Allow conda_install over multiple tool paths.

galaxyproject · Oct 4, 2016 · 2e4e5fc0442a20744254ee27cf4590b963773644 · 2e4e5fc
1 parent f0da66f
commit 2e4e5fc0442a20744254ee27cf4590b963773644
Unified Split

Showing with 15 additions and 10 deletions.

+1 −1 planemo/commands/cmd_conda_env.py

+3 −3 planemo/commands/cmd_conda_install.py

+11 −6 planemo/conda.py
diff --git a/planemo/commands/cmd_conda_env.py b/planemo/commands/cmd_conda_env.py
@@ -46,7 +46,7 @@ def cli(ctx, path, **kwds):
    """
    conda_context = build_conda_context(ctx, use_planemo_shell_exec=False, **kwds)
    conda_targets = collect_conda_targets(
-  
-        path, conda_context=conda_context
+  
+        ctx, path, conda_context=conda_context
    )
    installed_conda_targets = conda_util.filter_installed_targets(
        conda_targets, conda_context=conda_context

diff --git a/planemo/commands/cmd_conda_install.py b/planemo/commands/cmd_conda_install.py
@@ -11,11 +11,11 @@
 @click.command('conda_install')
-  
-@options.optional_tools_arg()
+  
+@options.optional_tools_arg(multiple=True)
 @options.conda_target_options()
 @options.conda_auto_init_option()
 @command_function
-  
-def cli(ctx, path, **kwds):
+  
+def cli(ctx, paths, **kwds):
    """Install conda packages for tool requirements."""
    conda_context = build_conda_context(ctx, **kwds)
    if not conda_context.is_conda_installed():
@@ -36,7 +36,7 @@ def cli(ctx, path, **kwds):
            raise ExitCodeException(EXIT_CODE_FAILED_DEPENDENCIES)
    return_codes = []
-  
-    for conda_target in collect_conda_targets(path):
+  
+    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

diff --git a/planemo/conda.py b/planemo/conda.py
@@ -7,9 +7,9 @@
 import os
 from galaxy.tools.deps import conda_util
-  
-from galaxy.tools.loader_directory import load_tool_sources_from_path
 from planemo.io import shell
+  
+from planemo.tools import yield_tool_sources_on_paths
 def build_conda_context(ctx, **kwds):
@@ -29,13 +29,18 @@ def build_conda_context(ctx, **kwds):
                                   shell_exec=shell_exec)
-  
-def collect_conda_targets(path, found_tool_callback=None, conda_context=None):
-  
-    """Load CondaTarget objects from supplied artifact sources."""
-  
-    conda_targets = []
-  
-    for (tool_path, tool_source) in load_tool_sources_from_path(path):
+  
+def collect_conda_targets(ctx, paths, found_tool_callback=None, conda_context=None):
+  
+    """Load CondaTarget objects from supplied artifact sources.
+  
+
+  
+    If a tool contains more than one requirement, the requirements will each
+  
+    appear once in the output.
+  
+    """
+  
+    conda_targets = set([])
+  
+    for (tool_path, tool_source) in yield_tool_sources_on_paths(ctx, paths):
        if found_tool_callback:
            found_tool_callback(tool_path)
-  
-        conda_targets.extend(tool_source_conda_targets(tool_source))
+  
+        for target in tool_source_conda_targets(tool_source):
+  
+            conda_targets.add(target)
    return conda_targets