CHG: Pinning NumPy version as temporary fix for GitHub CI issues; cle…

…anup

.github/workflows/common-workflow.yml

@@ -6,7 +6,7 @@ on:
       os:
         required: true
         type: string
-      build_type: 
+      build_type:
         required: true
         type: string
       build_command:
@@ -29,80 +29,80 @@ on:
         type: string
 env:
   ISSM_DIR: ${{ github.workspace }}
-  
+
 jobs:
   build:
-    name: build-ISSM-${{ inputs.os }}-${{ inputs.build_type}}
+    name: build-ISSM-${{ inputs.os }}-${{ inputs.build_type }}
     runs-on: ${{ inputs.os }}
     outputs:
-      test_matrix: ${{ steps.creatTestMatrix.outputs.test_output }}
+      test_matrix: ${{ steps.createTestMatrix.outputs.test_output }}
     steps:
-      - name: Check out repository code
+      - name: Check out copy of repository
         uses: actions/checkout@v4
-          
-      - name: Cache externalpackages
+
+      - name: Cache external packages
         uses: actions/cache@v3
         id: cache-externalpackages
         env:
-          cache-name: cache-externalpackages-${{ inputs.build_type}}
+          cache-name: cache-externalpackages-${{ inputs.build_type }}
         with:
           path: |
             ${{ env.ISSM_DIR }}/externalpackages/
             !${{ env.ISSM_DIR }}/externalpackages/petsc/src/
           key: ${{ runner.os }}-build-${{ env.cache-name }}
-          
-      - name: Prepare External Packages
-        if: ${{ steps.cache-externalpackages.outputs.cache-hit != 'true'}}
+
+      - name: Prepare external packages
+        if: ${{ steps.cache-externalpackages.outputs.cache-hit != 'true' }}
         run: |
           ${{ inputs.ext_install_command }}
 
       - name: Get MATLAB
-        if: ${{inputs.interface == 'matlab'}}
-        id:   setup-matlab
+        if: ${{ inputs.interface == 'matlab' }}
+        id: setup-matlab
         uses: matlab-actions/setup-matlab@v2
         with:
           release: R2023b
           cache: true
 
-      - name: Prepare python
+      - name: Prepare Python
         if: contains( inputs.interface, 'python')
         uses: actions/setup-python@v5
         id: setup-python
         with:
           python-version: ${{ inputs.python_version }}
 
-      - name: Install dependencies
-        if: contains( inputs.interface, 'python')
+      - name: Install Python dependencies
+        if: contains(inputs.interface, 'python')
         run: |
           sudo apt-get install libpython${{ inputs.python_version }}-dev
           sudo apt-get install python3-dev
           python -m pip install --upgrade pip
           sudo apt-get update && sudo apt-get install -y python-tk python3-tk
-          python -m pip install numpy scipy matplotlib nose
+          python -m pip install numpy==2.1.0 scipy matplotlib nose
 
-      - name: build ISSM
+      - name: Build ISSM
         run: |
           export MATLAB_ROOT=${{ steps.setup-matlab.outputs.matlabroot }}
           export PYTHON_ROOT=${{ env.pythonLocation }}
           export NUMPY_ROOT=${{ env.LD_LIBRARY_PATH }}/python3.11/site-packages/numpy
-          ${{ inputs.build_command}}
+          ${{ inputs.build_command }}
 
