burnman-cpp 0.6.0__tar.gz → 0.11.1__tar.gz

{burnman_cpp-0.6.0 → burnman_cpp-0.11.1}/.github/workflows/benchmarks.yml

@@ -43,7 +43,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y --no-install-recommends \
             cmake g++ catch2 libeigen3-dev libgsl-dev \
-            libcdd-dev libgmp-dev libnlopt-cxx-dev
+            libcdd-dev libgmp-dev libnlopt-cxx-dev libhdf5-dev
 
       - name: Configure benchmarks
         run: |
@@ -96,7 +96,7 @@ jobs:
         uses: actions/checkout@v7
         with:
           repository: geodynamics/burnman
-          ref: e2cfac31052273b3fa9d5ce905978e97723005e9
+          ref: b7c54ccf7bfd8583158c6dffe210c004b9570f4d
           path: build/python-burnman-reference
           persist-credentials: false
 

{burnman_cpp-0.6.0 → burnman_cpp-0.11.1}/.github/workflows/tests.yml

@@ -20,7 +20,7 @@ jobs:
   cpp:
     name: C++ tests
     runs-on: ubuntu-24.04
-    timeout-minutes: 20
+    timeout-minutes: 60
     steps:
       - name: Check out repository
         uses: actions/checkout@v7
@@ -32,7 +32,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y --no-install-recommends \
             cmake g++ catch2 libeigen3-dev libgsl-dev \
-            libcdd-dev libgmp-dev libnlopt-cxx-dev
+            libcdd-dev libgmp-dev libnlopt-cxx-dev libhdf5-dev
 
       - name: Configure C++ tests
         run: |
@@ -51,7 +51,7 @@ jobs:
   python:
     name: Python ${{ matrix.python-version }} tests
     runs-on: ubuntu-24.04
-    timeout-minutes: 20
+    timeout-minutes: 60
     strategy:
       fail-fast: false
       matrix:
@@ -80,7 +80,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y --no-install-recommends \
             cmake g++ libeigen3-dev libgsl-dev \
-            libcdd-dev libgmp-dev libnlopt-cxx-dev
+            libcdd-dev libgmp-dev libnlopt-cxx-dev libhdf5-dev
 
       - name: Build and install Python package
         run: python -m pip install '.[test,examples]' -Ccmake.define.BURNMAN_WARNINGS_AS_ERRORS=ON
@@ -92,7 +92,7 @@ jobs:
   reference:
     name: Pinned Python BurnMan reference
     runs-on: ubuntu-24.04
-    timeout-minutes: 20
+    timeout-minutes: 60
     env:
       CMAKE_BUILD_PARALLEL_LEVEL: "2"
       MPLBACKEND: Agg
@@ -110,7 +110,7 @@ jobs:
         uses: actions/checkout@v7
         with:
           repository: geodynamics/burnman
-          ref: e2cfac31052273b3fa9d5ce905978e97723005e9
+          ref: b7c54ccf7bfd8583158c6dffe210c004b9570f4d
           path: build/python-burnman-reference
           persist-credentials: false
 
@@ -128,12 +128,12 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y --no-install-recommends \
             cmake g++ clang-format libeigen3-dev libgsl-dev \
-            libcdd-dev libgmp-dev libnlopt-cxx-dev
+            libcdd-dev libgmp-dev libnlopt-cxx-dev libhdf5-dev
 
       - name: Install wrapper and reference dependencies
         run: |
           python -m pip install '.[test,examples]' -Ccmake.define.BURNMAN_WARNINGS_AS_ERRORS=ON
-          python -m pip install -e 'build/python-burnman-reference[dev]'
+          python -m pip install -e 'build/python-burnman-reference[dev]' h5py
 
       - name: Audit stored reference values and mineral catalogue
         env:
@@ -141,6 +141,7 @@ jobs:
         run: |
           python tools/check_reference_data.py
           python tools/export_example_minerals.py --check
+          python tools/export_covariance_data.py --check
           python tools/generate_ps1994_reference.py --reference build/python-burnman-reference
 
