gamut-format 1.0.0__tar.gz

gamut_format-1.0.0/.gitignore

@@ -0,0 +1,28 @@
+# Python
+__pycache__/
+*.pyc
+*.egg-info/
+dist/
+wheelhouse/
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+
+# Build trees and built libraries
+build/
+build-*/
+python/gamut/_native/
+matlab/*.mex*
+
+# Julia
+julia/Manifest.toml
+
+# Files the tests and benchmarks write
+*.gamut
+!docs/**/*.gamut
+bench/results/raw/
+
+.DS_Store
+matlab/libgamut.*
+matlab/gamut.dll
+matlab/gamut.lib

gamut_format-1.0.0/CHANGELOG.md

@@ -0,0 +1,31 @@
+# Changelog
+
+## 1.0.0 (2026-10-18)
+
+Version 1 of the format, `gamut/1`, and a new implementation. Before
+version 1 the format and its libraries were called mestra (the 0.1 series
+on PyPI).
+
+The format ([SPEC.md](SPEC.md)) is redesigned around the study: a run
+table with roles, statuses and splits; a shared mesh whose geometry is
+fixed, per run or per member of a family, or a mesh per run; fields as one
+block of runs × nodes; uncertainty and derivatives as relations; and model
+files of the same shape as data. Files of the earlier `mestra/0` are
+refused with a message naming their version.
+
+A C++ core with a C interface implements the format, and Python, MATLAB
+and Julia are layers over it, so every language gives the same answers.
+The Python wheels link HDF5 statically, so the core never meets another
+HDF5 in the same process.
+
+Python has `create`, `open`, `append`, `extract`, `write_copy`,
+`validate`, `create_model` and `evaluate`; the `gamut` command line
+(`info`, `validate`, `build`, `append`, `get`); and `gamut-vtk`, which
+turns a folder of VTK runs into a study and back. MATLAB, Julia and C++
+(the header-only `gamut/gamut.hpp`) have the same calls in each language's
+spelling, and C programs use the C interface, `gamut/gamut.h`.
+
+Readers check sizes before using memory, never follow links and load no
+HDF5 plugins ([security](docs/security.md)). The guide has fourteen pages,
+each held to a runnable example by the tests, and the
+[benchmarks](docs/benchmarks.md) cover two studies.

gamut_format-1.0.0/CITATION.cff

@@ -0,0 +1,34 @@
+cff-version: 1.2.0
+message: >-
+  If you use Gamut in published work, please cite it as below, and
+  name the format version your files declare (the root attribute
+  `format`, for example "gamut/1").
+title: "Gamut: an open file format for simulation studies"
+type: software
+version: 1.0.0
+date-released: 2026-10-18
+authors:
+  - name: "Bijective Systems"
+repository-code: "https://github.com/bijective-systems-org/gamut"
+url: "https://github.com/bijective-systems-org/gamut"
+license: Apache-2.0
+abstract: >-
+  Gamut is an open file format for the results of a parametric
+  simulation study and the models fitted to it. One HDF5 file, laid
+  out as a valid netCDF-4 file, holds the run table (parameters with
+  roles, labels, statuses, splits and scalar results, every number with
+  its units), the mesh the fields live on, the fields themselves as one
+  block of runs by nodes when the runs share a mesh, uncertainty and
+  gradients beside the values they describe, and fitted models in the
+  same terms as the data. One C++ core, with Python, MATLAB, Julia and C
+  interfaces, implements the specification, and a shared corpus of
+  valid, broken and hostile files holds every language to it.
+keywords:
+  - simulation data
+  - parametric study
+  - surrogate model
+  - HDF5
+  - netCDF-4
+  - mesh
+  - scientific machine learning
+  - uncertainty quantification

