Allow selection of python version when starting managed Galaxy

planemo/galaxy/run.py

@@ -6,7 +6,10 @@
 from six.moves import shlex_quote
 
 from planemo.io import info, shell_join
-from planemo.virtualenv import create_command
+from planemo.virtualenv import (
+    create_command,
+    DEFAULT_PYTHON_VERSION,
+)
 
 
 # Activate galaxy's virtualenv if present (needed for tests say but not for
@@ -39,7 +42,7 @@ def setup_venv(ctx, kwds):
         return ""
 
     create_template_params = {
-        'create_virtualenv': create_command("$GALAXY_VIRTUAL_ENV")
+        'create_virtualenv': create_command("$GALAXY_VIRTUAL_ENV", kwds.get('galaxy_python_version', None))
     }
     return shell_join(
         locate_galaxy_virtualenv(ctx, kwds),
@@ -55,6 +58,9 @@ def locate_galaxy_virtualenv(ctx, kwds):
         workspace = ctx.workspace
         galaxy_branch = kwds.get("galaxy_branch") or "master"
         shared_venv_path = os.path.join(workspace, "gx_venv")
+        galaxy_python_version = kwds.get('galaxy_python_version', DEFAULT_PYTHON_VERSION)
+        if galaxy_python_version != DEFAULT_PYTHON_VERSION:
+            shared_venv_path = "%s_%s" % (shared_venv_path, galaxy_python_version)
         if galaxy_branch != "master":
             shared_venv_path = "%s_%s" % (shared_venv_path, galaxy_branch)
         venv_command = CACHED_VIRTUAL_ENV_COMMAND % shlex_quote(shared_venv_path)

planemo/options.py

@@ -129,6 +129,16 @@ def galaxy_email_option():
     )
 
 
+def galaxy_python_version():
+    return planemo_option(
+        '--galaxy_python_version',
+        use_global_config=True,
+        default='2.7',
+        type=click.Choice(['2', '2.7', '3', '3.3', '3.4', '3.5', '3.6', '3.7']),
+        help="Python version to start Galaxy under",
+    )
+
+
 def galaxy_root_option():
     return planemo_option(
         "--galaxy_root",
@@ -1059,6 +1069,7 @@ def galaxy_config_options():
 def galaxy_target_options():
     return _compose(
         galaxy_root_option(),
+        galaxy_python_version(),
         galaxy_database_seed_option(),
         extra_tools_option(),
         install_galaxy_option(),

planemo/virtualenv.py

@@ -9,6 +9,9 @@
 from galaxy.tools.deps.commands import which
 
 
+DEFAULT_PYTHON_VERSION = "2.7"
+
+
 def create_and_exit(virtualenv_path, **kwds):
     sys.argv = ["virtualenv", virtualenv_path]
     python = kwds.get("python", None)
@@ -17,7 +20,7 @@ def create_and_exit(virtualenv_path, **kwds):
     return virtualenv.main()
 
 
-def create_command(virtualenv_path):
+def create_command(virtualenv_path, galaxy_python_version=None):
     """ If virtualenv is on Planemo's path use it, otherwise use the planemo
     subcommand virtualenv to create the virtualenv.
     """
@@ -34,11 +37,13 @@ def create_command(virtualenv_path):
 
     command = base_command
 
-    # If planemo is running in a Python 3 environment but Python 2.7
-    # is available for Galaxy, use it.
-    python27 = which("python2.7")
-    if python27:
-        python27 = os.path.abspath(python27)
-        command.extend(["-p", python27])
+    # Create a virtualenv with the selected python version.
+    # default to 2.7
+    if galaxy_python_version is None:
+        galaxy_python_version = DEFAULT_PYTHON_VERSION
+    python = which("python%s" % galaxy_python_version)
+    if python:
+        python = os.path.abspath(python)
+        command.extend(["-p", python])
     command.append(virtualenv_path)
     return " ".join(command)

tests/test_cmd_serve.py

@@ -13,6 +13,7 @@
     PROJECT_TEMPLATES_DIR,
     skip_if_environ,
     skip_unless_environ,
+    skip_unless_executable,
     target_galaxy_branch,
     TEST_DATA_DIR,
     TEST_REPOS_DIR,
@@ -28,6 +29,12 @@ class ServeTestCase(CliTestCase):
     def test_serve(self):
         self._launch_thread_and_wait(self._run)
 
+    @skip_if_environ("PLANEMO_SKIP_GALAXY_TEST")
+    @skip_unless_executable("python3")
+    def test_serve_python3(self):
+        extra_args = ['--galaxy_python_version', '3', '--galaxy_branch', 'release_18.09']
+        self._launch_thread_and_wait(self._run, extra_args)
+
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
     @mark.tests_galaxy_branch
     def test_serve_daemon(self):