From 377a733d970ad96364af576a1448142bcb49e1a6 Mon Sep 17 00:00:00 2001
From: Arjun Chennu <achennu@mpi-bremen.de>
Date: Thu, 19 Dec 2019 13:09:28 +0100
Subject: [PATCH 1/3] Bugfix in dataview update_irradiance

Handle case when irradiance is a dict format
---
 microbenthos/dataview/base.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/microbenthos/dataview/base.py b/microbenthos/dataview/base.py
index dbd49c9..b020db5 100644
--- a/microbenthos/dataview/base.py
+++ b/microbenthos/dataview/base.py
@@ -364,9 +364,10 @@ def update_irradiance(self):
             self.logger.debug('No irradiance info found')
 
         else:
-
             # load irradiance cycle info
-            linfo = dict(irradiance.attrs)
+            # irradiance might be hdf.Dataset or a dict
+            linfo = dict(getattr(irradiance, 'attrs',
+                                 irradiance['metadata']))
             self.diel_period = PhysicalField(linfo['hours_total'])
             self.diel_zenith = PhysicalField(linfo['zenith_time'])
 

From 6f930bd6dedc419f7d5959cfa098f60cf3cc7723 Mon Sep 17 00:00:00 2001
From: Arjun Chennu <achennu@mpi-bremen.de>
Date: Thu, 19 Dec 2019 13:09:58 +0100
Subject: [PATCH 2/3] Fixes in cli for export & added --version

export model command roundtrips better
---
 microbenthos/cli.py | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/microbenthos/cli.py b/microbenthos/cli.py
index af1b3de..19b0560 100644
--- a/microbenthos/cli.py
+++ b/microbenthos/cli.py
@@ -6,6 +6,7 @@
 
 import click
 from pathlib import Path
+from . import __version__
 
 try:
     import click_completion
@@ -173,6 +174,7 @@ def _simtime_total_callback(ctx, param, value):
 @click.option('--logger',
               help='Set specified logger to loglevel (example: microbenthos.model 20)',
               multiple=True, type=(str, click.IntRange(10, 40)))
+@click.version_option(version=__version__)
 def cli(verbosity, logger):
     """Console entry point for microbenthos"""
     loglevel = 0
@@ -288,6 +290,11 @@ def cli_simulate(model_file, output_dir, exporter, overwrite, compression,
     click.echo('Loading model from {}'.format(model_file))
     with open(model_file, 'r') as fp:
         defs = yaml.unsafe_load(fp)
+
+    if 'model' not in defs and 'domain' in defs:
+        # model is not under a separate key, so insert it under "model"
+        defs = dict(model=defs)
+
     if 'simulation' not in defs:
         defs['simulation'] = {}
 
@@ -475,7 +482,8 @@ def export_video(datafile, outfile, overwrite,
 
 @export.command('model')
 @click.argument('model_file', type=click.File())
-@click.option('--key', help='Load this key from the input file')
+@click.option('--key', help='Load this key from the input file',
+              default="model")
 @click.option('-v', '--verbose', is_flag=True, default=False,
               help='Set this to see verbose output')
 def export_model(model_file, key, verbose):
@@ -502,9 +510,12 @@ def export_model(model_file, key, verbose):
         from pprint import pformat
         if verbose:
             click.secho('Validated dictionary!', fg='green')
-
+        model_definition = dict(model=valid)
         click.secho(
-            yaml.dump(valid, indent=4, explicit_start=True, explicit_end=True),
+            yaml.dump(model_definition,
+                      indent=4,
+                      explicit_start=True,
+                      explicit_end=True),
             fg='yellow')
 
     except ValueError:

From 5155c034c4e8885f9ac731b42760bfe1302fc469 Mon Sep 17 00:00:00 2001
From: Arjun Chennu <achennu@mpi-bremen.de>
Date: Thu, 19 Dec 2019 17:29:17 +0100
Subject: [PATCH 3/3] Bump version: 0.13 --> 0.14

---
 .bumpversion.cfg         | 2 +-
 docs/conf.py             | 4 ++--
 microbenthos/__init__.py | 2 +-
 setup.py                 | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index aaf1ffe..ef57a9d 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.13
+current_version = 0.14
 commit = False
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)(\.(?P<patch>\d+))?
diff --git a/docs/conf.py b/docs/conf.py
index e98bf1f..0c72b13 100755
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -87,9 +87,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "0.13"
+version = "0.14"
 # The full version, including alpha/beta/rc tags.
-release = "0.13"
+release = "0.14"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/microbenthos/__init__.py b/microbenthos/__init__.py
index df0af76..72b10fe 100644
--- a/microbenthos/__init__.py
+++ b/microbenthos/__init__.py
@@ -3,7 +3,7 @@
 
 __author__ = """Arjun Chennu"""
 __email__ = 'achennu@mpi-bremen.de'
-__version__ = '0.13'
+__version__ = '0.14'
 
 import logging
 
diff --git a/setup.py b/setup.py
index af6276f..f8dafc4 100644
--- a/setup.py
+++ b/setup.py
@@ -44,7 +44,7 @@ def get_description():
 
 setup(
     name='microbenthos',
-    version='0.13',
+    version='0.14',
     description= \
         "Modeling framework for microbenthic habitats useful for studies in "
         "biogeochemistry and marine microbial ecology.",