gamut_format-1.0.0/CMakeLists.txt

@@ -0,0 +1,176 @@
+cmake_minimum_required(VERSION 3.16)
+project(gamut VERSION 1.0.0 LANGUAGES C CXX)
+
+# The shared core of spec version 1: one C++ library behind a plain C
+# interface (include/gamut/gamut.h).  Python, MATLAB and Julia bind to
+# that interface; nothing else is exported.
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+set(CMAKE_CXX_VISIBILITY_PRESET hidden)
+set(CMAKE_VISIBILITY_INLINES_HIDDEN ON)
+
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE)
+endif()
+
+option(GAMUT_BUILD_TESTS "Build the core's unit tests" ON)
+option(GAMUT_SANITIZE "Build with the address and undefined sanitizers" OFF)
+# A process may hold another HDF5 (h5py's, MATLAB's).  Where symbols share
+# one namespace (Linux), a core linked to a shared HDF5 can bind to the
+# other copy; linked statically, with only gamut_* exported, it cannot.
+option(GAMUT_STATIC_HDF5 "Link HDF5 statically into the core" OFF)
+if(GAMUT_STATIC_HDF5)
+  set(HDF5_USE_STATIC_LIBRARIES ON)
+  set(ZLIB_USE_STATIC_LIBS ON)
+  # With the C runtime linked statically, as tools/build_deps.sh builds
+  # HDF5 and zlib, the DLL needs no Visual C++ redistributable.
+  set(CMAKE_MSVC_RUNTIME_LIBRARY MultiThreaded)
+endif()
+
+# No multiply and add may fuse into one rounding step: the built-in
+# nearest-neighbour model must give bit-identical distances everywhere.
+if(MSVC)
+  set(GAMUT_WARNINGS /W4 /permissive-)
+  set(GAMUT_FP_FLAGS /fp:precise)
+else()
+  set(GAMUT_WARNINGS -Wall -Wextra -Wpedantic -Wshadow -Wconversion
+                      -Wsign-conversion)
+  set(GAMUT_FP_FLAGS -ffp-contract=off)
+endif()
+set(GAMUT_SANITIZER_FLAGS "")
+if(GAMUT_SANITIZE)
+  set(GAMUT_SANITIZER_FLAGS -fsanitize=address,undefined
+                             -fno-omit-frame-pointer
+                             -fno-sanitize-recover=undefined)
+  add_link_options(-fsanitize=address,undefined)
+endif()
+
+find_package(HDF5 REQUIRED COMPONENTS C HL)
+# 1.12 brought the object-token API the core uses; packages bundle 1.14.
+if(HDF5_VERSION AND HDF5_VERSION VERSION_LESS 1.12)
+  message(FATAL_ERROR "the Gamut core needs HDF5 1.12 or later; found ${HDF5_VERSION}. "
+                      "Point HDF5_ROOT at a newer HDF5.")
+endif()
+find_package(ZLIB REQUIRED)
+find_package(Threads REQUIRED)
+
+set(GAMUT_CORE_SOURCES
+  src/types.cpp
+  src/names.cpp
+  src/units.cpp
+  src/sha256.cpp
+  src/h5.cpp
+  src/chunk.cpp
+  src/schema.cpp
+  src/reader.cpp
+  src/writer.cpp
+  src/parallel.cpp
+  src/validate.cpp
+  src/value.cpp
+  src/codec.cpp
+  src/nearest.cpp
+  src/evaluate.cpp
+  src/copy.cpp
+  src/select.cpp
+  src/capi.cpp
+)
+
+# The objects once, linked into the shared library the bindings load and
+# into the unit tests, which reach the internals directly.
+add_library(gamut_core_objects OBJECT ${GAMUT_CORE_SOURCES})
+set_target_properties(gamut_core_objects PROPERTIES POSITION_INDEPENDENT_CODE ON)
+target_include_directories(gamut_core_objects
+  PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/include ${CMAKE_CURRENT_SOURCE_DIR}/src
+         ${HDF5_INCLUDE_DIRS})
+target_compile_definitions(gamut_core_objects PRIVATE GAMUT_BUILDING ${HDF5_DEFINITIONS})
+if(GAMUT_STATIC_HDF5)
+  # The core owns its HDF5, and so may set it up (no filter plugins).
+  set(GAMUT_OWN_HDF5 GAMUT_OWN_HDF5)
+endif()
+target_compile_definitions(gamut_core_objects PRIVATE ${GAMUT_OWN_HDF5})
+target_compile_options(gamut_core_objects PRIVATE ${GAMUT_WARNINGS}
+                       ${GAMUT_FP_FLAGS} ${GAMUT_SANITIZER_FLAGS})
+
+add_library(gamut SHARED $<TARGET_OBJECTS:gamut_core_objects>)
+target_include_directories(gamut PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+target_link_libraries(gamut PRIVATE ${HDF5_HL_LIBRARIES} ${HDF5_C_LIBRARIES} ZLIB::ZLIB
+                      Threads::Threads ${CMAKE_DL_LIBS})
+# Nothing but the C interface leaves the library, whatever is linked into it.
+if(APPLE)
+  target_link_options(gamut PRIVATE
+    "LINKER:-exported_symbols_list,${CMAKE_CURRENT_SOURCE_DIR}/exports.txt")
+elseif(UNIX)
+  target_link_options(gamut PRIVATE "LINKER:--version-script=${CMAKE_CURRENT_SOURCE_DIR}/exports.map")
+  if(NOT GAMUT_SANITIZE)
+    target_link_options(gamut PRIVATE "LINKER:--no-undefined")
+  endif()
+endif()
+set_target_properties(gamut PROPERTIES OUTPUT_NAME gamut)
