From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: Add setup.py
Forwarded: https://github.com/WorkflowConversion/CTDConverter/pull/40
Index: ctdconverter/convert.py
===================================================================
--- ctdconverter.orig/convert.py
+++ ctdconverter/convert.py
@@ -8,7 +8,7 @@ from argparse import RawDescriptionHelpF
 from common.exceptions import ApplicationException, ModelError
 
 __all__ = []
-__version__ = 2.0
+__version__ = '2.0'
 __date__ = '2014-09-17'
 __updated__ = '2017-08-09'
 
@@ -269,4 +269,4 @@ def validate_and_prepare_common_argument
 
 
 if __name__ == "__main__":
-    sys.exit(main())
\ No newline at end of file
+    sys.exit(main())
Index: ctdconverter/setup.py
===================================================================
--- /dev/null
+++ ctdconverter/setup.py
@@ -0,0 +1,170 @@
+"""A setuptools based setup module.
+
+See:
+https://packaging.python.org/en/latest/distributing.html
+https://github.com/pypa/sampleproject
+"""
+
+# Always prefer setuptools over distutils
+from setuptools import setup, find_packages
+# To use a consistent encoding
+from codecs import open
+from os import path
+import re
+
+here = path.abspath(path.dirname(__file__))
+
+# Get the long description from the README file
+with open(path.join(here, 'README.md'), encoding='utf-8') as f:
+    long_description = f.read()
+
+def read(*parts):
+    with open(path.join(here, *parts), 'r') as fp:
+        return fp.read()
+
+def find_version(*file_paths):
+    version_file = read(*file_paths)
+    version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
+                              version_file, re.M)
+    if version_match:
+        return version_match.group(1)
+    raise RuntimeError("Unable to find version string.")
+
+# Arguments marked as "Required" below must be included for upload to PyPI.
+# Fields marked as "Optional" may be commented out.
+
+setup(
+    # This is the name of your project. The first time you publish this
+    # package, this name will be registered for you. It will determine how
+    # users can install this project, e.g.:
+    #
+    # $ pip install sampleproject
+    #
+    # And where it will live on PyPI: https://pypi.org/project/sampleproject/
+    name='ctdconverter',  # Required
+
+    # Versions should comply with PEP 440:
+    # https://www.python.org/dev/peps/pep-0440/
+    #
+    # For a discussion on single-sourcing the version across setup.py and the
+    # project code, see
+    # https://packaging.python.org/en/latest/single_source_version.html
+    version=find_version("convert.py"),  # Required
+
+    # This is a one-line description or tagline of what your project does. This
+    # corresponds to the "Summary" metadata field:
+    # https://packaging.python.org/specifications/core-metadata/#summary
+    description='Convert CTD files into Galaxy tool and CWL CommandLineTool files',  # Required
+
+    # This is an optional longer description of your project that represents
+    # the body of text which users will see when they visit PyPI.
+    #
+    # Often, this is the same as your README, so you can just read it in from
+    # that file directly (as we have already done above)
+    #
+    # This field corresponds to the "Description" metadata field:
+    # https://packaging.python.org/specifications/core-metadata/#description-optional
+    long_description=long_description,  # Optional
+
+    # This should be a valid link to your project's main homepage.
+    #
+    # This field corresponds to the "Home-Page" metadata field:
+    # https://packaging.python.org/specifications/core-metadata/#home-page-optional
+    url='https://github.com/WorkflowConversion/CTDConverter',  # Optional
+
+    # This should be your name or the name of the organization which owns the
+    # project.
+    author='The WorkflowConversion team',  # Optional
+
+    # This should be a valid email address corresponding to the author listed
+    # above.
+    # author_email='authors@example.com',  # Optional
+
+    # Classifiers help users find your project by categorizing it.
+    #
+    # For a list of valid classifiers, see
+    # https://pypi.python.org/pypi?%3Aaction=list_classifiers
+    classifiers=[  # Optional
+        # How mature is this project? Common values are
+        #   3 - Alpha
+        #   4 - Beta
+        #   5 - Production/Stable
+        'Development Status :: 3 - Alpha',
+
+        # Indicate who your project is intended for
+        'Intended Audience :: Developers',
+        'Topic :: Software Development :: Build Tools',
+
+        'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
+        'License :: OSI Approved :: Apache Software License',
+
+        # Specify the Python versions you support here. In particular, ensure
+        # that you indicate whether you support Python 2, Python 3 or both.
+        'Programming Language :: Python :: 2',
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+    ],
+
+    # This field adds keywords for your project which will appear on the
+    # project page. What does your project relate to?
+    #
+    # Note that this is a string of words separated by whitespace, not a list.
+    keywords='CTD CWL CommonWL Galaxy Workflows WorkflowConversion',  # Optional
+
+    # You can just specify package directories manually here if your project is
+    # simple. Or you can use find_packages().
+    #
+    # Alternatively, if you just want to distribute a single Python file, use
+    # the `py_modules` argument instead as follows, which will expect a file
+    # called `my_module.py` to exist:
+    #
+    py_modules=["convert"],
+    #
+    packages=find_packages(exclude=['contrib', 'docs', 'tests']),  # Required
+
+    # This field lists other packages that your project depends on to run.
+    # Any package you put here will be installed by pip when your project is
+    # installed, so they must be valid existing projects.
+    #
+    # For an analysis of "install_requires" vs pip's requirements files see:
+    # https://packaging.python.org/en/latest/requirements.html
+    install_requires=['lxml', 'ruamel.yaml', 'ctdopts', 'pkg_resources'],
+
+    # List additional groups of dependencies here (e.g. development
+    # dependencies). Users will be able to install these using the "extras"
+    # syntax, for example:
+    #
+    #   $ pip install sampleproject[dev]
+    #
+    # Similar to `install_requires` above, these must be valid existing
+    # projects.
+    # extras_require={  # Optional
+    #     'dev': ['check-manifest'],
+    #     'test': ['coverage'],
+    # },
+
+    # If there are data files included in your packages that need to be
+    # installed, specify them here.
+    #
+    # If using Python 2.6 or earlier, then these have to be included in
+    # MANIFEST.in as well.
+    package_data={  # Optional
+        'ctdconverter': ['galaxy/macros.xml'],
+    },
+
+    # To provide executable scripts, use entry points in preference to the
+    # "scripts" keyword. Entry points provide cross-platform support and allow
+    # `pip` to create the appropriate form of executable for the target
+    # platform.
+    #
+    # For example, the following would provide a command called `sample` which
+    # executes the function `main` from this package when invoked:
+    entry_points={  # Optional
+        'console_scripts': [
+            'CTDConverter=convert:main',
+        ],
+    },
+)