Refactoring pygeosx to geos-python-interface

.github/workflows/python-package.yml

@@ -16,7 +16,7 @@ jobs:
       max-parallel: 3
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
-        package-name: ["geos-ats", "geos-mesh", "geos-timehistory", "geos-xml-tools", "hdf5-wrapper", "pygeos-tools"]
+        package-name: ["geos-ats", "geos-mesh", "geos-timehistory", "geos-xml-tools", "hdf5-wrapper", "geos-python-interface-tools"]
 
     steps:
     - uses: actions/checkout@v3

docs/conf.py

@@ -18,7 +18,7 @@
 
 # Add python modules to be documented
 python_root = '..'
-python_modules = ( 'geos-xml-tools', 'geos-mesh', 'geos-ats', 'hdf5-wrapper', 'pygeos-tools', 'geos-timehistory' )
+python_modules = ( 'geos-xml-tools', 'geos-mesh', 'geos-ats', 'hdf5-wrapper', 'geos-python-interface-tools', 'geos-timehistory' )
 for m in python_modules:
     sys.path.insert( 0, os.path.abspath( os.path.join( python_root, m, 'src' ) ) )
 
@@ -47,7 +47,7 @@
     'sphinxarg.ext', 'sphinx.ext.napoleon', 'sphinxcontrib.programoutput'
 ]
 
-autodoc_mock_imports = [ "pygeosx", "pylvarray", "meshio", "lxml", "mpi4py", "h5py", "ats", "scipy" ]
+autodoc_mock_imports = [ "geos_python_interface", "pylvarray", "meshio", "lxml", "mpi4py", "h5py", "ats", "scipy" ]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:

docs/geos-python-interface-tools.rst

@@ -0,0 +1,24 @@
+
+GEOS Python Interface Tools
+-----------------------------
+
+The `geos-python-interface-tools` python package adds a variety of tools for working with geos_python_interface objects.
+These include common operations such as setting the value of geosx wrappers with python functions, parallel communication, and file IO.
+Examples using these tools can be found here: `geos_python_interface Examples <https://geosx-geosx.readthedocs-hosted.com/en/latest/docs/sphinx/advancedExamples/geos_python_interfaceExamples/Index.html>`_ .
+
+
+API
+^^^^^
+
+.. automodule:: geos.geos_python_interface_tools.wrapper
+    :members:
+
+.. automodule:: geos.geos_python_interface_tools.file_io
+    :members:
+
+.. automodule:: geos.geos_python_interface_tools.mesh_interpolation
+    :members:
+
+.. automodule:: geos.geos_python_interface_tools.well_log
+    :members:
+

docs/index.rst

@@ -22,7 +22,7 @@ The ats setup command also sets up the python tools:
     make ats_environment
 
 
-These will attempt to install the required packages into the python distribution indicated via the `Python3_EXECUTABLE` cmake variable (also used by pygeosx).
+These will attempt to install the required packages into the python distribution indicated via the `Python3_EXECUTABLE` cmake variable (also used by geos_python_interface).
 If any package dependencies are missing, then the install script will attempt to fetch them from the internet using pip.
 After installation, these packages will be available for import within the associated python distribution, and a set of console scripts will be available within the GEOS build bin directory.
 
@@ -84,6 +84,6 @@ Packages
 
     geos-xml-tools
 
-    pygeos-tools
+    geos-python-interface-tools
 
     geos-timehistory

pygeos-tools/pyproject.toml → geos-python-interface-tools/pyproject.toml

@@ -3,9 +3,9 @@ requires = ["setuptools>=42", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "pygeos-tools"
+name = "geos-python-interface-tools"
 version = "0.1.0"
-description = "Tools for interacting with pygeosx"
+description = "Tools for interacting with geos_python_interface"
 maintainers = [
     {name = "Christopher Sherman", email = "[email protected]" }
 ]

pygeos-tools/src/geos/pygeos_tools/wrapper.py → geos-python-interface-tools/src/geos/geos_python_interface_tools/wrapper.py

@@ -3,7 +3,7 @@
 from mpi4py import MPI
 import matplotlib.pyplot as plt
 import pylvarray
-import pygeosx
+import geos_python_interface
 
 # Get the MPI rank
 comm = MPI.COMM_WORLD
@@ -16,7 +16,7 @@ def get_wrapper( problem, target_key, write_flag=False ):
 
     Args:
         filename (str): Catalog file name
-        problem (pygeosx.Group): GEOSX problem handle
+        problem (geos_python_interface.Group): GEOSX problem handle
         target_key (str): Key for the target wrapper
         write_flag (bool): Sets write mode (default=False)
 
