restore py3 commits

doc/conf.py

@@ -12,16 +12,20 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys, os
+import sys
+import os
 
 from mock import Mock as MagicMock
 
+
 class Mock(MagicMock):
     __all__ = []
     __version__ = "1.6"
+
     @classmethod
     def __getattr__(cls, name):
-            return Mock()
+        return Mock()
+
 
 # Mock modules so that we can build on readthedocs.org
 MOCK_MODULES = ['pcraster']
@@ -47,20 +51,20 @@ def __getattr__(cls, name):
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = ['sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.autosectionlabel',
-    ]
+              'sphinx.ext.autosummary',
+              'sphinx.ext.todo',
+              'sphinx.ext.coverage',
+              'sphinx.ext.viewcode',
+              'sphinx.ext.mathjax',
+              'sphinx.ext.napoleon',
+              'sphinx.ext.autosectionlabel',
+              ]
 
 napoleon_google_docstring = False
 napoleon_use_param = False
 napoleon_use_ivar = True
 
-todo_include_todos=True
+todo_include_todos = True
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -211,7 +215,6 @@ def __getattr__(cls, name):
 ]
 
 
-
 # -- Options for Epub output ----------------------------------------------
 
 # Bibliographic Dublin Core info.
@@ -231,5 +234,3 @@ def __getattr__(cls, name):
 
 # A list of files that should not be packed into the epub file.
 epub_exclude_files = ['search.html']
-
-

doc/running_GLOFRIM.rst

@@ -104,16 +104,27 @@ communicate with that model via BMI. Add only models which are part of the (coup
 .. note::
     CMF only listens to the configuration file if it is called *input_flood.nam*, therefore the original configuration file should be called different, for instance input_flood.nam.org.
 
-The **coupling** section contains general settings for the exchanges between models.::
+The **coupling** section contains general settings for the exchanges between models.
+**dt** indicates the time step at which information should be exchanged between models. This usually should be at least one full time step of the model that runs with the largest time step.
+In the example we assume that a WFlow model dictates daily time steps, and that a coupled lisflood model
+has smaller time steps. The section furthermore contains projections of the different model instances. These can be provided in EPSG code (e.g. "EPSG:4326" would indicate regular WGS84 lat lon projection) or as proj string, as shown in the example.::
 
     [coupling]
     # timestep for exchanges [sec]
     dt=86400
+    WFL=+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs
+    LFP=+proj=utm +zone=34 +south +ellps=WGS84 +datum=WGS84 +units=m +no_defs
 
-The **exchanges** section contains the information about how the models communicate on run time. This part has a slightly complex syntax as it contains a lot of information. 
+
+The **exchanges** section contains the information about how the models communicate on run time. This part has a slightly complex syntax as it contains a lot of information.
 Every line indicates one exchange from the left (upstream/get) model.variable to the right (downstream/set) model.variable. This can be further extended by multipliers which can be model variables 
-or scalar values in order to make sure the variable units match. Finally behind the @ the spatial location to get (upstream) and set (downstream) the model variables. 
-Current options are @1d,  @1d_us (the most upstream 1d cells or nodes) and @grid_us (the upstream cell for each grid cell)::
+or scalar values in order to make sure the variable units match. Behind the @ the spatial location to get (upstream) and set (downstream) the model variables.
+Current options are @1d,  @1d_us (the most upstream 1d cells or nodes) and @grid_us (the upstream cell for each grid cell). Finally, behind the location of the downstream/set model, a user may set a `|` sign and then specify the grid cell coordinates (in the projection of the model) in python list form, that should be coupled with the upstream grid cells of the upstream/get model. This should be done as follows::
+
+    [[x1, y1], [x2, y2], [x3, y3], ...., [xn, yn]]
+
+
+GLOFRIM will then only couple these specific grid cells rather than automatically lookup which cells are coupled. This is an important feature when river networks of the upstream/get and downstream/set models are not entirely commensurate. Examples are provided below::
 
     [exchanges]
     # setup exchanges which are executed during the coupled update function. 
@@ -129,6 +140,12 @@ Current options are @1d,  @1d_us (the most upstream 1d cells or nodes) and @grid
     PCR.runoff*cellArea=DFM.rain*ba*1000@1d
     PCR.discharge*86400@grid_us=DFM.rain*ba*1000@1d_us
 
+    # Example 3: upstream WFL discharge (RiverRunoff) is fed into a limited set of user specified LFP grid cells at the upstream bounds of the model domain.
+    # The user must ensure that the selected grid cells are overlapping with the intended
+    # WFL major streams.
+    WFL.RiverRunoff*86400@grid_us=LFP.SGCQin*86400@1d_us|[[677250, 8346250], [733250, 8428750], [839750, 8398750], [688750, 8452250], [792750, 8295750]]
+
+
 .. note::
     Note that only fluxes were tested as receiving variables. While states can be used as well, their rather static nature (i.e. using m3 instead of m3/s)
     can lead to numerical stabilities per time step. Careful testing of the established model coupling is thus necessary!

