BF: orchestrators: Fetch with --recurse-submodules=no

By default 'git fetch' will try to fetch submodules if the recorded
commit isn't available locally.  Avoid this because 1) with the
upcoming 0.13 release of Datalad, update() try to fetch an commit even
if it isn't in a ref that's brought down by the initial fetch [*] and
2) submodule.c hard codes 'origin' as a fallback to fetch from, so the
fetch is likely to fail, as 'run' names remotes by the resource name.

[*] See DataLad's dbd84e5662 (ENH: update: Try to fetch submodule
    commit explicitly if needed, 2020-02-07).

Fixes gh-499.

Author: kyleam

reproman/support/jobs/orchestrators.py

@@ -921,7 +921,8 @@ def fetch(self, on_remote_finish=None):
         ref = self.job_refname
         lgr.info("Updating local dataset with changes from '%s'",
                  resource_name)
-        self.ds.repo.fetch(resource_name, "{0}:{0}".format(ref))
+        self.ds.repo.fetch(resource_name, "{0}:{0}".format(ref),
+                           recurse_submodules="no")
         self.ds.update(sibling=resource_name,
                        merge=True, recursive=True)
         lgr.info("Getting outputs from '%s'", resource_name)

reproman/support/jobs/tests/test_orchestrators.py

@@ -647,3 +647,21 @@ def test_orc_datalad_concurrent_slurm(check_orc_datalad_concurrent, ssh_slurm):
     check_orc_datalad_concurrent(ssh_slurm,
                                  orcs.DataladLocalRunOrchestrator,
                                  "slurm")
+
+
+def test_orc_datalad_pair_submodule(job_spec, dataset, shell):
+    # Smoke test that triggers the failure from gh-499
+    with chpwd(dataset.path):
+        dataset.create("sub")
+        dataset.save()
+
+        job_spec["_resolved_command_str"] = "sh -c 'echo foo >sub/foo'"
+        job_spec["inputs"] = []
+        job_spec["outputs"] = []
+
+        orc = orcs.DataladPairOrchestrator(
+            shell, submission_type="local", job_spec=job_spec)
+        orc.prepare_remote()
+        orc.submit()
+        orc.follow()
+        orc.fetch()