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.
Files changed (86) hide show
  1. massim-0.1.0/.clangd +3 -0
  2. massim-0.1.0/.gitignore +28 -0
  3. massim-0.1.0/.python-version +1 -0
  4. massim-0.1.0/CMakeLists.txt +57 -0
  5. massim-0.1.0/CMakePresets.json +36 -0
  6. massim-0.1.0/EMERGE_baseline_strict.pkl +0 -0
  7. massim-0.1.0/IntegrateBetaCurve.nb +1456 -0
  8. massim-0.1.0/PKG-INFO +29 -0
  9. massim-0.1.0/README.md +14 -0
  10. massim-0.1.0/build_notes.txt +6 -0
  11. massim-0.1.0/cmake_install.cmake +95 -0
  12. massim-0.1.0/emerge_baseline.py +50 -0
  13. massim-0.1.0/emerge_masses.csv +28216 -0
  14. massim-0.1.0/emerge_sep_masses.csv +26457 -0
  15. massim-0.1.0/metabs.csv +28216 -0
  16. massim-0.1.0/old_pyproj +36 -0
  17. massim-0.1.0/profile_prof.py +230 -0
  18. massim-0.1.0/pyproject.toml +42 -0
  19. massim-0.1.0/setup.cfg +2 -0
  20. massim-0.1.0/simulations/diversity.py +93 -0
  21. massim-0.1.0/src/.clang-format +322 -0
  22. massim-0.1.0/src/cpp/common.h +68 -0
  23. massim-0.1.0/src/cpp/dataframe.h +95 -0
  24. massim-0.1.0/src/cpp/distribution.cpp +383 -0
  25. massim-0.1.0/src/cpp/distribution.h +415 -0
  26. massim-0.1.0/src/cpp/gradient_response.cpp +7 -0
  27. massim-0.1.0/src/cpp/gradient_response.h +161 -0
  28. massim-0.1.0/src/cpp/mass_tracker.cpp +16 -0
  29. massim-0.1.0/src/cpp/mass_tracker.h +504 -0
  30. massim-0.1.0/src/cpp/mass_transformer.cpp +400 -0
  31. massim-0.1.0/src/cpp/mass_transformer.h +335 -0
  32. massim-0.1.0/src/cpp/metrics.cpp +90 -0
  33. massim-0.1.0/src/cpp/metrics.h +20 -0
  34. massim-0.1.0/src/cpp/profile_generator.cpp +236 -0
  35. massim-0.1.0/src/cpp/profile_generator.h +166 -0
  36. massim-0.1.0/src/cpp/rng.h +53 -0
  37. massim-0.1.0/src/cpp/smallmap.h +221 -0
  38. massim-0.1.0/src/cpp/spectra.h +128 -0
  39. massim-0.1.0/src/cpp/tests/profile_prof.cpp +60 -0
  40. massim-0.1.0/src/cpp/tests/smallmap_test.cpp +153 -0
  41. massim-0.1.0/src/cpp/utils.cpp +151 -0
  42. massim-0.1.0/src/cpp/utils.h +36 -0
  43. massim-0.1.0/src/main.cpp +258 -0
  44. massim-0.1.0/src/massim/__init__.py +60 -0
  45. massim-0.1.0/src/massim/all.py +18 -0
  46. massim-0.1.0/src/massim/data/common_xfrms_emerge2.csv +109 -0
  47. massim-0.1.0/src/massim/data/common_xfrms_emerge_full.csv +109 -0
  48. massim-0.1.0/src/massim/data/common_xfrms_emerge_nonredundant.csv +45 -0
  49. massim-0.1.0/src/massim/data/common_xfrms_emerge_rawprob.csv +109 -0
  50. massim-0.1.0/src/massim/data/common_xfrms_emerge_trunc.csv +62 -0
  51. massim-0.1.0/src/massim/data/emerge_beta_fit.csv +326 -0
  52. massim-0.1.0/src/massim/data/emerge_intensity_icdf.npy +0 -0
  53. massim-0.1.0/src/massim/data/emerge_intensity_icdf_2D.npy +0 -0
