Uw2 pixi

.gitattributes

@@ -3,3 +3,5 @@
 *.ipynb	diff=jupyternotebook
 
 *.ipynb	merge=jupyternotebook
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.gitignore

@@ -106,3 +106,7 @@ docs/test/Pressure_Error.png
 
 docs/test/uplift/buildMount.txt
 docs/test/temp.h5
+
+# pixi environments
+.pixi
+*.egg-info

clean.sh

@@ -3,6 +3,7 @@
 set -x  # show commands
 
 rm -fr build
+
 find src -name '*.so' -exec rm {} +
 find src -name '*.__pycache__' -exec rm -r {} +
 find src -name '*.egg-info' -exec rm -r {} +

pixi.toml

@@ -0,0 +1,40 @@
+[workspace]
+authors = ["Julian Giordani <julian.giordani@sydney.edu.au>"]
+channels = [
+  "conda-forge",
+  "https://prefix.dev/pixi-build-backends"
+]
+name = "uw2-pixi"
+platforms = ["linux-64", "osx-arm64"]
+
+[tasks]
+build = "pip install ."
+test = "pytest ./docs/pytests/tests.py ./docs/pytests/test_examples.py ./docs/pytests/test_user_guide.py"
+
+[dependencies]
+petsc = "3.21.*"
+python = "3.11.*"
+numpy = "<2"
+pint = ">=0.24.4,<0.25"
+cmake = ">=4.0.3,<5"
+swig = ">=4"
+pkg-config = ">=0.29.2,<0.30"
+compilers = ">=1.10.0,<2"
+scipy = ">=1.16.0,<2"
+mpi4py = ">=4.1.0,<5"
+libxml2 = ">=2.13.8,<3"
+ninja = ">=1.13.0,<2"
+mesalib = ">=25.0.5,<26"
+mpich = ">=4.3.1,<5"
+hdf5 = { version = "*", build = "mpi*" }
+h5py = { version = "*", build = "mpi*" }
+pip = ">=25.1.1,<26"
+pytest = ">=8.4.1,<9"
+nbmake = ">=1.5.5,<2"
+jupytext = ">=1.17.2,<2"
+jupyterlab = ">=4.4.4,<5"
+matplotlib = ">=3.10.5,<4"
+#[host-dependencies]
+c-compiler = "*"
+cxx-compiler = "*"
+make = "*"

pixi_dev_notes.md

@@ -0,0 +1,10 @@
+## Pixi notes
+
+Pixi is a new package manager for building Underworld2. It uses `conda-forge` and `PyPI` under the source packages. It installs them in consistent reproducible environments much like `conda`, but with the addedd benefit of lock files for deterministic builds. 
+
+### Basic commands
+
+`pixi install` to install an environment of uw2
+`pixi run build` to build uw2 in the environment
+`pixi run test` to run the uw2 tests in the pixi environment
+`pixi shell` (in the same directory as `pixi.toml`) to enter into the environment.

src/underworld/_version.py

@@ -1 +1 @@
-__version__ = "2.17.0"
+__version__ = "2.17.1"

src/underworld/libUnderworld/CMakeLists.txt

@@ -1,14 +1,18 @@
 cmake_minimum_required(VERSION 3.16)
+cmake_policy(SET CMP0078 OLD)
+
+# Set some Global options for CMAKE 
 set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(Python_FIND_VIRTUALENV ONLY)
-cmake_policy(SET CMP0078 OLD)
+option(BUILD_SHARED_LIBS "Build using shared libraries" ON)
 
 project(Underworld)
+
+# Required dependencies
 find_package(PkgConfig REQUIRED)
 find_package(LibXml2 REQUIRED)
 find_package(MPI REQUIRED)
-
 find_package(Python3 COMPONENTS Interpreter Development NumPy REQUIRED)
 find_package(SWIG 4.0 COMPONENTS python REQUIRED)
 
@@ -24,6 +28,7 @@ else(DEFINED ENV{PETSC_DIR})
 endif()
 message(STATUS "Checking for PETSc using $PKG_CONFIG_PATH=$ENV{PKG_CONFIG_PATH}")
 