       - name: Run complete Python suite with the pinned reference

{burnman_cpp-0.6.0 → burnman_cpp-0.11.1}/.gitignore

@@ -29,3 +29,4 @@ examples/*_output/
 /benchmark-report.xml
 /python_assemblage_benchmarks.csv
 /python_mineral_benchmarks.csv
+benchmarks/*/results/

{burnman_cpp-0.6.0 → burnman_cpp-0.11.1}/CMakeLists.txt

@@ -13,7 +13,7 @@ endif()
 file(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/pyproject.toml" BURNMAN_VERSION_LINE
      REGEX "^version = ")
 string(REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+" BURNMAN_VERSION "${BURNMAN_VERSION_LINE}")
-project(burnman_cpp VERSION ${BURNMAN_VERSION} LANGUAGES CXX)
+project(burnman_cpp VERSION ${BURNMAN_VERSION} LANGUAGES C CXX)
 
 option(BURNMAN_BUILD_PYTHON "Build the Python extension" ON)
 option(BURNMAN_BUILD_TESTS "Build the C++ unit tests" OFF)
@@ -39,6 +39,7 @@ set(BURNMAN_WHEEL_DEPENDENCIES "" CACHE PATH "Private prefix for wheel dependenc
 if(BURNMAN_WHEEL_DEPENDENCIES)
   list(PREPEND CMAKE_PREFIX_PATH "${BURNMAN_WHEEL_DEPENDENCIES}")
   set(GSL_ROOT_DIR "${BURNMAN_WHEEL_DEPENDENCIES}")
+  set(HDF5_ROOT "${BURNMAN_WHEEL_DEPENDENCIES}")
 endif()
 if(APPLE)
   list(APPEND CMAKE_PREFIX_PATH /opt/homebrew /usr/local)
@@ -48,6 +49,7 @@ if(Eigen3_VERSION VERSION_LESS 3.4)
   message(FATAL_ERROR "BurnMan requires Eigen >= 3.4 (found ${Eigen3_VERSION})")
 endif()
 find_package(GSL REQUIRED)
+find_package(HDF5 1.10 REQUIRED COMPONENTS C)
 find_path(NLOPT_INCLUDE_DIR NAMES nlopt.hpp REQUIRED)
 find_library(NLOPT_LIBRARY NAMES nlopt REQUIRED)
 find_path(CDD_INCLUDE_DIR NAMES cdd.h PATH_SUFFIXES cddlib cdd REQUIRED)
@@ -62,6 +64,26 @@ target_include_directories(burnman_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/inclu
 target_link_libraries(burnman_core PUBLIC Eigen3::Eigen GSL::gsl GSL::gslcblas)
 target_include_directories(burnman_core SYSTEM PRIVATE ${CDD_INCLUDE_DIR} ${GMP_INCLUDE_DIR} ${NLOPT_INCLUDE_DIR})
 target_link_libraries(burnman_core PUBLIC ${CDD_GMP_LIBRARY} ${GMP_LIBRARY} ${NLOPT_LIBRARY})
+target_include_directories(burnman_core SYSTEM BEFORE PRIVATE ${HDF5_INCLUDE_DIRS})
+target_link_libraries(burnman_core PUBLIC ${HDF5_LIBRARIES})
+
+# Embed the HDF5 file images for standalone C++ and installed Python use.
+# CMake performs this step without requiring h5py or a Python interpreter.
+function(burnman_covariance_data name dataset)
+  set(input "${CMAKE_CURRENT_SOURCE_DIR}/src/data/input_covariance/${dataset}_cov.h5")
+  set(output "${CMAKE_CURRENT_BINARY_DIR}/generated/${name}_covariance_data.hpp")
+  set(script "${CMAKE_CURRENT_SOURCE_DIR}/cmake/EmbedCovariance.cmake")
+  add_custom_command(OUTPUT "${output}"
+    COMMAND "${CMAKE_COMMAND}" "-DNAME=${name}" "-DINPUT=${input}"
+            "-DOUTPUT=${output}" -P "${script}"
+    DEPENDS "${input}" "${script}"
+    VERBATIM)
+  target_sources(burnman_core PRIVATE "${output}")
+endfunction()
+burnman_covariance_data(HP_2011_ds62 HP_2011_ds62)
+burnman_covariance_data(HGP_2018_ds633 HGP_2018_ds633)
+burnman_covariance_data(HPx_ds636 HPx_ds636)
+target_include_directories(burnman_core PRIVATE "${CMAKE_CURRENT_BINARY_DIR}/generated")
 set_target_properties(burnman_core PROPERTIES POSITION_INDEPENDENT_CODE ON)
 burnman_compiler_warnings(burnman_core)
 
