--- a/env/lib/python3.7/site-packages/planemo/cli.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,332 +0,0 @@
-"""The module describes a CLI framework extending ``click``."""
-import functools
-import logging.config
-import os
-import shutil
-import sys
-import traceback
-
-import click
-from six.moves.urllib.request import urlopen
-
-from planemo import __version__
-from planemo.exit_codes import ExitCodeException
-from planemo.galaxy import profiles
-from .config import (
-    OptionSource,
-    read_global_config,
-)
-from .io import error
-
-
-CONTEXT_SETTINGS = dict(auto_envvar_prefix='PLANEMO')
-COMMAND_ALIASES = {
-    "l": "lint",
-    "o": "open",
-    "t": "test",
-    "s": "serve",
-}
-
-
-class Context(object):
-    """Describe context of Planemo computation.
-
-    Handles cross cutting concerns for Planemo such as verbose log
-    tracking, the definition of the Planemo workspace (``~/.planemo``),
-    and the global configuraton defined in ``~/.planemo.yml``.
-    """
-
-    def __init__(self):
-        """Construct a Context object using execution environment."""
-        self.home = os.getcwd()
-        self._global_config = None
-        # Will be set by planemo CLI driver
-        self.verbose = False
-        self.planemo_config = None
-        self.planemo_directory = None
-        self.option_source = {}
-
-    def set_option_source(self, param_name, option_source, force=False):
-        """Specify how an option was set."""
-        if not force:
-            assert param_name not in self.option_source, "No option source for [%s]" % param_name
-        self.option_source[param_name] = option_source
-
-    def get_option_source(self, param_name):
-        """Return OptionSource value indicating how the option was set."""
-        assert param_name in self.option_source, "No option source for [%s]" % param_name
-        return self.option_source[param_name]
-
-    @property
-    def global_config(self):
-        """Read Planemo's global configuration.
-
-        As defined most simply by ~/.planemo.yml.
-        """
-        if self._global_config is None:
-            self._global_config = read_global_config(self.planemo_config)
-        return self._global_config or {}
-
-    def log(self, msg, *args):
-        """Log a message to stderr."""
-        if args:
-            msg %= args
-        click.echo(msg, file=sys.stderr)
-
-    def vlog(self, msg, *args, **kwds):
-        """Log a message to stderr only if verbose is enabled."""
-        if self.verbose:
-            self.log(msg, *args)
-            if kwds.get("exception", False):
-                traceback.print_exc(file=sys.stderr)
-
-    @property
-    def workspace(self):
-        """Create and return Planemo's workspace.
-
-        By default this will be ``~/.planemo``.
-        """
-        if not self.planemo_directory:
-            raise Exception("No planemo workspace defined.")
-        workspace = self.planemo_directory
-        return self._ensure_directory(workspace, "workspace")
-
-    @property
-    def galaxy_profiles_directory(self):
-        """Create a return a directory for storing Galaxy profiles."""
-        path = os.path.join(self.workspace, "profiles")
-        return self._ensure_directory(path, "Galaxy profiles")
-
-    def _ensure_directory(self, path, name):
-        if not os.path.exists(path):
-            os.makedirs(path)
-        if not os.path.isdir(path):
-            template = "Planemo %s directory [%s] unavailable."
-            message = template % (name, path)
-            raise Exception(message)
-        return path
-
-    def exit(self, exit_code):
-        """Exit planemo with the supplied exit code."""
-        self.vlog("Exiting planemo with exit code [%d]" % exit_code)
-        raise ExitCodeException(exit_code)
-
-    def cache_download(self, url, destination):
-        cache = os.path.join(self.workspace, "cache")
-        if not os.path.exists(cache):
-            os.makedirs(cache)
-        filename = os.path.basename(url)
-        cache_destination = os.path.join(cache, filename)
-        if not os.path.exists(cache_destination):
-            with urlopen(url) as fh:
-                content = fh.read()
-            if len(content) == 0:
-                raise Exception("Failed to download [%s]." % url)
-            with open(cache_destination, "wb") as f:
-                f.write(content)
-
-        shutil.copy(cache_destination, destination)
-
-
-pass_context = click.make_pass_decorator(Context, ensure=True)
-cmd_folder = os.path.abspath(os.path.join(os.path.dirname(__file__),
-                                          'commands'))
-
-
-def list_cmds():
-    """List planemo commands from commands folder."""
-    rv = []
-    for filename in os.listdir(cmd_folder):
-        if filename.endswith('.py') and \
-           filename.startswith('cmd_'):
-            rv.append(filename[len("cmd_"):-len(".py")])
-    rv.sort()
-    return rv
-
-
-def name_to_command(name):
-    """Convert a subcommand name to the cli function for that command.
-
-    Command <X> is defined by the method 'planemo.commands.cmd_<x>:cli',
-    this method uses `__import__` to load and return that method.
-    """
-    try:
-        if sys.version_info[0] == 2:
-            name = name.encode('ascii', 'replace')
-        mod_name = 'planemo.commands.cmd_' + name
-        mod = __import__(mod_name, None, None, ['cli'])
-    except ImportError as e:
-        error("Problem loading command %s, exception %s" % (name, e))
-        return
-    return mod.cli
-
-
-class PlanemoCLI(click.MultiCommand):
-
-    def list_commands(self, ctx):
-        return list_cmds()
-
-    def get_command(self, ctx, name):
-        if name in COMMAND_ALIASES:
-            name = COMMAND_ALIASES[name]
-        return name_to_command(name)
-
-
-def command_function(f):
-    """Extension point for processing kwds after click callbacks."""
