Merge branch 'housekeeping_2025-09-29' into 'development'

housekeeping 2025-09-29

See merge request damask/DAMASK!1134

Author: Javier Velo

.github/workflows/Fortran.yml

@@ -2,7 +2,7 @@ name: Grid and Mesh Solver
 on: [push]
 
 env:
-  PETSC_VERSION: '3.23.3'
+  PETSC_VERSION: '3.24.0'
   HOMEBREW_NO_ANALYTICS: 'ON'     # Make Homebrew installation a little quicker
   HOMEBREW_NO_AUTO_UPDATE: 'ON'
   HOMEBREW_NO_BOTTLE_SOURCE_FALLBACK: 'ON'
@@ -17,7 +17,7 @@ jobs:
 
     strategy:
       matrix:
-        gcc_v: [11, 12, 13, 14, 15]
+        gcc_v: [11, 12, 13, 14]
       fail-fast: false
 
     env:
@@ -29,7 +29,6 @@ jobs:
 
       - name: GCC - Install
         run: |
-          sudo add-apt-repository ppa:ubuntu-toolchain-r/test
           sudo apt-get update
           sudo apt-get install liblapack-dev
           sudo apt-get install -y gcc-${GCC_V} gfortran-${GCC_V} g++-${GCC_V}

.gitlab-ci.yml

@@ -136,8 +136,9 @@ core:
     - |
       COMMITS=$(git log --reverse --format=format:%H origin/${CI_MERGE_REQUEST_TARGET_BRANCH_NAME}..${CI_COMMIT_SHA}~)
       for COMMIT in ${COMMITS};do
-        echo ${COMMIT}
+        printf "%b" "\e[1;32m::\nchecking commit ${COMMIT}\n::\e[0m\n"
         git checkout ${COMMIT}
+        git submodule update --init
         cmake -DGRID=ON -DMESH=ON -B build && cmake --build build --parallel 4 --target install
       done
 
@@ -149,7 +150,8 @@ processing:
       source env/DAMASK.sh
       COMMITS=$(git log --reverse --format=format:%H origin/$CI_MERGE_REQUEST_TARGET_BRANCH_NAME..$CI_COMMIT_SHA)
       for COMMIT in ${COMMITS};do
-        echo ${COMMIT}
+        printf "%b" "\e[1;32m::\nchecking commit ${COMMIT}\n::.\e[0m\n"
+        git checkout ${COMMIT}
         python -c 'import damask;print(damask.__version__)'
       done
 
@@ -270,8 +272,8 @@ unittest_oneapi_previous:
 .compile:
   stage: core
   before_script:
+    - ${PETSC_DIR}/lib/petsc/bin/petscversion
     - tail +$(grep -n 'Configure Actions.*' /petsc/configure.log | cut -f 1 -d:) /petsc/configure.log
-    - head -n 10 /petsc/include/petscversion.h | tail -n 6
     - source env/DAMASK.sh
     - cd PRIVATE/testing
 
@@ -320,8 +322,8 @@ Marc_compile:
 .configexamples_debug:
   stage: core
   before_script:
+    - ${PETSC_DIR}/lib/petsc/bin/petscversion
     - tail +$(grep -n 'Configure Actions.*' /petsc/configure.log | cut -f 1 -d:) /petsc/configure.log
-    - head -n 10 /petsc/include/petscversion.h | tail -n 6
     - source env/DAMASK.sh
     - cmake -B builddir -DGRID=ON -DCMAKE_BUILD_TYPE=DEBUG
     - cmake --build builddir --target install

CMakeLists.txt

@@ -1,5 +1,6 @@
 cmake_minimum_required(VERSION 3.18.0)
 set(CMAKE_CXX_STANDARD 23)
+set(CMAKE_C_STANDARD 17)
 include(FindPkgConfig REQUIRED)
 
 if(DEFINED ENV{PETSC_DIR})
@@ -11,7 +12,7 @@ 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}")
-set(PETSC_VERSION_MINOR_MIN "15")
+set(PETSC_VERSION_MINOR_MIN "19")
 set(PETSC_VERSION_MINOR_MAX "24")
 
 pkg_check_modules(PETSC_MIN REQUIRED PETSc>=3.${PETSC_VERSION_MINOR_MIN}.0 QUIET) #CMake does not support version range
@@ -39,17 +40,18 @@ project(DAMASK
         HOMEPAGE_URL https://damask-multiphysics.org
         LANGUAGES Fortran C CXX VERSION "${DAMASK_VERSION_CMAKE}")
 
