Prepare for release 0.3.1

README.md

@@ -27,14 +27,17 @@ Getting PyGeoStudio started requires Python and making GeoStudio recognized by P
 
 ## Examples
 
-Examples are provided in the folder `example`. 
+Examples are provided in the folder `examples`. 
 It contains:
 
 * Access the SEEP output of solved analysis and export it for processing with Paraview
 * Making plots with Matplotlib
+* Calibrate some properties
 * Change geometry, and material and reinforcement properties
 * Run parametric study
 
+For more details, see the "Examples" section in the [documentation](https://pygeostudio.readthedocs.io/en/stable/)
+
 
 ## Contributing
 

docs/source/conf.py

@@ -13,7 +13,7 @@
 project = 'PyGeoStudio'
 copyright = '2023, Moïse Rousseau'
 author = 'Moïse Rouseau'
-release = '0.4.0'
+release = '0.3.1'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/source/index.rst

@@ -31,7 +31,7 @@ Features
    * - Launch parametric study
      - OK
    * - Launch automatic calibration
-     - TODO
+     - See Examples
    * - Launch sensitivity analysis with true design of experiment
      - TODO
    * - Uncertainty analysis through bayesian framework

docs/source/user_guide.rst

@@ -16,7 +16,7 @@ PyGeoStudio interfaces the GeoStudio file un Python using the main Python class
 
     import PyGeoStudio as pgs
     src_file = "Reinforcement with Anchors.gsz"
-    geofile = pgs.GeoStudioFile(src_file,mode='r')
+    geofile = pgs.GeoStudioFile(src_file)
 
 The ``GeoStudioFile`` class then parse the study and create a copy in the computer memory that is accessible with Python (the ``geofile`` object in the code block above).
 Therefore, every change made through Python does not affect the input file but rather its representation in the memory.
@@ -32,7 +32,7 @@ It contains numerous attribute, method and subclasses which handle each feature
 The figure below shows how to access the different feature of a study.
 
 .. figure:: class_overview.png
-   :scale: 60 %
+   :scale: 70 %
 
    Overview of accessing GeoStudio properties through PyGeoStudio
 
@@ -55,8 +55,11 @@ Write back the modified study
 
 .. code-block:: python
 
+    # Overwrite study
+    geofile.save()
+    # Or save in a new file
     out_file = "./rapid_drawdown_changed_perm.gsz"
-    geofile.writeGeoStudioFile(out_file)
+    geofile.saveAs(out_file)
 
 
 Classes description (by alphabetical order)

examples/calibrations/1D_unsaturated_column_VG_parameter.py

@@ -3,6 +3,11 @@
 ============================
 """
 
+# %%
+# **This example is not yet working, as fitting Van Genuchten parameter is a complex task.
+# In the present version of the file, we use a gradient descent-like algorithm, which is unsuccessful because the objective function may have multiple local optimum.
+# Therefore, the next step is to use global algorithm such as differential evolution or simuated annealing**
+
 import PyGeoStudio as pgs
 import numpy as np
 
@@ -26,8 +31,7 @@
 PWPdata += np.random.normal(0.,0.2,len(PWPdata)) #add some noise to measurement with std dev of 0.5 KPa
 
 # %%
-#
-#set the X data 
+# Set the X data
 N = 100 # number of data point
 psi = np.logspace(-1,4,N) #suction from 0.1 to 1000 KPa
 WCfunction.resizeXYData(N)

setup.py

@@ -9,7 +9,7 @@
 
 setup(
     name='PyGeoStudio', 
-    version='0.3.0',  # Required
+    version='0.3.1',  # Required
     description='Python library allowing reading/writing GeoStudio .gsz files',
     long_description=long_description,
     long_description_content_type='text/markdown',