Merge branch 'housekeeping_2024-12-17' into 'development'

housekeeping 2024-12-17

See merge request damask/DAMASK!1014

Author: dmentock

.github/workflows/Fortran.yml

@@ -17,7 +17,7 @@ jobs:
 
     strategy:
       matrix:
-        gcc_v: [9, 10, 11, 12, 13]
+        gcc_v: [11, 12, 13]
       fail-fast: false
 
     env:

.gitlab-ci.yml

@@ -79,6 +79,18 @@ pytest:
     - python3 -m pytest -v --cov=damask --cov-report=xml --damaskroot=${DAMASK_ROOT}
     - coverage report --fail-under=90 --show-missing
 
+doctest:
+  stage: python
+  tags:
+    - matesting2-container-runner
+  image: git.damask-multiphysics.org:5050/damask/damask:python310_2407
+  before_script: []
+  script:
+    - export DAMASK_ROOT=$(pwd)
+    - PYTHONPATH=${DAMASK_ROOT}/python:$PYTHONPATH
+    - cd python
+    - python3 -m pytest -v --doctest-modules -k 'not result and not configmaterial and not orientation and not rotation and not geomgrid' damask
+
 mypy:
   stage: python
   tags:

CMakeLists.txt

@@ -10,7 +10,7 @@ endif()
 # Dummy project to determine compiler names and version
 project(Prerequisites LANGUAGES)
 set(ENV{PKG_CONFIG_PATH} "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/pkgconfig:$ENV{PKG_CONFIG_PATH}")
-pkg_check_modules(PETSC_MIN REQUIRED PETSc>=3.12.0 QUIET) #CMake does not support version range
+pkg_check_modules(PETSC_MIN REQUIRED PETSc>=3.15.0 QUIET) #CMake does not support version range
 pkg_check_modules(PETSC REQUIRED PETSc<3.23.0)
 
 pkg_get_variable(CMAKE_Fortran_COMPILER PETSc fcompiler)
@@ -20,7 +20,7 @@ pkg_get_variable(CMAKE_C_COMPILER PETSc ccompiler)
 string(TOUPPER "${DAMASK_SOLVER}" DAMASK_SOLVER_UPPER)
 string(TOLOWER "${DAMASK_SOLVER}" DAMASK_SOLVER_LOWER)
 if("${DAMASK_SOLVER_UPPER}" MATCHES "^(GRID|MESH|TEST)$")
-    project("damask-${DAMASK_SOLVER_LOWER}" HOMEPAGE_URL https://damask.mpie.de LANGUAGES Fortran C)
+    project("damask-${DAMASK_SOLVER_LOWER}" HOMEPAGE_URL https://damask-multiphysics.org LANGUAGES Fortran C)
 else()
     message(FATAL_ERROR "Invalid solver: DAMASK_SOLVER=${DAMASK_SOLVER}")
 endif()
@@ -33,15 +33,18 @@ set(ENV{PKG_CONFIG_PATH} "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/externalpackages:$ENV
 pkg_check_modules(HDF5 hdf5)
 pkg_check_modules(FFTW3 fftw3)
 pkg_check_modules(fYAML libfyaml)
-pkg_check_modules(zlib zlib)
+if(DAMASK_SOLVER_UPPER STREQUAL "GRID")
+    pkg_check_modules(zlib zlib)
+endif()
 
 file(STRINGS ${PROJECT_SOURCE_DIR}/VERSION DAMASK_VERSION)
 
 message("\nBuilding ${CMAKE_PROJECT_NAME} ${DAMASK_VERSION}\n")
 
 add_definitions(-DPETSC)
-add_definitions(-DDAMASKVERSION="${DAMASK_VERSION}")
-add_definitions(-DCMAKE_SYSTEM="${CMAKE_SYSTEM}")
+add_definitions(-DDAMASK_VERSION="${DAMASK_VERSION}")
+add_definitions(-DCMAKE_SYSTEM_NAME="${CMAKE_SYSTEM_NAME}")
+add_definitions(-DCMAKE_SYSTEM_PROCESSOR="${CMAKE_SYSTEM_PROCESSOR}")
 if(PETSC_VERSION VERSION_EQUAL 3.17.0)
    add_definitions("-DCHKERRQ=PetscCall")
 endif()
@@ -126,7 +129,10 @@ endif()
 
 set(CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE} "${CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE}} ${PETSC_INCLUDES} ${BUILDCMD_POST}")
 
-set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} <OBJECTS> -o <TARGET> <LINK_LIBRARIES> -L${PETSC_LIBRARY_DIRS} -lpetsc ${PETSC_EXTERNAL_LIB} -lz")
+set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} <OBJECTS> -o <TARGET> <LINK_LIBRARIES> -L${PETSC_LIBRARY_DIRS} -lpetsc ${PETSC_EXTERNAL_LIB}")
+if(DAMASK_SOLVER_UPPER STREQUAL "GRID")
+    set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} -lz")
+endif()
 
 if(fYAML_FOUND STREQUAL "1")
     set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} -L${fYAML_LIBRARY_DIRS}")