+# gamut.hpp needs C++17 in the programs that include it.
+target_compile_features(gamut INTERFACE cxx_std_17)
+
+if(GAMUT_BUILD_TESTS)
+  enable_testing()
+  add_executable(core_unit_tests tests/unit_tests.cpp $<TARGET_OBJECTS:gamut_core_objects>)
+  target_include_directories(core_unit_tests PRIVATE
+    ${CMAKE_CURRENT_SOURCE_DIR}/include ${CMAKE_CURRENT_SOURCE_DIR}/src ${HDF5_INCLUDE_DIRS})
+  target_compile_definitions(core_unit_tests PRIVATE ${HDF5_DEFINITIONS} ${GAMUT_OWN_HDF5})
+  target_compile_options(core_unit_tests PRIVATE ${GAMUT_WARNINGS}
+                         ${GAMUT_FP_FLAGS} ${GAMUT_SANITIZER_FLAGS})
+  target_link_libraries(core_unit_tests PRIVATE ${HDF5_HL_LIBRARIES} ${HDF5_C_LIBRARIES}
+                        ZLIB::ZLIB Threads::Threads)
+  add_test(NAME core_unit_tests COMMAND core_unit_tests
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+  add_executable(core_writer_reader_tests tests/writer_reader_tests.cpp
+                 $<TARGET_OBJECTS:gamut_core_objects>)
+  target_include_directories(core_writer_reader_tests PRIVATE
+    ${CMAKE_CURRENT_SOURCE_DIR}/include ${CMAKE_CURRENT_SOURCE_DIR}/src ${HDF5_INCLUDE_DIRS})
+  target_compile_definitions(core_writer_reader_tests PRIVATE ${HDF5_DEFINITIONS} ${GAMUT_OWN_HDF5})
+  target_compile_options(core_writer_reader_tests PRIVATE ${GAMUT_WARNINGS}
+                         ${GAMUT_FP_FLAGS} ${GAMUT_SANITIZER_FLAGS})
+  target_link_libraries(core_writer_reader_tests PRIVATE ${HDF5_HL_LIBRARIES} ${HDF5_C_LIBRARIES}
+                        ZLIB::ZLIB Threads::Threads)
+  add_test(NAME core_writer_reader_tests COMMAND core_writer_reader_tests
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+  # The C++ interface, linked to the shared library as a program using it is.
+  add_executable(header_tests tests/header_tests.cpp)
+  target_include_directories(header_tests PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
+  target_compile_options(header_tests PRIVATE ${GAMUT_WARNINGS} ${GAMUT_SANITIZER_FLAGS})
+  target_link_libraries(header_tests PRIVATE gamut)
+  add_test(NAME header_tests COMMAND header_tests WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+endif()
+
+# Installing.  A Python wheel (scikit-build-core) takes the library alone,
+# beside the package; otherwise the header, the library and a CMake package
+# (find_package(gamut) gives gamut::gamut).  Linked to a shared HDF5
+# outside the install (a source build), the library keeps the path to it.
+set_target_properties(gamut PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE)
+if(SKBUILD)
+  # On Windows the import library (gamut.lib) goes too, so MATLAB's gateway
+  # can be built against the wheel's core.
+  install(TARGETS gamut LIBRARY DESTINATION gamut/_native RUNTIME DESTINATION gamut/_native
+                         ARCHIVE DESTINATION gamut/_native)
+else()
+  include(GNUInstallDirs)
+  include(CMakePackageConfigHelpers)
+  target_include_directories(gamut INTERFACE $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
+  install(TARGETS gamut EXPORT gamutTargets
+          LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+          ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+          RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
+  install(FILES include/gamut/gamut.h include/gamut/gamut.hpp DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/gamut)
+  install(EXPORT gamutTargets NAMESPACE gamut::
+          DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/gamut)
+  file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/gamutConfig.cmake.in
+       "@PACKAGE_INIT@\ninclude(\"\${CMAKE_CURRENT_LIST_DIR}/gamutTargets.cmake\")\n")
+  configure_package_config_file(${CMAKE_CURRENT_BINARY_DIR}/gamutConfig.cmake.in
+                                ${CMAKE_CURRENT_BINARY_DIR}/gamutConfig.cmake
+                                INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/gamut)
+  write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/gamutConfigVersion.cmake
+                                   COMPATIBILITY SameMajorVersion)
+  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/gamutConfig.cmake
+                ${CMAKE_CURRENT_BINARY_DIR}/gamutConfigVersion.cmake
+          DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/gamut)
+endif()

