Merge pull request #196 from epigen/dev

Fix failure summarization message and allow non-string argument to option in pipeline_args

doc/source/changelog.rst

@@ -1,6 +1,14 @@
 Changelog
 ******************************
 
+- **v0.7.1** (*2017-11-15*):
+
+  - Fixed
+
+      - No longer falsely display that there's a submission failure.
+
+      - Allow non-string values to be unquoted in the ``pipeline_args`` section.
+
 - **v0.7** (*2017-11-15*):
 
   - New

looper/_version.py

@@ -1 +1 @@
-__version__ = "0.7.0"
+__version__ = "0.7.1"

looper/looper.py

@@ -522,7 +522,7 @@ def __call__(self, args, remaining_args):
                 samples_by_reason[SUBMISSION_FAILURE_MESSAGE] |= fails
                 failed_samples_by_pipeline[pl_key] |= fails
 
-        failed_sub_samples = samples_by_reason[SUBMISSION_FAILURE_MESSAGE]
+        failed_sub_samples = samples_by_reason.get(SUBMISSION_FAILURE_MESSAGE)
         if failed_sub_samples:
             _LOGGER.info("\n{} samples with at least one failed job submission: {}".
                          format(len(failed_sub_samples),

looper/models.py

@@ -1196,8 +1196,15 @@ def get_arg_string(self, pipeline_name):
 
         def make_optarg_text(opt, arg):
             """ Transform flag/option into CLI-ready text version. """
-            return "{} {}".format(opt, _os.path.expandvars(arg)) \
-                    if arg else opt
+            if arg:
+                try:
+                    arg = _os.path.expandvars(arg)
+                except TypeError:
+                    # Rely on direct string formatting of arg.
+                    pass
+                return "{} {}".format(opt, arg)
+            else:
+                return opt
 
         def create_argtext(name):
             """ Create command-line argstring text from config section. """