Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/deps.py @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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1 import tempfile
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2 from string import Template
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3
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4 import click
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5 from six import iteritems
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6
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7 from planemo.conda import build_conda_context
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8
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9 CONDA_DEPENDENCY_RESOLUTION_CONF = """<dependency_resolvers>
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10 <conda ${attributes} />
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11 <conda versionless="true" ${attributes} />
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12 </dependency_resolvers>
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13 """
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14
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15 # Like Conda resolution above, but allow tool shed packages to be used for
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16 # shed_serve and shed_test.
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17 DEFAULT_DEPENDENCY_RESOLUTION_CONF = """<dependency_resolvers>
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18 <tool_shed_packages />
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19 <conda ${attributes} />
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20 <conda versionless="true" ${attributes} />
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21 </dependency_resolvers>
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22 """
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23
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24 NO_DEPENDENCY_RESOLUTION_CONF = """<dependency_resolvers>
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25 </dependency_resolvers>
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26 """
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27
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28 BREW_DEPENDENCY_RESOLUTION_CONF = """<dependency_resolvers>
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29 <homebrew />
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30 <!--
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31 <homebrew versionless="true" />
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32 -->
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33 </dependency_resolvers>
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34 """
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35
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36 SHED_DEPENDENCY_RESOLUTION_CONF = """<dependency_resolvers>
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37 <tool_shed_tap />
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38 </dependency_resolvers>
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39 """
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40
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41 # Provide some shortcuts for simple/common dependency resolutions strategies.
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42 STOCK_DEPENDENCY_RESOLUTION_STRATEGIES = {
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43 "brew_dependency_resolution": BREW_DEPENDENCY_RESOLUTION_CONF,
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44 "shed_dependency_resolution": SHED_DEPENDENCY_RESOLUTION_CONF,
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45 "conda_dependency_resolution": CONDA_DEPENDENCY_RESOLUTION_CONF,
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46 "no_dependency_resolution": NO_DEPENDENCY_RESOLUTION_CONF,
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47 "default_dependency_resolution": DEFAULT_DEPENDENCY_RESOLUTION_CONF,
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48 }
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49
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50
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51 def ensure_dependency_resolvers_conf_configured(ctx, kwds, resolvers_conf=None):
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52 """Use supplied CLI options (kwds) to find or build a dependency resolvers file.
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53
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54 Set new path in kwds if needed.
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55 """
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56 _validate_dependency_resolution_options(kwds)
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57 always_specify_attribute = object()
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58
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59 dependency_attribute_kwds = {
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60 'conda_prefix': None,
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61 'conda_exec': None,
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62 'conda_debug': False,
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63 'conda_copy_dependencies': False,
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64 'conda_auto_init': always_specify_attribute,
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65 'conda_auto_install': always_specify_attribute,
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66 'conda_ensure_channels': '',
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67 'conda_use_local': False,
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68 }
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69 attributes = []
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70
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71 def add_attribute(key, value):
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72 attributes.append('%s="%s"' % (key, value))
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73
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74 conda_prefix_specified = False
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75 for key, default_value in iteritems(dependency_attribute_kwds):
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76 value = kwds.get(key, default_value)
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77 if value != default_value:
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78 conda_prefix_specified = conda_prefix_specified or (key == "conda_prefix")
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79 # Strip leading prefix (conda_) off attributes
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80 attribute_key = "_".join(key.split("_")[1:])
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81 add_attribute(attribute_key, value)
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82
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83 conda_context = build_conda_context(ctx, **kwds)
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84 if not conda_prefix_specified:
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85 add_attribute("prefix", conda_context.conda_prefix)
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86 add_attribute("condarc_override", conda_context.condarc_override)
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87
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88 attribute_str = " ".join(attributes)
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89
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90 if kwds.get("dependency_resolvers_config_file", None):
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91 resolution_type = "__explicit__"
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92 else:
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93 resolution_type = "default_dependency_resolution"
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94 for key in STOCK_DEPENDENCY_RESOLUTION_STRATEGIES:
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95 if kwds.get(key):
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96 resolution_type = key
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97
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98 if resolution_type != "__explicit__":
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99 # Planemo manages the dependency resolve conf file.
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100 template_str = STOCK_DEPENDENCY_RESOLUTION_STRATEGIES[resolution_type]
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101 conf_contents = Template(template_str).safe_substitute({
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102 'attributes': attribute_str
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103 })
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104 if resolvers_conf is None:
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105 resolvers_conf = tempfile.NamedTemporaryFile(delete=False).name
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106 with open(resolvers_conf, "w") as fh:
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107 fh.write(conf_contents)
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108 ctx.vlog(
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109 "Writing dependency_resolvers_config_file to path %s with contents [%s]",
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110 resolvers_conf,
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111 conf_contents,
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112 )
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113 kwds["dependency_resolvers_config_file"] = resolvers_conf
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114
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115
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116 def _validate_dependency_resolution_options(kwds):
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117 resolutions_strategies = [
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118 "brew_dependency_resolution",
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119 "dependency_resolvers_config_file",
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120 "shed_dependency_resolution",
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121 "conda_dependency_resolution",
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122 ]
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123
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124 selected_strategies = 0
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125 for key in resolutions_strategies:
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shellac
parents:
diff changeset
126 if kwds.get(key):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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127 selected_strategies += 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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128
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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129 if selected_strategies > 1:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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130 message = "At most one option from [%s] may be specified"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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131 raise click.UsageError(message % resolutions_strategies)