-if(NOT ${CMAKE_C_COMPILER_ID} STREQUAL ${CMAKE_Fortran_COMPILER_ID})
-  message(FATAL_ERROR "C compiler (${CMAKE_C_COMPILER_ID}) does not match Fortran compiler (${CMAKE_Fortran_COMPILER_ID})")
-endif()
-if(NOT ${CMAKE_CXX_COMPILER_ID} STREQUAL ${CMAKE_Fortran_COMPILER_ID})
-  message(FATAL_ERROR "C++ compiler (${CMAKE_CXX_COMPILER_ID}) does not match Fortran compiler (${CMAKE_Fortran_COMPILER_ID})")
+if(NOT ${CMAKE_Fortran_COMPILER_ID} STREQUAL "LLVMFlang")
+  if(NOT ${CMAKE_C_COMPILER_ID} STREQUAL ${CMAKE_Fortran_COMPILER_ID})
+    message(FATAL_ERROR "C compiler (${CMAKE_C_COMPILER_ID}) does not match Fortran compiler (${CMAKE_Fortran_COMPILER_ID})")
+  endif()
+  if(NOT ${CMAKE_CXX_COMPILER_ID} STREQUAL ${CMAKE_Fortran_COMPILER_ID})
+    message(FATAL_ERROR "C++ compiler (${CMAKE_CXX_COMPILER_ID}) does not match Fortran compiler (${CMAKE_Fortran_COMPILER_ID})")
+  endif()
 endif()
 
 set(CMAKE_Fortran_PREPROCESS "ON")
 
 # EXPERIMENTAL: This might help to detect external packages in future if PETSc is not aware of them
-set(ENV{PKG_CONFIG_PATH} "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/externalpackages:$ENV{PKG_CONFIG_PATH}")
 pkg_check_modules(HDF5 hdf5)
 pkg_check_modules(fYAML libfyaml)
 pkg_check_modules(LAPACK lapack)

PRIVATE

@@ -24,7 +24,7 @@ else()
 endif()
 
 if(CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 12)
-  add_definitions(-DOLD_STYLE_C_TO_FORTRAN_STRING)
+  add_compile_definitions(OLD_STYLE_C_TO_FORTRAN_STRING)
 endif()
 
 #------------------------------------------------------------------------------------------------

cmake/Compiler-GNU.cmake

@@ -89,7 +89,6 @@ fi
 export DAMASK_ROOT
 export PYTHONPATH=$DAMASK_ROOT/python:$PYTHONPATH
 
-for var in BASE STAT SOLVER BRANCH; do
+for var in BASE STAT SOLVER BRANCH ENV_ROOT; do
   unset "${var}"
 done
-unset "ENV_ROOT"

env/DAMASK.sh

@@ -79,7 +79,6 @@ fi
 export DAMASK_ROOT
 export PYTHONPATH=$DAMASK_ROOT/python:$PYTHONPATH
 
-for var in SOLVER BRANCH; do
+for var in SOLVER BRANCH ENV_ROOT; do
   unset "${var}"
 done
-unset "ENV_ROOT"

env/DAMASK.zsh

@@ -9,12 +9,12 @@
 
 from pathlib import Path as _Path
 import re as _re
-import logging
+import logging as _logging
 
-logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')
+_logging.basicConfig(level=_logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')
 
 name = 'damask'
-with open(_Path(__file__).parent/_Path('VERSION')) as _f:
+with open(_Path(__file__).parent/'VERSION') as _f:
     version = _re.sub(r'^v','',_f.readline().strip())
     __version__ = version
 

python/damask/__init__.py

@@ -6,6 +6,7 @@
 from itertools import chain
 
 import numpy as np
+from numpy import typing as npt
 import scipy.interpolate as interp
 import matplotlib as mpl
 if os.name == 'posix' and 'DISPLAY' not in os.environ:
@@ -618,7 +619,7 @@ def adjust_hue(msh_sat, m_unsat):
 
 
     @staticmethod
-    def _hsv2rgb(hsv: np.ndarray) -> np.ndarray:
+    def _hsv2rgb(hsv: npt.NDArray[np.floating]) -> npt.NDArray[np.floating]:
         """
         Hue Saturation Value to Red Green Blue.
 
