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}",
+] )