Drop nose

[nsoranzo]

It's deprecated and unmaintained, and breaks under Python 3.10 (xref. galaxyproject/planemo#1234 ).

TODO:

• lib/galaxy_test/base/instrument.py
• lib/galaxy_test/driver/driver_util.py
• Fix converter tests

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these contributions under Galaxy's current license.
• I agree to allow the Galaxy committers to license these and all my past contributions to the core galaxy codebase under the MIT license. If this condition is an issue, uncheck and just let us know why with an e-mail to galaxy-committers@lists.galaxyproject.org.

[jmchilton]

This is needed by Planemo though right? Just making sure there is a plan for a new approach or does pytest accomplish capturing this data some other way?

[mvdbeek]

Only if we run tests via ./run_tests.sh, we could use LocalManagedGalaxyEngine in planemo, which would converge nicely with testing non-tool artefacts. I was wondering what your thoughts on that are.

[nsoranzo]

@jmchilton @mvdbeek What's the way forward here? Marius proposed on Matrix this patch for Planemo:

diff --git a/planemo/engine/test.py b/planemo/engine/test.py
index 0bfb4119..206dad37 100644
--- a/planemo/engine/test.py
+++ b/planemo/engine/test.py
@@ -17,18 +17,8 @@ def test_runnables(ctx, runnables, original_paths=None, **kwds):
     test_engine_testable = {RunnableType.galaxy_tool, RunnableType.galaxy_datamanager, RunnableType.directory}
     enable_test_engines = any(r.type not in test_engine_testable for r in runnables)
     enable_test_engines = enable_test_engines or engine_type != "galaxy"
-    if enable_test_engines:
-        ctx.vlog("Using test engine type %s" % engine_type)
-        with engine_context(ctx, **kwds) as engine:
-            test_data = engine.test(runnables)
-            ctx.vlog("engine.test returning [%s]" % test_data)
-            return_value = handle_reports_and_summary(ctx, test_data.structured_data, kwds=kwds)
-    else:
-        ctx.vlog("Running traditional Galaxy tool tests using run_tests.sh in Galaxy root %s" % engine_type)
-        kwds["for_tests"] = True
-        if kwds.get("update_test_data"):
-            non_copied_runnables = for_paths(original_paths)
-            kwds["test_data_target_dir"] = _find_test_data(non_copied_runnables, **kwds)
-        with galaxy_config(ctx, runnables, **kwds) as config:
-            return_value = run_in_config(ctx, config, **kwds)
-    return return_value
+    ctx.vlog("Using test engine type %s" % engine_type)
+    with engine_context(ctx, **kwds) as engine:
+        test_data = engine.test(runnables)
+        ctx.vlog("engine.test returning [%s]" % test_data)
+        return handle_reports_and_summary(ctx, test_data.structured_data, kwds=kwds)

Should we try to open a PR for planemo with this?

[nsoranzo]

After discussing this at the latest Backend WG meeting, I think the plan is:

• merge Run local galaxy via gravity planemo#1232
• release galaxy-* packages for 22.01 on PyPI
• release new Planemo

Then the converter tests for this PR should pass, and we can merge it. Please correct me if I'm wrong.

[nsoranzo]

It looks like that rebasing on top of #13977 broke the Toolshed tests added to lib/tool_shed/test/functional/ in that PR.
Also converter tests broke after the rebase (framework tests failure seems unrelated).
Help welcome!

[jmchilton]

Taking a quick look at that.