added protection against bad batch inputs with test

gaps/batch.py

@@ -48,6 +48,7 @@ def __init__(self, config):
         config : str
             File path to config json or csv (str).
         """
+
         self._job_tags = None
         self._base_dir, config = _load_batch_config(config)
         self._pipeline_fp = Path(config["pipeline_config"])
@@ -338,7 +339,7 @@ def _check_sets(config, base_dir):
 
 def _enumerated_product(args):
     """An enumerated product function."""
-    yield from zip(product(*(range(len(x)) for x in args)), product(*args))
+    return list(zip(product(*(range(len(x)) for x in args)), product(*args)))
 
 
 def _parse_config(config):
@@ -350,12 +351,30 @@ def _parse_config(config):
     for batch_set in config["sets"]:
         set_tag = batch_set.get("set_tag", "")
         args = batch_set["args"]
+
         if set_tag in sets:
             msg = f"Found multiple sets with the same set_tag: {set_tag!r}"
             raise gapsValueError(msg)
+
+        for key, value in args.items():
+            if isinstance(value, str):
+                msg = ('Batch arguments should be lists but found '
+                       f'"{key}": "{value}"')
+                raise gapsValueError(msg)
+
         sets.add(set_tag)
 
-        for inds, comb in _enumerated_product(args.values()):
+        products = _enumerated_product(args.values())
+        set_str = f' in set "{set_tag}"' if set_tag else ''
+        logger.info(f'Found {len(products)} batch projects{set_str}. '
+                    'Creating jobs...')
+        if len(products) > 1e3:
+            msg = (f'Large number of batch jobs found: {len(products)}! '
+                   'Proceeding, but consider double checking your config.')
+            warn(msg)
+            logger.warning(msg)
+
+        for inds, comb in products:
             arg_combo = dict(zip(args, comb))
             arg_inds = dict(zip(args, inds))
             tag_arg_comb = {

gaps/cli/documentation.py

@@ -132,6 +132,16 @@
 
 Parameters
 ----------
+logging : dict, optional
+    Dictionary containing keyword-argument pairs to pass to
+    `init_logger <https://tinyurl.com/47hakp7f/>`_. This
+    initializes logging for the submission portion of the
+    pipeline. Note, however, that each step (command) will
+    **also** record the submission step log output to a
+    common "project" log file, so it's only ever necessary
+    to use this input if you want a different (lower) level
+    of verbosity than the `log_level` specified in the
+    config for the step of the pipeline being executed.
 pipeline_config : str
     Path to the pipeline configuration defining the commands to
     run for every parametric set.
@@ -163,8 +173,8 @@
             include an underscore, as that is provided during
             concatenation.
 
-
 """
+
 _BATCH_ARGS_DICT = """.. tabs::
 
                 .. group-tab:: JSON/JSON5
@@ -602,6 +612,10 @@ def _batch_command_help():  # pragma: no cover
 
     format_inputs = {}
     template_config = {
+        "logging": {
+            "log_file": None,
+            "log_level": "INFO"
+        },
         "pipeline_config": CommandDocumentation.REQUIRED_TAG,
         "sets": [
             {

tests/test_batch.py

@@ -541,5 +541,24 @@ def test_batch_csv_setup(csv_batch_config):
     assert count_2 == count_0, "Batch did not clear all job files!"
 
 
+def test_bad_str_arg(typical_batch_config):
+    """Test that a string in a batch argument will raise an error (argument
+    parameterizations should be lists)"""
+
+    batch_dir = typical_batch_config.parent
+
+    config = ConfigType.JSON.load(typical_batch_config)
+    config['sets'][0]['args']['project_points'] = 'bad_str'
+    with open(typical_batch_config, 'w') as f:
+        ConfigType.JSON.dump(config, f)
+
+    count_0 = len(list(batch_dir.glob("*")))
+    assert count_0 == 8, "Unknown starting files detected!"
+
+    with pytest.raises(gapsValueError) as exc_info:
+        BatchJob(typical_batch_config).run(dry_run=True)
+        assert 'Batch arguments should be lists' in str(exc_info)
+
+
 if __name__ == "__main__":
     pytest.main(["-q", "--show-capture=all", Path(__file__), "-rapP"])