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annotate env/lib/python3.7/site-packages/ephemeris-0.10.5.dist-info/METADATA @ 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 Metadata-Version: 2.1
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2 Name: ephemeris
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3 Version: 0.10.5
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4 Summary: Ephemeris is an opinionated library and set of scripts for managing the bootstrapping of Galaxy project plugins - tools, index data, and workflows.
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5 Home-page: https://github.com/galaxyproject/ephemeris
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6 Author: Galaxy Project and Community
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7 Author-email: jmchilton@gmail.com
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8 License: AFL
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9 Keywords: galaxy
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10 Platform: UNKNOWN
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11 Classifier: Development Status :: 5 - Production/Stable
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12 Classifier: Intended Audience :: Developers
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13 Classifier: Environment :: Console
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14 Classifier: License :: OSI Approved :: Academic Free License (AFL)
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15 Classifier: Operating System :: POSIX
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16 Classifier: Topic :: Software Development
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17 Classifier: Topic :: Software Development :: Code Generators
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18 Classifier: Topic :: Software Development :: Testing
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19 Classifier: Natural Language :: English
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20 Classifier: Programming Language :: Python :: 2
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21 Classifier: Programming Language :: Python :: 2.7
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22 Requires-Dist: six (>=1.9.0)
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23 Requires-Dist: PyYAML
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24 Requires-Dist: bioblend (>=0.10.0)
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25 Requires-Dist: Jinja2
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26 Requires-Dist: galaxy-tool-util (>=19.9.0.dev5)
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27 Requires-Dist: futures ; python_version < "3"
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29
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30 .. image:: https://readthedocs.org/projects/pip/badge/?version=latest
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31 :target: https://ephemeris.readthedocs.org
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32
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33 .. image:: https://badge.fury.io/py/ephemeris.svg
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34 :target: https://pypi.python.org/pypi/ephemeris/
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35
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36 .. image:: https://travis-ci.org/galaxyproject/ephemeris.png?branch=master
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37 :target: https://travis-ci.org/galaxyproject/ephemeris
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38
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39 .. image:: https://api.codacy.com/project/badge/Coverage/e12102174b4e452c871cd2bafedaec60
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40 :target: https://www.codacy.com/app/galaxyproject/ephemeris?utm_source=github.com&utm_medium=referral&utm_content=galaxyproject/ephemeris&utm_campaign=Badge_Coverage
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41
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42 .. image:: https://api.codacy.com/project/badge/Grade/e12102174b4e452c871cd2bafedaec60
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43 :target: https://www.codacy.com/app/galaxyproject/ephemeris?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=galaxyproject/ephemeris&amp;utm_campaign=Badge_Grade
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44
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45 Ephemeris is a small Python library and set of scripts for managing the
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46 bootstrapping of Galaxy_ plugins - tools, index data, and workflows.
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47
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48 * Free software: Academic Free License version 3.0
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49 * Documentation: https://ephemeris.readthedocs.org.
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50 * Code: https://github.com/galaxyproject/ephemeris
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51
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52
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53 .. _Galaxy: http://galaxyproject.org/
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54 .. _GitHub: https://github.com/
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55 .. _Docker: https://www.docker.com/
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56 .. _Homebrew: http://brew.sh/
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57 .. _linuxbrew: https://github.com/Homebrew/linuxbrew
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58 .. _Vagrant: https://www.vagrantup.com/
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59 .. _Travis CI: http://travis-ci.org/
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63
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64 History
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65 -------
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66
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67 .. to_doc
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68
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69 ---------------------
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70 0.10.5 (2020-02-29)
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71 ---------------------
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72
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73 * Fix `shed-tools test -t workflow_tools.yml` (thanks to `@nsoranzo`_). `Pull
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74 Request 155`_
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75 * Fix installing tool dependencies from yaml list (thanks to `@mvdbeek`_).
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76 `Pull Request 154`_
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77 * Cast exceptions to string using unicodify (thanks to `@mvdbeek`_). `Pull
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78 Request 150`_
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79 * Add description when creating folders with setup_data_libraries (thanks to
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80 `@abretaud`_). `Pull Request 149`_
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81
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82 ---------------------
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83 0.10.4 (2019-10-05)
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84 ---------------------
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85
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86 * When polling for repo install status, ensure the correct revision is being
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87 checked (thanks to `@natefoo`_). `Pull Request 146`_
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88 * Add install_tool_deps command (thanks to `@innovate-invent`_). `Pull Request
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89 145`_
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90
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91 ---------------------
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92 0.10.3 (2019-07-18)
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93 ---------------------
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94
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95 * Add install-tool-deps command that will install tool dependencies
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96 (thanks to `@innovate-invent`_). `Pull Request 130`_
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97 * Require galaxy-tool-util instead of galaxy-lib (thanks to `@nsoranzo`_).
