Merge pull request #94 from ContactEngineering/DOC/23_api

MAINT/23 api

.github/workflows/test.yml

@@ -15,12 +15,12 @@ on:
 jobs:
   tests:
     runs-on: ubuntu-20.04
-    timeout-minutes: 45
+    timeout-minutes: 90
 
     strategy:
       matrix:
-        mpi: ['yes', 'no']
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        mpi: ['no'] # FIXME!!  error when installing netCDF, not finding mpi4py see issue #95
+        python-version: ['3.8','3.9','3.10','3.11']
         mpi4py-version: [3.1.4]
         netcdf4-python-version: [1.6.3]
 
@@ -41,6 +41,7 @@ jobs:
         python3 -m venv venv
         source venv/bin/activate
         python3 -m pip install --upgrade pip pip-tools
+        
         if [ "${{ matrix.mpi }}" == "yes" ]; then
           sudo apt-get install -y \
             openmpi-bin \
@@ -76,6 +77,7 @@ jobs:
           echo "Installing ${MUSPECTRE_VERSION}"
           pip install -v --no-binary muspectre ${MUSPECTRE_VERSION}
         else
+          # Serial installation of muSpectre with FFTW support
           sudo apt-get install -y \
             libfftw3-dev \
             libnetcdf-dev
@@ -88,6 +90,8 @@ jobs:
         fi
         python3 -m pip install build
         python3 -m pip list
+        
+        # export LD_LIBRARY_PATH=$PWD/venv/lib/python${{ matrix.python-version }}/site-packages/.muspectre.mesonpy.libs/ 
 
     - name: Install extension module
       run: |
@@ -97,6 +101,7 @@ jobs:
     - name: Test with pytest
       run: |
         source venv/bin/activate
+ 
         python3 .check_netcdf_capabilities.py ${{ matrix.mpi }}
         python3 .check_mufft_capabilities.py ${{ matrix.mpi }}
         python3 -m pip list

Adhesion/ReferenceSolutions/JKR.py

@@ -120,7 +120,7 @@ def _contact_radius_from_penetration_force(
 
     for the contact radius :math:`a`.
 
-    If you want to determine the energy release rate, call `JKR.nonequilibrium_elastic_energy_release_rate`
+    If you want to determine the energy release rate, call `JKR.elastic_energy_release_rate`
     using the penetration and the contact radius afterwards.
 
     Parameters
@@ -185,7 +185,7 @@ def contact_radius(force=None,
 
       for the contact radius :math:`a`.
 
-      If you want to determine the energy release rate, call `JKR.nonequilibrium_elastic_energy_release_rate`
+      If you want to determine the energy release rate, call `JKR.elastic_energy_release_rate`
       using the penetration and the contact radius afterwards.
 
     Parameters
@@ -421,7 +421,7 @@ def equilibrium_elastic_energy(contact_radius):
 #       * (1/5 + (1 - R * np.sqrt(9 * np.pi * w / (2*a**3 * Es)))**2)
 
 
-def nonequilibrium_elastic_energy(penetration, contact_radius):
+def elastic_energy(penetration, contact_radius):
     r"""
 
     .. math::

pyproject.toml

@@ -20,9 +20,9 @@ requires-python = ">=3.8.0"
 dynamic = [ "version" ]
 dependencies = [
     "numpy>=1.16.3",
-    "scipy>=1.9.0",
+    "scipy>=1.9.0,<1.11.0",
     "NuMPI>=0.3.1",
-    "muSpectre>=0.25.1",
+    "muSpectre>=0.26.4",
     "SurfaceTopography>=1.3.0",
     "ContactMechanics>=1.1.0",
     "netCDF4"

test/ReferenceSolutions/test_sphere_jkr.py

@@ -265,7 +265,7 @@ def test_equilibrium_elastic_energy_vs_nonequilibrium():
     Eel = JKR.equilibrium_elastic_energy(a)
 
     np.testing.assert_allclose(Eel,
-                               JKR.nonequilibrium_elastic_energy(
+                               JKR.elastic_energy(
                                    JKR.penetration(a), a))