eg, '
+             '/home/C-PAC/run5/outputs:/outputs).\nUse absolute paths for '
+             'both paths.\n\nThis flag can take multiple arguments so cannot '
+             'be\nthe final argument before the command argument (i.e.,\nrun '
+             'or any other command that does not start with - or --)\n'
+    )
+
+    parser.add_argument(
+        '--platform',
+        choices=['docker', 'singularity'],
+        help='If neither platform nor image is specified,\ncpac will try '
+        'Docker first, then try\nSingularity if Docker fails.'
+    )
 
     parser.add_argument(
         '--image',
         help='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.'
+             '"fcpindi/c-pac").\nWill attempt to pull from Singularity Hub or '
+             'Docker Hub if not provided.\nIf image is specified but platform '
+             'is not, platform is\nassumed to be Singularity if image is a '
+             'path or \nDocker if image is an image name.'
     )
 
     parser.add_argument(
         '--tag',
-        help='tag of the Docker image to use (eg, "latest" or "nightly"). '
+        help='tag of the Docker image to use (eg, "latest" or "nightly").'
     )
 
     parser.add_argument(
-        '--version',
-        action='version',
-        version='cpac {ver}'.format(ver=__version__)
+        '--working_dir',
+        default=cwd,
+        help='working directory',
+        metavar='PATH'
+    )
+
+    parser.add_argument(
+        '--temp_dir',
+        default='/tmp',
+        help='directory for temporary files',
+        metavar='PATH'
     )
 
     parser.add_argument(
@@ -77,45 +133,6 @@ def parse_args(args):
         const=logging.DEBUG
     )
 
-    parser.add_argument(
-        '--working_dir',
-        default=cwd,
-        help="working directory",
-        metavar="PATH"
-    )
-
-    parser.add_argument(
-        '--temp_dir',
-        default='/tmp',
-        help="directory for temporary files",
-        metavar="PATH"
-    )
-
-    parser.add_argument(
-        '--output_dir',
-        default=os.path.join(cwd, 'outputs'),
-        help="directory where output files should be stored",
-        metavar="PATH"
-    )
-
-    parser.add_argument(
-        '-o', '--container_option',
-        dest='container_option',
-        nargs='+',
-        help="parameters and flags to pass through to Docker or Singularity",
-        metavar="OPT"
-    )
-
-    parser.add_argument(
-        '-B', '--custom_binding',
-        dest="custom_binding",
-        nargs="+",
-        help="directory to bind to container with a different path than the "
-             "real path in the format real_path:container_path (eg, "
-             "/home/C-PAC/run5/outputs:/outputs). Use absolute paths for both "
-             "paths"
-    )
-
     subparsers = parser.add_subparsers(dest='command')
 
     run_parser = subparsers.add_parser(