Implement --no_cleanup option for test & serve commands.

Prevents deletion of temporary files created for/by Galaxy. Might be useful for debugging stuff (#80 (comment)) - probably would be a whole lot more useful for debugging if we also dropped a little shell script in that directory that allowed resuming Galaxy from that state.

docs/commands/serve.rst

@@ -36,6 +36,8 @@ instances.
                                       execute command with.
       --install_galaxy                Download and configure a disposable copy of
                                       Galaxy from github.
+      --no_cleanup                    Do not cleanup temp files created for and by
+                                      Galaxy.
       --test_data DIRECTORY           test-data directory to for specified
                                       tool(s).
       --dependency_resolvers_config_file PATH

docs/commands/test.rst

@@ -61,6 +61,8 @@ please careful and do not try this against production Galaxy instances.
                                       execute command with.
       --install_galaxy                Download and configure a disposable copy of
                                       Galaxy from github.
+      --no_cleanup                    Do not cleanup temp files created for and by
+                                      Galaxy.
       --test_data DIRECTORY           test-data directory to for specified
                                       tool(s).
       --tool_data_table PATH          tool_data_table_conf.xml file to for

docs/commands/tool_factory.rst

@@ -26,6 +26,8 @@ http://www.ncbi.nlm.nih.gov/pubmed/23024011.
                                       execute command with.
       --install_galaxy                Download and configure a disposable copy of
                                       Galaxy from github.
+      --no_cleanup                    Do not cleanup temp files created for and by
+                                      Galaxy.
       --test_data DIRECTORY           test-data directory to for specified
                                       tool(s).
       --dependency_resolvers_config_file PATH

planemo/commands/cmd_serve.py

@@ -9,6 +9,7 @@
 @options.optional_tools_arg()
 @options.galaxy_root_option()
 @options.install_galaxy_option()
+@options.no_cleanup_option()
 @options.test_data_option()
 @options.dependency_resolvers_option()
 @options.job_config_option()

planemo/commands/cmd_test.py

@@ -84,6 +84,7 @@
 )
 @options.galaxy_root_option()
 @options.install_galaxy_option()
+@options.no_cleanup_option()
 @options.test_data_option()
 @options.tool_data_table_option()
 @options.dependency_resolvers_option()

planemo/commands/cmd_tool_factory.py

@@ -9,6 +9,7 @@
 @click.command('tool_factory')
 @options.galaxy_root_option()
 @options.install_galaxy_option()
+@options.no_cleanup_option()
 @options.test_data_option()
 @options.dependency_resolvers_option()
 @options.job_config_option()

planemo/galaxy_config.py

@@ -200,7 +200,8 @@ def config_join(*args):
 
         yield GalaxyConfig(galaxy_root, config_directory, env, test_data_dir)
     finally:
-        if created_config_directory:
+        cleanup = not kwds.get("no_cleanup", False)
+        if created_config_directory and cleanup:
             shutil.rmtree(config_directory)
 
 

planemo/options.py

@@ -149,6 +149,14 @@ def optional_project_arg(exists=True):
     )
 
 
+def no_cleanup_option():
+    return click.option(
+        "--no_cleanup",
+        is_flag=True,
+        help=("Do not cleanup temp files created for and by Galaxy.")
+    )
+
+
 def docker_cmd_option():
     return click.option(
         '--docker_cmd',