docs: update Readme; release history; remove some commented out code …

…from wateruse.py

Readme.md

@@ -4,9 +4,9 @@ Modflow-setup
 Modflow-setup is a Python package for automating the setup of MODFLOW groundwater models from grid-independent source data including shapefiles, rasters, and other MODFLOW models that are geo-located. Input data and model construction options are summarized in a single configuration file. Source data are read from their native formats and mapped to a regular finite difference grid specified in the configuration file. An external array-based [Flopy](https://github.com/modflowpy/flopy) model instance with the desired packages is created from the sampled source data and configuration settings. MODFLOW input can then be written from the flopy model instance.
 
 
-### Version 0.2
-![Tests](https://github.com/aleaf/modflow-setup/workflows/Tests/badge.svg)
-[![codecov](https://codecov.io/gh/aleaf/modflow-setup/branch/develop/graph/badge.svg?token=aWN47DYeIv)](https://codecov.io/gh/aleaf/modflow-setup)
+### Version 0.3
+![Tests](https://github.com/doi-usgs/modflow-setup/workflows/Tests/badge.svg)
+[![codecov](https://codecov.io/gh/doi-usgs/modflow-setup/branch/develop/graph/badge.svg?token=aWN47DYeIv)](https://codecov.io/gh/doi-usgs/modflow-setup)
 [![PyPI version](https://badge.fury.io/py/modflow-setup.svg)](https://badge.fury.io/py/modflow-setup)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/doi-usgs/modflow-setup/develop?urlpath=lab/tree/examples)
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
@@ -17,9 +17,9 @@ Modflow-setup is a Python package for automating the setup of MODFLOW groundwate
 
 Getting Started
 -----------------------------------------------
-For more details, see the [modflow-setup documentation](https://aleaf.github.io/modflow-setup/)
+For more details, see the [modflow-setup documentation](https://doi-usgs.github.io/modflow-setup/)
 
-Using a [yaml](https://en.wikipedia.org/wiki/YAML)-aware text editor, create a [configuration file](https://aleaf.github.io/modflow-setup/latest/config-file.html) similar to one of the examples in the [Configuration File Gallery](https://aleaf.github.io/modflow-setup/latest/config-file-gallery.html).
+Using a [yaml](https://en.wikipedia.org/wiki/YAML)-aware text editor, create a [configuration file](https://doi-usgs.github.io/modflow-setup/latest/config-file.html) similar to one of the examples in the [Configuration File Gallery](https://doi-usgs.github.io/modflow-setup/latest/config-file-gallery.html).
 
 The yaml file summarizes source data and parameter settings for setting up the various MODFLOW packages. To set up the model:
 
@@ -43,7 +43,7 @@ m.write_input()
 
 Installation
 -----------------------------------------------
-See the [Installation Instructions](https://aleaf.github.io/modflow-setup/latest/installation.html)
+See the [Installation Instructions](https://doi-usgs.github.io/modflow-setup/latest/installation.html)
 
 
 How to cite
@@ -54,6 +54,13 @@ Leaf AT and Fienen MN (2022) Modflow-setup: Robust automation of groundwater mod
 ###### Software/Code Citation for Modflow-setup
 Leaf, A.T. and Fienen, M.N. (2022). Modflow-setup version 0.1, U.S. Geological Survey Software Release, 30 Sep. 2022. https://doi.org/10.5066/P9O3QWQ1
 
+Applications of Modflow-setup
+-----------------------------------------------
+
+Fienen, M.N, and Corson-Dosch, N.T., 2021, Groundwater Model Archive and Workflow for Neversink/Rondout Basin, New York, Source Water Delineation: U.S. Geological Survey data release, https://doi.org/10.5066/P9HWSOHP.
+
+Fienen, M.N., Corson-Dosch, N.T., White, J.T., Leaf, A.T. and Hunt, R.J. (2022), Risk-Based Wellhead Protection Decision Support: A Repeatable Workflow Approach. Groundwater, 60: 71-86. https://doi.org/10.1111/gwat.13129
+
 MODFLOW Resources
 -----------------------------------------------
 

docs/source/release-history.rst

@@ -2,6 +2,15 @@
 Release History
 ===============
 
+Version 0.3.1 (2023-08-17)
+----------------------------------------
+* change 'boundname_col' argument in basic stress CSV input to 'boundname_column' for consistency with other inputs.
+* fix issue with layer assignment in SFR Package setup where idomain/ibound array wasn't getting passed to the SFRmaker `assign_layers()` function, which can be problematic for models with extensive inactive cells in their upper layers.
+* fix issue with model grid setup where `.prj` file for bounding box shapefile wasn't being written.
+* bug fixes for compatibility with `flopy>=3.4``
+* fixes to `grid.rasterize()` to better handle 64-bit integer and `object` dtypes
+* update example configuration files to use new length unit arguments in `sfrmaker>=0.11.1`
+
 
 Version 0.3.0 (2023-07-25)
 ----------------------------------------

mfsetup/wateruse.py

@@ -153,21 +153,6 @@ def read_wdnr_monthly_water_use(wu_file, wu_points, model,
                                        across_layers=False,
                                        distribute_by='transmissivity',
                                        minimum_layer_thickness=2.)
-    #isthin = well_info.laythick < minimum_layer_thickness
-    #well_info.loc[isthin, 'k'] = well_info.loc[isthin, 'ktop'].values
-    #well_info.loc[isthin, 'laythick'] = model.dis.thickness.array[well_info.k[isthin].values,
-    #                                                              well_info.i[isthin].values,
-    #                                                              well_info.j[isthin].values]
-    #isthin = well_info.laythick < minimum_layer_thickness
-    #well_info.loc[isthin, 'k'] = well_info.loc[isthin, 'kbotm'].values
-    #well_info.loc[isthin, 'laythick'] = model.dis.thickness.array[well_info.k[isthin].values,
-    #                                                              well_info.i[isthin].values,
-    #                                                              well_info.j[isthin].values]
-    #isthin = well_info.laythick < minimum_layer_thickness
-    #well_info.loc[isthin, 'k'] = 1
-    #well_info.loc[isthin, 'laythick'] = model.dis.thickness.array[well_info.k[isthin].values,
-    #                                                              well_info.i[isthin].values,
-    #                                                              well_info.j[isthin].values]
     isthin = well_info.laythick < minimum_layer_thickness
     assert not np.any(isthin)