refactor: change dependency settup (#73)

* change dependency of geos-posp

* Linting and typing fix

* update timehistory dependency

Author: mlemayTTE

README.md

@@ -49,53 +49,53 @@ The following package defines [Paraview](https://docs.paraview.org/) plugins tha
 GEOS Python packages dependency tree (inter-dependency and main external dependencies) is the following:
 
 ```
-|-- geos-ats
-|-- pygeos-tools
-|-- geos-utils
-|-- geos-geomechanics
-|   |-- geos-utils
-|
-|-- hdf5-wrapper
-|   |-- h5py
-|
-|-- geos-xml-tools
-|   |-- lxml
-|
-|-- geos-mesh
-|   |-- geos-utils
-|   |-- vtk
-|
-|-- geos-prep
-|   |-- geos-mesh
-|   |-- geos-xml-tools
-|
-|-- geos-posp
-|   |-- geos-mesh
-|   |-- geos-geomechanics
-|
-|-- time-history
-|   |-- hdf5-wrapper
-|
-|-- mesh-doctor
-|   |-- geos-prep
-|   |-- pyvista
-|
-|-- geos-trame
-|   |-- geos-xml-tools
-|   |-- geos-mesh
-|   |-- pyvista
-|   |-- trame
-|
-|-- geos-xml-viewer
-|   |-- geos-xml-tools
-|   |-- geos-mesh
-|   |-- pyvista
-|
-|-- geos-pv
-    |-- geos-prep
-    |-- geos-posp
-    |-- geos-xml-tools
-    |-- paraview
+├── geos-ats
+├── pygeos-tools
+├── geos-utils
+├── geos-geomechanics
+│   ├── geos-utils
+│
+├── hdf5-wrapper
+│   ├── h5py
+│
+├── geos-xml-tools
+│   ├── lxml
+│
+├── geos-mesh
+│   ├── geos-utils
+│   ├── vtk
+│
+├── geos-prep
+│   ├── geos-mesh
+│   ├── geos-xml-tools
+│
+├── geos-posp
+│   ├── geos-mesh
+│   ├── geos-geomechanics
+│
+├── time-history
+│   ├── hdf5-wrapper
+│
+├── mesh-doctor
+│   ├── geos-prep
+│   ├── pyvista
+│
+├── geos-trame
+│   ├── geos-xml-tools
+│   ├── geos-mesh
+│   ├── pyvista
+│   ├── trame
+│
+├── geos-xml-viewer
+│   ├── geos-xml-tools
+│   ├── geos-mesh
+│   ├── pyvista
+│
+├── geos-pv
+    ├── geos-prep
+    ├── geos-posp
+    ├── geos-xml-tools
+    ├── paraview
 ```
 
 See the [documentation](https://geosx-geosx.readthedocs-hosted.com/projects/geosx-geospythonpackages/en/latest/) for additional details about the packages and how to use them.
@@ -149,43 +149,26 @@ If you do not have the rights to push the code and open new PRs, consider openin
 Any new package must have the following architecture:
 
 ```
-package-name
-|-- pyproject.toml
-|-- setup.py
-|-- src
-|   |-- geos
-|       |-- package_name
-|           |-- file1.py
-|           |-- file1.py
-|-- tests
-    |-- test1.py
-    |-- test2.py
+package-name/
+├── pyproject.toml
+├── src
+│   ├── geos
+│       ├── package_name
+│           ├── file1.py
+│           ├── file1.py
+├── tests
+    ├── test1.py
+    ├── test2.py
 ```
 
-The *setup.py* file is optional. It is required if the package depends on another GEOS Python package located in the root directory. If you want a package1 to depend on package2, follow this [procedure](https://stackoverflow.com/questions/75159453/specifying-local-relative-dependency-in-pyproject-toml):
-
-* in the *package1/pyproject.py*, replace the tag `dependencies = ["external_packageX", "external_packageY",]` with `dynamic = ["dependencies"]`
-* create the *package1/setup.py* file
-* copy the following lines in the *setup.py* and update the dependencies
-  ```
-  from pathlib import Path
-  from setuptools import setup
-
-  # This is where you add any fancy path resolution to the local lib:
-  package_name = "geos-utils"
-  geos_utils_path: str = (Path(__file__).parent.parent / package_name).as_uri()
-
-  setup(
-      install_requires=[
-          "vtk >= 9.3",
-          "numpy >= 1.26",
-          "pandas >= 2.2",
-          "typing_extensions >= 4.12",
-          f"{package_name} @ {geos_utils_path}",
-      ]
-  )
-  ```
+If you want a package to depend on another GEOS Python package (let's say `geos-utils`), in the pyproject.toml the dependency takes the form:
 