+# Get CMAKE to find PETSc
 pkg_check_modules(PETSc PETSc)
 if(NOT PETSc_FOUND)
     message(FATAL_ERROR "Cannot find PETSc, please check that the PETSC_DIR environment " 
@@ -204,4 +209,5 @@ install(TARGETS ${target_sources}
     RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
     PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 
+# Now build the UW Swig wrappers (after C-code has been built). All swig stuff are in libUnderworldPY
 add_subdirectory(libUnderworldPy)

src/underworld/libUnderworld/libUnderworldPy/CMakeLists.txt

@@ -1,14 +1,7 @@
 
 # SWIG
-find_package(SWIG REQUIRED)
-find_package (Python COMPONENTS Interpreter Development)
+# load swig's cmake module
 include(${SWIG_USE_FILE})
-include_directories(${Python3_INCLUDE_DIRS})
-
-include_directories(../.)
-include_directories(${PETSc_INCLUDE_DIRS})
-include_directories(${LIBXML2_INCLUDE_DIR})
-include_directories(${Python3_NumPy_INCLUDE_DIRS})
 
 SET(UW_LIBRARIES
     Underworld
@@ -25,6 +18,7 @@ if(NOT APPLE)
     set(CMAKE_INSTALL_RPATH "\$ORIGIN")
 else()
     message(STATUS ">>> Apple")
+    set(CMAKE_MACOSX_RPATH TRUE)
     set(CMAKE_INSTALL_RPATH "@loader_path")
 endif()
 
@@ -35,89 +29,98 @@ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 
 SET(CMAKE_SWIG_FLAGS "-v" "-Wextra" "-O" "-c++" "-DSWIG_DO_NOT_WRAP")
 
-SET_SOURCE_FILES_PROPERTIES(Function.i PROPERTIES CPLUSPLUS ON)
-set_property(SOURCE Function.i PROPERTY SWIG_MODULE_NAME Function)
-SWIG_ADD_LIBRARY(Function TYPE SHARED LANGUAGE python SOURCES Function.i)
-SET_TARGET_PROPERTIES(${SWIG_MODULE_Function_REAL_NAME} PROPERTIES SUFFIX ".so")
-SWIG_LINK_LIBRARIES(Function PRIVATE ${UW_LIBRARIES})
-SWIG_LINK_LIBRARIES(Function PRIVATE ${PETSc_LINK_LIBRARIES})
-
-SET_SOURCE_FILES_PROPERTIES(c_arrays.i PROPERTIES CPLUSPLUS ON)
-set_property(SOURCE c_arrays.i PROPERTY SWIG_MODULE_NAME c_arrays)
-SWIG_ADD_LIBRARY(c_arrays TYPE SHARED LANGUAGE python SOURCES c_arrays.i)
-SET_TARGET_PROPERTIES(${SWIG_MODULE_c_arrays_REAL_NAME} PROPERTIES SUFFIX ".so")
-SWIG_LINK_LIBRARIES(c_arrays PRIVATE ${UW_LIBRARIES})
-SWIG_LINK_LIBRARIES(c_arrays PRIVATE ${PETSc_LINK_LIBRARIES})
-
-SET_SOURCE_FILES_PROPERTIES(c_pointers.i PROPERTIES CPLUSPLUS ON)
-set_property(SOURCE c_pointers.i PROPERTY SWIG_MODULE_NAME c_pointers)
-SWIG_ADD_LIBRARY(c_pointers TYPE SHARED LANGUAGE python SOURCES c_pointers.i)
-SET_TARGET_PROPERTIES(${SWIG_MODULE_c_pointers_REAL_NAME} PROPERTIES SUFFIX ".so")
-SWIG_LINK_LIBRARIES(c_pointers PRIVATE ${UW_LIBRARIES})
-SWIG_LINK_LIBRARIES(c_pointers PRIVATE ${PETSc_LINK_LIBRARIES})
-
-SET_SOURCE_FILES_PROPERTIES(gLucifer.i PROPERTIES CPLUSPLUS ON)
+message("Swig diagnostics:")
+get_property(dirs DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES)
+foreach(dir ${dirs})
+  message(STATUS "dir='${dir}'")
+endforeach()
+message(STATUS "UW_LIBRARIES=${UW_LIBRARIES}")
+message(STATUS "PETSc_LIBRARIES=${PETSc_LIBRARIES}")
+message("End Swig diagnostics:")
+
+set_source_files_properties(Function.i PROPERTIES
+    CPLUSPLUS ON
+    SWIG_MODULE_NAME Function)
+# This create swig module target, SWIG_MODULE_Function_REAL_NAME with CMP0078 != NEW
+swig_add_library(Function
+    TYPE SHARED
+    LANGUAGE python
+    SOURCES Function.i
+)
+set_target_properties(${SWIG_MODULE_Function_REAL_NAME} PROPERTIES 
+    SUFFIX ".so" )
+
+target_link_libraries(${SWIG_MODULE_Function_REAL_NAME}
+    PRIVATE ${UW_LIBRARIES}
+    PRIVATE ${PETSc_LIBRARIES})
+
+set_source_files_properties(c_arrays.i PROPERTIES 
+    CPLUSPLUS ON
+    SWIG_MODULE_NAME c_arrays)
+swig_add_library(c_arrays TYPE SHARED LANGUAGE python SOURCES c_arrays.i)
+set_target_properties(${SWIG_MODULE_c_arrays_REAL_NAME} PROPERTIES SUFFIX ".so")
+target_link_libraries(${SWIG_MODULE_c_arrays_REAL_NAME} PRIVATE ${UW_LIBRARIES} PRIVATE ${PETSc_LIBRARIES})
+
+set_source_files_properties(c_pointers.i PROPERTIES
+    CPLUSPLUS ON
+    SWIG_MODULE_NAME c_pointers)
+swig_add_library(c_pointers TYPE SHARED LANGUAGE python SOURCES c_pointers.i)
+set_target_properties(${SWIG_MODULE_c_pointers_REAL_NAME} PROPERTIES SUFFIX ".so")
+target_link_libraries(${SWIG_MODULE_c_pointers_REAL_NAME} PRIVATE ${UW_LIBRARIES} PRIVATE ${PETSc_LIBRARIES})
+
+set_source_files_properties(gLucifer.i PROPERTIES CPLUSPLUS ON)
 set_property(SOURCE gLucifer.i PROPERTY SWIG_MODULE_NAME gLucifer)
-SWIG_ADD_LIBRARY(gLucifer TYPE SHARED LANGUAGE python SOURCES gLucifer.i)
-SET_TARGET_PROPERTIES(${SWIG_MODULE_gLucifer_REAL_NAME} PROPERTIES SUFFIX ".so")
-SWIG_LINK_LIBRARIES(gLucifer PRIVATE ${UW_LIBRARIES})
-SWIG_LINK_LIBRARIES(gLucifer PRIVATE ${PETSc_LINK_LIBRARIES})
+swig_add_library(gLucifer TYPE SHARED LANGUAGE python SOURCES gLucifer.i)
+set_target_properties(${SWIG_MODULE_gLucifer_REAL_NAME} PROPERTIES SUFFIX ".so")
+target_link_libraries(${SWIG_MODULE_gLucifer_REAL_NAME} PRIVATE ${UW_LIBRARIES} PRIVATE ${PETSc_LIBRARIES})
 