PRIVATE

@@ -564,12 +564,9 @@ def from_Voronoi_tessellation(cells: IntSequence,
 
         """
         coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
-        tree = spatial.cKDTree(seeds,boxsize=size) if periodic else \
-               spatial.cKDTree(seeds)
-        try:
-            material_ = tree.query(coords, workers = int(os.environ.get('OMP_NUM_THREADS',4)))[1]
-        except TypeError:
-            material_ = tree.query(coords, n_jobs = int(os.environ.get('OMP_NUM_THREADS',4)))[1]    # scipy <1.6
+        tree = spatial.KDTree(seeds,boxsize=size) if periodic else \
+               spatial.KDTree(seeds)
+        material_ = tree.query(coords, workers = int(os.environ.get('OMP_NUM_THREADS',4)))[1]
 
         return GeomGrid(material = (material_ if material is None else np.array(material)[material_]).reshape(cells),
                         size     = size,

python/damask/_geomgrid.py

@@ -231,7 +231,7 @@ def allclose(self: MyType,
         return np.all(self.isclose(other,rtol,atol,equal_nan))
 
 
-    def __array__(self,*, copy: bool = None) -> np.ndarray:
+    def __array__(self,*, copy: Optional[bool] = None) -> np.ndarray:
         """Initializer for numpy."""
         return self.quaternion.copy() if copy is True else self.quaternion                          # noqa: E712
 

python/damask/_rotation.py

@@ -451,7 +451,6 @@ def save(self,
             writer.Write()
 
 
-    # Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data
     def set(self,
             label: Optional[str] = None,
             data: Union[None, np.ndarray, np.ma.MaskedArray] = None,

python/damask/_vtk.py

@@ -155,9 +155,9 @@ def from_grid(grid,
     # materials: 29
     >>> COG,matID = damask.seeds.from_grid(g,average=True)
     >>> distance,ID = scipy.spatial.KDTree(COG,boxsize=g.size).query(seeds)
-    >>> np.max(distance) / np.linalg.norm(g.size/g.cells)
+    >>> print(np.max(distance) / np.linalg.norm(g.size/g.cells))
     10.1
-    >>> (ID == matID).all()
+    >>> print((ID == matID).all())
     True
 
     """

python/damask/seeds.py

@@ -1,5 +1,7 @@
 [mypy]
 warn_redundant_casts = True
+plugins = numpy.typing.mypy_plugin
+
 [mypy-scipy.*]
 ignore_missing_imports = True
 [mypy-h5py.*]

python/mypy.ini

@@ -5,7 +5,7 @@
 !> @author Philip Eisenlohr, Max-Planck-Institut für Eisenforschung GmbH
 !> @brief Parse command line interface for PETSc-based solvers
 !--------------------------------------------------------------------------------------------------
-#define PETSC_MINOR_MIN 12
+#define PETSC_MINOR_MIN 15
 #define PETSC_MINOR_MAX 22
 
 module CLI
@@ -109,19 +109,18 @@ subroutine CLI_init()
   print'(1x,a)', 'https://doi.org/'//PETSc_DOI
 #endif
 #endif
-  print'(/,1x,a)', 'Version: '//DAMASKVERSION
+  print'(/,1x,a)', 'Version: '//DAMASK_VERSION
 
+  ! https://github.com/jeffhammond/HPCInfo/blob/master/docs/Preprocessor-Macros.md
   print'(/,1x,a)', 'Compiled with: '//compiler_version()
-  print'(1x,a)',   'Compiled on: '//CMAKE_SYSTEM
   print'(1x,a)',   'Compiler options: '//compiler_options()
+  print'(1x,a)',   'Compiled for: '//CMAKE_SYSTEM_NAME//' on '//CMAKE_SYSTEM_PROCESSOR
+  print'(1x,a,1x,i0,a,i0,a,i0)', &
+                   'PETSc version:',PETSC_VERSION_MAJOR,'.',PETSC_VERSION_MINOR,'.',PETSC_VERSION_SUBMINOR
 
-  ! https://github.com/jeffhammond/HPCInfo/blob/master/docs/Preprocessor-Macros.md
-  print'(/,1x,a)', 'Compiled on: '//__DATE__//' at '//__TIME__
-
-  print'(/,1x,a,1x,i0,a,i0,a,i0)', &
-                'PETSc version:',PETSC_VERSION_MAJOR,'.',PETSC_VERSION_MINOR,'.',PETSC_VERSION_SUBMINOR
+  print'(/,1x,a)', 'Compiled at: '//__DATE__//' at '//__TIME__
 
-  call date_and_time(values = dateAndTime)
+   call date_and_time(values = dateAndTime)
   print'(/,1x,a,1x,2(i2.2,a),i4.4)', 'Date:',dateAndTime(3),'/',dateAndTime(2),'/',dateAndTime(1)
   print'(1x,a,1x,2(i2.2,a),i2.2)',   'Time:',dateAndTime(5),':',dateAndTime(6),':',dateAndTime(7)