+```
+dependencies = [
+    ...
+    "geos-utils @ file:./geos-utils",
+]
+```
 
 Release
 -------

geos-geomechanics/pyproject.toml

@@ -21,7 +21,13 @@ classifiers = [
     "Development Status :: 4 - Beta",
     "Programming Language :: Python"
 ]
-dynamic = ["dependencies"]
+dependencies=[
+    "vtk >= 9.3",
+    "numpy >= 1.26",
+    "pandas >= 2.2",
+    "typing_extensions >= 4.12",
+    "geos-utils @ file:./geos-utils",
+]
 requires-python = ">= 3.10"
 
 [project.optional-dependencies]

geos-geomechanics/setup.py

@@ -31,7 +31,8 @@ def specificGravity( density: npt.NDArray[ np.float64 ], specificDensity: float
 
     if abs( specificDensity ) < EPSILON:
         return np.full_like( density, np.nan )
-    return ( density / specificDensity ).astype( np.float64 )
+
+    return ( density / specificDensity ).astype( float )
 
 
 # https://en.wikipedia.org/wiki/Elastic_modulus
@@ -626,7 +627,7 @@ def criticalPorePressure(
     stressVector: npt.NDArray[ np.float64 ],
     rockCohesion: float,
     frictionAngle: float = 0.0,
-) -> npt.NDArray[ np.float64 ]:
+) -> npt.NDArray[ np.floating[ Any ] ]:
     r"""Compute the critical pore pressure.
 
     Fracturing can occur in areas where Critical pore pressure is greater than
@@ -665,9 +666,10 @@ def criticalPorePressure(
         maximumPrincipalStress[ i ] = p1
 
     # assertion frictionAngle < np.pi/2., so sin(frictionAngle) != 1
-    cohesiveTerm: npt.NDArray[ np.float64 ] = ( rockCohesion * np.cos( frictionAngle ) /
-                                                ( 1 - np.sin( frictionAngle ) ) )
-    residualTerm: npt.NDArray[ np.floating[ Any ] ] = ( 3 * minimumPrincipalStress - maximumPrincipalStress ) / 2.0
+    cohesiveTerm: npt.NDArray[ np.floating[ Any ] ] = ( rockCohesion * np.cos( frictionAngle ) /
+                                                        ( 1.0 - np.sin( frictionAngle ) ) )
+    residualTerm: npt.NDArray[ np.floating[ Any ] ] = ( 3.0 * minimumPrincipalStress - maximumPrincipalStress ) / 2.0
+
     return cohesiveTerm + residualTerm
 
 
@@ -852,14 +854,14 @@ def shearCapacityUtilization( traction: npt.NDArray[ np.float64 ], rockCohesion:
     for i in range( traction.shape[ 0 ] ):
         tractionVec: npt.NDArray[ np.float64 ] = traction[ i ]
         # use -1 to agree with Geos convention (i.e., compression with negative stress)
-        stressNormal: npt.NDArray[ np.float64 ] = -1.0 * tractionVec[ 0 ]
+        stressNormal: float = -1.0 * tractionVec[ 0 ]
 
         # compute failure envelope
         mohrCoulomb: MohrCoulomb = MohrCoulomb( rockCohesion, frictionAngle )
         tauFailure: float = float( mohrCoulomb.computeShearStress( stressNormal ) )
         scu_i: float = np.nan
         if tauFailure > 0:
-            scu_i = np.abs( tractionVec[ 1 ] ) / tauFailure
+            scu_i = abs( tractionVec[ 1 ] ) / tauFailure
         # compute SCU
         scu[ i ] = scu_i
     return scu

geos-geomechanics/src/geos/geomechanics/processing/geomechanicsCalculatorFunctions.py

@@ -29,8 +29,18 @@ keywords = [
     "GEOS",
     "Simulation",
 ]
-dynamic = ["dependencies"]
-requires-python = ">= 3.9"
+
+requires-python = ">= 3.10"
+
+dependencies = [
+    "vtk >= 9.3",
+    "numpy >= 1.26",
+    "pandas >= 2.2",
+    "typing_extensions >= 4.12",
+    "geos-utils @ file:./geos-utils",
+    "geos-geomechanics @ file:./geos-geomechanics",
+]
+
 
 [project.urls]
 Homepage = "https://github.com/GEOS-DEV/geosPythonPackages"

geos-posp/pyproject.toml

@@ -17,7 +17,12 @@ classifiers = [
 ]
 
 requires-python = ">=3.9"
-dynamic = ["dependencies"]
+dependencies = [
+    "matplotlib",
+    "h5py",
+    "numpy",
+    "hdf5-wrapper @ file:./hdf5-wrapper",
+]
 
 [project.scripts]
     plot-timehistory = "geos.timehistory.plot:main"