@@ -635,7 +636,7 @@ def _hsv2rgb(hsv: np.ndarray) -> np.ndarray:
         return np.array(colorsys.hsv_to_rgb(hsv[0]/360.,hsv[1],hsv[2]))
 
     @staticmethod
-    def _rgb2hsv(rgb: np.ndarray) -> np.ndarray:
+    def _rgb2hsv(rgb: npt.NDArray[np.floating]) -> npt.NDArray[np.floating]:
         """
         Red Green Blue to Hue Saturation Value.
 
@@ -654,7 +655,7 @@ def _rgb2hsv(rgb: np.ndarray) -> np.ndarray:
 
 
     @staticmethod
-    def _hsl2rgb(hsl: np.ndarray) -> np.ndarray:
+    def _hsl2rgb(hsl: npt.NDArray[np.floating]) -> npt.NDArray[np.floating]:
         """
         Hue Saturation Luminance to Red Green Blue.
 
@@ -671,7 +672,7 @@ def _hsl2rgb(hsl: np.ndarray) -> np.ndarray:
         return np.array(colorsys.hls_to_rgb(hsl[0]/360.,hsl[2],hsl[1]))
 
     @staticmethod
-    def _rgb2hsl(rgb: np.ndarray) -> np.ndarray:
+    def _rgb2hsl(rgb: npt.NDArray[np.floating]) -> npt.NDArray[np.floating]:
         """
         Red Green Blue to Hue Saturation Luminance.
 
@@ -690,7 +691,7 @@ def _rgb2hsl(rgb: np.ndarray) -> np.ndarray:
 
 
     @staticmethod
-    def _xyz2rgb(xyz: np.ndarray) -> np.ndarray:
+    def _xyz2rgb(xyz: npt.NDArray[np.floating]) -> npt.NDArray[np.floating]:
         """
         CIEXYZ to Red Green Blue.
 
@@ -719,7 +720,7 @@ def _xyz2rgb(xyz: np.ndarray) -> np.ndarray:
         return np.clip(rgb,0.,1.)
 
     @staticmethod
-    def _rgb2xyz(rgb: np.ndarray) -> np.ndarray:
+    def _rgb2xyz(rgb: npt.NDArray[np.floating]) -> npt.NDArray[np.floating]:
         """
         Red Green Blue to CIEXYZ.
 
@@ -746,8 +747,8 @@ def _rgb2xyz(rgb: np.ndarray) -> np.ndarray:
 
 
     @staticmethod
-    def _lab2xyz(lab: np.ndarray,
-                 ref_white: np.ndarray = _REF_WHITE) -> np.ndarray:
+    def _lab2xyz(lab: npt.NDArray[np.floating],
+                 ref_white: npt.NDArray[np.floating] = _REF_WHITE) -> npt.NDArray[np.floating]:
         """
         CIELAB to CIEXYZ.
 
@@ -778,8 +779,8 @@ def _lab2xyz(lab: np.ndarray,
                         ])*ref_white
 
     @staticmethod
-    def _xyz2lab(xyz: np.ndarray,
-                 ref_white: np.ndarray = _REF_WHITE) -> np.ndarray:
+    def _xyz2lab(xyz: npt.NDArray[np.floating],
+                 ref_white: npt.NDArray[np.floating] = _REF_WHITE) -> npt.NDArray[np.floating]:
         """
         CIEXYZ to CIELAB.
 
@@ -812,7 +813,7 @@ def _xyz2lab(xyz: np.ndarray,
 
 
     @staticmethod
-    def _lab2msh(lab: np.ndarray) -> np.ndarray:
+    def _lab2msh(lab: npt.NDArray[np.floating]) -> npt.NDArray[np.floating]:
         """
         CIELAB to Msh.
 