  54. massim-0.1.0/src/massim/data/emerge_masses.csv +66436 -0
  55. massim-0.1.0/src/massim/data/emerge_masses_count.csv +54292 -0
  56. massim-0.1.0/src/massim/data/emerge_masses_filt.csv +31932 -0
  57. massim-0.1.0/src/massim/data/emerge_nonredundant.csv +43 -0
  58. massim-0.1.0/src/massim/data/emerge_nonredundant2.csv +40 -0
  59. massim-0.1.0/src/massim/data/emerge_nonredundant3.csv +38 -0
  60. massim-0.1.0/src/massim/data/kegg_rxns.csv +1254 -0
  61. massim-0.1.0/src/massim/data/kegg_xfrms.csv +1255 -0
  62. massim-0.1.0/src/massim/data/transf_key_fe.csv +110 -0
  63. massim-0.1.0/src/massim/data/xfrms_emerge_full.csv +109 -0
  64. massim-0.1.0/src/massim/data_analysis.py +2115 -0
  65. massim-0.1.0/src/massim/distributions.py +1017 -0
  66. massim-0.1.0/src/massim/experiment.py +2211 -0
  67. massim-0.1.0/src/massim/filters.py +148 -0
  68. massim-0.1.0/src/massim/gradient_response.py +395 -0
  69. massim-0.1.0/src/massim/graph_based.py +117 -0
  70. massim-0.1.0/src/massim/graph_util.py +217 -0
  71. massim-0.1.0/src/massim/mass_distribution.py +94 -0
  72. massim-0.1.0/src/massim/metric.py +42 -0
  73. massim-0.1.0/src/massim/noise.py +283 -0
  74. massim-0.1.0/src/massim/parser.py +38 -0
  75. massim-0.1.0/src/massim/plotting.py +87 -0
  76. massim-0.1.0/src/massim/profile.py +1271 -0
  77. massim-0.1.0/src/massim/py.typed +0 -0
  78. massim-0.1.0/src/massim/sampling.py +659 -0
  79. massim-0.1.0/src/massim/simulator.py +131 -0
  80. massim-0.1.0/src/massim/species_config.py +621 -0
  81. massim-0.1.0/src/massim/stats.py +287 -0
  82. massim-0.1.0/src/massim/transformations.py +113 -0
  83. massim-0.1.0/src/massim/utils.py +102 -0
  84. massim-0.1.0/src/massim/vspecies.py +0 -0
  85. massim-0.1.0/std.pcm +0 -0
  86. massim-0.1.0/uv.lock +855 -0
massim-0.1.0/.clangd ADDED
@@ -0,0 +1,3 @@
1
+ CompileFlags:
2
+ Add: [-std=c++20]
3
+
@@ -0,0 +1,28 @@
1
+ # Python-generated files
2
+ __pycache__/
3
+ *.py[oc]
4
+ build/
5
+ dist/
6
+ wheels/
7
+ *.egg-info
8
+
9
+ # Emacs temp
10
+ *~
11
+ \#*\#
12
+ .\#*
13
+
14
+ # Virtual environments
15
+ .venv
16
+
17
+ # My test programs
18
+ tst_*.py
19
+ scratch.py
20
+
21
+ # Misc:
22
+ .DS_Store
23
+ CMakeCache.txt
24
+ CMakeFiles
25
+ .cache
26
+ mprofile_*.dat
27
+ *.pyi
28
+ compile_commands.json
@@ -0,0 +1 @@
1
+ 3.12
@@ -0,0 +1,57 @@
1
+ cmake_minimum_required(VERSION 4.0)
2
+ set(CMAKE_EXPERIMENTAL_CXX_IMPORT_STD "451f2fe2-a8a2-47c3-bc32-94786d8fc91b")
3
+ set(CXX_MODULE_STD 1)
4
+
5
+ project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX)
6
+ set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
7
+
8
+ set(PYBIND11_FINDPYTHON ON)
9
+ find_package(pybind11 CONFIG REQUIRED)
10
+
11