gamut_format-1.0.0/CONTRIBUTING.md

@@ -0,0 +1,76 @@
+# Contributing
+
+The [specification](SPEC.md) and the [corpus](corpus) define Gamut. The
+C++ core in `src/` implements them once; Python, MATLAB, Julia and the C++
+header are thin layers over its C interface. A change of behaviour starts from the
+specification and the corpus, never from one language.
+
+## A bug
+
+Describe what happened and what you expected, with the smallest file or
+script that shows it, and the output of `gamut --version`. A fix comes
+with a test at the layer that owns the problem: the core's tests for the
+core, the language's tests for its layer, the corpus for anything every
+language must agree on.
+
+## A change to the format
+
+Open an issue first, with:
+
+1. a real study or workflow that the format cannot hold today;
+2. the meaning proposed, and what readers that do not know it will do;
+3. whether it is an addition within version 1 (SPEC.md section 17: a
+   reader that does not know it reports W5 and goes on) or needs a new
+   major version;
+4. the corpus cases that pin it.
+
+The specification, the corpus and the core change together.
+
+## Building and running the checks
+
+The core needs CMake 3.16 or later, a C++17 compiler and HDF5 1.12 or
+later (or `tools/build_deps.sh` and `-DGAMUT_STATIC_HDF5=ON`, as in
+[installing](docs/install.md)). From the top of a checkout:
+
+```bash
+cmake -S . -B build -DHDF5_ROOT=/path/to/hdf5
+cmake --build build -j2
+./build/core_unit_tests && ./build/core_writer_reader_tests
+(cd build && ./header_tests)
+```
+
+Python finds the core in `build/` when run from the checkout:
+
+```bash
+pip install numpy pytest h5py pint xarray netCDF4 pyvista pandas
+cd python && python -m pytest -q tests
+```
+
+The tests also run every script in `examples/`, check that each page of
+`docs/guide/` quotes its example and shows what it prints, run the
+command-line page's sessions, and build the C example. Change an example
+and its page together.
+
+Julia's tests, and the corpus from Python and Julia (the Julia check needs
+the JSON package in its environment):
+
+```bash
+julia --project=julia -e 'include("julia/test/runtests.jl")'
+python corpus/generate.py /tmp/corpus
+GAMUT_LIBRARY=build/libgamut.so python corpus/check.py /tmp/corpus
+julia --project=<an environment with JSON and Gamut> julia/test/check_corpus.jl /tmp/corpus
+```
+
+In MATLAB, from `matlab/`: `build_mex`, then `run_tests`, then
+`corpus='/tmp/corpus'; run('tests/check_corpus.m')`.
+
+`tools/damaged_files.py` measures how readers meet damaged files, and
+`bench/` holds the benchmarks (`bench/figures.py` rebuilds the benchmark
+page's tables and figures from `bench/results/`).
+
+## Style
+
+Code reads like the code around it: plain names, few comments, each
+saying why. Messages say what is wrong and what to do, with the rule
+(`E7`) when one applies. Documentation is short and tested where it can
+be.

gamut_format-1.0.0/LICENSE

@@ -0,0 +1,202 @@
+
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+
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+   APPENDIX: How to apply the Apache License to your work.
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