-SET_SOURCE_FILES_PROPERTIES(petsc.i PROPERTIES CPLUSPLUS ON)
+set_source_files_properties(petsc.i PROPERTIES CPLUSPLUS ON)
 set_property(SOURCE petsc.i PROPERTY SWIG_MODULE_NAME petsc)
-SWIG_ADD_LIBRARY(petsc TYPE SHARED LANGUAGE python SOURCES petsc.i)
-SET_TARGET_PROPERTIES(${SWIG_MODULE_petsc_REAL_NAME} PROPERTIES SUFFIX ".so")
-SWIG_LINK_LIBRARIES(petsc PRIVATE ${UW_LIBRARIES})
-SWIG_LINK_LIBRARIES(petsc PRIVATE ${PETSc_LINK_LIBRARIES})
+swig_add_library(petsc TYPE SHARED LANGUAGE python SOURCES petsc.i)
+set_target_properties(${SWIG_MODULE_petsc_REAL_NAME} PROPERTIES SUFFIX ".so")
+target_link_libraries(${SWIG_MODULE_petsc_REAL_NAME} PRIVATE ${UW_LIBRARIES} PRIVATE ${PETSc_LIBRARIES})
 
-SET_SOURCE_FILES_PROPERTIES(PICellerator.i PROPERTIES CPLUSPLUS ON)
+set_source_files_properties(PICellerator.i PROPERTIES CPLUSPLUS ON)
 set_property(SOURCE PICellerator.i PROPERTY SWIG_MODULE_NAME PICellerator)
-SWIG_ADD_LIBRARY(PICellerator TYPE SHARED LANGUAGE python SOURCES PICellerator.i)
-SET_TARGET_PROPERTIES(${SWIG_MODULE_PICellerator_REAL_NAME} PROPERTIES SUFFIX ".so")
-SWIG_LINK_LIBRARIES(PICellerator PRIVATE ${UW_LIBRARIES})
-SWIG_LINK_LIBRARIES(PICellerator PRIVATE ${PETSc_LINK_LIBRARIES})
+swig_add_library(PICellerator TYPE SHARED LANGUAGE python SOURCES PICellerator.i)
+set_target_properties(${SWIG_MODULE_PICellerator_REAL_NAME} PROPERTIES SUFFIX ".so")
+target_link_libraries(${SWIG_MODULE_PICellerator_REAL_NAME} PRIVATE ${UW_LIBRARIES} PRIVATE ${PETSc_LIBRARIES})
 
