refactor: Create geos-geomechanics package (#66)

* Move geomechanics processes to dedicated package

* Update dependencies

* Move tests to geomechanics package

* Update build process

* Correction to build process

* Update documentation

* Build typo and missing files

* Doc automodule typo

* Add module path to sys path for PV plugins

* Typo in module import

* Fix import path and move line to top of file

* linting

* Fix doc

* Consistency with other packages pyproject.toml

Author: paloma-martinez

docs/conf.py

@@ -17,8 +17,8 @@
 
 # Add python modules to be documented
 python_root = '..'
-python_modules = ( 'geos-ats', 'geos-mesh', 'geos-posp', 'geos-timehistory', 'geos-utils', 'geos-xml-tools', 
-                   'hdf5-wrapper', 'pygeos-tools' )
+python_modules = ( 'geos-ats', 'geos-mesh', 'geos-posp', 'geos-timehistory', 'geos-utils', 'geos-xml-tools', 'hdf5-wrapper',
+                   'pygeos-tools', 'geos-geomechanics' )
 for m in python_modules:
     sys.path.insert( 0, os.path.abspath( os.path.join( python_root, m, 'src' ) ) )
 

docs/geos-geomechanics.rst

@@ -0,0 +1,10 @@
+GEOS Post-Processing tools
+=============================
+
+.. toctree::
+   :maxdepth: 5
+   :caption: Contents:
+
+   ./geos_geomechanics_docs/home.rst
+
+   ./geos_geomechanics_docs/modules.rst

docs/geos_geomechanics_docs/home.rst

@@ -0,0 +1,4 @@
+GEOS Geomechanics Tools
+=========================
+
+This package contains geomechanics functions and data models.

docs/geos_geomechanics_docs/model.rst

@@ -0,0 +1,19 @@
+Geomechanics models
+======================
+This 
+
+geos.geomechanics.model.MohrCircle module
+------------------------------------------
+
+.. automodule:: geos.geomechanics.model.MohrCircle
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+geos.geomechanics.model.MohrCoulomb module
+-------------------------------------------
+
+.. automodule:: geos.geomechanics.model.MohrCoulomb
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/geos_geomechanics_docs/modules.rst

@@ -0,0 +1,10 @@
+GEOS geomechanics tools
+=========================
+
+.. toctree::
+   :maxdepth: 5
+   
+   model
+   
+   processing
+

docs/geos_geomechanics_docs/processing.rst

@@ -0,0 +1,11 @@
+Processing
+============
+The processing part of `geos-geomechanics` package contains functions tools to compute geomechanical properties.
+
+geos.geomechanics.processing.geomechanicsCalculatorFunctions module
+---------------------------------------------------------------------
+
+.. automodule:: geos.geomechanics.processing.geomechanicsCalculatorFunctions
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/index.rst

@@ -84,6 +84,8 @@ Packages
 
     geos-posp
 
+    geos-geomechanics
+
     geos-timehistory
 
     geos-utils

geos-geomechanics/pyproject.toml

@@ -0,0 +1,56 @@
+[build-system]
+requires = ["setuptools>=61.2"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["geos_geomechanics*"]
+exclude = ['tests*']
+
+[project]
+name = "geos-geomechanics"
+version = "0.1.0"
+description = "Geomechanics models and processing tools"
+authors = [{name = "GEOS contributors" }]
+maintainers = [{name = "Martin Lemay", email = "[email protected]"}]
+license = {text = "Apache-2.0"}
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Programming Language :: Python"
+]
+dynamic = ["dependencies"]
+requires-python = ">= 3.10"
+
+[project.optional-dependencies]
+build = [
+  "build ~= 1.2"
+]
+dev = [
+    "yapf",
+    "mypy",
+]
+test = [
+   "pytest",
+]
+
+[project.scripts]
+
+
+[tool.pytest.ini_options]
+addopts = "--import-mode=importlib"
+console_output_style = "count"
+pythonpath = ["src"]
+python_classes = "Test"
+python_files = "test*.py"
+python_functions = "test*"
+testpaths = ["tests"]
+norecursedirs = "bin"
+filterwarnings = []
+
+
+[tool.coverage.run]
+branch = true
+source = ["src/geos"]

