update gui branche with latest main (#255)

* fixed dependencies for python 3.13 (#236)

* test with timing function

* Add devcontainer for use in codespaces (#240)

* devcontainer added

* Update Dockerfile

* Update Dockerfile

* Update devcontainer.json

* Update Dockerfile

* fixed dependencies for python 3.13 (#236) (#239)

* Update Dockerfile

* remove abundant stuff

* Add devcontainer for use in codespaces (#240) (#242)

* devcontainer added

* Update Dockerfile

* Update Dockerfile

* Update devcontainer.json

* Update Dockerfile

* fixed dependencies for python 3.13 (#236) (#239)

* Update Dockerfile

* remove abundant stuff

* Update Dockerfile (#243)

This patch updates the dockerfile for the codespace to be compatible with developer mode.
You need to manual install python in dev model after the docker is created.

* Cleanup main (#245)

* delete abundant files

* deleted:    aeolis/examples/vanWesten2024/blowout/figure_grid_initialization.png
deleted:    aeolis/examples/vanWesten2024/blowout/figure_params_initialization.png
deleted:    aeolis/examples/vanWesten2024/blowout/figure_timeseries_initialization.png

* Update pyproject.toml

* Update README.md

* Update CITATION.cff

* Update release info (#246)

* Update pyproject.toml

* Update CITATION.cff

* Update README.md

* Update Python version and dependencies in installation guide

* Implement error message for missing ne_file

Added error handling for missing 'ne_file' when using Avalanching.

* Print message for aeolis installation in Dockerfile

Add message indicating manual installation of aeolis

* Update vegetation parameters in constants.py (#250)

* Update vegetation parameters in constants.py

Removes unused V_Lat parameter
solves #120 
Changes default for veg_min_elevation to -10 to avoid unwanted use of this functionality.

* Update aeolis/constants.py

Co-authored-by: Copilot <[email protected]>

---------

Co-authored-by: Copilot <[email protected]>

---------

Co-authored-by: Copilot <[email protected]>

Author: Sierd

.devcontainer/Dockerfile

@@ -0,0 +1,25 @@
+FROM continuumio/miniconda3
+
+# Set the working directory
+
+# WORKDIR /workspace
+
+# Install Python
+RUN conda install python -y
+
+# Copy the project files
+# COPY . .
+
+# Install the necessary packages
+
+# RUN pip install .
+
+# Clean up
+RUN conda clean -afy
+
+# Set the default command
+CMD ["bash"]
+
+# print a message to indicate that the container is ready
+RUN echo "The container is ready to use but you need to install aeolis manualy. You can run 'pip instal . -e' to run in editable mode."
+

.devcontainer/devcontainer.json

@@ -0,0 +1,7 @@
+{
+  "name": "AEOLIS Development Container",
+  "build": {
+    "dockerfile": "Dockerfile",
+    "context": ".."
+  }
+}

CITATION.cff

@@ -69,5 +69,5 @@ keywords:
   - sediment
 license: GPL-3.0
 commit: 0adaedfc8015f18b3b551bed1dda38d630cd8c95
-version: 3.0.0.rc3
-date-released: '2023-10-18'
+version: 3.0.1
+date-released: '2025-07-11'

README.md

@@ -91,7 +91,7 @@ Read our [Contribution Guidelines](CONTRIBUTING.md) to know how you can help to
 
 Please, cite this software as follows:
 
-*de Vries, S., Hallin, C., van IJzendoorn, C., van Westen, B., Cohn, N., Strypsteen, G., Skaden, J., Agrawal, N., & Garcia Alvarez, M. (2023). AeoLiS (Version 3.0.0.rc2) [Computer software]. https://github.com/openearth/aeolis-python*
+*de Vries, S., Hallin, C., van IJzendoorn, C., van Westen, B., Cohn, N., Strypsteen, G., Skaden, J., Agrawal, N., & Garcia Alvarez, M. (2023). AeoLiS (Version 3.0.1) [Computer software]. https://github.com/openearth/aeolis-python*
 