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98 `Pull Request 143`_
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99 * Release to PyPI on tag (thanks to `@mvdbeek`_). `Pull Request 142`_
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100 * Make Data library creation more robust
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101 (thanks to `@erasche`_). `Pull Request 138`_
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102 * Make tool testing more robust (thanks to
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103 `@mvdbeek`_). `Pull Request 137`_, `Pull Request 136`_
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104
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105 ---------------------
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106 0.10.2 (2019-06-04)
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107 ---------------------
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108
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109 * Fix default message check (thanks to `@mvdbeek`_). `Pull Request 135`_
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110
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111 ---------------------
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112 0.10.1 (2019-06-04)
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113 ---------------------
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114
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115 * Fix timeout handling when installing repositories
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116 (thanks to `@mvdbeek`_). `Pull Request 134`_
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117
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118 ---------------------
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119 0.10.0 (2019-05-29)
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120 ---------------------
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121
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122 * fix doc building and regenerate (thanks to `@martenson`_). `Pull Request
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123 129`_
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124 * fix default for 'parallel_tests' typo (thanks to `@martenson`_). `Pull
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125 Request 127`_
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126 * Include some additional stats for xunit reporting (thanks to `@mvdbeek`_).
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127 `Pull Request 126`_
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128 * Handle timeout gracefully for UWSGI connection (thanks to `@pcm32`_). `Pull
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129 Request 123`_
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130 * Update Docs for User Name (Should be Email) (thanks to `@rdvelazquez`_).
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131 `Pull Request 122`_
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132 * remove the python invocation from usage examples (thanks to `@martenson`_).
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133 `Pull Request 121`_
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134 * Fix crash when too_with_panel is empty (thanks to `@jvanbraekel`_). `Pull
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135 Request 120`_
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136 * Test tools in parallel, with regular user permissions, without a shared
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137 filesystem (thanks to `@mvdbeek`_). `Pull Request 118`_
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138 * use latest documentation dependencies to fix documentation build issue
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139 (thanks to `@rhpvorderman`_). `Pull Request 114`_
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140 * Refactor shed tool functionality. Removed deprecated options from
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141 shed-tools CLI.
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142 shed-tools update now also accepts tool list, so tools in galaxy can
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143 be selectively updated. Improved algorithm leads to much faster
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144 skipping of already installed tools, which makes the installation
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145 of tools much faster on an already populated galaxy.
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146 (thanks to `@rhpvorderman`_).
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147 `Pull Request 104`_
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148 * Add ``pytest``, enable coverage testing (thanks to `@rhpvorderman`_).
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149 `Pull Request 105`_
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150 * Make ``setup_data_libraries.py`` check for existence before recreation of
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151 libraries.
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152 (thanks to `@Slugger70`_).
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153 `Pull Request 103`_
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154 * Catch failures on requests to the installed repo list when doing post-
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155 timeout spinning on installation in ``shed-tools`` (thanks to `@natefoo`_).
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156 `Pull Request 97`_
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157 * Fix coverage reporting on codacy (thanks to `@rhpvorderman`_).
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158 `Pull Request 106`_
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159 * Run-data-managers now outputs stderr of failed jobs (thanks to `@rhpvorderman`_).
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160 `Pull Request 110`_
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161
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162 ---------------------
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163 0.9.0 (2018-05-23)
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164 ---------------------
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165
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166 * Update data managers when updating tools (thanks to `@rhpvorderman`_).
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167 `Pull Request 78`_, `Issue 69`_
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168 * Run data managers aggressive parallelization and refactoring (thanks to
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169 `@rhpvorderman`_).
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170 `Pull Request 79`_
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171 * Makes publishing of imported workflows available (thanks to `@pcm32`_).
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172 `Pull Request 74`_
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173 * Add option to test tools on update/install for Galaxy 18.05 (thanks to `@jmchilton`_).
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174 `Pull Request 81`_
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175 * Upload 2.0 support for data library creation (thanks to `@jmchilton`_).
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176 `Pull Request 89`_
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177 * Fixes to revision parsing in tools.yaml (thanks to `@bgruening`_).
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178 `Pull Request 70`_
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179 * Add Codacy monitoring and badge (thanks to `@jmchilton`_).
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180 `Pull Request 73`_
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181 * Fix typo in project organization document (thanks to `@blankenberg`_).
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182 `Pull Request 86`_
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183 * Fix hardcoded log paths (thanks to `@rhpvorderman`_).
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184 `Pull Request 85`_
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185 * Fix ``shed-tools`` update argparse handling (thanks to `@rhpvorderman`_).
