Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/github_util.py @ 4:79f47841a781 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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0
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1 """Utilities for interacting with Github."""
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2 from __future__ import absolute_import
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3
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4 import os
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5
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6 from galaxy.tool_util.deps.commands import which
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7
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8 from planemo import git
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9 from planemo.io import (
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10 communicate,
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11 IS_OS_X,
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12 untar_to,
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13 )
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14
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15 try:
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16 import github
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17 has_github_lib = True
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18 except ImportError:
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19 github = None
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20 has_github_lib = False
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21
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22 HUB_VERSION = "2.2.8"
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23
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24 NO_GITHUB_DEP_ERROR = ("Cannot use github functionality - "
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25 "PyGithub library not available.")
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26 FAILED_TO_DOWNLOAD_HUB = "No hub executable available and it could not be installed."
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27
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28
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29 def get_github_config(ctx, allow_anonymous=False):
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30 """Return a :class:`planemo.github_util.GithubConfig` for given configuration."""
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31 global_github_config = _get_raw_github_config(ctx)
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32 return GithubConfig(global_github_config, allow_anonymous=allow_anonymous)
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33
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34
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35 def clone_fork_branch(ctx, target, path, **kwds):
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36 """Clone, fork, and branch a repository ahead of building a pull request."""
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37 git.checkout(
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38 ctx,
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39 target,
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40 path,
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41 branch=kwds.get("branch", None),
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42 remote="origin",
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43 from_branch="master"
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44 )
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45 if kwds.get("fork"):
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46 try:
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47 fork(ctx, path, **kwds)
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48 except Exception:
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49 pass
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50
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51
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52 def fork(ctx, path, **kwds):
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53 """Fork the target repository using ``hub``."""
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54 hub_path = ensure_hub(ctx, **kwds)
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55 hub_env = get_hub_env(ctx, path, **kwds)
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56 cmd = [hub_path, "fork"]
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57 communicate(cmd, env=hub_env)
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58
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59
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60 def pull_request(ctx, path, message=None, **kwds):
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61 """Create a pull request against the origin of the path using ``hub``."""
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62 hub_path = ensure_hub(ctx, **kwds)
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63 hub_env = get_hub_env(ctx, path, **kwds)
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64 cmd = [hub_path, "pull-request"]
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65 if message is not None:
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66 cmd.extend(["-m", message])
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67 communicate(cmd, env=hub_env)
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68
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69
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70 def get_hub_env(ctx, path, **kwds):
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71 """Return a environment dictionary to run hub with given user and repository target."""
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72 env = git.git_env_for(path).copy()
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73 github_config = _get_raw_github_config(ctx)
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74 if github_config is not None:
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75 if "username" in github_config:
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76 env["GITHUB_USER"] = github_config["username"]
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77 if "password" in github_config:
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78 env["GITHUB_PASSWORD"] = github_config["password"]
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79
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80 return env
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81
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82
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83 def ensure_hub(ctx, **kwds):
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84 """Ensure ``hub`` is on the system ``PATH``.
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85
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86 This method will ensure ``hub`` is installed if it isn't available.
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87
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88 For more information on ``hub`` checkout ...
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89 """
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90 hub_path = which("hub")
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91 if not hub_path:
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92 planemo_hub_path = os.path.join(ctx.workspace, "hub")
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93 if not os.path.exists(planemo_hub_path):
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94 _try_download_hub(planemo_hub_path)
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95
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96 if not os.path.exists(planemo_hub_path):
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97 raise Exception(FAILED_TO_DOWNLOAD_HUB)
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98
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99 hub_path = planemo_hub_path
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100 return hub_path
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101
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102
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103 def _try_download_hub(planemo_hub_path):
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104 link = _hub_link()
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105 # Strip URL base and .tgz at the end.
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106 basename = link.split("/")[-1].rsplit(".", 1)[0]
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107 untar_to(link, tar_args=['-zxvf', '-', "%s/bin/hub" % basename], path=planemo_hub_path)
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108 communicate(["chmod", "+x", planemo_hub_path])
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109
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110
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111 def _get_raw_github_config(ctx):
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112 """Return a :class:`planemo.github_util.GithubConfig` for given configuration."""
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113 if "github" not in ctx.global_config:
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114 if "GITHUB_USER" in os.environ and "GITHUB_PASSWORD" in os.environ:
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115 return {
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116 "username": os.environ["GITHUB_USER"],
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117 "password": os.environ["GITHUB_PASSWORD"],
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118 }
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119 if "github" not in ctx.global_config:
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120 raise Exception("github account not found in planemo config and GITHUB_USER / GITHUB_PASSWORD environment variables unset")
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121 return ctx.global_config["github"]
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122
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123
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124 class GithubConfig(object):
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125 """Abstraction around a Github account.
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126
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127 Required to use ``github`` module methods that require authorization.
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128 """
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129
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130 def __init__(self, config, allow_anonymous=False):
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131 if not has_github_lib:
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132 raise Exception(NO_GITHUB_DEP_ERROR)
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133 if "username" not in config or "password" not in config:
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134 if not allow_anonymous:
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135 raise Exception("github authentication unavailable")
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136 github_object = github.Github()
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137 else:
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138 github_object = github.Github(config["username"], config["password"])
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139 self._github = github_object
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140
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141
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142 def _hub_link():
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143 if IS_OS_X:
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144 template_link = "https://github.com/github/hub/releases/download/v%s/hub-darwin-amd64-%s.tgz"
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145 else:
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146 template_link = "https://github.com/github/hub/releases/download/v%s/hub-linux-amd64-%s.tgz"
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147 return template_link % (HUB_VERSION, HUB_VERSION)
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148
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149
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150 def publish_as_gist_file(ctx, path, name="index"):
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151 """Publish a gist.
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152
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153 More information on gists at http://gist.github.com/.
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154 """
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155 github_config = get_github_config(ctx, allow_anonymous=False)
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156 user = github_config._github.get_user()
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157 with open(path, "r") as fh:
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158 content = fh.read()
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159 content_file = github.InputFileContent(content)
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160 gist = user.create_gist(False, {name: content_file})
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161 return gist.files[name].raw_url
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162
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163
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164 def get_repository_object(ctx, name):
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165 github_object = get_github_config(ctx, allow_anonymous=True)
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166 return github_object._github.get_repo(name)
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167
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168
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169 __all__ = (
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170 "clone_fork_branch",
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171 "ensure_hub",
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172 "fork",
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173 "get_github_config",
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174 "get_hub_env",
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175 "publish_as_gist_file",
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176 )