 ## Acknowlegdements
 

aeolis/constants.py

@@ -300,7 +300,6 @@
     'hveg_max'                      : 1.,                 # [m] Max height of vegetation
     'dzb_opt'                       : 0.,                 # [m/year] Sediment burial for optimal growth
     'V_ver'                         : 0.,                 # [m/year] Vertical growth potential
-    'V_lat'                         : 0.,                 # [m/year] Lateral growth
     'germinate'                     : 0.,                 # [1/year] Possibility of germination per year
     'lateral'                       : 0.,                 # [1/year] Posibility of lateral expension per year
     'veg_gamma'                     : 1.,                 # [-] Constant on influence of sediment burial
@@ -332,7 +331,7 @@
     'alfa'                          : 0,                  # [deg] Real-world grid cell orientation wrt the North (clockwise)
     'dune_toe_elevation'            : 3,                  # Choose dune toe elevation, only used in the PH12 dune erosion solver
     'beach_slope'                   : 0.1,                # Define the beach slope, only used in the PH12 dune erosion solver
-    'veg_min_elevation'             : 3,                  # Choose the minimum elevation where vegetation can grow
+    'veg_min_elevation'             : -10.,               # Minimum elevation (m) where vegetation can grow; default -10 disables restriction (allows vegetation everywhere). Set to a higher value to enforce a minimum elevation for vegetation growth.
     'vegshear_type'                 : 'raupach',          # Choose the Raupach grid based solver (1D or 2D) or the Okin approach (1D only)
     'okin_c1_veg'                   : 0.48,               #x/h spatial reduction factor in Okin model for use with vegetation
     'okin_c1_fence'                 : 0.48,               #x/h spatial reduction factor in Okin model for use with sand fence module

aeolis/inout.py

@@ -117,6 +117,13 @@ def read_configfile(configfile, parse_files=True, load_defaults=True):
     # set default for nsavetimes, if not given
     if 'nsavetimes' in p and not p['nsavetimes']:
         p['nsavetimes'] = int(p['dzb_interval']/p['dt'])
+
+    # catch some incompatible parameter combinations.
+    if (p['ne_file'] is None) and (p['process_avalanche'] == True):
+        print('Please provide a valid ne_file path in the configuration file when using Avalanching.')
+        print('Code does not proceed until this is provided.')
+        print('Hint: If you do not have a ne_file, you can create one with all zeros, with the same dimensions as your grid.')        
+        exit("Exiting due to error")       
 
     return p
 
@@ -603,4 +610,4 @@ def output_sedtrails(s, p):
         savemat(os.path.join('sedtrails_output', str(int(time)).zfill(12) + '.mat'), mdic)
     else:
         mdic = {'us': us, 'un': un, 'dzb': dzb, 'pickup': pickup}
-        savemat(os.path.join('sedtrails_output', str(int(time)).zfill(12) + '.mat'), mdic)
+        savemat(os.path.join('sedtrails_output', str(int(time)).zfill(12) + '.mat'), mdic)

aeolis/vegetation.py

@@ -28,23 +28,13 @@
 import logging
 from scipy import ndimage, misc
 import numpy as np
-import math
-#import matplotlib.pyplot as plt
 from aeolis.wind import *
 import aeolis.rotation
 
 # package modules
 import aeolis.wind
-#from aeolis.utils import *
 
 import numpy as np
-from scipy.integrate import quad
-from scipy.integrate import romberg
-from scipy.optimize import root_scalar
-from scipy.signal import convolve
-from scipy.special import sici
-from scipy.special import erfi
-import matplotlib.pyplot as plt
 
 # initialize logger
 logger = logging.getLogger(__name__)

aeolis/wind.py

@@ -28,18 +28,9 @@
 
 import numpy as np
 import logging
-import operator
-#import scipy.special
-#import scipy.interpolate
-from scipy import ndimage, misc
-import matplotlib.pyplot as plt
-from scipy.integrate import quad
-from scipy.integrate import romberg
+
+from scipy import ndimage
 from scipy.optimize import root_scalar
-from scipy.signal import convolve
-from scipy.special import sici
-from scipy.special import erfi
-from scipy.interpolate import griddata
 
 
 # package modules

docs/user/installation.rst

@@ -8,18 +8,19 @@ AeoLiS is a Python package that can be installed from PyPI or from source. For t
 Requirements
 ------------
 
-- Python 3.8 or newer 
+- Python 3.9 or newer 
 - pip 22.0 or newer
 - netCDF4
 
 Dependencies
 """"""""""""
 
-- docopt==0.6.1
+- docopt
+- typer
 - bmi-python
 - netCDF4
 - scipy
-- numpy<1.24,>=1.18
+- numpy
 - matplotlib
 - numba
 
@@ -59,8 +60,8 @@ Example from command line:
 
 .. code:: shell
 
-   aeolis params.txt
+   aeolis run params.txt
 
 .. note::
 
-   Model parameters and other configuration is passed in a `params.txt`. See the :ref:`default settings` for more details.  
+   Model parameters and other configuration is passed in a `params.txt`. See the :ref:`default settings` for more details.  

pyproject.toml

@@ -12,7 +12,7 @@ exclude = [
 
 [project]
 name = "aeolis"
-version = "3.0.0.rc3"
+version = "3.0.1"
 authors = [
   { name="Sierd de Vries", email="[email protected]" },
 ]
@@ -31,7 +31,7 @@ dependencies = [
   "bmi-python",
   "netCDF4",
   "scipy",
-  "numpy<1.24,>=1.18",
+  "numpy",
   "matplotlib",
   "numba",
 ]