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comparison env/lib/python3.7/site-packages/planemo/deps.py @ 5:9b1c78e6ba9c draft default tip

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"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author shellac
date Mon, 01 Jun 2020 08:59:25 -0400
parents 79f47841a781
children
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4:79f47841a781 5:9b1c78e6ba9c
1 import tempfile
2 from string import Template
3
4 import click
5 from six import iteritems
6
7 from planemo.conda import build_conda_context
8
9 CONDA_DEPENDENCY_RESOLUTION_CONF = """<dependency_resolvers>
10 <conda ${attributes} />
11 <conda versionless="true" ${attributes} />
12 </dependency_resolvers>
13 """
14
15 # Like Conda resolution above, but allow tool shed packages to be used for
16 # shed_serve and shed_test.
17 DEFAULT_DEPENDENCY_RESOLUTION_CONF = """<dependency_resolvers>
18 <tool_shed_packages />
19 <conda ${attributes} />
20 <conda versionless="true" ${attributes} />
21 </dependency_resolvers>
22 """
23
24 NO_DEPENDENCY_RESOLUTION_CONF = """<dependency_resolvers>
25 </dependency_resolvers>
26 """
27
28 BREW_DEPENDENCY_RESOLUTION_CONF = """<dependency_resolvers>
29 <homebrew />
30 <!--
31 <homebrew versionless="true" />
32 -->
33 </dependency_resolvers>
34 """
35
36 SHED_DEPENDENCY_RESOLUTION_CONF = """<dependency_resolvers>
37 <tool_shed_tap />
38 </dependency_resolvers>
39 """
40
41 # Provide some shortcuts for simple/common dependency resolutions strategies.
42 STOCK_DEPENDENCY_RESOLUTION_STRATEGIES = {
43 "brew_dependency_resolution": BREW_DEPENDENCY_RESOLUTION_CONF,
44 "shed_dependency_resolution": SHED_DEPENDENCY_RESOLUTION_CONF,
45 "conda_dependency_resolution": CONDA_DEPENDENCY_RESOLUTION_CONF,
46 "no_dependency_resolution": NO_DEPENDENCY_RESOLUTION_CONF,
47 "default_dependency_resolution": DEFAULT_DEPENDENCY_RESOLUTION_CONF,
48 }
49
50
51 def ensure_dependency_resolvers_conf_configured(ctx, kwds, resolvers_conf=None):
52 """Use supplied CLI options (kwds) to find or build a dependency resolvers file.
53
54 Set new path in kwds if needed.
55 """
56 _validate_dependency_resolution_options(kwds)
57 always_specify_attribute = object()
58
59 dependency_attribute_kwds = {
60 'conda_prefix': None,
61 'conda_exec': None,
62 'conda_debug': False,
63 'conda_copy_dependencies': False,
64 'conda_auto_init': always_specify_attribute,
65 'conda_auto_install': always_specify_attribute,
66 'conda_ensure_channels': '',
67 'conda_use_local': False,
68 }
69 attributes = []
70
71 def add_attribute(key, value):
72 attributes.append('%s="%s"' % (key, value))
73
74 conda_prefix_specified = False
75 for key, default_value in iteritems(dependency_attribute_kwds):
76 value = kwds.get(key, default_value)
77 if value != default_value:
78 conda_prefix_specified = conda_prefix_specified or (key == "conda_prefix")
79 # Strip leading prefix (conda_) off attributes
80 attribute_key = "_".join(key.split("_")[1:])
81 add_attribute(attribute_key, value)
82
83 conda_context = build_conda_context(ctx, **kwds)
84 if not conda_prefix_specified:
85 add_attribute("prefix", conda_context.conda_prefix)
86 add_attribute("condarc_override", conda_context.condarc_override)
87
88 attribute_str = " ".join(attributes)
89
90 if kwds.get("dependency_resolvers_config_file", None):
91 resolution_type = "__explicit__"
92 else:
93 resolution_type = "default_dependency_resolution"
94 for key in STOCK_DEPENDENCY_RESOLUTION_STRATEGIES:
95 if kwds.get(key):
96 resolution_type = key
97
98 if resolution_type != "__explicit__":
99 # Planemo manages the dependency resolve conf file.
100 template_str = STOCK_DEPENDENCY_RESOLUTION_STRATEGIES[resolution_type]
101 conf_contents = Template(template_str).safe_substitute({
102 'attributes': attribute_str
103 })
104 if resolvers_conf is None:
105 resolvers_conf = tempfile.NamedTemporaryFile(delete=False).name
106 with open(resolvers_conf, "w") as fh:
107 fh.write(conf_contents)
108 ctx.vlog(
109 "Writing dependency_resolvers_config_file to path %s with contents [%s]",
110 resolvers_conf,
111 conf_contents,
112 )
113 kwds["dependency_resolvers_config_file"] = resolvers_conf
114
115
116 def _validate_dependency_resolution_options(kwds):
117 resolutions_strategies = [
118 "brew_dependency_resolution",
119 "dependency_resolvers_config_file",
120 "shed_dependency_resolution",
121 "conda_dependency_resolution",
122 ]
123
124 selected_strategies = 0
125 for key in resolutions_strategies:
126 if kwds.get(key):
127 selected_strategies += 1
128
129 if selected_strategies > 1:
130 message = "At most one option from [%s] may be specified"
131 raise click.UsageError(message % resolutions_strategies)