geos-geomechanics/setup.py

@@ -0,0 +1,13 @@
+from pathlib import Path
+from setuptools import setup
+
+# This is where you add any fancy path resolution to the local lib:
+geos_utils_path: str = ( Path( __file__ ).parent.parent / "geos-utils" ).as_uri()
+
+setup( install_requires=[
+    "vtk >= 9.3",
+    "numpy >= 1.26",
+    "pandas >= 2.2",
+    "typing_extensions >= 4.12",
+    f"geos-utils @ {geos_utils_path}",
+] )

geos-geomechanics/src/geos/geomechanics/__init__.py

@@ -1,119 +1,115 @@
-# SPDX-License-Identifier: Apache-2.0
-# SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
-# SPDX-FileContributor: Alexandre Benedicto, Martin Lemay
-import numpy as np
-import numpy.typing as npt
-from typing_extensions import Self
-
-from geos_posp.processing.geomechanicsCalculatorFunctions import (
-    computeStressPrincipalComponentsFromStressVector,
-)
-
-__doc__ = """
-MohrCircle module define the Mohr's circle parameters.
-
-Inputs are a 6 component stress vector, a circle id, and the mechanical
-convention used for compression.
-The class computes principal components from stress vector during initialization.
-Accessors get access to these 3 principal components as well as circle center
-and radius.
-
-To use the object:
-
-.. code-block:: python
-
-    from processing.MohrCircle import MohrCircle
-
-    # create the object
-    stressVector :npt.NDArray[np.float64]
-    circleId :str
-    mohrCircle :MohrCircle = MohrCircle(circleId)
-
-    # either directly set principal components (p3 <= p2 <= p1)
-    mohrCircle.SetPrincipalComponents(p3, p2, p1)
-    # or compute them from stress vector
-    mohrCircle.computePrincipalComponents(stressVector)
-
-    # access to members
-    id :str = mohrCircle.getCircleId()
-    p1, p2, p3 :float = mohrCircle.getPrincipalComponents()
-    radius :float = mohrCircle.getCircleRadius()
-    center :float = mohrCircle.getCircleCenter()
-"""
-
-
-class MohrCircle:
-    def __init__(self: Self, circleId: str) -> None:
-        """Compute Mohr's Circle from input stress.
-
-        Args:
-            circleId (str): Mohr's circle id.
-        """
-        self.m_circleId: str = circleId
-
-        self.m_p1: float = 0.0
-        self.m_p2: float = 0.0
-        self.m_p3: float = 0.0
-
-    def __str__(self: Self) -> str:
-        """Overload of __str__ method."""
-        return self.m_circleId
-
-    def __repr__(self: Self) -> str:
-        """Overload of __repr__ method."""
-        return self.m_circleId
-
-    def setCircleId(self: Self, circleId: str) -> None:
-        """Set circle Id variable.
-
-        Args:
-            circleId (str): circle Id.
-        """
-        self.m_circleId = circleId
-
-    def getCircleId(self: Self) -> str:
-        """Access the Id of the Mohr circle.
-
-        Returns:
-            str: Id of the Mohr circle
-        """
-        return self.m_circleId
-
-    def getCircleRadius(self: Self) -> float:
-        """Compute and return Mohr's circle radius from principal components."""
-        return (self.m_p1 - self.m_p3) / 2.0
-
-    def getCircleCenter(self: Self) -> float:
-        """Compute and return Mohr's circle center from principal components."""
-        return (self.m_p1 + self.m_p3) / 2.0
-
-    def getPrincipalComponents(self: Self) -> tuple[float, float, float]:
-        """Get Moh's circle principal components."""
-        return (self.m_p3, self.m_p2, self.m_p1)
-
-    def setPrincipalComponents(self: Self, p3: float, p2: float, p1: float) -> None:
-        """Set principal components.
-
-        Args:
-            p3 (float): first component. Must be the lowest.
-            p2 (float): second component.
-            p1 (float): third component. Must be the greatest.
-        """
-        assert (p3 <= p2) and (p2 <= p1), "Component order is wrong."
-        self.m_p3 = p3
-        self.m_p2 = p2
-        self.m_p1 = p1
-
-    def computePrincipalComponents(
-        self: Self, stressVector: npt.NDArray[np.float64]
-    ) -> None:
-        """Calculate principal components.
-
-        Args:
-            stressVector (npt.NDArray[np.float64]): 6 components stress vector
