├── .github └── workflows │ ├── build_wheels.yml │ └── run_test.yml ├── .gitignore ├── .readthedocs.yaml ├── .vscode └── settings.json ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── api_pipe.rst │ ├── classical_api.rst │ ├── classical_entropy_similarity.rst │ ├── classical_spectral_entropy.rst │ ├── classical_useful_functions.rst │ ├── conf.py │ ├── entropy_search_advanced_usage.rst │ ├── entropy_search_api.rst │ ├── entropy_search_basic_usage.rst │ ├── entropy_search_examples.rst │ ├── entropy_search_quickstart.rst │ ├── entropy_search_useful_functions.rst │ ├── index.rst │ └── install.rst ├── examples ├── example-2.py ├── example-multiple_cores.py ├── example-search_mona-with_pickle_functions.py ├── example-search_mona-with_read_write_functions-low_memory_usage.py ├── example-search_mona-with_read_write_functions.py ├── example-with_individual_search_function.py └── example.py ├── languages ├── c │ ├── CMakeLists.txt │ ├── CleanSpectrum.c │ ├── CleanSpectrum.h │ ├── Example.c │ ├── SpectralEntropy.c │ └── SpectralEntropy.h ├── javascript │ ├── CleanSpectrum.c │ ├── CleanSpectrum.h │ ├── MSEntropy.c │ ├── SpectralEntropy.c │ ├── SpectralEntropy.h │ ├── compile_to_mjs.sh │ ├── compile_to_wasm.sh │ ├── example.html │ ├── example.js │ ├── msentropy.js │ ├── msentropy.mjs │ └── msentropy.wasm └── r │ ├── DESCRIPTION │ ├── NAMESPACE │ ├── R │ ├── RcppExports.R │ └── msentropy_similarity.R │ ├── Read-and-delete-me │ ├── man │ ├── calculate_entropy_similarity.Rd │ ├── calculate_spectral_entropy.Rd │ ├── calculate_unweighted_entropy_similarity.Rd │ ├── clean_spectrum.Rd │ └── msentropy_similarity.Rd │ ├── msentropy_0.1.4.tar.gz │ ├── src │ ├── CleanSpectrum.c │ ├── CleanSpectrum.h │ ├── RcppExports.cpp │ ├── SpectralEntropy.c │ ├── SpectralEntropy.h │ └── entropy.cpp │ └── tests │ ├── testthat.R │ └── testthat │ └── test_msentropy_similarity.R ├── ms_entropy ├── __init__.py ├── entropy_search │ ├── __init__.py │ ├── fast_flash_entropy_search.py │ ├── fast_flash_entropy_search_cpython.pyx │ ├── flash_entropy_search.py │ ├── flash_entropy_search_core.py │ ├── flash_entropy_search_core_for_dynamic_indexing.py │ ├── flash_entropy_search_core_low_memory.py │ └── flash_entropy_search_core_medium_memory.py ├── file_io │ ├── __init__.py │ ├── lbm2_file.py │ ├── mgf_file.py │ ├── msp_file.py │ ├── mzml_file.py │ ├── shared.py │ └── spec_file.py ├── spectra │ ├── CleanSpectrum.c │ ├── CleanSpectrum.h │ ├── SpectralEntropy.c │ ├── SpectralEntropy.h │ ├── __init__.py │ ├── entropy.py │ ├── entropy_cython.pyx │ ├── entropy_numba.py │ └── tools.py └── version.py ├── pack_for_python.sh ├── pack_for_r.sh ├── pyproject.toml ├── requirements.txt ├── setup.cfg ├── setup.py └── tests ├── ms_entropy ├── test_dynamic_search.py ├── test_entropy.py └── test_entropy_search.py /.github/workflows/build_wheels.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/.github/workflows/build_wheels.yml -------------------------------------------------------------------------------- /.github/workflows/run_test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/.github/workflows/run_test.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /.vscode/settings.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/.vscode/settings.json -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/README.md -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/requirements.txt -------------------------------------------------------------------------------- /docs/source/api_pipe.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/source/api_pipe.rst -------------------------------------------------------------------------------- /docs/source/classical_api.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/source/classical_api.rst -------------------------------------------------------------------------------- /docs/source/classical_entropy_similarity.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/source/classical_entropy_similarity.rst -------------------------------------------------------------------------------- /docs/source/classical_spectral_entropy.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/source/classical_spectral_entropy.rst -------------------------------------------------------------------------------- /docs/source/classical_useful_functions.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/source/classical_useful_functions.rst -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/source/conf.py -------------------------------------------------------------------------------- /docs/source/entropy_search_advanced_usage.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/source/entropy_search_advanced_usage.rst -------------------------------------------------------------------------------- /docs/source/entropy_search_api.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/source/entropy_search_api.rst -------------------------------------------------------------------------------- /docs/source/entropy_search_basic_usage.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/source/entropy_search_basic_usage.rst -------------------------------------------------------------------------------- /docs/source/entropy_search_examples.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/source/entropy_search_examples.rst -------------------------------------------------------------------------------- /docs/source/entropy_search_quickstart.