-    @functools.wraps(f)
-    def handle_blended_options(*args, **kwds):
-        profile = kwds.get("profile", None)
-        if profile:
-            ctx = args[0]
-            profile_defaults = profiles.ensure_profile(
-                ctx, profile, **kwds
-            )
-            _setup_profile_options(ctx, profile_defaults, kwds)
-
-        _setup_galaxy_source_options(args[0], kwds)
-
-        try:
-            return f(*args, **kwds)
-        except ExitCodeException as e:
-            sys.exit(e.exit_code)
-
-    return pass_context(handle_blended_options)
-
-
-EXCLUSIVE_OPTIONS_LIST = [
-]
-
-
-def _setup_galaxy_source_options(ctx, kwds):
-    for exclusive_options in EXCLUSIVE_OPTIONS_LIST:
-        option_source = {}
-        for option in exclusive_options:
-            if option in kwds:
-                option_source[option] = ctx.get_option_source(option)
-            else:
-                option_source[option] = None
-
-        most_authoratative_source = None
-        most_authoratative_source_options = []
-        for key, value in option_source.items():
-            if value is None:
-                continue
-            if most_authoratative_source is None or value.value < most_authoratative_source.value:
-                most_authoratative_source = value
-                most_authoratative_source_options = [key]
-            elif value == most_authoratative_source:
-                most_authoratative_source_options.append(key)
-
-        if most_authoratative_source != OptionSource.default and len(most_authoratative_source_options) > 1:
-            raise click.UsageError("Cannot specify multiple of %s" % most_authoratative_source_options)
-
-        for option in exclusive_options:
-            if option in kwds and option not in most_authoratative_source_options:
-                del kwds[option]
-
-
-def _setup_profile_options(ctx, profile_defaults, kwds):
-    for key, value in profile_defaults.items():
-        option_present = key in kwds
-        option_cli_specified = option_present and (ctx.get_option_source(key) == OptionSource.cli)
-        use_profile_option = not option_present or not option_cli_specified
-        if use_profile_option:
-            kwds[key] = value
-            ctx.set_option_source(
-                key, OptionSource.profile, force=True
-            )
-
-
-@click.command(cls=PlanemoCLI, context_settings=CONTEXT_SETTINGS)
-@click.version_option(__version__)
-@click.option('-v', '--verbose', is_flag=True,
-              help='Enables verbose mode.')
-@click.option('--config',
-              default="~/.planemo.yml",
-              envvar="PLANEMO_GLOBAL_CONFIG_PATH",
-              help="Planemo configuration YAML file.")
-@click.option('--directory',
-              default="~/.planemo",
-              envvar="PLANEMO_GLOBAL_WORKSPACE",
-              help="Workspace for planemo.")
-@pass_context
-def planemo(ctx, config, directory, verbose, configure_logging=True):
-    """A command-line toolkit for building tools and workflows for Galaxy.
-
-    Check out the full documentation for Planemo online
-    http://planemo.readthedocs.org or open with ``planemo docs``.
-
-    All the individual planemo commands support the ``--help`` option, for
-    example use ``planemo lint --help`` for more details on checking tools.
-    """
-    ctx.verbose = verbose
-    if configure_logging:
-        logging_config = {
-            'version': 1,
-            'disable_existing_loggers': False,
-            'formatters': {
-                'verbose': {
-                    'format': '%(name)s %(levelname)s %(asctime)s: %(message)s'
-                },
-                'simple': {
-                    'format': '%(name)s %(levelname)s: %(message)s'
-                },
-            },
-            'handlers': {
-                'console': {
-                    'level': 'DEBUG',
-                    'class': 'logging.StreamHandler',
-                    'formatter': 'simple' if not verbose else 'verbose'
-                },
-            },
-            'loggers': {
-                # Suppress CWL is beta warning, for Planemo purposes - it is absolutely not.
-                'galaxy.tools.parser.factory': {
-                    'handlers': ['console'],
-                    'propagate': False,
-                    'level': 'ERROR' if not verbose else "DEBUG",
-                },
-                'galaxy.tools.deps.commands': {
-                    'handlers': ['console'],
-                    'propagate': False,
-                    'level': 'ERROR' if not verbose else "DEBUG",
-                },
-                'galaxy': {
-                    'handlers': ['console'],
-                    'propagate': False,
-                    'level': 'INFO' if not verbose else "DEBUG",
-                },
-                # @jmchilton
-                # I'm fixing up Planemo's lint functionality for CWL and I keep seeing this for the
-                # schema metadata stuff (e.g. in the workflows repo). "rdflib.term WARNING:
-                # http://schema.org/docs/!DOCTYPE html does not look like a valid URI, trying to
-                # serialize this will break.". I'm going to suppress this warning I think, or are the
-                # examples wrong and should declare their namespaces differently in some way?
-                # @mr-c
-                # That particular warning is worth suppressing. A PR to silence it permanently would be very welcome!
-                # https://github.com/RDFLib/rdflib/blob/master/rdflib/term.py#L225
-                'rdflib.term': {
-                    'handlers': ['console'],
-                    'propagate': False,
-                    'level': 'ERROR' if not verbose else "DEBUG",
-                }
-            },
-            'root': {
-                'handlers': ['console'],
-                'propagate': False,
-                'level': 'WARNING' if not verbose else "DEBUG",
-            }
-        }
-        logging.config.dictConfig(logging_config)
-    ctx.planemo_config = os.path.expanduser(config)
-    ctx.planemo_directory = os.path.expanduser(directory)
-
-
-__all__ = (
-    "command_function",
-    "Context",
-    "list_cmds",
-    "name_to_command",
-    "planemo",
-)