Merge pull request #102 from ContactEngineering/24_v0.92.0

DOC: Updated ChangeLog.md and Flake8 for upcoming release
ContactEngineering · Jan 14, 2024 · b9bbb0b · b9bbb0b
2 parents e1de72c + 7549e71
commit b9bbb0b
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Showing 26 changed files with 282 additions and 372 deletions.
diff --git a/.check_mufft_capabilities.py b/.check_mufft_capabilities.py
@@ -10,5 +10,5 @@
 
 if mpi_required:
     # Make sure that we have the parallel version running
-    #assert muFFT.__has_parallel4_support__
+    # assert muFFT.__has_parallel4_support__
     assert muFFT.has_mpi
diff --git a/.check_netcdf_capabilities.py b/.check_netcdf_capabilities.py
@@ -14,5 +14,5 @@
 
 if mpi_required:
     # Make sure that we have the parallel version running
-    #assert netCDF4.__has_parallel4_support__
+    # assert netCDF4.__has_parallel4_support__
     assert netCDF4.__has_pnetcdf_support__
diff --git a/.github/workflows/flake8.yml b/.github/workflows/flake8.yml
@@ -11,29 +11,17 @@ on:
       - '**'
 
 jobs:
-  tests:
+  flake8:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-      with:
-        fetch-depth: 0
-        submodules: recursive
-
-    - name: Set up python3 ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install dependencies
-      run: |
-        sudo apt-get update -qy
-        sudo apt-get install -y python3-pip
-
-    - name: Build extension module
-      run: |
-        python3 -m pip install ".[test]"
-
-    - name: Flake8 via pytest
-      run: |
-        python3 -m pytest --flake8 -m flake8 --verbose --full-trace -s
+      - name: Check out source repository
+        uses: actions/checkout@v4
+      - name: Set up Python environment
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+      - name: flake8 Lint
+        uses: py-actions/flake8@v2
+        with:
+          exclude: "docs/examples/*"
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -14,95 +14,63 @@ on:
 
 jobs:
   tests:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     timeout-minutes: 90
 
     strategy:
       matrix:
-        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]
+        mpi: [ 'yes', 'no' ]
+        python-version: [ '3.8', '3.9', '3.10', '3.11', '3.12' ]
+        mpi4py-version: [ 3.1.5 ]
+        netcdf4-python-version: [ 1.6.2 ]
+        muspectre-version: [ 0.26.4 ]
 
-    steps:
-    - uses: actions/checkout@v3
-      with:
-        fetch-depth: 0
-        submodules: recursive
 
-    - name: Set up python3 ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          submodules: recursive
 
-    - name: Install dependencies
-      run: |
-        sudo apt-get update -qy
-        python3 -m venv venv
-        source venv/bin/activate
-        python3 -m pip install --upgrade pip pip-tools
-        
-        if [ "${{ matrix.mpi }}" == "yes" ]; then
-          sudo apt-get install -y \
-            openmpi-bin \
-            libopenmpi-dev \
-            libfftw3-dev \
-            libfftw3-mpi-dev \
-            libhdf5-mpi-dev \
-            libpnetcdf-dev \
-            libnetcdf-pnetcdf-dev \
-            meson \
-            ninja-build
-          # Compute mpi4py and muSpectre versions
-          pip-compile pyproject.toml
-          NUMPY_VERSION=$(grep 'numpy==' requirements.txt)
-          MUSPECTRE_VERSION=$(grep 'muspectre==' requirements.txt)
-          # Install numpy
-          echo "Installing ${NUMPY_VERSION}"
-          pip install -v ${NUMPY_VERSION}
-          # Install mpi4py
-          echo "Installing mpi4py==${{ matrix.mpi4py-version }}"
-          CC=mpicc python3 -m pip install -v \
-            --no-binary mpi4py \
-            mpi4py==${{ matrix.mpi4py-version }}
-          # Install netCDF4 with MPI support
-          echo "Installing netCD4==${{ matrix.netcdf4-python-version }}"
-          CC=mpicc NETCDF4_DIR=/usr/lib/x86_64-linux-gnu/netcdf/pnetcdf python3 -m pip install -v \
-            --no-binary mpi4py --no-binary netCDF4 --no-binary muspectre \
-            ${NUMPY_VERSION} \
-            mpi4py==${{ matrix.mpi4py-version }} \
-            netCDF4==${{ matrix.netcdf4-python-version }} \
-            ${MUSPECTRE_VERSION}
-          # Manually install muSpectre with MPI enabled
-          echo "Installing ${MUSPECTRE_VERSION}"
-          pip install -v --no-binary muspectre ${MUSPECTRE_VERSION}
-        else
-          # Serial installation of muSpectre with FFTW support
-          sudo apt-get install -y \
-            libfftw3-dev \
-            libnetcdf-dev
-          # Compute muSpectre version
-          pip-compile pyproject.toml
-          MUSPECTRE_VERSION=$(grep 'muspectre==' requirements.txt)
-          # Manually install muSpectre with FFTW support
-          echo "Installing ${MUSPECTRE_VERSION}"
-          pip install -v --no-binary muspectre ${MUSPECTRE_VERSION}
-        fi
-        python3 -m pip install build
-        python3 -m pip list
-        
-        # export LD_LIBRARY_PATH=$PWD/venv/lib/python${{ matrix.python-version }}/site-packages/.muspectre.mesonpy.libs/ 
+      - name: Set up python3 ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
 