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186 `Pull Request 88`_
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187 * Fix a few lint issues (thanks to `@jmchilton`_).
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188 `Pull Request 90`_
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189
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190 ---------------------
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191 0.8.0 (2017-12-29)
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192 ---------------------
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193
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194 * Many new documentation enhancements (thanks to @rhpvorderman, and others)
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195 * rename of shed-install to shed-tools and add a new --latest and --revision argument (thanks to @rhpvorderman)
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196 * many fixes and new tests by (thanks to @mvdbeek)
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197 * Parallelization of run-data-managers (thanks to @rhpvorderman)
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198 * run-data-managers now uses more advanced templating for less repetitive input yamls (thanks to @rhpvorderman)
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199 * run-data-managers now checks if a genome index is already present before running the data manager (thanks to @rhpvorderman)
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200 * ephemeris will now use https by default instead of http (thanks to @bgruening)
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201
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202 ---------------------
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203 0.7.0 (2017-06-27)
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204 ---------------------
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205
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206 * Many new documentation enhancements (thanks to @rhpvorderman, @erasche, and others) -
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207 docs are now published to https://readthedocs.org/projects/ephemeris/.
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208 * Fix problem with empty list options related to running data managers (thanks to @rhpvorderman).
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209 * Enable data managers to run with API keys (thanks to @rhpvorderman).
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210 * Add sleep command to wait for a Galaxy API to become available (thanks to @erasche).
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211 * Preserve readable order of keys while processing tool lists (thanks to @drosofff).
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212
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213 ---------------------
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214 0.6.1 (2017-04-17)
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215 ---------------------
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216
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217 * Add Python 2 and 3 testing for all scripts against galaxy-docker-stable along with various
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218 refactoring to reduce code duplication and Python 3 fixes. `#36
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219 <https://github.com/galaxyproject/ephemeris/pull/36>`__
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220
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221 ---------------------
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222 0.6.0 (2017-04-10)
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223 ---------------------
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224
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225 * Add new connection options for setting up data libraries.
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226
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227 ---------------------
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228 0.5.1 (2017-04-07)
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229 ---------------------
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230
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231 * Fix new ``run-data-managers`` CLI entrypoint.
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232
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233 ---------------------
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234 0.5.0 (2017-04-06)
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235 ---------------------
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236
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237 * Add ``run-data-managers`` tool to trigger DM with multiple values and in order. `#30 <https://github.com/galaxyproject/ephemeris/pull/30>`_
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238 * The workflow install tool now supports a directory of workflows. `#27 <https://github.com/galaxyproject/ephemeris/pull/27>`_
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239 * enable global options in a tool yaml files, like `install_resolver_dependencies: true` `#26 <https://github.com/galaxyproject/ephemeris/pull/26>`_
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240 * Mention mimum required galaxy versions. `#23 <https://github.com/galaxyproject/ephemeris/pull/23>`_ (thanks to @mvdbeek)
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241
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242
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243 ---------------------
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244 0.4.0 (2016-09-07)
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245 ---------------------
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246
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247 * Be more generic in determining a server time-out (thanks to @afgane).
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248 * Get tool list entrypoint and improvements (thanks to @mvdbeek).
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249 * Rename ``tool_panel_section_name`` to ``tool_panel_section_label`` like
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250 ansible-galaxy-tools (thanks to @nturaga).
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251 * Add missing file ``tool_list.yaml.sample`` (thanks to @nturaga).
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252
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253 ---------------------
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254 0.3.0 (2016-08-26)
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255 ---------------------
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256
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257 * More robust shed-install script, install dependencies by default, improve logging
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258 (thanks to @mvdbeek).
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259
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260 ---------------------
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261 0.2.0 (2016-08-15)
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262 ---------------------
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263
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264 * Add tool generate a tool list from a Galaxy workflow file
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265 (thanks to @drosofff).
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266 * Fix various code quality issues including adding beta support
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267 for Python 3 (thanks in part to @mvdbeek).
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268
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269 ---------------------
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270 0.1.0 (2016-06-15)
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271 ---------------------
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272
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273 * Setup project, pull in scripts from `ansible-galaxy-tools
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274 <https://github.com/galaxyproject/ansible-galaxy-tools>`__
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275 and adapt them for usage as a library.