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/source/entropy_search_quickstart.rst -------------------------------------------------------------------------------- /docs/source/entropy_search_useful_functions.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/source/entropy_search_useful_functions.rst -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/source/index.rst -------------------------------------------------------------------------------- /docs/source/install.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/docs/source/install.rst -------------------------------------------------------------------------------- /examples/example-2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/examples/example-2.py -------------------------------------------------------------------------------- /examples/example-multiple_cores.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/examples/example-multiple_cores.py -------------------------------------------------------------------------------- /examples/example-search_mona-with_pickle_functions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/examples/example-search_mona-with_pickle_functions.py -------------------------------------------------------------------------------- /examples/example-search_mona-with_read_write_functions-low_memory_usage.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/examples/example-search_mona-with_read_write_functions-low_memory_usage.py -------------------------------------------------------------------------------- /examples/example-search_mona-with_read_write_functions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/examples/example-search_mona-with_read_write_functions.py -------------------------------------------------------------------------------- /examples/example-with_individual_search_function.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/examples/example-with_individual_search_function.py -------------------------------------------------------------------------------- /examples/example.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/examples/example.py -------------------------------------------------------------------------------- /languages/c/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/c/CMakeLists.txt -------------------------------------------------------------------------------- /languages/c/CleanSpectrum.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/c/CleanSpectrum.c -------------------------------------------------------------------------------- /languages/c/CleanSpectrum.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/c/CleanSpectrum.h -------------------------------------------------------------------------------- /languages/c/Example.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/c/Example.c -------------------------------------------------------------------------------- /languages/c/SpectralEntropy.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/c/SpectralEntropy.c -------------------------------------------------------------------------------- /languages/c/SpectralEntropy.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/c/SpectralEntropy.h -------------------------------------------------------------------------------- /languages/javascript/CleanSpectrum.c: -------------------------------------------------------------------------------- 1 | ../c/CleanSpectrum.c -------------------------------------------------------------------------------- /languages/javascript/CleanSpectrum.h: -------------------------------------------------------------------------------- 1 | ../c/CleanSpectrum.h -------------------------------------------------------------------------------- /languages/javascript/MSEntropy.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/javascript/MSEntropy.c -------------------------------------------------------------------------------- /languages/javascript/SpectralEntropy.c: -------------------------------------------------------------------------------- 1 | ../c/SpectralEntropy.c -------------------------------------------------------------------------------- /languages/javascript/SpectralEntropy.h: -------------------------------------------------------------------------------- 1 | ../c/SpectralEntropy.h -------------------------------------------------------------------------------- /languages/javascript/compile_to_mjs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/javascript/compile_to_mjs.sh -------------------------------------------------------------------------------- /languages/javascript/compile_to_wasm.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/javascript/compile_to_wasm.sh -------------------------------------------------------------------------------- /languages/javascript/example.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/javascript/example.html -------------------------------------------------------------------------------- /languages/javascript/example.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/javascript/example.js -------------------------------------------------------------------------------- /languages/javascript/msentropy.