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From: Michael R. Crusoe <michael.crusoe@gmail.com>
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Subject: Add setup.py
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Forwarded: https://github.com/WorkflowConversion/CTDConverter/pull/40
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--- ctdconverter.orig/common/utils.py
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+++ ctdconverter/common/utils.py
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@@ -7,7 +7,7 @@
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from string import strip
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from logger import info, error, warning
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-from common.exceptions import ApplicationException
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+from .exceptions import ApplicationException
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from CTDopts.CTDopts import CTDModel, ParameterGroup
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--- ctdconverter.orig/convert.py
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+++ ctdconverter/convert.py
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@@ -8,7 +8,7 @@
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from common.exceptions import ApplicationException, ModelError
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@@ -1,14 +1,14 @@
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import os
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import sys
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import traceback
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-import common.utils as utils
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+import .common.utils as utils
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from argparse import ArgumentParser
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from argparse import RawDescriptionHelpFormatter
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-from common.exceptions import ApplicationException, ModelError
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+from . import common.exceptions as exceptions
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__all__ = []
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-__version__ = 2.0
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__date__ = '2014-09-17'
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__updated__ = '2017-08-09'
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@@ -222,13 +222,13 @@
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print("Interrupted...")
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return 0
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- except ApplicationException, e:
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+ except exceptions.ApplicationException, e:
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traceback.print_exc()
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utils.error("CTDConverter could not complete the requested operation.", 0)
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utils.error("Reason: " + e.msg, 0)
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return 1
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- except ModelError, e:
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+ except exceptions.ModelError, e:
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traceback.print_exc()
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utils.error("There seems to be a problem with one of your input CTDs.", 0)
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utils.error("Reason: " + e.msg, 0)
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@@ -250,13 +250,13 @@
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# if input is a single file, we expect output to be a file (and not a dir that already exists)
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if len(args.input_files) == 1:
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if os.path.isdir(args.output_destination):
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- raise ApplicationException("If a single input file is provided, output (%s) is expected to be a file "
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+ raise exceptions.ApplicationException("If a single input file is provided, output (%s) is expected to be a file "
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"and not a folder.\n" % args.output_destination)
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# if input is a list of files, we expect output to be a folder
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if len(args.input_files) > 1:
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if not os.path.isdir(args.output_destination):
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- raise ApplicationException("If several input files are provided, output (%s) is expected to be an "
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+ raise exceptions.ApplicationException("If several input files are provided, output (%s) is expected to be an "
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"existing directory.\n" % args.output_destination)
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# check that the provided input files, if provided, contain a valid file path
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@@ -269,4 +269,4 @@
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- sys.exit(main())
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\ No newline at end of file
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+ sys.exit(main())
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--- ctdconverter.orig/cwl/converter.py
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+++ ctdconverter/cwl/converter.py
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@@ -12,7 +12,7 @@
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import ruamel.yaml as yaml
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from CTDopts.CTDopts import _InFile, _OutFile, ParameterGroup, _Choices, _NumericRange, _FileFormat, ModelError, _Null
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-from common import utils, logger
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+from ..common import utils, logger
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# all cwl-related properties are defined here
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--- ctdconverter.orig/galaxy/converter.py
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+++ ctdconverter/galaxy/converter.py
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@@ -8,8 +8,8 @@
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from lxml import etree
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from lxml.etree import SubElement, Element, ElementTree, ParseError, parse
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-from common import utils, logger
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-from common.exceptions import ApplicationException, InvalidModelException
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+from ..common import utils, logger
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+from ..common.exceptions import ApplicationException, InvalidModelException
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from CTDopts.CTDopts import _InFile, _OutFile, ParameterGroup, _Choices, _NumericRange, _FileFormat, ModelError, _Null
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--- /dev/null
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+++ ctdconverter/__main__.py
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@@ -0,0 +1,6 @@
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+from __future__ import absolute_import
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+import sys
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+
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+from . import convert
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+
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+sys.exit(convert.main())
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--- /dev/null
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+++ ctdconverter/setup.py
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@@ -0,0 +1,170 @@
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@@ -0,0 +1,167 @@
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+"""A setuptools based setup module.
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+
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+See:
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+ # This is a one-line description or tagline of what your project does. This
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+ # corresponds to the "Summary" metadata field:
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+ # https://packaging.python.org/specifications/core-metadata/#summary
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+ description='Convert CTD files into Galaxy tool and CWL CommandLineTool files', # Required
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+ description='Convert CTD files into Galaxy tool and CWL CommandLineTool '
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+ 'files', # Required
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+
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+ # This is an optional longer description of your project that represents
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+ # the body of text which users will see when they visit PyPI.
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+ #
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+ # This field corresponds to the "Description" metadata field:
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+ # https://packaging.python.org/specifications/core-metadata/#description-optional
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+ long_description=long_description, # Optional
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+ long_description=long_description,
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+
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+ # This should be a valid link to your project's main homepage.
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+ #
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+ # This field corresponds to the "Home-Page" metadata field:
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+ # https://packaging.python.org/specifications/core-metadata/#home-page-optional
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+ url='https://github.com/WorkflowConversion/CTDConverter', # Optional
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+ url='https://github.com/WorkflowConversion/CTDConverter',
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+
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+ # This should be your name or the name of the organization which owns the
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+ # project.
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+ author='The WorkflowConversion team', # Optional
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+ author='The WorkflowConversion team',
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+
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+ # This should be a valid email address corresponding to the author listed
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+ # above.
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+ #
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+ # For a list of valid classifiers, see
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+ # https://pypi.python.org/pypi?%3Aaction=list_classifiers
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+ classifiers=[ # Optional
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+ classifiers=[
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+ # How mature is this project? Common values are
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+ # 3 - Alpha
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+ # 4 - Beta
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+ # Note that this is a string of words separated by whitespace, not a list.
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+ keywords='CTD CWL CommonWL Galaxy Workflows WorkflowConversion', # Optional
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+
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+ # You can just specify package directories manually here if your project is
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+ # simple. Or you can use find_packages().
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+ #
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+ # Alternatively, if you just want to distribute a single Python file, use
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+ # the `py_modules` argument instead as follows, which will expect a file
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+ # called `my_module.py` to exist:
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+ #
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+ py_modules=["convert"],
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+ #
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+ packages=find_packages(exclude=['contrib', 'docs', 'tests']), # Required
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+ packages=['ctdconverter', 'ctdconverter.common', 'ctdconverter.galaxy',
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+ 'ctdconverter.cwl'], # Required
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+ package_dir={ 'ctdconverter': '.',
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+ 'ctdconverter.common': 'common',
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+ 'ctdconverter.galaxy': 'galaxy',
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+ 'ctdconverter.cwl': 'cwl'},
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+
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+ # This field lists other packages that your project depends on to run.
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+ # Any package you put here will be installed by pip when your project is
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+ #
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+ # If using Python 2.6 or earlier, then these have to be included in
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+ # MANIFEST.in as well.
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+ package_data={ # Optional
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+ package_data={
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+ 'ctdconverter': ['galaxy/macros.xml'],
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+ },
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+
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+ # executes the function `main` from this package when invoked:
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+ entry_points={ # Optional
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+ 'console_scripts': [
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+ 'CTDConverter=convert:main',
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+ 'CTDConverter=ctdconverter',
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+ ],
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+ },
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+)
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