Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/conda.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 """Planemo specific utilities for dealing with conda.
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2
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3 The extend galaxy-tool-util's features with planemo specific idioms.
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4 """
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5
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6 from __future__ import absolute_import
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7
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8 import collections
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9 import os
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10 import threading
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11
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12 from galaxy.tool_util.deps import conda_util
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13
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14 from planemo.exit_codes import EXIT_CODE_FAILED_DEPENDENCIES, ExitCodeException
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15 from planemo.io import error, shell
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16 from planemo.tools import yield_tool_sources_on_paths
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17
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18 MESSAGE_ERROR_FAILED_INSTALL = "Attempted to install conda and failed."
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19 MESSAGE_ERROR_CANNOT_INSTALL = "Cannot install Conda - perhaps due to a failed installation or permission problems."
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20 MESSAGE_ERROR_NOT_INSTALLING = "Conda not configured - run ``planemo conda_init`` or pass ``--conda_auto_init`` to continue."
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21
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22 BEST_PRACTICE_CHANNELS = ["conda-forge", "bioconda", "defaults"]
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23
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24
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25 def build_conda_context(ctx, **kwds):
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26 """Build a galaxy-tool-util CondaContext tailored to planemo use.
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27
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28 Using planemo's common command-line/global config options.
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29 """
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30 condarc_override_default = os.path.join(ctx.workspace, "condarc")
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31 conda_prefix = kwds.get("conda_prefix", None)
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32 use_planemo_shell = kwds.get("use_planemo_shell_exec", True)
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33 ensure_channels = kwds.get("conda_ensure_channels", "")
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34 condarc_override = kwds.get("condarc", condarc_override_default)
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35 use_local = kwds.get("conda_use_local", False)
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36 shell_exec = shell if use_planemo_shell else None
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37 conda_context = conda_util.CondaContext(conda_prefix=conda_prefix,
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38 ensure_channels=ensure_channels,
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39 condarc_override=condarc_override,
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40 use_local=use_local,
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41 shell_exec=shell_exec)
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42 handle_auto_init = kwds.get("handle_auto_init", False)
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43 if handle_auto_init and not conda_context.is_installed():
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44 auto_init = kwds.get("conda_auto_init", True)
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45 failed = True
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46 if auto_init:
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47 if conda_context.can_install_conda():
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48 if conda_util.install_conda(conda_context):
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49 error(MESSAGE_ERROR_FAILED_INSTALL)
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50 else:
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51 failed = False
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52 else:
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53 error(MESSAGE_ERROR_CANNOT_INSTALL)
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54 else:
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55 error(MESSAGE_ERROR_NOT_INSTALLING)
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56
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57 if failed:
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58 raise ExitCodeException(EXIT_CODE_FAILED_DEPENDENCIES)
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59 if handle_auto_init:
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60 conda_context.ensure_conda_build_installed_if_needed()
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61 return conda_context
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62
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63
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64 def collect_conda_targets(ctx, paths, recursive=False, found_tool_callback=None):
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65 """Load CondaTarget objects from supplied artifact sources.
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66
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67 If a tool contains more than one requirement, the requirements will each
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68 appear once in the output.
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69 """
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70 conda_targets = set([])
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71 real_paths = []
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72 for path in paths:
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73 if not os.path.exists(path):
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74 targets = target_str_to_targets(path)
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75 [conda_targets.add(_) for _ in targets]
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76 else:
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77 real_paths.append(path)
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78
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79 for (tool_path, tool_source) in yield_tool_sources_on_paths(ctx, real_paths, recursive=recursive, exclude_deprecated=True):
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80 if found_tool_callback:
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81 found_tool_callback(tool_path)
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82 for target in tool_source_conda_targets(tool_source):
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83 conda_targets.add(target)
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84 return conda_targets
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85
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86
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87 # Copied and modified from mulled stuff - need to syncronize these concepts.
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88 def target_str_to_targets(targets_raw):
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89 def parse_target(target_str):
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90 if "=" in target_str:
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91 package_name, version = target_str.split("=", 1)
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92 else:
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93 package_name = target_str
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94 version = None
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95 target = conda_util.CondaTarget(package_name, version)
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96 return target
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97
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98 targets = [parse_target(_) for _ in targets_raw.split(",")]
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99 return targets
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100
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101
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102 def collect_conda_target_lists(ctx, paths, recursive=False, found_tool_callback=None):
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103 """Load CondaTarget lists from supplied artifact sources.
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104
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105 If a tool contains more than one requirement, the requirements will all
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106 appear together as one list element of the output list.
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107 """
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108 conda_target_lists, _ = collect_conda_target_lists_and_tool_paths(ctx, paths, recursive=recursive, found_tool_callback=found_tool_callback)
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109 return conda_target_lists
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110
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111
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112 def collect_conda_target_lists_and_tool_paths(ctx, paths, recursive=False, found_tool_callback=None):
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113 """Load CondaTarget lists from supplied artifact sources.
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114
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115 If a tool contains more than one requirement, the requirements will all
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116 appear together as one list element of the output list.
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117 """
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118 conda_target_lists = set([])
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119 tool_paths = collections.defaultdict(list)
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120 for (tool_path, tool_source) in yield_tool_sources_on_paths(ctx, paths, recursive=recursive, yield_load_errors=False):
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121 if found_tool_callback:
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122 found_tool_callback(tool_path)
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123 targets = frozenset(tool_source_conda_targets(tool_source))
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124 conda_target_lists.add(targets)
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125 tool_paths[targets].append(tool_path)
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126
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127 # Turn them into lists so the order matches before returning...
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128 conda_target_lists = list(conda_target_lists)
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129 conda_target_tool_paths = [tool_paths[c] for c in conda_target_lists]
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130
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131 return conda_target_lists, conda_target_tool_paths
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132
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133
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134 def tool_source_conda_targets(tool_source):
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135 """Load CondaTarget object from supplied abstract tool source."""
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136 requirements, _ = tool_source.parse_requirements_and_containers()
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137 return conda_util.requirements_to_conda_targets(requirements)
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138
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139
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140 best_practice_search_first = threading.local()
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141
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142
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143 def best_practice_search(conda_target, conda_context=None, platform=None):
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144 # Call it in offline mode after the first time.
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145 try:
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146 best_practice_search_first.previously_called
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147 # TODO: Undo this...
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148 offline = False
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149 except AttributeError:
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150 best_practice_search_first.previously_called = True
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151 offline = False
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152
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153 if not conda_context:
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154 conda_context = conda_util.CondaContext()
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155 return conda_util.best_search_result(
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156 conda_target,
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157 conda_context=conda_context,
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158 channels_override=BEST_PRACTICE_CHANNELS,
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159 offline=offline,
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160 platform=platform,
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161 )
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162
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163
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164 __all__ = (
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165 "BEST_PRACTICE_CHANNELS",
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166 "best_practice_search",
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167 "build_conda_context",
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168 "collect_conda_targets",
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169 "collect_conda_target_lists",
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170 "collect_conda_target_lists_and_tool_paths",
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171 "tool_source_conda_targets",
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172 )