-SET_SOURCE_FILES_PROPERTIES(Solvers.i PROPERTIES CPLUSPLUS ON)
+set_source_files_properties(Solvers.i PROPERTIES CPLUSPLUS ON)
 set_property(SOURCE Solvers.i PROPERTY SWIG_MODULE_NAME Solvers)
-SWIG_ADD_LIBRARY(Solvers TYPE SHARED LANGUAGE python SOURCES Solvers.i)
-SET_TARGET_PROPERTIES(${SWIG_MODULE_Solvers_REAL_NAME} PROPERTIES SUFFIX ".so")
-SWIG_LINK_LIBRARIES(Solvers PRIVATE ${UW_LIBRARIES})
-SWIG_LINK_LIBRARIES(Solvers PRIVATE ${PETSc_LINK_LIBRARIES})
+swig_add_library(Solvers TYPE SHARED LANGUAGE python SOURCES Solvers.i)
+set_target_properties(${SWIG_MODULE_Solvers_REAL_NAME} PROPERTIES SUFFIX ".so")
+target_link_libraries(${SWIG_MODULE_Solvers_REAL_NAME} PRIVATE ${UW_LIBRARIES} PRIVATE ${PETSc_LIBRARIES})
 
-SET_SOURCE_FILES_PROPERTIES(StgDomain.i PROPERTIES CPLUSPLUS ON)
+set_source_files_properties(StgDomain.i PROPERTIES CPLUSPLUS ON)
 set_property(SOURCE StgDomain.i PROPERTY SWIG_MODULE_NAME StgDomain)
-SWIG_ADD_LIBRARY(StgDomain TYPE SHARED LANGUAGE python SOURCES StgDomain.i)
-SET_TARGET_PROPERTIES(${SWIG_MODULE_StgDomain_REAL_NAME} PROPERTIES SUFFIX ".so")
-SWIG_LINK_LIBRARIES(StgDomain PRIVATE ${UW_LIBRARIES})
-SWIG_LINK_LIBRARIES(StgDomain PRIVATE ${PETSc_LINK_LIBRARIES})
+swig_add_library(StgDomain TYPE SHARED LANGUAGE python SOURCES StgDomain.i)
+set_target_properties(${SWIG_MODULE_StgDomain_REAL_NAME} PROPERTIES SUFFIX ".so")
+target_link_libraries(${SWIG_MODULE_StgDomain_REAL_NAME} PRIVATE ${UW_LIBRARIES} PRIVATE ${PETSc_LIBRARIES})
 
-SET_SOURCE_FILES_PROPERTIES(StGermain.i PROPERTIES CPLUSPLUS ON)
+set_source_files_properties(StGermain.i PROPERTIES CPLUSPLUS ON)
 set_property(SOURCE StGermain.i PROPERTY SWIG_MODULE_NAME StGermain)
-SWIG_ADD_LIBRARY(StGermain TYPE SHARED LANGUAGE python SOURCES StGermain.i)
-SET_TARGET_PROPERTIES(${SWIG_MODULE_StGermain_REAL_NAME} PROPERTIES SUFFIX ".so")
-SWIG_LINK_LIBRARIES(StGermain PRIVATE ${UW_LIBRARIES})
-SWIG_LINK_LIBRARIES(StGermain PRIVATE ${PETSc_LINK_LIBRARIES})
+swig_add_library(StGermain TYPE SHARED LANGUAGE python SOURCES StGermain.i)
+set_target_properties(${SWIG_MODULE_StGermain_REAL_NAME} PROPERTIES SUFFIX ".so")
+target_link_libraries(${SWIG_MODULE_StGermain_REAL_NAME} PRIVATE ${UW_LIBRARIES} PRIVATE ${PETSc_LIBRARIES})
 