@@ -839,7 +840,7 @@ def _lab2msh(lab: np.ndarray) -> np.ndarray:
                         ])
 
     @staticmethod
-    def _msh2lab(msh: np.ndarray) -> np.ndarray:
+    def _msh2lab(msh: npt.NDArray[np.floating]) -> npt.NDArray[np.floating]:
         """
         Msh to CIELAB.
 
@@ -865,7 +866,7 @@ def _msh2lab(msh: np.ndarray) -> np.ndarray:
                         ])
 
     @staticmethod
-    def _lab2rgb(lab: np.ndarray) -> np.ndarray:
+    def _lab2rgb(lab: npt.NDArray[np.floating]) -> npt.NDArray[np.floating]:
         """
         CIELAB to Red Green Blue.
 
@@ -882,7 +883,7 @@ def _lab2rgb(lab: np.ndarray) -> np.ndarray:
         return Colormap._xyz2rgb(Colormap._lab2xyz(lab))
 
     @staticmethod
-    def _rgb2lab(rgb: np.ndarray) -> np.ndarray:
+    def _rgb2lab(rgb: npt.NDArray[np.floating]) -> npt.NDArray[np.floating]:
         """
         Red Green Blue to CIELAB.
 
@@ -899,7 +900,7 @@ def _rgb2lab(rgb: np.ndarray) -> np.ndarray:
         return Colormap._xyz2lab(Colormap._rgb2xyz(rgb))
 
     @staticmethod
-    def _msh2rgb(msh: np.ndarray) -> np.ndarray:
+    def _msh2rgb(msh: npt.NDArray[np.floating]) -> npt.NDArray[np.floating]:
         """
         Msh to Red Green Blue.
 
@@ -916,7 +917,7 @@ def _msh2rgb(msh: np.ndarray) -> np.ndarray:
         return Colormap._lab2rgb(Colormap._msh2lab(msh))
 
     @staticmethod
-    def _rgb2msh(rgb: np.ndarray) -> np.ndarray:
+    def _rgb2msh(rgb: npt.NDArray[np.floating]) -> npt.NDArray[np.floating]:
         """
         Red Green Blue to Msh.
 
@@ -933,7 +934,7 @@ def _rgb2msh(rgb: np.ndarray) -> np.ndarray:
         return Colormap._lab2msh(Colormap._rgb2lab(rgb))
 
     @staticmethod
-    def _hsv2msh(hsv: np.ndarray) -> np.ndarray:
+    def _hsv2msh(hsv: npt.NDArray[np.floating]) -> npt.NDArray[np.floating]:
         """
         Hue Saturation Value to msh.
 
@@ -950,7 +951,7 @@ def _hsv2msh(hsv: np.ndarray) -> np.ndarray:
         return Colormap._rgb2msh(Colormap._hsv2rgb(hsv))
 
     @staticmethod
-    def _hsl2msh(hsl: np.ndarray) -> np.ndarray:
+    def _hsl2msh(hsl: npt.NDArray[np.floating]) -> npt.NDArray[np.floating]:
         """
         Hue Saturation Luminance to Msh.
 
@@ -967,7 +968,7 @@ def _hsl2msh(hsl: np.ndarray) -> np.ndarray:
         return Colormap._rgb2msh(Colormap._hsl2rgb(hsl))
 
     @staticmethod
-    def _xyz2msh(xyz: np.ndarray) -> np.ndarray:
+    def _xyz2msh(xyz: npt.NDArray[np.floating]) -> npt.NDArray[np.floating]:
         """
         CIEXYZ to Msh.
 

python/damask/_colormap.py

@@ -124,8 +124,12 @@ def load_DREAM3D(fname: str,
 
         Homogenization and phase entries are emtpy and need to be
         defined separately.
+
+        Versions 8.0 and later of the DREAM.3D file format are not yet supported.
         """
         with h5py.File(fname, 'r') as f:
+            if (file_version := util.version(f.attrs['FileVersion'].decode()+'.0')) > '7.0.0':
+                raise ValueError(f'DREAM.3D file format {file_version} is not supported')
             b = util.DREAM3D_base_group(f) if base_group is None else base_group
             c = util.DREAM3D_cell_data_group(f) if cell_data is None else cell_data