Add --skip_venv flag for conda, other cases.

jmchilton · jmchilton · commit 9f3957d35521 · 2016-01-13T19:01:09.000Z
Fixes #377 ... or makes it possible to fix it anyway. To preserve conda's environment for test execution run planemo, first install Galaxy's depndencies into the conda environment using: % cd $GALAXY_ROOT % pip install requirements.txt % pip install -r lib/galaxy/dependencies/dev-requirements.txt Then run planemo test, serve, etc... with the --skip_venv flag. % planemo test --skip_venv .
diff --git a/planemo/galaxy_run.py b/planemo/galaxy_run.py
@@ -33,6 +33,9 @@
 
 
 def setup_venv(ctx, kwds):
+    if kwds.get("skip_venv", False):
+        return ""
+
     create_template_params = {
         'create_virtualenv': create_command("$GALAXY_VIRTUAL_ENV")
     }
@@ -67,7 +70,7 @@ def shell_if_wheels(command):
 
 def setup_common_startup_args():
     return set_variable_if_wheels(
-        "COMMON_STARTUP_ARGS", "--skip-venv --dev-wheels"
+        "COMMON_STARTUP_ARGS", "--dev-wheels"
     )
 
 
diff --git a/planemo/galaxy_serve.py b/planemo/galaxy_serve.py
@@ -17,9 +17,6 @@ def serve(ctx, paths, **kwds):
 
     with galaxy_config.galaxy_config(ctx, paths, **kwds) as config:
         # TODO: Allow running dockerized Galaxy here instead.
-        setup_common_startup_args = galaxy_run.set_variable_if_wheels(
-            "COMMON_STARTUP_ARGS", "--skip-venv"
-        )
         setup_venv_command = galaxy_run.setup_venv(ctx, kwds)
         run_script = os.path.join(config.galaxy_root, "run.sh")
         run_script += " $COMMON_STARTUP_ARGS"
@@ -33,7 +30,6 @@ def serve(ctx, paths, **kwds):
         cd_to_galaxy_command = "cd %s" % config.galaxy_root
         cmd = io.shell_join(
             cd_to_galaxy_command,
-            setup_common_startup_args,
             setup_venv_command,
             run_script,
         )
diff --git a/planemo/options.py b/planemo/options.py
@@ -18,6 +18,16 @@ def force_option(what="files"):
     )
 
 
+def skip_venv_option():
+    return click.option(
+        "--skip_venv",
+        is_flag=True,
+        help=("Do not create or source a virtualenv environment for Galaxy, "
+              "this should be used or instance to preserve an externally "
+              "configured virtual environment or conda environment.")
+    )
+
+
 def test_data_option():
     return click.option(
         "--test_data",
@@ -643,6 +653,7 @@ def galaxy_target_options():
         install_galaxy_option(),
         galaxy_branch_option(),
         galaxy_source_option(),
+        skip_venv_option(),
         no_cache_galaxy_option(),
         no_cleanup_option(),
         job_config_option(),

Original file line number	Diff line number	Diff line change
`@@ -33,6 +33,9 @@`
`33`	`33`
`34`	`34`
`35`	`35`	`def setup_venv(ctx, kwds):`
	`36`	`+ if kwds.get("skip_venv", False):`
	`37`	`+ return ""`
	`38`	`+`
`36`	`39`	`create_template_params = {`
`37`	`40`	`'create_virtualenv': create_command("$GALAXY_VIRTUAL_ENV")`
`38`	`41`	`}`
`@@ -67,7 +70,7 @@ def shell_if_wheels(command):`
`67`	`70`
`68`	`71`	`def setup_common_startup_args():`
`69`	`72`	`return set_variable_if_wheels(`
`70`		`- "COMMON_STARTUP_ARGS", "--skip-venv --dev-wheels"`
	`73`	`+ "COMMON_STARTUP_ARGS", "--dev-wheels"`
`71`	`74`	`)`
`72`	`75`
`73`	`76`