Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/gxformat2/lint.py @ 0:26e78fe6e8c4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 """Workflow linting entry point - main script."""
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2 import argparse
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3 import os
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4 import sys
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5
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6 from gxformat2._scripts import ensure_format2
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7 from gxformat2._yaml import ordered_load
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8 from gxformat2.linting import LintContext
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9 from gxformat2.markdown_parse import validate_galaxy_markdown
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10
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11 EXIT_CODE_SUCCESS = 0
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12 EXIT_CODE_LINT_FAILED = 1
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13 EXIT_CODE_FORMAT_ERROR = 2
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14 EXIT_CODE_FILE_PARSE_FAILED = 3
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15
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16 LINT_FAILED_NO_OUTPUTS = "Workflow contained no outputs"
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17 LINT_FAILED_OUTPUT_NO_LABEL = "Workflow contained output without a label"
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18
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19
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20 def ensure_key(lint_context, has_keys, key, has_class=None, has_value=None):
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21 if key not in has_keys:
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22 lint_context.error("expected to find key [{key}] but absent", key=key)
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23 return None
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24
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25 value = has_keys[key]
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26 return ensure_key_has_value(lint_context, has_keys, key, value, has_class=has_class, has_value=has_value)
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27
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28
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29 def ensure_key_if_present(lint_context, has_keys, key, default=None, has_class=None):
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30 if key not in has_keys:
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31 return default
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32
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33 value = has_keys[key]
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34 return ensure_key_has_value(lint_context, has_keys, key, value, has_class=has_class, has_value=None)
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35
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36
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37 def ensure_key_has_value(lint_context, has_keys, key, value, has_class=None, has_value=None):
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38 if has_class is not None and not isinstance(value, has_class):
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39 lint_context.error("expected value [{value}] with key [{key}] to be of class {clazz}", key=key, value=value, clazz=has_class)
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40 if has_value is not None and value != has_value:
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41 lint_context.error("expected value [{value}] with key [{key}] to be {expected_value}", key=key, value=value, expected_value=has_value)
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42 return value
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43
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44
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45 def _lint_step_errors(lint_context, step):
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46 step_errors = step.get("errors")
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47 if step_errors is not None:
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48 lint_context.warn("tool step contains error indicated during Galaxy export - %s" % step_errors)
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49
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50
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51 def lint_ga(lint_context, workflow_dict, path=None):
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52 """Lint a native/legacy style Galaxy workflow and populate the corresponding LintContext."""
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53 ensure_key(lint_context, workflow_dict, "format-version", has_value="0.1")
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54 ensure_key(lint_context, workflow_dict, "a_galaxy_workflow", has_value="true")
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55
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56 native_steps = ensure_key(lint_context, workflow_dict, "steps", has_class=dict) or {}
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57
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58 found_outputs = False
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59 found_output_without_label = False
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60 for order_index_str, step in native_steps.items():
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61 if not order_index_str.isdigit():
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62 lint_context.error("expected step_key to be integer not [{value}]", value=order_index_str)
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63
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64 workflow_outputs = ensure_key_if_present(lint_context, step, "workflow_outputs", default=[], has_class=list)
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65 for workflow_output in workflow_outputs:
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66 found_outputs = True
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67
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68 if not workflow_output.get("label"):
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69 found_output_without_label = True
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70
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71 step_type = step.get("type")
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72 if step_type == "subworkflow":
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73 subworkflow = ensure_key(lint_context, step, "subworkflow", has_class=dict)
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74 lint_ga(lint_context, subworkflow)
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75
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76 _lint_step_errors(lint_context, step)
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77 _lint_tool_if_present(lint_context, step)
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78
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79 _validate_report(lint_context, workflow_dict)
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80 if not found_outputs:
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81 lint_context.warn(LINT_FAILED_NO_OUTPUTS)
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82
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83 if found_output_without_label:
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84 lint_context.warn(LINT_FAILED_OUTPUT_NO_LABEL)
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85
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86 _lint_training(lint_context, workflow_dict)
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87
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88
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89 def lint_format2(lint_context, workflow_dict, path=None):
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90 """Lint a Format 2 Galaxy workflow and populate the corresponding LintContext."""