-SET_SOURCE_FILES_PROPERTIES(StGermain_Tools.i PROPERTIES CPLUSPLUS ON)
+set_source_files_properties(StGermain_Tools.i PROPERTIES CPLUSPLUS ON)
 set_property(SOURCE StGermain_Tools.i PROPERTY SWIG_MODULE_NAME StGermain_Tools)
-SWIG_ADD_LIBRARY(StGermain_Tools TYPE SHARED LANGUAGE python SOURCES StGermain_Tools.i StGermain_Tools.c)
-SET_TARGET_PROPERTIES(${SWIG_MODULE_StGermain_Tools_REAL_NAME} PROPERTIES SUFFIX ".so")
-SWIG_LINK_LIBRARIES(StGermain_Tools PRIVATE ${UW_LIBRARIES})
-SWIG_LINK_LIBRARIES(StGermain_Tools PRIVATE ${PETSc_LINK_LIBRARIES})
+swig_add_library(StGermain_Tools TYPE SHARED LANGUAGE python SOURCES StGermain_Tools.i StGermain_Tools.c)
+set_target_properties(${SWIG_MODULE_StGermain_Tools_REAL_NAME} PROPERTIES SUFFIX ".so")
+target_link_libraries(${SWIG_MODULE_StGermain_Tools_REAL_NAME} PRIVATE ${UW_LIBRARIES} PRIVATE ${PETSc_LIBRARIES})
 
-SET_SOURCE_FILES_PROPERTIES(StgFEM.i PROPERTIES CPLUSPLUS ON)
+set_source_files_properties(StgFEM.i PROPERTIES CPLUSPLUS ON)
 set_property(SOURCE StgFEM.i PROPERTY SWIG_MODULE_NAME StgFEM)
-SWIG_ADD_LIBRARY(StgFEM TYPE SHARED LANGUAGE python SOURCES StgFEM.i)
-SET_TARGET_PROPERTIES(${SWIG_MODULE_StgFEM_REAL_NAME} PROPERTIES SUFFIX ".so")
-SWIG_LINK_LIBRARIES(StgFEM PRIVATE ${UW_LIBRARIES})
-SWIG_LINK_LIBRARIES(StgFEM PRIVATE ${PETSc_LINK_LIBRARIES})
+swig_add_library(StgFEM TYPE SHARED LANGUAGE python SOURCES StgFEM.i)
+set_target_properties(${SWIG_MODULE_StgFEM_REAL_NAME} PROPERTIES SUFFIX ".so")
+target_link_libraries(${SWIG_MODULE_StgFEM_REAL_NAME} PRIVATE ${UW_LIBRARIES} PRIVATE ${PETSc_LIBRARIES})
 
-SET_SOURCE_FILES_PROPERTIES(Underworld.i PROPERTIES CPLUSPLUS ON)
+set_source_files_properties(Underworld.i PROPERTIES CPLUSPLUS ON)
 set_property(SOURCE Underworld.i PROPERTY SWIG_MODULE_NAME Underworld)
-SWIG_ADD_LIBRARY(Underworld TYPE SHARED LANGUAGE python SOURCES Underworld.i)
-SET_TARGET_PROPERTIES(${SWIG_MODULE_Underworld_REAL_NAME} PROPERTIES SUFFIX ".so")
-SWIG_LINK_LIBRARIES(Underworld PRIVATE ${UW_LIBRARIES})
-SWIG_LINK_LIBRARIES(Underworld PRIVATE ${PETSc_LINK_LIBRARIES})
+swig_add_library(Underworld TYPE SHARED LANGUAGE python SOURCES Underworld.i)
+set_target_properties(${SWIG_MODULE_Underworld_REAL_NAME} PROPERTIES SUFFIX ".so")
+target_link_libraries(${SWIG_MODULE_Underworld_REAL_NAME} PRIVATE ${UW_LIBRARIES} PRIVATE ${PETSc_LIBRARIES})
 
 # Handle where to install the resulting Python package
 if(CALL_FROM_SETUP_PY)
@@ -130,6 +133,7 @@ else()
     set(UW_INSTALL_PREFIX ${Python3_SITELIB})
 endif()
 
+# Find the SWIG_SUPPORT_FILES from each wrapping
 get_property(FUNCTION_PY_FILE TARGET ${SWIG_MODULE_Function_REAL_NAME} PROPERTY SWIG_SUPPORT_FILES)
 get_property(CARRAYS_PY_FILE TARGET ${SWIG_MODULE_c_arrays_REAL_NAME} PROPERTY SWIG_SUPPORT_FILES)
 get_property(CPOINTERS_PY_FILE TARGET ${SWIG_MODULE_c_pointers_REAL_NAME} PROPERTY SWIG_SUPPORT_FILES)
@@ -158,6 +162,7 @@ set(WRAPPER_FILES
     ${UNDERWORLD_PY_FILE}
 )
 
+# install the wrapper files
 install(FILES ${WRAPPER_FILES} DESTINATION "${UW_INSTALL_PREFIX}/libUnderworld/libUnderworldPy")