-                Stress vector must follow GEOS convention (XX, YY, ZZ, YZ, XZ, XY)
-        """
-        # get stress principal components
-        self.m_p3, self.m_p2, self.m_p1 = (
-            computeStressPrincipalComponentsFromStressVector(stressVector)
-        )
+# SPDX-License-Identifier: Apache-2.0
+# SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
+# SPDX-FileContributor: Alexandre Benedicto, Martin Lemay
+import numpy as np
+import numpy.typing as npt
+from typing_extensions import Self
+
+from geos.geomechanics.processing.geomechanicsCalculatorFunctions import (
+    computeStressPrincipalComponentsFromStressVector, )
+
+__doc__ = """
+MohrCircle module define the Mohr's circle parameters.
+
+Inputs are a 6 component stress vector, a circle id, and the mechanical
+convention used for compression.
+The class computes principal components from stress vector during initialization.
+Accessors get access to these 3 principal components as well as circle center
+and radius.
+
+To use the object:
+
+.. code-block:: python
+
+    from processing.MohrCircle import MohrCircle
+
+    # create the object
+    stressVector :npt.NDArray[np.float64]
+    circleId :str
+    mohrCircle :MohrCircle = MohrCircle(circleId)
+
+    # either directly set principal components (p3 <= p2 <= p1)
+    mohrCircle.SetPrincipalComponents(p3, p2, p1)
+    # or compute them from stress vector
+    mohrCircle.computePrincipalComponents(stressVector)
+
+    # access to members
+    id :str = mohrCircle.getCircleId()
+    p1, p2, p3 :float = mohrCircle.getPrincipalComponents()
+    radius :float = mohrCircle.getCircleRadius()
+    center :float = mohrCircle.getCircleCenter()
+"""
+
+
+class MohrCircle:
+
+    def __init__( self: Self, circleId: str ) -> None:
+        """Compute Mohr's Circle from input stress.
+
+        Args:
+            circleId (str): Mohr's circle id.
+        """
+        self.m_circleId: str = circleId
+
+        self.m_p1: float = 0.0
+        self.m_p2: float = 0.0
+        self.m_p3: float = 0.0
+
+    def __str__( self: Self ) -> str:
+        """Overload of __str__ method."""
+        return self.m_circleId
+
+    def __repr__( self: Self ) -> str:
+        """Overload of __repr__ method."""
+        return self.m_circleId
+
+    def setCircleId( self: Self, circleId: str ) -> None:
+        """Set circle Id variable.
+
+        Args:
+            circleId (str): circle Id.
+        """
+        self.m_circleId = circleId
+
+    def getCircleId( self: Self ) -> str:
+        """Access the Id of the Mohr circle.
+
+        Returns:
+            str: Id of the Mohr circle
+        """
+        return self.m_circleId
+
+    def getCircleRadius( self: Self ) -> float:
+        """Compute and return Mohr's circle radius from principal components."""
+        return ( self.m_p1 - self.m_p3 ) / 2.0
+
+    def getCircleCenter( self: Self ) -> float:
+        """Compute and return Mohr's circle center from principal components."""
+        return ( self.m_p1 + self.m_p3 ) / 2.0
+
+    def getPrincipalComponents( self: Self ) -> tuple[ float, float, float ]:
+        """Get Moh's circle principal components."""
+        return ( self.m_p3, self.m_p2, self.m_p1 )
+
+    def setPrincipalComponents( self: Self, p3: float, p2: float, p1: float ) -> None:
+        """Set principal components.
+
+        Args:
+            p3 (float): first component. Must be the lowest.
+            p2 (float): second component.
+            p1 (float): third component. Must be the greatest.
+        """
+        assert ( p3 <= p2 ) and ( p2 <= p1 ), "Component order is wrong."
+        self.m_p3 = p3
+        self.m_p2 = p2
+        self.m_p1 = p1
+
+    def computePrincipalComponents( self: Self, stressVector: npt.NDArray[ np.float64 ] ) -> None:
+        """Calculate principal components.
+
+        Args:
+            stressVector (npt.NDArray[np.float64]): 6 components stress vector
+                Stress vector must follow GEOS convention (XX, YY, ZZ, YZ, XZ, XY)
+        """
+        # get stress principal components
+        self.m_p3, self.m_p2, self.m_p1 = ( computeStressPrincipalComponentsFromStressVector( stressVector ) )