@@ -72,18 +94,31 @@ if(BURNMAN_BUILD_PYTHON)
     python/bindings/module.cpp
     python/bindings/params.cpp
     python/bindings/eos.cpp
+    python/bindings/thermal_components.cpp
     python/bindings/materials.cpp
     python/bindings/composition.cpp
+    python/bindings/linear_fitting.cpp
+    python/bindings/nonlinear_fitting.cpp
+    python/bindings/eos_fitting.cpp
+    python/bindings/composition_fitting.cpp
+    python/bindings/thermobarometry.cpp
+    python/bindings/chemistry.cpp
+    python/bindings/equilibrated_composite.cpp
     python/bindings/combined.cpp
     python/bindings/modifiers.cpp
     python/bindings/solutions.cpp
     python/bindings/minerals.cpp
     python/bindings/utils.cpp
     python/bindings/model_sets.cpp
+    python/bindings/seismic.cpp
+    python/bindings/geotherm.cpp
+    python/bindings/layer.cpp
+    python/bindings/planet.cpp
     python/bindings/polytope.cpp
     python/bindings/phase_diagram.cpp
     python/bindings/equilibration.cpp)
   target_link_libraries(_core PRIVATE burnman_core)
+  set_target_properties(_core PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE)
   target_compile_definitions(_core PRIVATE BURNMAN_VERSION="${PROJECT_VERSION}")
   burnman_compiler_warnings(_core)
   install(TARGETS _core LIBRARY DESTINATION burnman_cpp RUNTIME DESTINATION burnman_cpp)

{burnman_cpp-0.6.0 → burnman_cpp-0.11.1}/Makefile

@@ -1,12 +1,16 @@
-# Copyright (c) 2025 Benedict Heinen
+# ------------------------------------------------------
 #
-# This file is part of burnman_cpp and is licensed under the
-# GNU General Public License v3.0 or later. See the LICENSE file
-# or <https://www.gnu.org/licenses/> for details.
+# SPDX-License-Identifier: GPL-3.0-or-later
 #
-# burnman_cpp is based on BurnMan: <https://geodynamics.github.io/burnman/>
+# SPDX-FileCopyrightText: Copyright (C) 2025-2026 by the BurnMan Team.
 #
-# ------------------- END OF LICENSE SECTION -----------------
+# This file is part of BurnMan.
+#
+# Detailed license information governing the source code
+# and contributions can be found in the LICENSE document.
+#
+# ------------------------------------------------------
+
 # The native sources implement a library; Catch2 supplies main() for tests.
 TARGET_LIBRARY := libburnman.a
 TEST_EXEC := run_tests
@@ -14,6 +18,8 @@ BENCHMARK_EXEC := run_benchmarks
 
 # Compiler
 CXX := g++
+CMAKE ?= cmake
+PKG_CONFIG ?= pkg-config
 
 # Directories
 CWD := $(shell pwd)
@@ -32,11 +38,14 @@ INCLUDE_DIR_TEST := $(TEST_DIR)/include
 # GSL on MacOS installed via brew is in /opt/homebrew/lib
 EXTRA_INCLUDE ?= $(wildcard /opt/homebrew/include /opt/homebrew/include/eigen3 /opt/homebrew/opt/gsl/include /usr/local/include /usr/local/include/eigen3 /usr/include/eigen3)
 EXTRA_LIB ?= $(wildcard /usr/local/lib /opt/homebrew/lib)
-LDFLAGS_COMMON := -lgsl -lgslcblas -lcddgmp -lgmp -lnlopt -lm
+# Override these flags when HDF5 is installed outside pkg-config's search path.
+HDF5_CFLAGS ?= $(shell $(PKG_CONFIG) --cflags hdf5)
+HDF5_LIBS ?= $(shell $(PKG_CONFIG) --libs hdf5)
+LDFLAGS_COMMON := -lgsl -lgslcblas -lcddgmp -lgmp -lnlopt $(HDF5_LIBS) -lm
 LDFLAGS_TEST := -lCatch2Main -lCatch2
 
