ci: Update CI to include new packages, typing and tests

.github/workflows/python-package.yml

@@ -8,15 +8,39 @@ concurrency:
 
 
 jobs:
-  build:
+  # Checks if PR title follows conventional semantics
+  semantic_pull_request:    
+    permissions:
+      pull-requests: write  # for amannn/action-semantic-pull-request to analyze PRs and 
+      statuses: write  # for amannn/action-semantic-pull-request to mark status of analyzed PR
+      contents: read    
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check if the PR name has conventional semantics
+        if: github.event_name == 'pull_request'
+        uses: amannn/action-semantic-pull-request@v5.5.3
+        id: lint_pr_title
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          wip: true
+          # Configure that a scope doesn't need to be provided.
+          requireScope: false
+
+      - name: Skip the check on main branch
+        if:  github.ref_name == 'main'
+        run: |
+          echo "This is not a Pull-Request, skipping"
 
+  build:
     runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       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"]
+        python-version: ["3.10", "3.11", "3.12"]
+        package-name: ["geos-ats", "geos-mesh", "geos-posp", "geos-timehistory", "geos-trame", "geos-utils", "geos-xml-tools", "geos-xml-viewer", "hdf5-wrapper", "pygeos-tools"]
 
     steps:
     - uses: actions/checkout@v3
@@ -31,12 +55,15 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         python -m pip install pytest yapf toml
-        python -m pip install ${{ matrix.package-name }}/
+        python -m pip install ./${{ matrix.package-name }}/[test]
     - name: Lint with yapf
       # working-directory: ./${{ matrix.package-name }}
       run: |
-        yapf -r --diff ${{ matrix.package-name }} --style .style.yapf
-    # - name: Test with pytest
-    #   working-directory: ./${{ matrix.package-name }}
-    #   run: |
-    #     pytest
+        yapf -r --diff ./${{ matrix.package-name }} --style .style.yapf
+    - name: Test with pytest
+      #working-directory: ./${{ matrix.package-name }}
+      run:
+      # python -m pytest ./${{ matrix.package-name }} --doctest-modules --junitxml=junit/test-results.xml --cov-report=xml --cov-report=html |
+      # wrap pytest to avoid error when no tests in the package
+        sh -c 'python -m pytest ./${{ matrix.package-name }}; ret=$?; [ $ret = 5 ] && exit 0 || exit $ret'
+

.github/workflows/typing-check.yml

@@ -0,0 +1,43 @@
+name: "Pull Request Typing Check"
+on: 
+- pull_request
+
+# Cancels in-progress workflows for a PR when updated
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+
+jobs:
+  build:
+    runs-on: ubuntu-22.04
+    strategy:
+      fail-fast: false
+      max-parallel: 3
+      matrix:
+        # add packages to check typing
+        package-name: ["hdf5-geomechanics", "geos-posp", "geos-timehistory", "geos-utils", "geos-xml-tools", "hdf5-wrapper"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - uses: mpi4py/setup-mpi@v1
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+        cache: 'pip'
+    - name: Install package
+      # working-directory: ./${{ matrix.package-name }}
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install mypy ruff
+
+    - name: Typing check with mypy
+      #  working-directory: ./${{ matrix.package-name }}
+      run:  |
+        python -m mypy --config-file ./.mypy.ini --check-untyped-defs ./${{ matrix.package-name }}
+
+    - name: Format and linting check with ruff
+      #  working-directory: ./${{ matrix.package-name }}
+      run:  |
+        python -m ruff check --config .ruff.toml ./geos-utils

.mypy.ini

@@ -0,0 +1,19 @@
+[mypy]
+python_version = 3.10
+
+# strict = true
+warn_unreachable = true
+implicit_reexport = true
+show_error_codes = true
+show_column_numbers = true
+ignore_missing_imports = true
+warn_unused_configs = true
+allow_redefinition = false
+
+# ignore files in the tests directory
+[mypy-tests.*]
+ignore_errors = True
+
+# ignore files in the build directory
+[mypy-build.*]
+ignore_errors = True

.ruff.toml

@@ -0,0 +1,66 @@
+# Exclude a variety of commonly ignored directories.
+extend-exclude = ["tests/data"]
+
+line-length = 120
+indent-width = 4
+
+# Assume Python 3.9
+target-version = "py39"
+
+[lint]
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+select = [
+    "E",    # pycodestyle errors
+    "W",    # pycodestyle warnings
+    "F",    # pyflakes
+#    "UP",   # pyupgrade deactivate since python39
+    "B",    # flake8-bugbear        
+    "SIM",  # flake8-simplify        
+    "ANN",  # flake8-annotations        
+    "C4",   # flake8-comprehensions    
+#    "I",    # isort - manage by yapf
+    "D",    # pydocstyle    
+]
+
+ignore = [
+    "E501",  # line too long, handled by yapf
+    "B008",  # do not perform function calls in argument defaults
+    "C901",  # too complex
+    "W191",  # indentation contains tabs
+    "D100",
+    "D101",
+    "D104",  # Missing docstring in public package in __init__.py files
+    "UP007",
+    "ANN401",  # allows Any return
+]
+
+[lint.pydocstyle]
+convention = "google"
+
+[format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+# Enable auto-formatting of code examples in docstrings. Markdown,
+# reStructuredText code/literal blocks and doctests are all supported.
+docstring-code-format = true
+
+# Set the line length limit used when formatting code snippets in
+# docstrings.
+docstring-code-line-length = "dynamic"

