Allow conda_install to work with packages as well as just tools.

jmchilton · jmchilton · commit 8faf661f7020 · 2017-02-16T13:42:35.000-05:00
diff --git a/planemo/commands/cmd_conda_install.py b/planemo/commands/cmd_conda_install.py
@@ -10,8 +10,9 @@
 
 
 @click.command('conda_install')
-@options.optional_tools_arg(multiple=True)
+@options.optional_tools_or_packages_arg(multiple=True)
 @options.conda_target_options()
+@options.conda_global_option()
 @options.conda_auto_init_option()
 @command_function
 def cli(ctx, paths, **kwds):
@@ -21,7 +22,7 @@ def cli(ctx, paths, **kwds):
     for conda_target in collect_conda_targets(ctx, paths):
         ctx.log("Install conda target %s" % conda_target)
         return_code = conda_util.install_conda_target(
-            conda_target, conda_context=conda_context
+            conda_target, conda_context=conda_context, skip_environment=kwds.get("global", False)
         )
         return_codes.append(return_code)
     return coalesce_return_codes(return_codes, assert_at_least_one=True)
diff --git a/planemo/conda.py b/planemo/conda.py
@@ -60,14 +60,37 @@ def collect_conda_targets(ctx, paths, found_tool_callback=None, conda_context=No
     appear once in the output.
     """
     conda_targets = set([])
-    for (tool_path, tool_source) in yield_tool_sources_on_paths(ctx, paths):
+    real_paths = []
+    for path in paths:
+        if not os.path.exists(path):
+            targets = target_str_to_targets(path)
+            [conda_targets.add(_) for _ in targets]
+        else:
+            real_paths.append(path)
+
+    for (tool_path, tool_source) in yield_tool_sources_on_paths(ctx, real_paths):
         if found_tool_callback:
             found_tool_callback(tool_path)
         for target in tool_source_conda_targets(tool_source):
             conda_targets.add(target)
     return conda_targets
 
 
+# Copied and modified from mulled stuff - need to syncronize these concepts.
+def target_str_to_targets(targets_raw):
+    def parse_target(target_str):
+        if "=" in target_str:
+            package_name, version = target_str.split("=", 1)
+        else:
+            package_name = target_str
+            version = None
+        target = conda_util.CondaTarget(package_name, version)
+        return target
+
+    targets = [parse_target(_) for _ in targets_raw.split(",")]
+    return targets
+
+
 def collect_conda_target_lists(ctx, paths, found_tool_callback=None):
     """Load CondaTarget lists from supplied artifact sources.
 
diff --git a/planemo/options.py b/planemo/options.py
@@ -481,6 +481,18 @@ def conda_auto_init_option():
     )
 
 
+def conda_global_option():
+    return planemo_option(
+        "--global",
+        is_flag=True,
+        default=False,
+        help=("Install Conda dependencies globally instead of in requirement specific "
+              "environments packaged for tools. If the Conda bin directory is on your "
+              "PATH, tools may still use binaries but this is more designed for "
+              "interactive testing and debugging.")
+    )
+
+
 def required_tool_arg():
     """ Decorate click method as requiring the path to a single tool.
     """
@@ -514,6 +526,20 @@ def _optional_tools_default(ctx, param, value):
         return value
 
 
+def optional_tools_or_packages_arg(multiple=False):
+    """ Decorate click method as optionally taking in the path to a tool
+    or directory of tools or a Conda package. If no such argument is given
+    the current working directory will be treated as a directory of tools.
+    """
+    name = "paths" if multiple else "path"
+    nargs = -1 if multiple else 1
+    return click.argument(
+        name,
+        metavar="TARGET",
+        nargs=nargs,
+    )
+
+
 def optional_tools_arg(multiple=False):
     """ Decorate click method as optionally taking in the path to a tool
     or directory of tools. If no such argument is given the current working