       - name: Compile ISSM
         run: make -j4 install
 
       - name: Compress ISSM artifact
-        run: tar --exclude='./externalpackages/petsc/src' -cvf ISSM_artifact-${{ runner.os }}-${{ inputs.build_type}}.tar -C ${{ env.ISSM_DIR }}/ .
-        
+        run: tar --exclude='./externalpackages/petsc/src' -cvf ISSM_artifact-${{ runner.os }}-${{ inputs.build_type }}.tar -C ${{ env.ISSM_DIR }}/ .
+
       - name: Upload ISSM artifact
         uses: actions/upload-artifact@v4
         with:
           name: ISSM-${{ runner.os }}-${{ inputs.build_type }}
           path: ISSM_artifact-${{ runner.os }}-${{ inputs.build_type }}.tar
-          compression-level: 1          
-      - id: creatTestMatrix
+          compression-level: 1
+      - id: createTestMatrix
         run: |
           TESTS='${{ inputs.test_cases }}'
-          echo "test_output=$(jq -cn --argjson values "$TESTS" '{test_cases: $values}')" >> $GITHUB_OUTPUT  
+          echo "test_output=$(jq -cn --argjson values "$TESTS" '{test_cases: $values}')" >> $GITHUB_OUTPUT
   test:
     runs-on: ${{ inputs.os }}
     needs: build
@@ -113,26 +113,26 @@ jobs:
       - name: Download ISSM artifact
         uses: actions/download-artifact@v4
         with:
-          name: ISSM-${{ runner.os }}-${{ inputs.build_type}}
+          name: ISSM-${{ runner.os }}-${{ inputs.build_type }}
           path: ${{ env.ISSM_DIR }}
-      
-      - name: uncompress ISSM artifact
+
+      - name: Unpack ISSM artifact
         run: |
-          tar -xvf ISSM_artifact-${{ runner.os }}-${{ inputs.build_type}}.tar
+          tar -xvf ISSM_artifact-${{ runner.os }}-${{ inputs.build_type }}.tar
           source $ISSM_DIR/etc/environment.sh
         working-directory: ${{ env.ISSM_DIR }}
         shell: 'bash'
-          
+
       - name: Get MATLAB
-        if: ${{inputs.interface == 'matlab'}}
-        id:   setup-matlab
+        if: ${{ inputs.interface == 'matlab' }}
+        id: setup-matlab
         uses: matlab-actions/setup-matlab@v2
         with:
           release: R2023b
           cache: true
-          
+
       - name: Creating matlab_ci.m
-        if: ${{inputs.interface == 'matlab'}}
+        if: ${{ inputs.interface == 'matlab' }}
         run: |
           cat > ${ISSM_DIR}/matlab_ci.m << EOF
           % Go to the test directory
@@ -143,43 +143,43 @@ jobs:
           devpath;
 
           % Run tests
-          runme('exclude',[IdFromString('Dakota')],${{inputs.additional_options}} 'id',[${{matrix.test_cases}}],'quitonerror',1);
+          runme('exclude',[IdFromString('Dakota')],${{ inputs.additional_options }} 'id',[${{ matrix.test_cases }}],'quitonerror',1);
           quit(0);
           EOF
           cat ${ISSM_DIR}/matlab_ci.m
-          
+
       - name: Get run-matlab-command
-        if: ${{inputs.interface == 'matlab'}}
+        if: ${{ inputs.interface == 'matlab' }}
         run: |
           wget -O /usr/local/bin/run-matlab-command https://ssd.mathworks.com/supportfiles/ci/run-matlab-command/v2/glnxa64/run-matlab-command
           chmod +x /usr/local/bin/run-matlab-command
-          
+
       - name: Run MATLAB tests
         if: ${{inputs.interface == 'matlab'}}
         run: |
           source $ISSM_DIR/etc/environment.sh
           LD_PRELOAD=/lib/x86_64-linux-gnu/libstdc++.so.6:$ISSM_DIR/externalpackages/petsc/install/lib/libmpi.so:$ISSM_DIR/externalpackages/petsc/install/lib/libmpifort.so run-matlab-command "matlab_ci"
-  
-      - name: Prepare python
-        if: contains( inputs.interface, 'python')
+
+      - name: Prepare Python
+        if: contains(inputs.interface, 'python')
         uses: actions/setup-python@v5
         id: setup-python
         with:
           python-version: ${{ inputs.python_version }}
 