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', 'geos-geomechanics' )
+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' ) ) )
 
@@ -42,15 +42,16 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [ 'sphinx_design', 'sphinx_rtd_theme', 'sphinxarg.ext', 'sphinxcontrib.programoutput',
-               'sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon',
-               'sphinx.ext.todo', 'sphinx.ext.viewcode' ]
+extensions = [
+    'sphinx_design', 'sphinx_rtd_theme', 'sphinxarg.ext', 'sphinxcontrib.programoutput', 'sphinx.ext.autodoc',
+    'sphinx.ext.doctest', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.todo', 'sphinx.ext.viewcode'
+]
 
 autoclass_content = 'both'
 autodoc_mock_imports = [ "ats", "h5py", "lxml", "paraview", "pygeosx", "pylvarray", "meshio", "mpi4py", "scipy" ]
 autodoc_typehints = 'none'
 autodoc_typehints_format = 'short'
-suppress_warnings = [""]
+suppress_warnings = [ "" ]
 typehints_defaults = 'braces'
 
 # The suffix(es) of source filenames.

geos-ats/pyproject.toml

@@ -26,6 +26,7 @@ dependencies = [
     "pyyaml",
     "tqdm",
     "requests",
+    "scipy",
     "GitPython",
     "google-cloud-storage",
     "pip-system-certs",
@@ -51,3 +52,22 @@ include-package-data = true
 
 [tool.setuptools.package-data]
 "*" = ["*.js", "*.css", "*.zip"]
+
+[tool.pytest.ini_options]
+addopts = [
+    "--import-mode=importlib",
+]
+console_output_style = "count"
+python_classes = "Test"
+python_files = "tests_*.py"
+python_functions = "tests*"
+testpaths = ["tests"]
+pythonpath = [
+    "src",
+]
+norecursedirs = "bin"
+filterwarnings = []
+
+[tool.coverage.run]
+branch = true
+source = ["src/geos/"]

geos-geomechanics/src/geos/geomechanics/model/MohrCircle.py

@@ -5,7 +5,7 @@
 import numpy.typing as npt
 from typing_extensions import Self
 
-from geos.geomechanics.processing.geomechanicsCalculatorFunctions import (
+from geos_posp.processing.geomechanicsCalculatorFunctions import (
     computeStressPrincipalComponentsFromStressVector, )
 
 __doc__ = """

geos-geomechanics/src/geos/geomechanics/model/MohrCoulomb.py

@@ -92,5 +92,5 @@ def computeFailureEnvelop(
             element is the ordinates.
         """
         sigmaMin: float = ( self.m_sigmaMin if stressNormalMin is None else stressNormalMin )
-        stressNormal: npt.NDArray[ np.float64 ] = np.linspace( sigmaMin, stressNormalMax, n )
+        stressNormal: npt.NDArray[ np.float64 ] = np.linspace( sigmaMin, stressNormalMax, n ).astype( np.float64 )
         return ( stressNormal, np.array( self.computeShearStress( stressNormal ) ) )

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

@@ -1,10 +1,11 @@
 # SPDX-License-Identifier: Apache-2.0
 # # SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
 # SPDX-FileContributor: Alexandre Benedicto, Martin Lemay
+from typing import Any
 import numpy as np
 import numpy.typing as npt
 
-from geos.geomechanics.model.MohrCoulomb import MohrCoulomb
+from geos_posp.processing.MohrCoulomb import MohrCoulomb
 from geos.utils.algebraFunctions import getAttributeMatrixFromVector
 from geos.utils.PhysicalConstants import (
     EPSILON, )
@@ -30,7 +31,7 @@ def specificGravity( density: npt.NDArray[ np.float64 ], specificDensity: float
 
     if abs( specificDensity ) < EPSILON:
         return np.full_like( density, np.nan )
-    return density / specificDensity
+    return ( density / specificDensity ).astype( np.float64 )
 
 
 # https://en.wikipedia.org/wiki/Elastic_modulus
@@ -666,7 +667,7 @@ def criticalPorePressure(
     # 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.float64 ] = ( 3 * minimumPrincipalStress - maximumPrincipalStress ) / 2.0
+    residualTerm: npt.NDArray[ np.floating[ Any ] ] = ( 3 * minimumPrincipalStress - maximumPrincipalStress ) / 2.0
     return cohesiveTerm + residualTerm
 