 # Expand to paths
-INCLUDE_FLAGS_COMMON := -I$(INCLUDE_DIR) $(addprefix -isystem , $(EXTRA_INCLUDE))
+INCLUDE_FLAGS_COMMON := -I$(INCLUDE_DIR) $(HDF5_CFLAGS) $(addprefix -isystem , $(EXTRA_INCLUDE))
 INCLUDE_FLAGS_TEST := -I$(INCLUDE_DIR_TEST)
 LIB_PATHS := $(addprefix -L, $(EXTRA_LIB))
 
@@ -94,6 +103,12 @@ ifeq ($(PROFILE), 1)
 	MODE_BUILD_DIR := $(MODE_BUILD_DIR)-profile
 endif
 
+# Covariance images are generated for this build mode before their reader.
+COVARIANCE_BUILD_DIR := $(MODE_BUILD_DIR)/generated
+COVARIANCE_EMBED_SCRIPT := $(CWD)/cmake/EmbedCovariance.cmake
+COVARIANCE_HEADERS := $(addprefix $(COVARIANCE_BUILD_DIR)/,HP_2011_ds62_covariance_data.hpp HGP_2018_ds633_covariance_data.hpp HPx_ds636_covariance_data.hpp)
+CPPFLAGS += -I$(COVARIANCE_BUILD_DIR)
+
 # Find source files
 SOURCES := $(shell find $(SRC_DIR) -name '*.cpp')
 TEST_SOURCES := $(shell find $(TEST_DIR) -name '*.cpp')
@@ -115,6 +130,15 @@ BENCHMARK_TARGET := $(BIN_DIR)/$(BENCHMARK_EXEC)$(BIN_SUFFIX)
 # Default rule
 all: $(TARGET)
 
+$(COVARIANCE_BUILD_DIR)/HP_2011_ds62_covariance_data.hpp: $(SRC_DIR)/data/input_covariance/HP_2011_ds62_cov.h5
+$(COVARIANCE_BUILD_DIR)/HGP_2018_ds633_covariance_data.hpp: $(SRC_DIR)/data/input_covariance/HGP_2018_ds633_cov.h5
+$(COVARIANCE_BUILD_DIR)/HPx_ds636_covariance_data.hpp: $(SRC_DIR)/data/input_covariance/HPx_ds636_cov.h5
+
+$(COVARIANCE_HEADERS): $(COVARIANCE_EMBED_SCRIPT)
+	$(CMAKE) "-DNAME=$(patsubst %_covariance_data.hpp,%,$(notdir $@))" "-DINPUT=$(filter %.h5,$^)" "-DOUTPUT=$@" -P "$(COVARIANCE_EMBED_SCRIPT)"
+
+$(MODE_BUILD_DIR)/src/data/covariance.o: $(COVARIANCE_HEADERS)
+
 # Archive the native library; linking an executable would require main().
 $(TARGET) : $(OBJECTS) | $(BIN_DIR)
 	$(AR) rcs $@ $^

{burnman_cpp-0.6.0 → burnman_cpp-0.11.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: burnman_cpp
-Version: 0.6.0
+Version: 0.11.1
 Summary: Python bindings for the BurnMan C++ mineral physics library
 Author-Email: The BurnMan Team <bob.myhill@bristol.ac.uk>
 License-Expression: GPL-3.0-or-later
@@ -22,6 +22,7 @@ Provides-Extra: examples
 Requires-Dist: matplotlib>=3.6; extra == "examples"
 Provides-Extra: reference
 Requires-Dist: burnman>=2.1; extra == "reference"
+Requires-Dist: h5py>=3.8; extra == "reference"
 Description-Content-Type: text/markdown
 