-      - name: Install dependencies
+      - name: Install Python dependencies
         if: contains( inputs.interface, 'python')
         run: |
           python -m pip install --upgrade pip
           sudo apt-get update && sudo apt-get install -y python-tk python3-tk
-          python -m pip install numpy scipy matplotlib nose netCDF4
+          python -m pip install numpy==2.1.0 scipy matplotlib nose netCDF4
 
       - name: Run Python tests
-        if: contains( inputs.interface, 'python')
+        if: contains(inputs.interface, 'python')
         run: |
           export PYTHONPATH="${ISSM_DIR}/src/m/dev:${PYTHONPATH}"
-          export PYTHONSTARTUP="${PYTHONPATH}/devpath.py"
+          export PYTHONSTARTUP="${ISSM_DIR}/src/m/dev/devpath.py"
           export PYTHONUNBUFFERED=1
           source $ISSM_DIR/etc/environment.sh
           cd $ISSM_DIR/test/NightlyRun
-          LD_PRELOAD=/lib/x86_64-linux-gnu/libstdc++.so.6:$ISSM_DIR/externalpackages/petsc/install/lib/libmpi.so:$ISSM_DIR/externalpackages/petsc/install/lib/libmpifort.so ./runme.py --output=nightly --rank=1 --numprocs=1 --id {{matrix.test_cases}} --exclude Dakota 234 418 420
+          LD_PRELOAD=/lib/x86_64-linux-gnu/libstdc++.so.6:$ISSM_DIR/externalpackages/petsc/install/lib/libmpi.so:$ISSM_DIR/externalpackages/petsc/install/lib/libmpifort.so ./runme.py --output=nightly --rank=1 --numprocs=1 --id ${{ matrix.test_cases }} --exclude Dakota 234 418 420

.github/workflows/ubuntu-python.yml

@@ -44,7 +44,7 @@ jobs:
         cd $ISSM_DIR/externalpackages/m1qn3    && ./install-linux.sh
         cd $ISSM_DIR/externalpackages/petsc    && ./install-3.22-linux.sh
         cd $ISSM_DIR/externalpackages/semic    && ./install.sh
-      test_cases: '["range(101,216)", "range(217,400)", "range(401, 900)"]'
+      test_cases: '["101:399", "401:899"]'
       additional_options: " "
     secrets: inherit
     name: build-test-ubuntu-python

jenkins/jenkins.sh

@@ -397,7 +397,7 @@ if [ $PYTHON_TEST -eq 1 ]; then
 	else
 		export PYTHONPATH="${ISSM_DIR}/src/m/dev:${PYTHONPATH}"
 	fi
-	export PYTHONSTARTUP="${PYTHONPATH}/devpath.py"
+	export PYTHONSTARTUP="${ISSM_DIR}/src/m/dev/devpath.py"
 	export PYTHONUNBUFFERED=1 # We don't want Python to buffer otherwise issm.exe output is not captured
 	for (( i=1;i<=$NUMCPUS_RUN;i++ ))
 	do

jenkins/mac-intel-full

@@ -23,7 +23,7 @@ ISSM_CONFIG='\
 	--with-python-version=3.9 \
 	--with-python-dir=/System/Volumes/Data/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9 \
 	--with-python-numpy-dir=${HOME}/.venv/issm/lib/python3.9/site-packages/numpy \
-	--with-fortran-lib="-L/usr/local/Cellar/gcc/14.1.0_2/lib/gcc/current -lgfortran" \
+	--with-fortran-lib="-L/usr/local/Cellar/gcc/14.2.0_1/lib/gcc/current -lgfortran" \
 	--with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \
 	--with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
 	--with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
@@ -59,7 +59,7 @@ EXTERNALPACKAGES="
 	hdf5		install-1.sh
 	netcdf		install-4.sh
 	proj		install-6.sh
-	gdal		install-3-python.sh
+	gdal		install-3-mac-python.sh
 	gshhg		install.sh
 	gmt			install-6-mac.sh
 	gmsh		install-4-mac.sh

src/m/geometry/GetAreas.py

@@ -2,36 +2,34 @@
 
 
 def GetAreas(index, x, y, z=np.array([])):
-    """
-    GETAREAS - compute areas or volumes of elements
+    """GetAreas - compute areas or volumes of elements
 
