Merge branch 'release_24.0' into release_24.1

Author: nsoranzo

lib/galaxy/jobs/handler.py

@@ -188,6 +188,7 @@ def grab_unhandled_items(self):
             self.setup_query()
 
         with self.app.model.engine.connect() as conn:
+            conn = conn.execution_options(**self._grab_conn_opts)
             with conn.begin() as trans:
                 try:
                     proxy = conn.execute(self._grab_query)

lib/galaxy/tool_util/deps/mulled/invfile.lua

@@ -88,14 +88,13 @@ inv.task('build')
     .using(conda_image)
         .withHostConfig({binds = bind_args})
         .run('/bin/sh', '-c', preinstall
-            .. conda_bin .. ' create --quiet --yes -p /usr/local/env --copy  && '
             .. conda_bin .. ' install '
             .. channel_args .. ' '
             .. target_args
-            .. ' --strict-channel-priority -p /usr/local/env --copy --yes '
+            .. ' --strict-channel-priority -p /usr/local --copy --yes '
             .. verbose
             .. postinstall)
-    .wrap('build/dist/env')
+    .wrap('build/dist')
         .at('/usr/local')
         .inImage(destination_base_image)
         .as(repo)

lib/galaxy/tool_util/deps/mulled/mulled_build.py

@@ -314,11 +314,11 @@ def mull_targets(
         if conda_version is not None:
             specs.append(f"conda={conda_version}")
         if mamba_version is not None:
-            specs.append(f"mamba={mamba_version}")
             if mamba_version == "" and not specs:
                 # If nothing but mamba without a specific version is requested,
                 # then only run conda install if mamba is not already installed.
                 mamba_test = "[ '[]' = \"$( conda list --json --full-name mamba )\" ]"
+            specs.append(f"mamba={mamba_version}")
         conda_install = f"""conda install {verbose} --yes {" ".join(f"'{spec}'" for spec in specs)}"""
         involucro_args.extend(["-set", f"PREINSTALL=if {mamba_test} ; then {conda_install} ; fi"])