--- a/env/lib/python3.7/site-packages/planemo/conda.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,172 +0,0 @@
-"""Planemo specific utilities for dealing with conda.
-
-The extend galaxy-tool-util's features with planemo specific idioms.
-"""
-
-from __future__ import absolute_import
-
-import collections
-import os
-import threading
-
-from galaxy.tool_util.deps import conda_util
-
-from planemo.exit_codes import EXIT_CODE_FAILED_DEPENDENCIES, ExitCodeException
-from planemo.io import error, shell
-from planemo.tools import yield_tool_sources_on_paths
-
-MESSAGE_ERROR_FAILED_INSTALL = "Attempted to install conda and failed."
-MESSAGE_ERROR_CANNOT_INSTALL = "Cannot install Conda - perhaps due to a failed installation or permission problems."
-MESSAGE_ERROR_NOT_INSTALLING = "Conda not configured - run ``planemo conda_init`` or pass ``--conda_auto_init`` to continue."
-
-BEST_PRACTICE_CHANNELS = ["conda-forge", "bioconda", "defaults"]
-
-
-def build_conda_context(ctx, **kwds):
-    """Build a galaxy-tool-util CondaContext tailored to planemo use.
-
-    Using planemo's common command-line/global config options.
-    """
-    condarc_override_default = os.path.join(ctx.workspace, "condarc")
-    conda_prefix = kwds.get("conda_prefix", None)
-    use_planemo_shell = kwds.get("use_planemo_shell_exec", True)
-    ensure_channels = kwds.get("conda_ensure_channels", "")
-    condarc_override = kwds.get("condarc", condarc_override_default)
-    use_local = kwds.get("conda_use_local", False)
-    shell_exec = shell if use_planemo_shell else None
-    conda_context = conda_util.CondaContext(conda_prefix=conda_prefix,
-                                            ensure_channels=ensure_channels,
-                                            condarc_override=condarc_override,
-                                            use_local=use_local,
-                                            shell_exec=shell_exec)
-    handle_auto_init = kwds.get("handle_auto_init", False)
-    if handle_auto_init and not conda_context.is_installed():
-        auto_init = kwds.get("conda_auto_init", True)
-        failed = True
-        if auto_init:
-            if conda_context.can_install_conda():
-                if conda_util.install_conda(conda_context):
-                    error(MESSAGE_ERROR_FAILED_INSTALL)
-                else:
-                    failed = False
-            else:
-                error(MESSAGE_ERROR_CANNOT_INSTALL)
-        else:
-            error(MESSAGE_ERROR_NOT_INSTALLING)
-
-        if failed:
-            raise ExitCodeException(EXIT_CODE_FAILED_DEPENDENCIES)
-    if handle_auto_init:
-        conda_context.ensure_conda_build_installed_if_needed()
-    return conda_context
-
-
-def collect_conda_targets(ctx, paths, recursive=False, found_tool_callback=None):
-    """Load CondaTarget objects from supplied artifact sources.
-
-    If a tool contains more than one requirement, the requirements will each
-    appear once in the output.
-    """
-    conda_targets = set([])
-    real_paths = []
-    for path in paths:
-        if not os.path.exists(path):
-            targets = target_str_to_targets(path)
-            [conda_targets.add(_) for _ in targets]
-        else:
-            real_paths.append(path)
-
-    for (tool_path, tool_source) in yield_tool_sources_on_paths(ctx, real_paths, recursive=recursive, exclude_deprecated=True):
-        if found_tool_callback:
-            found_tool_callback(tool_path)
-        for target in tool_source_conda_targets(tool_source):
-            conda_targets.add(target)
-    return conda_targets
-
-
-# Copied and modified from mulled stuff - need to syncronize these concepts.
-def target_str_to_targets(targets_raw):
-    def parse_target(target_str):
-        if "=" in target_str:
-            package_name, version = target_str.split("=", 1)
-        else:
-            package_name = target_str
-            version = None
-        target = conda_util.CondaTarget(package_name, version)
-        return target
-
-    targets = [parse_target(_) for _ in targets_raw.split(",")]
-    return targets
-
-
-def collect_conda_target_lists(ctx, paths, recursive=False, found_tool_callback=None):
-    """Load CondaTarget lists from supplied artifact sources.
-
-    If a tool contains more than one requirement, the requirements will all
-    appear together as one list element of the output list.
-    """
-    conda_target_lists, _ = collect_conda_target_lists_and_tool_paths(ctx, paths, recursive=recursive, found_tool_callback=found_tool_callback)
-    return conda_target_lists
-
-
-def collect_conda_target_lists_and_tool_paths(ctx, paths, recursive=False, found_tool_callback=None):
-    """Load CondaTarget lists from supplied artifact sources.
-
-    If a tool contains more than one requirement, the requirements will all
-    appear together as one list element of the output list.
-    """
-    conda_target_lists = set([])
-    tool_paths = collections.defaultdict(list)
-    for (tool_path, tool_source) in yield_tool_sources_on_paths(ctx, paths, recursive=recursive, yield_load_errors=False):
-        if found_tool_callback:
-            found_tool_callback(tool_path)
-        targets = frozenset(tool_source_conda_targets(tool_source))
-        conda_target_lists.add(targets)
-        tool_paths[targets].append(tool_path)
-
-    # Turn them into lists so the order matches before returning...
-    conda_target_lists = list(conda_target_lists)
-    conda_target_tool_paths = [tool_paths[c] for c in conda_target_lists]
-
-    return conda_target_lists, conda_target_tool_paths
-
-
-def tool_source_conda_targets(tool_source):
-    """Load CondaTarget object from supplied abstract tool source."""
-    requirements, _ = tool_source.parse_requirements_and_containers()
-    return conda_util.requirements_to_conda_targets(requirements)
-
-
-best_practice_search_first = threading.local()
-
-
-def best_practice_search(conda_target, conda_context=None, platform=None):
-    # Call it in offline mode after the first time.
-    try:
-        best_practice_search_first.previously_called
-        # TODO: Undo this...
-        offline = False
-    except AttributeError:
-        best_practice_search_first.previously_called = True
-        offline = False
-
-    if not conda_context:
-        conda_context = conda_util.CondaContext()
-    return conda_util.best_search_result(
-        conda_target,
-        conda_context=conda_context,
-        channels_override=BEST_PRACTICE_CHANNELS,
-        offline=offline,
-        platform=platform,
-    )
-
-
-__all__ = (
-    "BEST_PRACTICE_CHANNELS",
-    "best_practice_search",
-    "build_conda_context",
-    "collect_conda_targets",
-    "collect_conda_target_lists",
-    "collect_conda_target_lists_and_tool_paths",
-    "tool_source_conda_targets",
-)