massim 0.1.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- massim-0.1.0/.clangd +3 -0
- massim-0.1.0/.gitignore +28 -0
- massim-0.1.0/.python-version +1 -0
- massim-0.1.0/CMakeLists.txt +57 -0
- massim-0.1.0/CMakePresets.json +36 -0
- massim-0.1.0/EMERGE_baseline_strict.pkl +0 -0
- massim-0.1.0/IntegrateBetaCurve.nb +1456 -0
- massim-0.1.0/PKG-INFO +29 -0
- massim-0.1.0/README.md +14 -0
- massim-0.1.0/build_notes.txt +6 -0
- massim-0.1.0/cmake_install.cmake +95 -0
- massim-0.1.0/emerge_baseline.py +50 -0
- massim-0.1.0/emerge_masses.csv +28216 -0
- massim-0.1.0/emerge_sep_masses.csv +26457 -0
- massim-0.1.0/metabs.csv +28216 -0
- massim-0.1.0/old_pyproj +36 -0
- massim-0.1.0/profile_prof.py +230 -0
- massim-0.1.0/pyproject.toml +42 -0
- massim-0.1.0/setup.cfg +2 -0
- massim-0.1.0/simulations/diversity.py +93 -0
- massim-0.1.0/src/.clang-format +322 -0
- massim-0.1.0/src/cpp/common.h +68 -0
- massim-0.1.0/src/cpp/dataframe.h +95 -0
- massim-0.1.0/src/cpp/distribution.cpp +383 -0
- massim-0.1.0/src/cpp/distribution.h +415 -0
- massim-0.1.0/src/cpp/gradient_response.cpp +7 -0
- massim-0.1.0/src/cpp/gradient_response.h +161 -0
- massim-0.1.0/src/cpp/mass_tracker.cpp +16 -0
- massim-0.1.0/src/cpp/mass_tracker.h +504 -0
- massim-0.1.0/src/cpp/mass_transformer.cpp +400 -0
- massim-0.1.0/src/cpp/mass_transformer.h +335 -0
- massim-0.1.0/src/cpp/metrics.cpp +90 -0
- massim-0.1.0/src/cpp/metrics.h +20 -0
- massim-0.1.0/src/cpp/profile_generator.cpp +236 -0
- massim-0.1.0/src/cpp/profile_generator.h +166 -0
- massim-0.1.0/src/cpp/rng.h +53 -0
- massim-0.1.0/src/cpp/smallmap.h +221 -0
- massim-0.1.0/src/cpp/spectra.h +128 -0
- massim-0.1.0/src/cpp/tests/profile_prof.cpp +60 -0
- massim-0.1.0/src/cpp/tests/smallmap_test.cpp +153 -0
- massim-0.1.0/src/cpp/utils.cpp +151 -0
- massim-0.1.0/src/cpp/utils.h +36 -0
- massim-0.1.0/src/main.cpp +258 -0
- massim-0.1.0/src/massim/__init__.py +60 -0
- massim-0.1.0/src/massim/all.py +18 -0
- massim-0.1.0/src/massim/data/common_xfrms_emerge2.csv +109 -0
- massim-0.1.0/src/massim/data/common_xfrms_emerge_full.csv +109 -0
- massim-0.1.0/src/massim/data/common_xfrms_emerge_nonredundant.csv +45 -0
- massim-0.1.0/src/massim/data/common_xfrms_emerge_rawprob.csv +109 -0
- massim-0.1.0/src/massim/data/common_xfrms_emerge_trunc.csv +62 -0
- massim-0.1.0/src/massim/data/emerge_beta_fit.csv +326 -0
- massim-0.1.0/src/massim/data/emerge_intensity_icdf.npy +0 -0
- massim-0.1.0/src/massim/data/emerge_intensity_icdf_2D.npy +0 -0
- massim-0.1.0/src/massim/data/emerge_masses.csv +66436 -0
- massim-0.1.0/src/massim/data/emerge_masses_count.csv +54292 -0
- massim-0.1.0/src/massim/data/emerge_masses_filt.csv +31932 -0
- massim-0.1.0/src/massim/data/emerge_nonredundant.csv +43 -0
- massim-0.1.0/src/massim/data/emerge_nonredundant2.csv +40 -0
- massim-0.1.0/src/massim/data/emerge_nonredundant3.csv +38 -0
- massim-0.1.0/src/massim/data/kegg_rxns.csv +1254 -0
- massim-0.1.0/src/massim/data/kegg_xfrms.csv +1255 -0
- massim-0.1.0/src/massim/data/transf_key_fe.csv +110 -0
- massim-0.1.0/src/massim/data/xfrms_emerge_full.csv +109 -0
- massim-0.1.0/src/massim/data_analysis.py +2115 -0
- massim-0.1.0/src/massim/distributions.py +1017 -0
- massim-0.1.0/src/massim/experiment.py +2211 -0
- massim-0.1.0/src/massim/filters.py +148 -0
- massim-0.1.0/src/massim/gradient_response.py +395 -0
- massim-0.1.0/src/massim/graph_based.py +117 -0
- massim-0.1.0/src/massim/graph_util.py +217 -0
- massim-0.1.0/src/massim/mass_distribution.py +94 -0
- massim-0.1.0/src/massim/metric.py +42 -0
- massim-0.1.0/src/massim/noise.py +283 -0
- massim-0.1.0/src/massim/parser.py +38 -0
- massim-0.1.0/src/massim/plotting.py +87 -0
- massim-0.1.0/src/massim/profile.py +1271 -0
- massim-0.1.0/src/massim/py.typed +0 -0
- massim-0.1.0/src/massim/sampling.py +659 -0
- massim-0.1.0/src/massim/simulator.py +131 -0
- massim-0.1.0/src/massim/species_config.py +621 -0
- massim-0.1.0/src/massim/stats.py +287 -0
- massim-0.1.0/src/massim/transformations.py +113 -0
- massim-0.1.0/src/massim/utils.py +102 -0
- massim-0.1.0/src/massim/vspecies.py +0 -0
- massim-0.1.0/std.pcm +0 -0
- massim-0.1.0/uv.lock +855 -0
massim-0.1.0/.clangd
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massim-0.1.0/.gitignore
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# Python-generated files
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__pycache__/
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*.py[oc]
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build/
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dist/
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wheels/
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*.egg-info
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# Emacs temp
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*~
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\#*\#
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.\#*
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# Virtual environments
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.venv
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# My test programs
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tst_*.py
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scratch.py
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# Misc:
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.DS_Store
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CMakeCache.txt
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CMakeFiles
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.cache
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mprofile_*.dat
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*.pyi
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compile_commands.json
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3.12
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cmake_minimum_required(VERSION 4.0)
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set(CMAKE_EXPERIMENTAL_CXX_IMPORT_STD "451f2fe2-a8a2-47c3-bc32-94786d8fc91b")
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set(CXX_MODULE_STD 1)
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project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX)