-       compute areas of triangular elements or volumes
-       of pentahedrons
+    compute areas of triangular elements or volumes of pentahedrons
 
-       Usage:
-          areas  =GetAreas(index, x, y)
-          volumes = GetAreas(index, x, y, z)
+    Usage:
+        areas = GetAreas(index, x, y)
+        volumes = GetAreas(index, x, y, z)
 
-       Examples:
-          areas  =GetAreas(md.mesh.elements, md.mesh.x, md.mesh.y)
-          volumes = GetAreas(md.mesh.elements, md.mesh.x, md.mesh.y, md.z)
+    Examples:
+        areas = GetAreas(md.mesh.elements, md.mesh.x, md.mesh.y)
+        volumes = GetAreas(md.mesh.elements, md.mesh.x, md.mesh.y, md.z)
     """
 
-    #get number of elements and number of nodes
-    nels = np.size(index, axis=0)
-    nods = np.size(x)
+    # Get number of elements and number of nodes
+    nels = np.shape(index)[0]
+    nods = np.shape(x)[0]
 
-    #some checks
-    if np.size(y) != nods or (z and np.size(z) != nods):
-        raise TypeError("GetAreas error message: x, y and z do not have the same length.")
+    # Some checks
+    if np.shape(y)[0] != nods or (z and np.shape(z)[0] != nods):
+        raise TypeError('GetAreas error message: x, y and z do not have the same length.')
     if np.max(index) > nods:
-        raise TypeError("GetAreas error message: index should not have values above %d." % nods)
-    if (not z and np.size(index, axis=1) != 3):
-        raise TypeError("GetAreas error message: index should have 3 columns for 2d meshes.")
-    if (z and np.size(index, axis=1) != 6):
-        raise TypeError("GetAreas error message: index should have 6 columns for 3d meshes.")
+        raise TypeError('GetAreas error message: index should not have values above {}.'.format(nods))
+    if (not z and np.shape(index)[1] != 3):
+        raise TypeError('GetAreas error message: index should have 3 columns for 2d meshes.')
+    if (z and np.shape(index)[1] != 6):
+        raise TypeError('GetAreas error message: index should have 6 columns for 3d meshes.')
 
-    #initialization
+    # Initialization
     areas = np.zeros(nels)
     x1 = x[index[:, 0] - 1]
     x2 = x[index[:, 1] - 1]
@@ -40,12 +38,12 @@ def GetAreas(index, x, y, z=np.array([])):
     y2 = y[index[:, 1] - 1]
     y3 = y[index[:, 2] - 1]
 
-    #compute the volume of each element
+    # Compute the volume of each element
     if not z:
-        #compute the surface of the triangle
+        # Compute the surface of the triangle
         areas = (0.5 * ((x2 - x1) * (y3 - y1) - (y2 - y1) * (x3 - x1)))
     else:
-        #V = area(triangle) * 1 / 3(z1 + z2 + z3)
+        # V = area(triangle) * 1/3(z1 + z2 + z3)
         thickness = np.mean(z[index[:, 3:6] - 1]) - np.mean(z[index[:, 0:3] - 1])
         areas = (0.5 * ((x2 - x1) * (y3 - y1) - (y2 - y1) * (x3 - x1))) * thickness
 

src/m/mesh/rifts/meshprocessrifts.py

@@ -7,7 +7,7 @@
 
 
 def meshprocessrifts(md, domainoutline):
-    """MESHPROCESSRIFTS - process mesh when rifts are present
+    """meshprocessrifts - process mesh when rifts are present
 
     split rifts inside mesh (rifts are defined by presence of
     segments inside the domain outline)
@@ -28,20 +28,20 @@ def meshprocessrifts(md, domainoutline):
     md.mesh.segments = md.mesh.segments.astype(int)
     md.mesh.segmentmarkers = md.mesh.segmentmarkers.astype(int)
     if not isinstance(md.rifts.riftstruct, list) or not md.rifts.riftstruct:
-        raise RuntimeError("ProcessRifts did not find any rift")
+        raise RuntimeError('ProcessRifts did not find any rift')
 
