Install repos for all tested artifacts

Author: mvdbeek

planemo/engine/galaxy.py

@@ -47,10 +47,9 @@ class GalaxyEngine(BaseEngine, metaclass=abc.ABCMeta):
     def _run(self, runnables, job_paths):
         """Run job in Galaxy."""
         results = []
-        for runnable, job_path in zip(runnables, job_paths):
-            self._ctx.vlog(f"Serving artifact [{runnable}] with Galaxy.")
-            with self.ensure_runnables_served([runnable]) as config:
-                self._ctx.vlog(f"Running job path [{job_path}]")
+        with self.ensure_runnables_served(runnables) as config:
+            for runnable, job_path in zip(runnables, job_paths):
+                self._ctx.log(f"Running [{runnable}] - [{job_path}] with Galaxy.")
                 if self._ctx.verbose:
                     self._ctx.log(f"Running Galaxy with API configuration [{config.user_api_config}]")
                 run_response = execute(self._ctx, config, runnable, job_path, **self._kwds)

planemo/galaxy/workflows.py

@@ -8,6 +8,7 @@
     Dict,
     List,
 )
+from typing import TYPE_CHECKING
 from urllib.parse import urlparse
 
 import yaml
@@ -27,11 +28,20 @@
 
 from planemo.galaxy.api import gi
 from planemo.io import warn
+from typing_extensions import NamedTuple
+
+if TYPE_CHECKING:
+    from ephemeris.shed_tools import InstallRepoDict
 
 FAILED_REPOSITORIES_MESSAGE = "Failed to install one or more repositories."
 GALAXY_WORKFLOWS_PREFIX = "gxid://workflows/"
 
 
+class InstalledShedRepos(NamedTuple):
+    installed_repositories: List["InstallRepoDict"]
+    updated_repositories: List["InstallRepoDict"]
+
+
 def load_shed_repos(runnable):
     if runnable.type.name != "galaxy_workflow":
         return []