 # burnman_cpp
@@ -52,32 +53,114 @@ Python authors (as of 2025, from the [BurnMan README](https://github.com/geodyna
 
 ### Published Python wheels
 
-Install the published package with:
+Using Python 3.10 or newer, install the published package into your chosen
+Python environment:
 
 ```sh
 python -m pip install --upgrade pip
 python -m pip install burnman_cpp
 ```
 
-If no matching wheel is available, pip builds from source and needs the dependencies below.
+A virtual environment is optional. To use one, run these commands before
+installing:
 
-### Building from source
+```sh
+python -m venv .venv
+source .venv/bin/activate
+```
 
-Source builds require:
+Pip installs NumPy and SciPy automatically. Published wheels bundle the native
+libraries, so a compiler and native development packages are only needed when
+building from source. If no matching wheel is available, pip builds from source
+and needs the dependencies below.
 
-- A C++17 compiler, such as GCC or Clang.
-- CMake 3.18 or newer.
-- Eigen 3.4 or newer, GSL, NLopt with its C++ headers, cddlib with its GMP
-  library (`cddgmp`), and GMP.
-- Python 3.10 or newer and its development headers for the Python package.
-- Catch2 3.4 or newer for C++ tests and benchmarks.
+### Building from source
 
-On Ubuntu:
+#### Native dependencies
+
+Both the C++ library and Python source builds require:
+
+- **C and C++17 compiler toolchain**, such as GCC or Clang: compiles the native
+  library and, for Python builds, the extension module. CMake also checks for
+  a C compiler when locating HDF5.
+- **CMake 3.18 or newer**: configures the build, locates native dependencies and
+  embeds the covariance datasets. The supplied Makefile also uses CMake for
+  the data embedding step.
+- **Eigen 3.4 or newer**: supplies matrix and vector operations, linear solvers
+  and decompositions for compositions, reactions, solution models and fitting.
+- **GSL (GNU Scientific Library)**: provides root finding, numerical
+  integration, special functions and splines for equations of state and radial
+  planet profiles.
+- **NLopt, including its C++ header `nlopt.hpp`**: performs constrained
+  optimisation for relaxed solutions, fitting, thermobarometry and phase
+  stability calculations.
+- **cddlib, including its GMP-backed library `cddgmp`**: converts composition
+  constraints into polytope vertices for solution and assemblage calculations.
+- **GMP (GNU Multiple Precision Arithmetic Library)**: provides the exact
+  rational arithmetic used by cddlib and the polytope code to handle chemical
+  composition constraints.
+- **HDF5 1.10 or newer, with its C development headers and gzip/deflate support**:
+  reads the embedded endmember energy covariance datasets for HP_2011_ds62,
+  HGP_2018_ds633 and HPx_ds636. These data are embedded during the build and
+  read in memory.
+
+Additional tools depend on the build and checks you choose:
+
+- **Make**: runs the supplied Makefile. CMake builds also need a build tool,
+  such as Make or Ninja.
+- **pkg-config**: lets the Makefile discover HDF5 compiler and linker flags.
+  It is optional for CMake builds.
+- **Catch2 3.4 or newer**: supplies the C++ unit test runner and performance
+  benchmark framework. It is only required when building those targets.
+- **Git**: downloads the source repository and the optional pinned Python
+  BurnMan reference checkout.
+
+#### Python dependencies
+
+For the Python package, also install:
+
+- **Python 3.10 or newer, including its development headers**: runs the package
+  and lets the extension compile against Python.
+- **pip**: builds and installs the Python package and its Python dependencies.
+
+Pip installs these build and runtime dependencies automatically, as specified in
+[pyproject.toml](pyproject.toml):
+
+- **scikit-build-core 0.11 or newer** (build): connects pip's package build
+  process to CMake and packages the compiled extension.
+- **pybind11 3.0 or newer** (build): exposes the C++ classes and functions to
+  Python, including conversions between Eigen matrices and NumPy arrays.
+- **NumPy 1.23 or newer** (runtime): provides arrays for compositions, material
+  properties, covariance matrices and thermodynamic grids.
+- **SciPy 1.9 or newer** (runtime): provides interpolation, sparse matrices,
+  optimisation and smoothing for potential grids and ASPECT table exports.
+
+Optional Python dependencies are installed through extras:
+
+- **pytest 7 or newer** (`test`): runs the Python test suite.
+- **Matplotlib 3.6 or newer** (`examples`): plots examples, phase diagrams and
+  diagnostic figures; it is also needed by the plotting tests.
+- **Python BurnMan 2.1 or newer** (`reference`): enables adapters and comparisons
+  with the original implementation. The reference tests below use a specific
+  Git commit for reproducibility.
+- **h5py 3.8 or newer** (`reference`): exports and checks the HDF5 covariance
+  source files. Ordinary builds and covariance access use native HDF5 directly.
+
+#### Install system dependencies
+
+On Ubuntu 24.04, install the native dependencies and Python development tools:
 
 ```sh
 sudo apt-get update
-sudo apt-get install -y build-essential cmake python3-dev \
-  libeigen3-dev libgsl-dev libnlopt-cxx-dev libcdd-dev libgmp-dev catch2
+sudo apt-get install -y build-essential cmake git pkg-config \
+  python3-dev python3-pip python3-venv \
+  libeigen3-dev libgsl-dev libnlopt-cxx-dev libcdd-dev libgmp-dev libhdf5-dev
+```
+
+For C++ tests and benchmarks, also install Catch2:
+
+```sh
+sudo apt-get install -y catch2
 ```
 