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91 from gxformat2.schema.v19_09 import load_document
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92 from schema_salad.exceptions import SchemaSaladException
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93 try:
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94 load_document("file://" + os.path.normpath(path))
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95 except SchemaSaladException as e:
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96 lint_context.error("Validation failed " + str(e))
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97
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98 steps = ensure_key_if_present(lint_context, workflow_dict, 'steps', default={}, has_class=dict)
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99 for key, step in steps.items():
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100 _lint_step_errors(lint_context, step)
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101 _lint_tool_if_present(lint_context, step)
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102
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103 _validate_report(lint_context, workflow_dict)
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104 _lint_training(lint_context, workflow_dict)
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105
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106
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107 def _lint_tool_if_present(lint_context, step_dict):
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108 tool_id = step_dict.get('tool_id')
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109 if tool_id and 'testtoolshed' in tool_id:
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110 lint_context.warn('Step references a tool from the test tool shed, this should be replaced with a production tool')
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111
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112
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113 def _validate_report(lint_context, workflow_dict):
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114 report_dict = ensure_key_if_present(lint_context, workflow_dict, "report", default=None, has_class=dict)
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115 if report_dict is not None:
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116 markdown = ensure_key(lint_context, report_dict, "markdown", has_class=str)
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117 if isinstance(markdown, str):
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118 try:
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119 validate_galaxy_markdown(markdown)
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120 except ValueError as e:
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121 lint_context.error("Report markdown validation failed [%s]" % e)
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122
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123
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124 def _lint_training(lint_context, workflow_dict):
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125 if lint_context.training_topic is None:
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126 return
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127
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128 if "tags" not in workflow_dict:
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129 lint_context.warn("Missing tag(s).")
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130 else:
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131 tags = workflow_dict["tags"]
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132 if lint_context.training_topic not in tags:
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133 lint_context.warn("Missing expected training topic (%s) as workflow tag." % lint_context.training_topic)
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134 # Move up into individual lints - all workflows should have docs.
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135 format2_dict = ensure_format2(workflow_dict)
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136 if "doc" not in format2_dict:
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137 lint_context.warn("Missing workflow documentation (annotation or doc element)")
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138 elif not format2_dict["doc"]:
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139 lint_context.warn("Empty workflow documentation (annotation or doc element)")
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140
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141
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142 def main(argv=None):
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143 """Script entry point for linting workflows."""
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144 if argv is None:
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145 argv = sys.argv
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146 args = _parser().parse_args(argv[1:])
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147 path = args.path
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148 with open(path, "r") as f:
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149 try:
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150 workflow_dict = ordered_load(f)
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151 except Exception:
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152 return EXIT_CODE_FILE_PARSE_FAILED
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153 workflow_class = workflow_dict.get("class")
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154 lint_func = lint_format2 if workflow_class == "GalaxyWorkflow" else lint_ga
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155 lint_context = LintContext(training_topic=args.training_topic)
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156 lint_func(lint_context, workflow_dict, path=path)
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157 lint_context.print_messages()
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158 if lint_context.found_errors:
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159 return EXIT_CODE_FORMAT_ERROR
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160 elif lint_context.found_warns:
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161 return EXIT_CODE_LINT_FAILED
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162 else:
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163 return EXIT_CODE_SUCCESS
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164
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165
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166 def _parser():
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167 parser = argparse.ArgumentParser()
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168 parser.add_argument("--training-topic",
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169 required=False,
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170 help='If this is a training workflow, specify a training topic.')
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171 parser.add_argument('path', metavar='PATH', type=str,
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172 help='workflow path')
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173 return parser
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174
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175
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176 if __name__ == "__main__":
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177 sys.exit(main())
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178
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179
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180 __all__ = ('main', 'lint_format2', 'lint_ga')