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/javascript/msentropy.js -------------------------------------------------------------------------------- /languages/javascript/msentropy.mjs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/javascript/msentropy.mjs -------------------------------------------------------------------------------- /languages/javascript/msentropy.wasm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/javascript/msentropy.wasm -------------------------------------------------------------------------------- /languages/r/DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/r/DESCRIPTION -------------------------------------------------------------------------------- /languages/r/NAMESPACE: -------------------------------------------------------------------------------- 1 | useDynLib(msentropy, .registration=TRUE) 2 | importFrom(Rcpp, evalCpp) 3 | exportPattern("^[[:alpha:]]+") 4 | -------------------------------------------------------------------------------- /languages/r/R/RcppExports.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/r/R/RcppExports.R -------------------------------------------------------------------------------- /languages/r/R/msentropy_similarity.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/r/R/msentropy_similarity.R -------------------------------------------------------------------------------- /languages/r/Read-and-delete-me: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/r/Read-and-delete-me -------------------------------------------------------------------------------- /languages/r/man/calculate_entropy_similarity.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/r/man/calculate_entropy_similarity.Rd -------------------------------------------------------------------------------- /languages/r/man/calculate_spectral_entropy.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/r/man/calculate_spectral_entropy.Rd -------------------------------------------------------------------------------- /languages/r/man/calculate_unweighted_entropy_similarity.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/r/man/calculate_unweighted_entropy_similarity.Rd -------------------------------------------------------------------------------- /languages/r/man/clean_spectrum.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/r/man/clean_spectrum.Rd -------------------------------------------------------------------------------- /languages/r/man/msentropy_similarity.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/r/man/msentropy_similarity.Rd -------------------------------------------------------------------------------- /languages/r/msentropy_0.1.4.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/r/msentropy_0.1.4.tar.gz -------------------------------------------------------------------------------- /languages/r/src/CleanSpectrum.c: -------------------------------------------------------------------------------- 1 | ../../c/CleanSpectrum.c -------------------------------------------------------------------------------- /languages/r/src/CleanSpectrum.h: -------------------------------------------------------------------------------- 1 | ../../c/CleanSpectrum.h -------------------------------------------------------------------------------- /languages/r/src/RcppExports.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/r/src/RcppExports.cpp -------------------------------------------------------------------------------- /languages/r/src/SpectralEntropy.c: -------------------------------------------------------------------------------- 1 | ../../c/SpectralEntropy.c -------------------------------------------------------------------------------- /languages/r/src/SpectralEntropy.h: -------------------------------------------------------------------------------- 1 | ../../c/SpectralEntropy.h -------------------------------------------------------------------------------- /languages/r/src/entropy.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/r/src/entropy.cpp -------------------------------------------------------------------------------- /languages/r/tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/r/tests/testthat.R -------------------------------------------------------------------------------- /languages/r/tests/testthat/test_msentropy_similarity.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/languages/r/tests/testthat/test_msentropy_similarity.R -------------------------------------------------------------------------------- /ms_entropy/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/__init__.py -------------------------------------------------------------------------------- /ms_entropy/entropy_search/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/entropy_search/__init__.py -------------------------------------------------------------------------------- /ms_entropy/entropy_search/fast_flash_entropy_search.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/entropy_search/fast_flash_entropy_search.py -------------------------------------------------------------------------------- /ms_entropy/entropy_search/fast_flash_entropy_search_cpython.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/entropy_search/fast_flash_entropy_search_cpython.pyx -------------------------------------------------------------------------------- /ms_entropy/entropy_search/flash_entropy_search.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/entropy_search/flash_entropy_search.py -------------------------------------------------------------------------------- /ms_entropy/entropy_search/flash_entropy_search_core.