-    - name: Install extension module
-      run: |
-        source venv/bin/activate
-        python3 -m pip install .[test]
+      - name: Install dependencies and extension module
+        run: |
+          set -x
+          sudo apt-get update -qy
+          sudo apt-get install -y python3-dev python3-venv libfftw3-dev libopenblas-dev
+          python3 -m venv venv
+          source venv/bin/activate
+          python3 -m pip install --upgrade pip
+          python3 -m pip install flit numpy pip-tools setuptools wheel
+          if [ "${{ matrix.mpi }}" == "yes" ]; then
+            # We now need to recompile some modules to link with native MPI
+            sudo apt-get install openmpi-bin libopenmpi-dev libfftw3-mpi-dev libhdf5-mpi-dev libpnetcdf-dev libnetcdf-pnetcdf-dev
+            # Install mpi4py first (because netCDF4 depends on it)
+            export NETCDF4_DIR=/usr/lib/x86_64-linux-gnu/netcdf/pnetcdf
+            export CC=mpicc
+            python3 -m pip install -v --no-binary mpi4py mpi4py==${{ matrix.mpi4py-version }}
+          else
+            sudo apt-get install libhdf5-dev libnetcdf-dev
+          fi
+          python3 -m pip install -v cython
+          python3 -m pip install -v --no-build-isolation --no-binary netCDF4 netCDF4==${{ matrix.netcdf4-python-version }}
+          # We need to force compilation of muSpectre; otherwise it will download a binary wheel which has no FFTW
+          # support, but we need this for the half-complex tests
+          python3 -m pip install -v --no-binary muSpectre muSpectre==${{ matrix.muspectre-version }}
+          python3 -m pip install -v .[test]
+          # Check that NetCDF install was not overriden
+          python3 .check_netcdf_capabilities.py ${{ matrix.mpi }}
+          python3 .check_mufft_capabilities.py ${{ matrix.mpi }}
 
-    - name: Test with pytest
-      run: |
-        source venv/bin/activate
- 
-        python3 .check_netcdf_capabilities.py ${{ matrix.mpi }}
-        python3 .check_mufft_capabilities.py ${{ matrix.mpi }}
-        python3 -m pip list
-        if [ "${{ matrix.mpi }}" == "yes" ]; then python3 run-tests.py --no-build --verbose --full-trace; else python3 -m pytest --verbose --full-trace -s; fi
+      - name: Test with pytest
+        run: |
+          source venv/bin/activate        
+          if [ "${{ matrix.mpi }}" == "yes" ]; then
+            python3 run-tests.py --no-build --verbose --full-trace
+          else
+            python3 -m pytest --verbose --full-trace -s
+          fi
diff --git a/.github/workflows/test_examples.yml b/.github/workflows/test_examples.yml
@@ -14,62 +14,56 @@ on:
 
 jobs:
   tests:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     timeout-minutes: 40
 
     strategy:
       matrix:
         python-version: ['3.8', '3.9', '3.10']
 
     steps:
-    - uses: actions/checkout@v3
-      with:
-        fetch-depth: 0
-        submodules: recursive
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          submodules: recursive
 