+
12
+ find_package(OpenMP REQUIRED)
13
+
14
+ file(GLOB SOURCES "src/cpp/*.cpp")
15
+ find_package (Eigen3 3.3 REQUIRED NO_MODULE)
16
+ add_library(cmassim STATIC ${SOURCES})
17
+ target_include_directories(cmassim PRIVATE)
18
+ set_property(TARGET cmassim PROPERTY CXX_STANDARD 23)
19
+ target_compile_options(cmassim PRIVATE)
20
+ target_link_libraries (cmassim Eigen3::Eigen)
21
+
22
+ # Install the dyl
23
+ install(
24
+ TARGETS cmassim
25
+ EXPORT cmassimTargets
26
+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
27
+
28
+
29
+
30
+ find_package (Eigen3 3.3 REQUIRED)
31
+ include_directories( ${EIGEN3_INCLUDE_DIRS} )
32
+ pybind11_add_module(_core MODULE src/main.cpp)
33
+ target_include_directories(_core PRIVATE)
34
+ set_property(TARGET _core PROPERTY CXX_STANDARD 23)
35
+ target_link_libraries(_core PRIVATE)
36
+ target_link_libraries(_core PRIVATE cmassim)
37
+ install(TARGETS _core cmassim DESTINATION ${SKBUILD_PROJECT_NAME})
38
+
39
+
40
+
41
+ # Extra test apps
42
+ add_executable(prof_test "src/cpp/tests/profile_prof.cpp")
43
+ set_property(TARGET prof_test PROPERTY CXX_STANDARD 23)
44
+ target_compile_options(prof_test PRIVATE -fexperimental-library)
45
+ target_compile_features(prof_test PRIVATE cxx_std_23 INTERFACE cxx_std_23)
46
+ target_link_libraries (prof_test cmassim Eigen3::Eigen -fexperimental-library OpenMP::OpenMP_CXX)
47
+
48
+ add_executable(smallmap_test "src/cpp/tests/smallmap_test.cpp")
49
+ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
50
+ set_property(TARGET smallmap_test PROPERTY CXX_STANDARD 23)
51
+ target_compile_options(smallmap_test PRIVATE -fexperimental-library)
52
+ target_compile_features(smallmap_test PRIVATE cxx_std_23 INTERFACE cxx_std_23)
53
+ target_link_libraries (smallmap_test cmassim Eigen3::Eigen -fexperimental-library OpenMP::OpenMP_CXX)
54
+
55
+
56
+ # find_package(cmassim CONFIG)
57
+
@@ -0,0 +1,36 @@
1
+ {
2
+ "version": 6,
3
+ "configurePresets": [
4
+ {
5
+ "name": "debug",
6
+ "displayName": "Debug",
7
+ "generator": "Ninja",
8
+ "binaryDir": "build/debug",
9
+ "cacheVariables": {
10
+ "CMAKE_BUILD_TYPE": "Debug",
11
+ "SKBUILD_PROJECT_NAME": "massim"
12
+ }
13
+ },
14
+ {
15
+ "name": "release",
16
+ "displayName": "Release",
17
+ "generator": "Ninja",
18
+ "binaryDir": "build/release",
19
+ "cacheVariables": {
20
+ "CMAKE_BUILD_TYPE": "Release",
21
+ "SKBUILD_PROJECT_NAME": "massim"
22
+ }
23
+ }
24
+ ,
25
+ {
26
+ "name": "reldebug",
27
+ "displayName": "RelWithDebInfo",
28
+ "generator": "Ninja",
29
+ "binaryDir": "build/reldebug",
30
+ "cacheVariables": {
31
+ "CMAKE_BUILD_TYPE": "RelWithDebInfo",
32
+ "SKBUILD_PROJECT_NAME": "massim"
33
+ }
34
+ }
35
+ ]
36
+ }
File without changes