planemo uses internal gx_venv even if galaxy_root brings its own .venv #1343
Description
To reproduce rename planemo's .planemo/gx_venv*, then run e.g. planemo test with --galaxy_root set to an existing instance of Galaxy with its .venv set up.
Expected behavior: planemo should use the root Galaxy's .venv
Actual behavior: planemo fails after completing all tests with
Traceback (most recent call last):
File "/home/wolma/planemo_39/bin/planemo", line 8, in <module>
sys.exit(planemo())
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/click/decorators.py", line 84, in new_func
return ctx.invoke(f, obj, *args, **kwargs)
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/planemo/cli.py", line 102, in handle_blended_options
return f(*args, **kwds)
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/planemo/commands/cmd_test.py", line 75, in cli
return_value = test_runnables(ctx, runnables, original_paths=uris, **kwds)
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/planemo/engine/test.py", line 13, in test_runnables
test_data = engine.test(runnables, test_timeout=kwds.get("test_timeout"))
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/planemo/engine/interface.py", line 76, in test
test_results = self._collect_test_results(test_cases, test_timeout)
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/planemo/engine/interface.py", line 90, in _collect_test_results
run_responses = self._run_test_cases(test_cases, test_timeout)
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/planemo/engine/galaxy.py", line 119, in _run_test_cases
pass
File "/usr/lib64/python3.9/contextlib.py", line 126, in __exit__
next(self.gen)
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/planemo/engine/galaxy.py", line 137, in ensure_runnables_served
yield config
File "/usr/lib64/python3.9/contextlib.py", line 126, in __exit__
next(self.gen)
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/planemo/galaxy/serve.py", line 91, in serve_daemon
config.kill()
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/planemo/galaxy/config.py", line 1049, in kill
stop_gravity(virtual_env=self.virtual_env_dir, gravity_state_dir=self.gravity_state_dir, env=self.env)
File "/home/wolma/planemo_39/lib64/python3.9/site-packages/planemo/io.py", line 206, in stop_gravity
subprocess.check_call([gravity_bin, "--state-dir", gravity_state_dir, "shutdown"], env=environ)
File "/usr/lib64/python3.9/subprocess.py", line 368, in check_call
retcode = call(*popenargs, **kwargs)
File "/usr/lib64/python3.9/subprocess.py", line 349, in call
with Popen(*popenargs, **kwargs) as p:
File "/usr/lib64/python3.9/subprocess.py", line 951, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/usr/lib64/python3.9/subprocess.py", line 1821, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: '/home/wolma/.planemo/gx_venv_3/bin/galaxyctl'
because it looks for gravity in the expected planemo-internal place.
A workaround when you haven't set up the planemo venv is to run planemo with --no_cache_galaxy, but since planemo manages to start gravity no matter what, it should also be able to stop it again.