-    - name: Set up python3 ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
+      - name: Set up python3 ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
 
-    - name: Install dependencies
-      run: |
-        sudo apt-get update -qy
-        python3 -m venv venv
-        source venv/bin/activate
-        python3 -m pip install --upgrade pip pip-tools
-        
-        # Serial installation of muSpectre with FFTW support
-        sudo apt-get install -y \
-            libfftw3-dev \
-            libnetcdf-dev
-          # Compute muSpectre version
-          pip-compile pyproject.toml
-          MUSPECTRE_VERSION=$(grep 'muspectre==' requirements.txt)
-          # Manually install muSpectre with FFTW support
-          echo "Installing ${MUSPECTRE_VERSION}"
-          pip install -v --no-binary muspectre ${MUSPECTRE_VERSION}
-        
-        python3 -m pip install build
-        python3 -m pip list
+      - name: Install dependencies and extension module
+        run: |
+          set -x
+          sudo apt-get update -qy
+          sudo apt-get install -y python3-dev python3-venv libfftw3-dev libopenblas-dev
+          python3 -m venv venv
+          source venv/bin/activate
+          python3 -m pip install --upgrade pip
+          python3 -m pip install flit numpy pip-tools setuptools wheel
+          sudo apt-get install libhdf5-dev libnetcdf-dev
+          python3 -m pip install -v .[test]
+          # Check that NetCDF install was not overriden
+          python3 .check_netcdf_capabilities.py no
+          python3 .check_mufft_capabilities.py no
 
-    - name: Install extension module
-      run: |
-        source venv/bin/activate
-        python3 -m pip install .[test]
+      - name: Install extension module
+        run: |
+          source venv/bin/activate
+          python3 -m pip install .[test]
 
-    - name: Test example files
-      run: |
-        source venv/bin/activate
-        python3 -m pip install jupytext
-        python3 -m pip list
-        cd docs/examples
-        for f in *.ipynb
-        do
-            jupytext --check  pytest --warn-only $f
-        done
-
-        for f in *.py
-        do
-            jupytext --check pytest --warn-only $f
-        done
+      - name: Test example files
+        run: |
+          source venv/bin/activate
+          python3 -m pip install jupytext
+          python3 -m pip list
+          cd docs/examples
+          for f in *.ipynb
+          do
+              jupytext --check  pytest --warn-only $f
+          done
+  
+          for f in *.py
+          do
+              jupytext --check pytest --warn-only $f
+          done
diff --git a/Adhesion/ChangeLog.md b/Adhesion/ChangeLog.md
@@ -2,16 +2,12 @@
 Change log for Adhesion
 =======================
 
-v0.91.2 (27May23)
+v0.92.0 (14Jan24)
 -----------------
 - ENH: Analytical formulas for JKR contact 
-- DOC: Examples are now in documentation and stored as plain-text (jupytext) python files
-
-v0.91.1 (01Feb23)
------------------
-
 - BUG: Fixed discover of version when in a git repository that is not the
   source directory of SurfaceTopography
+- DOC: Examples are now in documentation and stored as plain-text (jupytext) python files
 
 v0.91.0 (03Jan23)
 -----------------

diff --git a/docs/conf.py b/docs/conf.py
@@ -20,6 +20,7 @@
 import os
 import sys
 import Adhesion
+
 sys.path.insert(0, os.path.abspath('../..'))
 
 # -- General configuration ------------------------------------------------
@@ -39,8 +40,6 @@
               "myst_nb"
               ]
 
-
-
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -86,7 +85,6 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
-
 # -- Options for HTML output ----------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -110,20 +108,19 @@
 #
 # This is required for the alabaster theme
 # refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
-#html_sidebars = {
+# html_sidebars = {
 #    '**': [
 #        'relations.html',  # needs 'show_related': True theme option to display
 #        'searchbox.html',
 #    ]
-#}
+# }
 
 
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'Adhesiondoc'
 
-
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {
@@ -152,7 +149,6 @@
      'Pastewka', 'manual'),
 ]
 
-
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
@@ -162,7 +158,6 @@
      authors, 1)
 ]
 
-
 # -- Options for Texinfo output -------------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples
@@ -181,5 +176,4 @@
     ".py": ["jupytext.reads", {"fmt": "py:percent"}],
 }
 
-
 nb_execution_timeout = 240