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set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
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set(PYBIND11_FINDPYTHON ON)
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find_package(pybind11 CONFIG REQUIRED)
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find_package(OpenMP REQUIRED)
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file(GLOB SOURCES "src/cpp/*.cpp")
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find_package (Eigen3 3.3 REQUIRED NO_MODULE)
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add_library(cmassim STATIC ${SOURCES})
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target_include_directories(cmassim PRIVATE)
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set_property(TARGET cmassim PROPERTY CXX_STANDARD 23)
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target_compile_options(cmassim PRIVATE)
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target_link_libraries (cmassim Eigen3::Eigen)
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# Install the dyl
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install(
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TARGETS cmassim
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EXPORT cmassimTargets
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LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
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find_package (Eigen3 3.3 REQUIRED)
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include_directories( ${EIGEN3_INCLUDE_DIRS} )
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pybind11_add_module(_core MODULE src/main.cpp)
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target_include_directories(_core PRIVATE)
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set_property(TARGET _core PROPERTY CXX_STANDARD 23)
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target_link_libraries(_core PRIVATE)
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target_link_libraries(_core PRIVATE cmassim)
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install(TARGETS _core cmassim DESTINATION ${SKBUILD_PROJECT_NAME})
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# Extra test apps
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add_executable(prof_test "src/cpp/tests/profile_prof.cpp")
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set_property(TARGET prof_test PROPERTY CXX_STANDARD 23)
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target_compile_options(prof_test PRIVATE -fexperimental-library)
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target_compile_features(prof_test PRIVATE cxx_std_23 INTERFACE cxx_std_23)
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target_link_libraries (prof_test cmassim Eigen3::Eigen -fexperimental-library OpenMP::OpenMP_CXX)
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add_executable(smallmap_test "src/cpp/tests/smallmap_test.cpp")
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SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
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set_property(TARGET smallmap_test PROPERTY CXX_STANDARD 23)
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target_compile_options(smallmap_test PRIVATE -fexperimental-library)
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target_compile_features(smallmap_test PRIVATE cxx_std_23 INTERFACE cxx_std_23)
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target_link_libraries (smallmap_test cmassim Eigen3::Eigen -fexperimental-library OpenMP::OpenMP_CXX)
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# find_package(cmassim CONFIG)
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{
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"version": 6,
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"configurePresets": [
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{
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"name": "debug",
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"displayName": "Debug",
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"generator": "Ninja",
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"binaryDir": "build/debug",
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"cacheVariables": {
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"CMAKE_BUILD_TYPE": "Debug",
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"SKBUILD_PROJECT_NAME": "massim"
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}
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},
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{
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"name": "release",
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"displayName": "Release",
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"generator": "Ninja",
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"binaryDir": "build/release",
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"cacheVariables": {
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"CMAKE_BUILD_TYPE": "Release",
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"SKBUILD_PROJECT_NAME": "massim"
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}
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}
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,
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{
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"name": "reldebug",
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"displayName": "RelWithDebInfo",
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"generator": "Ninja",
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"binaryDir": "build/reldebug",
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"cacheVariables": {
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"CMAKE_BUILD_TYPE": "RelWithDebInfo",
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"SKBUILD_PROJECT_NAME": "massim"
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}
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}
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]
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}
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