 On macOS, install the Xcode command-line tools if needed, then install the
@@ -85,10 +168,18 @@ dependencies with [Homebrew](https://brew.sh):
 
 ```sh
 xcode-select --install
-brew install python cmake eigen gsl nlopt cddlib gmp catch2
+brew install python cmake pkg-config eigen gsl nlopt cddlib gmp hdf5
 ```
 
-Clone the repository:
+For C++ tests and benchmarks, also install Catch2:
+
+```sh
+brew install catch2
+```
+
+#### Build and install the Python package
+
+Clone the repository, then use your chosen Python environment:
 
 ```sh
 git clone https://github.com/bobmyhill/burnman_cpp.git
@@ -177,7 +268,9 @@ Make also accepts an optional `BUILD_MODE` argument. Available modes:
 
 Debug and test builds use separate outputs, such as `bin/run_tests_debug` and
 `bin/run_tests_test`. Use `CXX`, `EXTRA_INCLUDE` and `EXTRA_LIB` to override the
-compiler and dependency paths.
+compiler and dependency paths. If HDF5 is outside pkg-config's search path, set
+`PKG_CONFIG_PATH` to the directory containing `hdf5.pc`, or pass `HDF5_CFLAGS`
+and `HDF5_LIBS` explicitly to Make.
 
 ### Optional Python BurnMan reference comparisons
 
@@ -187,7 +280,7 @@ comparisons used by GitHub CI:
 
 ```sh
 git clone https://github.com/geodynamics/burnman.git build/python-burnman-reference
-git -C build/python-burnman-reference checkout e2cfac31052273b3fa9d5ce905978e97723005e9
+git -C build/python-burnman-reference checkout b7c54ccf7bfd8583158c6dffe210c004b9570f4d
 python -m pip install -e 'build/python-burnman-reference[dev]'
 export PYTHONPATH="$PWD/build/python-burnman-reference"
 export PYTHONDONTWRITEBYTECODE=1
@@ -198,6 +291,9 @@ MPLBACKEND=Agg python -m pytest -q -ra python/tests
 
 Install the same formatter versions used by GitHub CI:
 
+- **clang-format**: formats C++ sources and headers.
+- **Black**: formats Python sources.
+
 ```sh
 python -m pip install -r contrib/utilities/requirements-format.txt
 ```
@@ -218,6 +314,13 @@ directory.
 Build, run and report performance benchmarks using the instructions in
 [benchmarks/README.md](benchmarks/README.md).
 
+The Python reporting tools use NumPy and Matplotlib, plus:
+
+- **pandas 1.5 or newer**: processes timing tables and CSV reports.
+
+Install the reporting dependencies with
+`python -m pip install -r benchmarks/requirements.txt`.
+
 ## License
 
 burnman_cpp is licensed under [GPL-3.0-or-later](LICENSE).