Merge branch 'dorelease' into 'master'

prepare for release

See merge request deltares/imod/imod-python!76

docs/changelog.rst

@@ -9,6 +9,9 @@ The format is based on `Keep a Changelog`_, and this project adheres to
 [Unreleased]
 ------------
 
+[0.9.0] - 2020-01-19
+--------------------
+
 Added
 ~~~~~
 -  IDF files representing data of arbitrary dimensionality can be opened and
@@ -19,11 +22,15 @@ Added
 -  Writing GDAL rasters using (:meth:`imod.rasterio.save`) and (:meth:`imod.rasterio.write`) auto-detects GDAL driver based on file extension
 -  64-bit IDF files can be opened (:meth:`imod.idf.open`)
 -  64-bit IDF files can be written using (:meth:`imod.idf.save`) and (:meth:`imod.idf.write`) using keyword ``dtype=np.float64``
+-  ``sel`` and ``isel`` methods to ``SeawatModel`` to support taking out a subdomain
+-  Docstrings for the Modflow 6 classes in :mod:`imod.mf6`
+-  :meth:`imod.select.upper_active_layer` function to get the upper active layer from ibound ``xr.DataArray``
 
 Changed
 ~~~~~~~
 
 -  :func:`imod.idf.read` is deprecated, use :mod:`imod.idf.open` instead
+-  :func:`imod.rasterio.read` is deprecated, use :mod:`imod.rasterio.open` instead
 
 Fixed
 ~~~~~

docs/index.rst

@@ -3,11 +3,23 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-iMOD-Python: work with iMOD MODFLOW models in Python
-====================================================
+iMOD-Python: make massive MODFLOW models
+========================================
 
-Work with `iMOD <https://oss.deltares.nl/web/imod>`__ MODFLOW models in
-Python.
+The imod Python package is designed to help you in your MODFLOW groundwater modeling efforts.
+It makes it easy to go from your raw data to a fully defined MODFLOW model, with the aim to make this process reproducable.
+Whether you want to build a simple 2D conceptual model, or a complex 3D regional model with millions of cells,
+imod-python scales automatically by making use of `dask <https://dask.org/>`__.
+
+By building on top of popular Python packages like `xarray <http://xarray.pydata.org/>`__, `pandas <http://pandas.pydata.org/>`__,
+`rasterio <https://rasterio.readthedocs.io/en/latest/>`__ and `geopandas <http://geopandas.org/>`__, a lot of functionality comes
+for free.
+
+Currently we support the creation of the following MODFLOW-based models:
+
+* `USGS MODFLOW 6 <https://www.usgs.gov/software/modflow-6-usgs-modular-hydrologic-model>`__ (:doc:`api/mf6`), structured grids only
+* `iMODFLOW <https://oss.deltares.nl/web/imod>`__ (:doc:`api/flow`)
+* `iMOD-WQ <https://oss.deltares.nl/web/imod>`__ (:doc:`api/wq`), which integrates SEAWAT (density-dependent groundwater flow) and MT3DMS (multi-species reactive transport calculations)
 
 Documentation: https://imod.xyz/
 
@@ -97,6 +109,20 @@ information see :doc:`installation`.
    # with dimensions time, layer, y, x
    da = imod.idf.open('path/to/results/head_*.idf')
 
+   # create a groundwater model
+   # abridged example, see examples for the full code
+   gwf_model = imod.mf6.GroundwaterFlowModel()
+   gwf_model["dis"] = imod.mf6.StructuredDiscretization(
+       top=200.0, bottom=bottom, idomain=idomain
+   )
+   gwf_model["chd"] = imod.mf6.ConstantHead(
+       head, print_input=True, print_flows=True, save_flows=True
+   )
+   simulation = imod.mf6.Modflow6Simulation("ex01-twri")
+   simulation["GWF_1"] = gwf_model
+   simulation.time_discretization(times=["2000-01-01", "2000-01-02"])
+   simulation.write(modeldir)
+
 Authors
 -------
 This Python package was written primarily by Martijn Visser and Huite Bootsma at Deltares.

imod/rasterio.py

@@ -8,6 +8,7 @@
 
 import glob
 import pathlib
+import warnings
 
 import numpy as np
 import xarray as xr
@@ -168,6 +169,14 @@ def _read(path, headersize, nrow, ncol, nodata, dtype):
         return a
 
 
+def read(path, use_cftime=False, pattern=None):
+    warnings.warn(
+        "The imod.rasterio.read() function is deprecated. Instead use imod.rasterio.open().",
+        FutureWarning,
+    )
+    return open(path, use_cftime=False, pattern=None).load()
+
+
 def open(path, use_cftime=False, pattern=None):
     r"""
     Open one or more GDAL supported raster files as an xarray.DataArray.

imod/select/layers.py

@@ -6,15 +6,22 @@
 
 def upper_active_layer(da, is_ibound=True, include_constant_head=False):
     """
-    Function to get the upper active layer from ibound xr.DataArray
+    Function to get the upper active layer from ibound xarray.DataArray
 
-    Parameters:
-    da : 3d xr.DataArray
-    is_ibound: da is interpreted as ibound, with values 0 inactive, 1, active, -1 chd
-                if False: upper_active_layer is interpreted as upper layer that has data
-    include_constant_head : also incluse chd cells? bool, default False
+    Parameters
+    ----------
+    da : xarray.DataArray
+        A 3D DataArray
+    is_ibound: bool, optional
+        If True, ``da`` is interpreted as ibound, with values 0: inactive, 1: active, -1 constant head.
+        If False, ``upper_active_layer`` is interpreted as first layer that has data.
+        Default is True.
+    include_constant_head : bool, optional
+        If True and ``is_ibound``, also include constant head cells.
+        Default is False.
 
-    Returns:
+    Returns
+    -------
     2d xr.DataArray of layernumber of upper active model layer
     """
     if is_ibound:

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name="imod",
-    description="Work with iMOD MODFLOW models",
+    description="Make massive MODFLOW models",
     long_description=long_description,
     url="https://gitlab.com/deltares/imod/imod-python",
     author="Martijn Visser",
@@ -50,7 +50,7 @@
         "Development Status :: 4 - Beta",
         "Intended Audience :: Developers",
         "Intended Audience :: Science/Research",
-        "Topic :: Scientific/Engineering",
+        "Topic :: Scientific/Engineering :: Hydrology",
         "License :: OSI Approved :: MIT License",
         "Programming Language :: Python :: 3",
         "Programming Language :: Python :: 3.6",