 
@@ -848,7 +849,8 @@ def shearCapacityUtilization( traction: npt.NDArray[ np.float64 ], rockCohesion:
     assert traction.shape[ 1 ] == 3, "Traction vector must have 3 components."
 
     scu: npt.NDArray[ np.float64 ] = np.full( traction.shape[ 0 ], np.nan )
-    for i, tractionVec in enumerate( traction ):
+    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 ]
 

geos-geomechanics/tests/testsFunctionsGeomechanicsCalculator.py

@@ -9,7 +9,6 @@
 
 import numpy as np
 import numpy.typing as npt
-import pandas as pd  # type: ignore[import-untyped]
 from typing_extensions import Self
 
 dir_path = os.path.dirname( os.path.realpath( __file__ ) )
@@ -247,9 +246,9 @@ def test_shearCapacityUtilization( self: Self ) -> None:
 
         # calculation
         obtained: npt.NDArray[ np.float64 ] = fcts.shearCapacityUtilization( traction, rockCohesion, frictionAngle )
-        expected: npt.NDArray[ np.float64 ] = np.array( [ 0.899, 0.923, 0.982, 1.004, 1.048 ] )
+        expected: list[ float ] = [ 0.899, 0.923, 0.982, 1.004, 1.048 ]
 
-        self.assertSequenceEqual( np.round( obtained, 3 ).flatten().tolist(), expected.tolist() )
+        self.assertSequenceEqual( np.round( obtained, 3 ).flatten().tolist(), expected )
 
     def test_computeStressPrincipalComponents( self: Self ) -> None:
         """Test calculation of stress principal components from stress tensor."""

geos-geomechanics/tests/testsMohrCircle.py

@@ -75,7 +75,7 @@ def test_MohrCoulombInit( self: Self ) -> None:
     def test_computeShearStress( self: Self ) -> None:
         """Test calculation of shear stress from normal stress."""
         # inputs
-        stressNormal: npt.NDArray[ np.float64 ] = np.linspace( 5.0e8, 1.0e9, 100 )
+        stressNormal: npt.NDArray[ np.float64 ] = np.linspace( 5.0e8, 1.0e9, 100 ).astype( float )
         # expected values
         expectedValues: npt.NDArray[ np.float64 ] = np.array( [
             888163490.0,
@@ -184,7 +184,7 @@ def test_computeShearStress( self: Self ) -> None:
         obtained: npt.NDArray[ np.float64 ] = np.array( mohrCoulomb.computeShearStress( stressNormal ) )
 
         # test results
-        self.assertSequenceEqual( expectedValues.tolist(), np.round( obtained ).tolist() )
+        self.assertSequenceEqual( expectedValues.tolist(), np.round( obtained ).tolist() )  # type: ignore[arg-type]
 
     def test_computeFailureEnvelop1( self: Self ) -> None:
         """Test calculation of failure envelop from minimum normal stress."""
@@ -221,8 +221,12 @@ def test_computeFailureEnvelop1( self: Self ) -> None:
         normalStressObtained, shearStressObtained = mohrCoulomb.computeFailureEnvelop( stressNormalMax, n=10 )
 
         # test results
-        self.assertSequenceEqual( normalStressExpected.tolist(), np.round( normalStressObtained ).tolist() )
-        self.assertSequenceEqual( shearStressExpected.tolist(), np.round( shearStressObtained ).tolist() )
+        self.assertSequenceEqual(
+            normalStressExpected.tolist(),  # type: ignore[arg-type]
+            np.round( normalStressObtained ).tolist() )
+        self.assertSequenceEqual(
+            shearStressExpected.tolist(),  # type: ignore[arg-type]
+            np.round( shearStressObtained ).tolist() )
 
     def test_computeFailureEnvelop2( self: Self ) -> None:
         """Test calculation of failure envelop in user-defined range."""
@@ -262,5 +266,9 @@ def test_computeFailureEnvelop2( self: Self ) -> None:
                                                                                        n=10 )
 
         # test results
-        self.assertSequenceEqual( normalStressExpected.tolist(), np.round( normalStressObtained ).tolist() )
-        self.assertSequenceEqual( shearStressExpected.tolist(), np.round( shearStressObtained ).tolist() )
+        self.assertSequenceEqual(
+            normalStressExpected.tolist(),  # type: ignore[arg-type]
+            np.round( normalStressObtained ).tolist() )
+        self.assertSequenceEqual(
+            shearStressExpected.tolist(),  # type: ignore[arg-type]
+            np.round( shearStressObtained ).tolist() )

geos-mesh/pyproject.toml

@@ -41,13 +41,5 @@ addopts = [
     "--import-mode=importlib",
 ]
 pythonpath = [
-    "checks", "parsing",
+    "src",
 ]
-
-[tool.mypy]
-python_version = "3.11"
-warn_return_any = true
-warn_unused_configs = true
-ignore_missing_imports = true
-allow_redefinition = true
-plugins = "numpy.typing.mypy_plugin"