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276
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277 .. github_links
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278 .. _Pull Request 155: https://github.com/galaxyproject/ephemeris/pull/155
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279 .. _Pull Request 154: https://github.com/galaxyproject/ephemeris/pull/154
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280 .. _Pull Request 150: https://github.com/galaxyproject/ephemeris/pull/150
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281 .. _Pull Request 149: https://github.com/galaxyproject/ephemeris/pull/149
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282 .. _Pull Request 146: https://github.com/galaxyproject/ephemeris/pull/146
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283 .. _Pull Request 145: https://github.com/galaxyproject/ephemeris/pull/145
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284 .. _Pull Request 130: https://github.com/galaxyproject/ephemeris/pull/130
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285 .. _Pull Request 143: https://github.com/galaxyproject/ephemeris/pull/143
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286 .. _Pull Request 142: https://github.com/galaxyproject/ephemeris/pull/142
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287 .. _Pull Request 138: https://github.com/galaxyproject/ephemeris/pull/138
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288 .. _Pull Request 137: https://github.com/galaxyproject/ephemeris/pull/137
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289 .. _Pull Request 136: https://github.com/galaxyproject/ephemeris/pull/136
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290 .. _Pull Request 135: https://github.com/galaxyproject/ephemeris/pull/135
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291 .. _Pull Request 134: https://github.com/galaxyproject/ephemeris/pull/134
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292 .. _Pull Request 129: https://github.com/galaxyproject/ephemeris/pull/129
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293 .. _Pull Request 127: https://github.com/galaxyproject/ephemeris/pull/127
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294 .. _Pull Request 126: https://github.com/galaxyproject/ephemeris/pull/126
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295 .. _Pull Request 123: https://github.com/galaxyproject/ephemeris/pull/123
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296 .. _Pull Request 122: https://github.com/galaxyproject/ephemeris/pull/122
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297 .. _Pull Request 121: https://github.com/galaxyproject/ephemeris/pull/121
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298 .. _Pull Request 120: https://github.com/galaxyproject/ephemeris/pull/120
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299 .. _Pull Request 118: https://github.com/galaxyproject/ephemeris/pull/118
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300 .. _Pull Request 114: https://github.com/galaxyproject/ephemeris/pull/114
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301 .. _Pull Request 97: https://github.com/galaxyproject/ephemeris/pull/97
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302 .. _Pull Request 103: https://github.com/galaxyproject/ephemeris/pull/103
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303 .. _Pull Request 104: https://github.com/galaxyproject/ephemeris/pull/104
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304 .. _Pull Request 105: https://github.com/galaxyproject/ephemeris/pull/105
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305 .. _Pull Request 106: https://github.com/galaxyproject/ephemeris/pull/106
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306 .. _Pull Request 110: https://github.com/galaxyproject/ephemeris/pull/110
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307 .. _Pull Request 74: https://github.com/galaxyproject/ephemeris/pull/74
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308 .. _Issue 69: https://github.com/galaxyproject/ephemeris/issues/69
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309 .. _Pull Request 73: https://github.com/galaxyproject/ephemeris/pull/73
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310 .. _Pull Request 78: https://github.com/galaxyproject/ephemeris/pull/78
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311 .. _Pull Request 70: https://github.com/galaxyproject/ephemeris/pull/70
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312 .. _Pull Request 86: https://github.com/galaxyproject/ephemeris/pull/86
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313 .. _Pull Request 79: https://github.com/galaxyproject/ephemeris/pull/79
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314 .. _Pull Request 85: https://github.com/galaxyproject/ephemeris/pull/85
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315 .. _Pull Request 81: https://github.com/galaxyproject/ephemeris/pull/81
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316 .. _Pull Request 90: https://github.com/galaxyproject/ephemeris/pull/90
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317 .. _Pull Request 89: https://github.com/galaxyproject/ephemeris/pull/89
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318 .. _Pull Request 88: https://github.com/galaxyproject/ephemeris/pull/88
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319 .. _@abretaud: https://github.com/abretaud
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320 .. _@bgruening: https://github.com/bgruening
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321 .. _@blankenberg: https://github.com/blankenberg
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322 .. _@rhpvorderman: https://github.com/rhpvorderman
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323 .. _@pcm32: https://github.com/pcm32
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324 .. _@jmchilton: https://github.com/jmchilton
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325 .. _@Slugger70: https://github.com/Slugger70
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326 .. _@natefoo: https://github.com/natefoo
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327 .. _@martenson: https://github.com/martenson
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328 .. _@mvdbeek: https://github.com/mvdbeek
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329 .. _@rdvelazquez: https://github.com/rdvelazquez
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330 .. _@jvanbraekel: https://github.com/jvanbraekel
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331 .. _@innovate-invent: https://github.com/innovate-invent
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332 .. _@erasche: https://github.com/erasche
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333 .. _@nsoranzo: https://github.com/nsoranzo
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334
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335 .. _bioblend: https://github.com/galaxyproject/bioblend/
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336 .. _nose: https://nose.readthedocs.org/en/latest/
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337
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338