Merge pull request #50 from pepkit/dev

v0.9.1 bugfix release

doc/source/changelog.rst

@@ -1,5 +1,12 @@
 Changelog
 ******************************
+- **v0.9.1** (*2018-06-30*):
+
+  - Fixed
+
+    - Fixed several bugs with ``looper summarize`` that caused failure on edge cases.
+
+
 - **v0.9.0** (*2018-06-25*):
 
   - New
@@ -8,7 +15,7 @@ Changelog
 
     - Add ``allow-duplicate-names`` command-line options
 
-    - Allow any variables in environment config files or other ``compute`` sections to be used in submission templates
+    - Allow any variables in environment config files or other ``compute`` sections to be used in submission templates. This allows looper to be used with containers.
 
     - Add nice universal project-level HTML reporting
 

doc/source/usage.rst

@@ -22,7 +22,7 @@ Here you can see the command-line usage instructions for the main looper command
 
 .. code-block:: none
 
-	version: 0.9.0-dev
+	version: 0.9.1
 	usage: looper [-h] [-V] [--logfile LOGFILE] [--verbosity {0,1,2,3,4}] [--dbg]
 	              {run,summarize,destroy,check,clean} ...
 	
@@ -53,7 +53,7 @@ Here you can see the command-line usage instructions for the main looper command
 
 .. code-block:: none
 
-	version: 0.9.0-dev
+	version: 0.9.1
 	usage: looper run [-h] [-t TIME_DELAY] [--ignore-flags]
 	                  [--allow-duplicate-names] [--compute COMPUTE] [--env ENV]
 	                  [--limit LIMIT] [--lump LUMP] [--lumpn LUMPN]
@@ -106,7 +106,7 @@ Here you can see the command-line usage instructions for the main looper command
 
 .. code-block:: none
 
-	version: 0.9.0-dev
+	version: 0.9.1
 	usage: looper summarize [-h] [--file-checks] [-d]
 	                        [--exclude-protocols [EXCLUDE_PROTOCOLS [EXCLUDE_PROTOCOLS ...]]
 	                        | --include-protocols
@@ -137,7 +137,7 @@ Here you can see the command-line usage instructions for the main looper command
 
 .. code-block:: none
 
-	version: 0.9.0-dev
+	version: 0.9.1
 	usage: looper destroy [-h] [--file-checks] [-d]
 	                      [--exclude-protocols [EXCLUDE_PROTOCOLS [EXCLUDE_PROTOCOLS ...]]
 	                      | --include-protocols
@@ -168,7 +168,7 @@ Here you can see the command-line usage instructions for the main looper command
 
 .. code-block:: none
 
-	version: 0.9.0-dev
+	version: 0.9.1
 	usage: looper check [-h] [-A] [-F [FLAGS [FLAGS ...]]] [--file-checks] [-d]
 	                    [--exclude-protocols [EXCLUDE_PROTOCOLS [EXCLUDE_PROTOCOLS ...]]
 	                    | --include-protocols
@@ -204,7 +204,7 @@ Here you can see the command-line usage instructions for the main looper command
 
 .. code-block:: none
 
-	version: 0.9.0-dev
+	version: 0.9.1
 	usage: looper clean [-h] [--file-checks] [-d]
 	                    [--exclude-protocols [EXCLUDE_PROTOCOLS [EXCLUDE_PROTOCOLS ...]]
 	                    | --include-protocols

looper/__init__.py

@@ -58,7 +58,7 @@ def setup_looper_logger(level, additional_locations=None, devmode=False):
     fmt = DEV_LOGGING_FMT if devmode else DEFAULT_LOGGING_FMT
 
     # Establish the logger.
-    LOOPER_LOGGER = logging.getLogger("looper")
+    LOOPER_LOGGER = logging.getLogger()
     # First remove any previously-added handlers
     LOOPER_LOGGER.handlers = []
     LOOPER_LOGGER.propagate = False
@@ -94,7 +94,10 @@ def setup_looper_logger(level, additional_locations=None, devmode=False):
 
     # Add the handlers.
     formatter = logging.Formatter(fmt=(fmt or DEFAULT_LOGGING_FMT))
+
     for loc in where:
+        if not loc:
+            continue
         if isinstance(loc, str):
             # File destination
             dirpath = os.path.abspath(os.path.dirname(loc))

looper/_version.py

@@ -1 +1 @@
-__version__ = "0.9.0"
+__version__ = "0.9.1"