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/entropy_search/flash_entropy_search_core.py -------------------------------------------------------------------------------- /ms_entropy/entropy_search/flash_entropy_search_core_for_dynamic_indexing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/entropy_search/flash_entropy_search_core_for_dynamic_indexing.py -------------------------------------------------------------------------------- /ms_entropy/entropy_search/flash_entropy_search_core_low_memory.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/entropy_search/flash_entropy_search_core_low_memory.py -------------------------------------------------------------------------------- /ms_entropy/entropy_search/flash_entropy_search_core_medium_memory.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/entropy_search/flash_entropy_search_core_medium_memory.py -------------------------------------------------------------------------------- /ms_entropy/file_io/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/file_io/__init__.py -------------------------------------------------------------------------------- /ms_entropy/file_io/lbm2_file.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/file_io/lbm2_file.py -------------------------------------------------------------------------------- /ms_entropy/file_io/mgf_file.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/file_io/mgf_file.py -------------------------------------------------------------------------------- /ms_entropy/file_io/msp_file.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/file_io/msp_file.py -------------------------------------------------------------------------------- /ms_entropy/file_io/mzml_file.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/file_io/mzml_file.py -------------------------------------------------------------------------------- /ms_entropy/file_io/shared.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/file_io/shared.py -------------------------------------------------------------------------------- /ms_entropy/file_io/spec_file.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/file_io/spec_file.py -------------------------------------------------------------------------------- /ms_entropy/spectra/CleanSpectrum.c: -------------------------------------------------------------------------------- 1 | ../../languages/c/CleanSpectrum.c -------------------------------------------------------------------------------- /ms_entropy/spectra/CleanSpectrum.h: -------------------------------------------------------------------------------- 1 | ../../languages/c/CleanSpectrum.h -------------------------------------------------------------------------------- /ms_entropy/spectra/SpectralEntropy.c: -------------------------------------------------------------------------------- 1 | ../../languages/c/SpectralEntropy.c -------------------------------------------------------------------------------- /ms_entropy/spectra/SpectralEntropy.h: -------------------------------------------------------------------------------- 1 | ../../languages/c/SpectralEntropy.h -------------------------------------------------------------------------------- /ms_entropy/spectra/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/spectra/__init__.py -------------------------------------------------------------------------------- /ms_entropy/spectra/entropy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/spectra/entropy.py -------------------------------------------------------------------------------- /ms_entropy/spectra/entropy_cython.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/spectra/entropy_cython.pyx -------------------------------------------------------------------------------- /ms_entropy/spectra/entropy_numba.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/spectra/entropy_numba.py -------------------------------------------------------------------------------- /ms_entropy/spectra/tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/ms_entropy/spectra/tools.py -------------------------------------------------------------------------------- /ms_entropy/version.py: -------------------------------------------------------------------------------- 1 | __version__ = '1.3.9' 2 | -------------------------------------------------------------------------------- /pack_for_python.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/pack_for_python.sh -------------------------------------------------------------------------------- /pack_for_r.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/pack_for_r.sh -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/pyproject.toml -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | -e .[dev,all] 2 | -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [build_ext] 2 | inplace=1 3 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/setup.py -------------------------------------------------------------------------------- /tests/ms_entropy: -------------------------------------------------------------------------------- 1 | ../ms_entropy -------------------------------------------------------------------------------- /tests/test_dynamic_search.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/tests/test_dynamic_search.py -------------------------------------------------------------------------------- /tests/test_entropy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/tests/test_entropy.py -------------------------------------------------------------------------------- /tests/test_entropy_search.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuanyueLi/MSEntropy/HEAD/tests/test_entropy_search.py --------------------------------------------------------------------------------