environment.yml

@@ -1,21 +1,22 @@
-name: glofrim
+name: glofrim3
 
 channels:
   - conda-forge
+  - defaults
 
 dependencies:
-  - python=2.7
-  - numpy==1.14.5
-  - netcdf4>=1.3.1
-  - rasterio>=1.0
-  - rtree>=0.8.3
-  - click>=6.7
-  - configparser>=3.5.0
-  - python-dateutil>=2.2
-  - pytz>=2014.3
-  - faulthandler>=2.3
-  - six>=1.6.1
-  - pip>=9.0.3
+  - configparser
+  - click>=7.0
+  - netcdf4>=1.4.2
+  - numpy
+  - pcraster
+  - pip>=20.0
+  - python>=3.7
+  - python-dateutil>=2.8
+  - pytz>=2019.3
+  - rasterio>=1.1
+  - rtree>=0.9.3
+  - six>=1.14
+  - wflow
   - pip:
-    - bmi-python
-    - git+https://github.com/openearth/glofrim.git
+    - bmi-python>=0.2.6

glofrim.ini

@@ -1,30 +1,29 @@
-[engines]
-# path to model engines; only required for the non-python models used
-# these settings can also be set in environment.env
-CMF = /home/dirk/Models/cama-flood_bmi_v3.6.2/src/libcama.so                
-DFM = /home/dirk/Models/dflowfm-1.1.201/lib/libdflowfm.so                  
-LFP = /home/dirk/repos/LISFLOOD-BMI/lisflood-bmi-v5.9/liblisflood.so
-
-[models]
-# alternative root dir for relative ini-file paths, by default the directory of this ini file is used; 
-# this setting can also be set in environment.env
-root_dir = /home/dirk/repos/model_test_data/test_Elbe                       
-# reference to inifiles
-# all referenced inifiles are run during update
-# format: model_short_name = path/to/configuratoin_file
-PCR=PCR_Elbe/setup_PCR_30min_Elbe.ini
-DFM=DFM_Elbe/Elbe_1way_1d2dFM_400m_3200m.mdu
-
-
-[coupling]
-# timestep for exchanges [sec]
-dt=86400
-
-[exchanges]
-# setup exchanges which are executed during the coupled update function. 
-# Note that the user should make sure that both sides should represent a volume [m3]
-# format: From_model.var1*var2*multiplier@index = To_model.var*multiplier@index
-# the multiplier is optional
-# if no index is set the whole 2D domain is coupled
-PCR.runoff*cellArea=DFM.rain*ba*0.1@1d
-PCR.discharge*86400@grid_us=DFM.rain*ba*0.1@1d_us
+[engines]
+# path to model engines; only required for the non-python models used
+# these settings can also be set in environment.env
+# CMF = /home/dirk/Models/cama-flood_bmi_v3.6.2/src/libcama.so                
+# DFM = /home/dirk/Models/dflowfm-1.1.201/lib/libdflowfm.so                  
+LFP = /home/hcwinsemius/lisflood/liblisflood.so
+
+[models]
+# alternative root dir for relative ini-file paths, by default the directory of this ini file is used; 
+# this setting can also be set in environment.env
+root_dir = /home/hcwinsemius/git/glofrim/tests/model_test_data
+# reference to inifiles
+# all referenced inifiles are run during update
+# format: model_short_name = path/to/configuratoin_file
+# PCR=PCR_Elbe/setup_PCR_30min_Elbe.ini
+# DFM=DFM_Elbe/Elbe_1way_1d2dFM_400m_3200m.mdu
+LFP=LFP_data/LFPmodel_Elbe.par
+
+[coupling]
+# timestep for exchanges [sec]
+dt=86400
+
+[exchanges]
+# setup exchanges which are executed during the coupled update function. 
+# Note that the user should make sure that both sides should represent a volume [m3]
+# format: From_model.var1*var2*multiplier@index = To_model.var*multiplier@index
+# the multiplier is optional
+# if no index is set the whole 2D domain is coupled
+# PCR.discharge*86400@grid_us=DFM.rain*ba*0.1@1d_us

glofrim/__init__.py

@@ -1,8 +1,9 @@
-from pcr_bmi import PCR
-from cmf_bmi import CMF
-from dfm_bmi import DFM
-from wfl_bmi import WFL
-from lfp_bmi import LFP
-from glofrim_bmi import Glofrim
-from spatial_coupling import SpatialCoupling
-from grids import UCGrid, UGrid, RGrid, Network1D
+from glofrim.pcr_bmi import PCR
+from glofrim.cmf_bmi import CMF
+from glofrim.dfm_bmi import DFM
+from glofrim.wfl_bmi import WFL
+from glofrim.lfp_bmi import LFP
+from glofrim.glofrim_bmi import Glofrim
+from glofrim.spatial_coupling import SpatialCoupling
+from glofrim.grids import UCGrid, UGrid, RGrid, Network1D
+from glofrim import nb