-    #Fill in rest of fields:
+    # Fill in rest of fields
     md.mesh.numberofelements = np.size(md.mesh.elements, axis=0)
     md.mesh.numberofvertices = np.size(md.mesh.x)
     md.mesh.vertexonboundary = np.zeros(np.size(md.mesh.x), int)
     md.mesh.vertexonboundary[md.mesh.segments[:, 0:2] - 1] = 1
 
-    #get coordinates of rift tips
+    # Get coordinates of rift tips
     for rift in md.rifts.riftstruct:
         rift['tip1coordinates'] = np.hstack((md.mesh.x[rift['tips'][0, 0].astype(int) - 1].reshape(-1, ), md.mesh.y[rift['tips'][0, 0].astype(int) - 1].reshape(-1, )))
         rift['tip2coordinates'] = np.hstack((md.mesh.x[rift['tips'][0, 1].astype(int) - 1].reshape(-1, ), md.mesh.y[rift['tips'][0, 1].astype(int) - 1].reshape(-1, )))
 
-    #In case we have rifts that open up the domain outline, we need to open them:
+    # In case we have rifts that open up the domain outline, we need to open them
     flags = ContourToMesh(md.mesh.elements, md.mesh.x, md.mesh.y, domainoutline, 'node', 0)
     found = 0
     for rift in md.rifts.riftstruct:
@@ -54,7 +54,7 @@ def meshprocessrifts(md, domainoutline):
     if found:
         md = meshprocessoutsiderifts(md, domainoutline)
 
-    #get elements that are not correctly oriented in the correct direction:
+    # Get elements that are not correctly oriented in the correct direction
     aires = GetAreas(md.mesh.elements, md.mesh.x, md.mesh.y)
     pos = np.nonzero(aires < 0)[0]
     md.mesh.elements[pos, :] = np.vstack((md.mesh.elements[pos, 1], md.mesh.elements[pos, 0], md.mesh.elements[pos, 2])).T

src/m/os/issmscpin.m

@@ -5,7 +5,7 @@ function issmscpin(host, login,port,path, packages)
 %
 % NOTE: If users again have issues with file list (i.e.
 %
-%   {<FILE1>,<FILE2>,...<FILEN>}
+%   {<FILE1>,<FILE2>,...,<FILEN>}
 %
 % ), note that this a bash'ism and default shell should be checked. View file 
 % history for potential fix (i.e. some combination of -O and -T options).

src/m/os/issmscpin.py

@@ -12,7 +12,7 @@ def issmscpin(host, login, port, path, packages):
 
     NOTE: If users again have issues with file list (i.e.
 
-        {<FILE1>,<FILE2>,...<FILEN>}
+        {<FILE1>,<FILE2>,...,<FILEN>}
 
     ), note that this a bash'ism and default shell should be checked. View file 
     history for potential fix (i.e. some combination of -O and -T options).

src/m/plot/plotmodel.py

@@ -12,13 +12,12 @@
 
 
 def plotmodel(md, *args):
-    '''
-    PLOTMODEL - At command prompt, type 'plotdoc()' for additional
+    """plotmodel - At command prompt, type 'plotdoc()' for additional
     documentation.
 
     TODO:
         - Fix 'plotdoc()', as it is not currently working.
-    '''
+    """
 
     #First process options
     options = plotoptions(*args)