@@ -44,7 +44,7 @@ def get_wrapper_par( problem, target_key, allgather=False, ghost_key='' ):
     Note: if ghost_key is set, it will try to remove any ghost elements
 
     Args:
-        problem (pygeosx.Group): GEOSX problem handle
+        problem (geos_python_interface.Group): GEOSX problem handle
         target_key (str): Key for the target wrapper
         allgather (bool): Flag to trigger allgather across ranks (False)
         ghost_key (str): Key for the corresponding ghost wrapper (default='')
@@ -112,7 +112,7 @@ def gather_wrapper( problem, key, ghost_key='' ):
     Get a global copy of a wrapper as a numpy ndarray on rank 0
 
     Args:
-        problem (pygeosx.Group): GEOSX problem handle
+        problem (geos_python_interface.Group): GEOSX problem handle
         target_key (str): Key for the target wrapper
 
     Returns:
@@ -126,7 +126,7 @@ def allgather_wrapper( problem, key, ghost_key='' ):
     Get a global copy of a wrapper as a numpy ndarray on all ranks
 
     Args:
-        problem (pygeosx.Group): GEOSX problem handle
+        problem (geos_python_interface.Group): GEOSX problem handle
         target_key (str): Key for the target wrapper
 
     Returns:
@@ -140,7 +140,7 @@ def get_global_value_range( problem, key ):
     Get the range of a target value across all processes
 
     Args:
-        problem (pygeosx.Group): GEOSX problem handle
+        problem (geos_python_interface.Group): GEOSX problem handle
         target_key (str): Key for the target wrapper
 
     Returns:
@@ -182,7 +182,7 @@ def print_global_value_range( problem, key, header, scale=1.0, precision='%1.4f'
     Print the range of a target value across all processes
 
     Args:
-        problem (pygeosx.Group): GEOSX problem handle
+        problem (geos_python_interface.Group): GEOSX problem handle
         target_key (str): Key for the target wrapper
         header (str): Header to print with the range
         scale (float): Multiply the range with this value before printing (default = 1.0)
@@ -214,7 +214,7 @@ def set_wrapper_to_value( problem, key, value ):
     Set the value of a wrapper
 
     Args:
-        problem (pygeosx.Group): GEOSX problem handle
+        problem (geos_python_interface.Group): GEOSX problem handle
         target_key (str): Key for the target wrapper
         value (float): Value to set the wrapper
     """
@@ -227,7 +227,7 @@ def set_wrapper_with_function( problem, target_key, input_keys, fn, target_index
     Set the value of a wrapper using a function
 
     Args:
-        problem (pygeosx.Group): GEOSX problem handle
+        problem (geos_python_interface.Group): GEOSX problem handle
         target_key (str): Key for the target wrapper
         input_keys (str, list): The input key(s)
         fn (function): Vectorized function used to calculate target values
@@ -275,7 +275,7 @@ def search_datastructure_wrappers_recursive( group, filters, matching_paths, lev
     Recursively search the group and its children for wrappers that match the filters
 
     Args:
-        problem (pygeosx.Group): GEOSX problem handle
+        problem (geos_python_interface.Group): GEOSX problem handle
         filters (list): a list of strings
         matching_paths (list): a list of matching values
     """
@@ -303,7 +303,7 @@ def get_matching_wrapper_path( problem, filters ):
     'a/b/c', 'c/b/a', 'd/e/c/f/b/a/a'
 
     Args:
-        problem (pygeosx.Group): GEOSX problem handle
+        problem (geos_python_interface.Group): GEOSX problem handle
         filters (list): a list of strings
 
     Returns:
@@ -336,7 +336,7 @@ def run_queries( problem, records ):
     'fhandle': plt.figure()  # A figure handle }}
 
     Args:
-        problem (pygeosx.Group): GEOSX problem handle
+        problem (geos_python_interface.Group): GEOSX problem handle
         records (dict): A dict of dicts that specifies the queries to run
     """
     for k in records.keys():

geos-xml-tools/src/geos/xml_tools/main.py

@@ -112,7 +112,7 @@ def preprocess_serial() -> None:
             compiled_name = args.compiled_name
         else:
             raise Exception(
-                'When applying the preprocessor in parallel (outside of pygeosx), the --compiled_name argument is required'
+                'When applying the preprocessor in parallel (outside of geos_python_interface), the --compiled_name argument is required'
             )
 
     # Note: the return value may be passed to sys.exit, and cause bash to report an error