Merge pull request #273 from ArtesiaWater/dev

Update to version 0.7.0

Author: rubencalje

.github/workflows/ci.yml

@@ -54,7 +54,6 @@ jobs:
         run: |
           py.test ./tests -m "not notebooks"
 
-
       - name: Run codacy-coverage-reporter
         uses: codacy/codacy-coverage-reporter-action@master
         with:

.gitignore

@@ -146,7 +146,13 @@ nlmod/bin/*
 !nlmod/bin/
 !nlmod/bin/mp7_2_002_provisional
 flowchartnlmod.pptx
-tests/data/
+
+tests/data/*
+!tests/data/**/
+tests/data/mfoutput/*
+!tests/data/mfoutput/vertex/*
+!tests/data/mfoutput/structured/*
+
 docs/examples/*/
 !docs/examples/data/
 !docs/examples/data/chloride_hbossche.nc

.prospector.yaml

@@ -26,4 +26,10 @@ pylint:
     - no-else-raise
     - too-many-arguments
     - too-many-locals
+    - too-many-branches
+    - too-many-statements
     - logging-fstring-interpolation
+
+mccabe:
+  disable:
+    - MC0001

.readthedocs.yml

@@ -7,9 +7,9 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.10"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
@@ -20,7 +20,6 @@ sphinx:
 
 # Optionally declare the Python requirements required to build your docs
 python:
-  system_packages: true
   install:
     - method: pip
       path: .

README.md

@@ -8,35 +8,67 @@
 [![PyPI version](https://badge.fury.io/py/nlmod.svg)](https://badge.fury.io/py/nlmod)
 [![Documentation Status](https://readthedocs.org/projects/nlmod/badge/?version=stable)](https://nlmod.readthedocs.io/en/stable/?badge=stable)
 
-Python package with functions to process, build and visualise MODFLOW models in the Netherlands.
+Python package to build, run and visualize MODFLOW 6 groundwater models in the Netherlands.
 
-The functions in nlmod have four main objectives:
+`nlmod` was built to allow users to write scripts to quickly download relevant data
+from publicly available sources, and build and post-process groundwater flow and
+transport models at different spatial and temporal scales to answer specific
+geohydrological questions. Scripting these steps, from downloading data to building
+groundwater models, makes models more reproducible and transparent.
+
+The functions in `nlmod` have four main objectives:
 
 1. Create and adapt the temporal and spatial discretization of a MODFLOW model using an xarray Dataset (`nlmod.dims`).
 2. Download and read data from external sources, project this data on the modelgrid and add this data to an xarray Dataset (`nlmod.read`).
-3. Use data in an xarray Dataset to build modflow packages using FloPy (`nlmod.gwf` for Modflow 6 and `nlmod.modpath` for Modpath).
+3. Use data in an xarray Dataset to build modflow packages for both groundwater flow and transport models using FloPy (`nlmod.sim`, `nlmod.gwf` and `nlmod.gwt` for Modflow 6 and `nlmod.modpath` for Modpath).
 4. Visualise modeldata in Python (`nlmod.plot`) or GIS software (`nlmod.gis`).
 
-More information can be found on the documentation-website: https://nlmod.readthedocs.io/.
+More information can be found on the documentation-website:
+https://nlmod.readthedocs.io/.
 
 ## Installation
 
 Install the module with pip:
 
 `pip install nlmod`
 
-`nlmod` has many required dependencies: `flopy`, `xarray`, `netcdf4`, `rasterio`, `rioxarray`, `affine`, `geopandas`, `owslib`, `hydropandas`, `shapely`, `pyshp`, `rtree`, `matplotlib`, `dask` and `colorama`. On top of that there are some optional dependecies, only needed (and imported) in a single method. Examples of this are `bottleneck` (used in calculate_gxg), `geocube` (used in add_min_ahn_to_gdf), `h5netcdf` (used for hdf5 files backend in xarray). To install the nlmod with the optional dependencies use:
+`nlmod` has the following required dependencies: 
+
+* `flopy`
+* `xarray`
+* `netcdf4`
+* `rasterio`
+* `rioxarray`
+* `affine`
+* `geopandas`
+* `owslib`
+* `hydropandas`
+* `shapely`
+* `pyshp`
+* `rtree`
+* `matplotlib`
+* `dask`
+* `colorama`
+
+There are some optional dependecies, only needed (and imported) in a single method.
+Examples of this are `bottleneck` (used in calculate_gxg), `geocube` (used in
+add_min_ahn_to_gdf), `h5netcdf` (used for hdf5 files backend in xarray), `scikit-image`
+(used in calculate_sea_coverage). To install `nlmod` with the optional dependencies use:
 
 `pip install nlmod[full]`
 
-When using pip the dependencies are automatically installed. Some dependencies are notoriously hard to install on certain platforms.
-Please see the [dependencies](https://github.com/ArtesiaWater/hydropandas#dependencies) section of the `hydropandas` package for more information on how to install these packages manually.
+When using pip the dependencies are automatically installed. Some dependencies are
+notoriously hard to install on certain platforms. Please see the
+[dependencies](https://github.com/ArtesiaWater/hydropandas#dependencies) section of the
+`hydropandas` package for more information on how to install these packages manually.
 
 ## Getting started
 
-If you are using nlmod for the first time you need to download the MODFLOW executables. You can easily download these executables by running this Python code:
+If you are using `nlmod` for the first time you need to download the MODFLOW
+executables. You can easily download these executables by running this Python code:
 
     import nlmod
 	nlmod.download_mfbinaries()
 
-After you've downloaded the executables you can run the Jupyter Notebooks in the examples folder. These notebooks illustrate how you to use the nlmod package.
+After you've downloaded the executables you can run the Jupyter Notebooks in the
+examples folder. These notebooks illustrate how to use the `nlmod` package.