Merge pull request #1265 from mvdbeek/autoupdate_cmd_fixes

Allow running autoupdate against external server

planemo/commands/cmd_autoupdate.py

@@ -73,6 +73,7 @@ def skip_requirements_option() -> Callable:
 @test_option()
 @skiplist_option()
 @skip_requirements_option()
+@options.serve_engine_option()
 @options.test_options()
 @options.galaxy_target_options()
 @options.galaxy_config_options()
@@ -81,6 +82,7 @@ def skip_requirements_option() -> Callable:
 @options.fail_level_option()
 @options.galaxy_url_option()
 @options.galaxy_user_key_option()
+@options.galaxy_admin_key_option()
 @command_function
 def cli(ctx, paths, **kwds):  # noqa C901
     """Auto-update tool requirements by checking against Conda and updating if newer versions are available."""
@@ -126,7 +128,7 @@ def cli(ctx, paths, **kwds):  # noqa C901
 
     if modified_workflows and not kwds.get("dry_run"):
         assert is_galaxy_engine(**kwds)
-        if kwds.get("engine") != "external_galaxy":
+        if kwds.get("engine") != "external_galaxy" or kwds.get("galaxy_admin_key"):
             kwds["install_most_recent_revision"] = True
             kwds["install_resolver_dependencies"] = False
             kwds["install_repository_dependencies"] = False

tests/test_cmd_autoupdate.py

@@ -82,10 +82,9 @@ def test_autoupdate_no_update_needed(self):
     def test_autoupdate_workflow(self):
         """Test autoupdate command for a workflow is needed."""
         with self._isolate_with_test_data("wf_repos/autoupdate_tests") as f:
-            wf_file = os.path.join(f, "diff-refactor-test.ga")
-            autoupdate_command = ["autoupdate", wf_file, "--galaxy_branch", "dev"]  # need >= 21.05
+            wf_file = os.path.realpath(os.path.join(f, "diff-refactor-test.ga"))
+            autoupdate_command = ["autoupdate", wf_file]
             result = self._runner.invoke(self._cli.planemo, autoupdate_command)
-
             assert f"Auto-updating workflow {wf_file}" in result.output
             with open(wf_file) as g:
                 wf = json.load(g)