pycompound 0.0.7__py3-none-any.whl → 0.0.8__py3-none-any.whl

app.py

@@ -1,11 +1,11 @@
 
 from shiny import App, ui, reactive, render
-from pycompound_fy7392.spec_lib_matching import run_spec_lib_matching_on_HRMS_data 
-from pycompound_fy7392.spec_lib_matching import run_spec_lib_matching_on_NRMS_data 
-from pycompound_fy7392.spec_lib_matching import tune_params_on_HRMS_data
-from pycompound_fy7392.spec_lib_matching import tune_params_on_NRMS_data
-from pycompound_fy7392.plot_spectra import generate_plots_on_HRMS_data
-from pycompound_fy7392.plot_spectra import generate_plots_on_NRMS_data
+from pycompound.spec_lib_matching import run_spec_lib_matching_on_HRMS_data 
+from pycompound.spec_lib_matching import run_spec_lib_matching_on_NRMS_data 
+from pycompound.spec_lib_matching import tune_params_on_HRMS_data
+from pycompound.spec_lib_matching import tune_params_on_NRMS_data
+from pycompound.plot_spectra import generate_plots_on_HRMS_data
+from pycompound.plot_spectra import generate_plots_on_NRMS_data
 from pathlib import Path
 import subprocess
 import traceback

pycompound/plot_spectra.py

@@ -96,8 +96,8 @@ def generate_plots_on_HRMS_data(query_data=None, reference_data=None, spectrum_I
         print(f'Error: spectrum_preprocessing_order must contain only \'C\', \'F\', \'M\', \'N\', \'L\', \'W\'.')
         sys.exit()
 
-    if similarity_measure not in ['cosine','shannon','renyi','tsallis','mixture','jaccard','dice','3w_jaccard','sokal_sneath','binary_cosine','mountford','mcconnaughey','driver_kroeber','simpson','braun_banquet','fager_mcgowan','kulczynski','interection','hamming','hellinger']:
-        print('\nError: similarity_measure must be either cosine, shannon, renyi, tsallis, mixture, jaccard, dice, 3w_jaccard, sokal_sneath, binary_cosine, mountford, mcconnaughey, driver_kroeber, simpson, braun_banquet, fager_mcgowan, kulczynski, interection, hamming, or hellinger.')
+    if similarity_measure not in ['cosine','shannon','renyi','tsallis','mixture','jaccard','dice','3w_jaccard','sokal_sneath','binary_cosine','mountford','mcconnaughey','driver_kroeber','simpson','braun_banquet','fager_mcgowan','kulczynski','intersection','hamming','hellinger']:
+        print('\nError: similarity_measure must be either cosine, shannon, renyi, tsallis, mixture, jaccard, dice, 3w_jaccard, sokal_sneath, binary_cosine, mountford, mcconnaughey, driver_kroeber, simpson, braun_banquet, fager_mcgowan, kulczynski, intersection, hamming, or hellinger.')
         sys.exit()
 
     if isinstance(int_min,int) is True:
@@ -400,8 +400,8 @@ def generate_plots_on_NRMS_data(query_data=None, reference_data=None, spectrum_I
         print(f'Error: spectrum_preprocessing_order must contain only \'F\', \'N\', \'W\', \'L\'.')
         sys.exit()
 
-    if similarity_measure not in ['cosine','shannon','renyi','tsallis','mixture','jaccard','dice','3w_jaccard','sokal_sneath','binary_cosine','mountford','mcconnaughey','driver_kroeber','simpson','braun_banquet','fager_mcgowan','kulczynski','interection','hamming','hellinger']:
-        print('\nError: similarity_measure must be either cosine, shannon, renyi, tsallis, mixture, jaccard, dice, 3w_jaccard, sokal_sneath, binary_cosine, mountford, mcconnaughey, driver_kroeber, simpson, braun_banquet, fager_mcgowan, kulczynski, interection, hamming, or hellinger.')
+    if similarity_measure not in ['cosine','shannon','renyi','tsallis','mixture','jaccard','dice','3w_jaccard','sokal_sneath','binary_cosine','mountford','mcconnaughey','driver_kroeber','simpson','braun_banquet','fager_mcgowan','kulczynski','intersection','hamming','hellinger']:
+        print('\nError: similarity_measure must be either cosine, shannon, renyi, tsallis, mixture, jaccard, dice, 3w_jaccard, sokal_sneath, binary_cosine, mountford, mcconnaughey, driver_kroeber, simpson, braun_banquet, fager_mcgowan, kulczynski, intersection, hamming, or hellinger.')
         sys.exit()
 
     if isinstance(int_min,int) is True:

{pycompound-0.0.7.dist-info → pycompound-0.0.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pycompound
-Version: 0.0.7
+Version: 0.0.8
 Summary: Python package to perform compound identification in mass spectrometry via spectral library matching.
 Author-email: Hunter Dlugas <fy7392@wayne.edu>
 License-Expression: MIT
@@ -23,4 +23,6 @@ Requires-Dist: joblib==1.5.2
 Dynamic: license-file
 
 # PyCompound
+
 A Python-based tool for spectral library matching, PyCompound is available as a Python package with a command-line interface (CLI) available and as a GUI application build with Python/Shiny. It performs spectral library matching to identify chemical compounds, offering a range of spectrum preprocessing transformations and similarity measures, including Cosine, three entropy-based similarity measures, and a plethora of binary similarity measures. PyCompound also includes functionality to tune parameters commonly used in a compound identification workflow given a query library of spectra with known ID. PyCompound supports both high-resolution mass spectrometry (HRMS) data (e.g., LC-MS/MS) and nominal-resolution mass spectrometry (NRMS) data (e.g., GC-MS). For the full documentation, see the GitHub repository https://github.com/hdlugas/pycompound.
+

{pycompound-0.0.7.dist-info → pycompound-0.0.8.dist-info}/RECORD

@@ -1,14 +1,14 @@
-app.py,sha256=PKiCJe_18EJIHvs0R7pl_Yf-XakZn5J0AAfI-AnGsX0,21535
+app.py,sha256=DCaQEp8_1-oldlhzEKo5HpKC2S-orV9gJxuSEHga9MY,21493
 pycompound/build_library.py,sha256=8ghpX8wfj6u-3V5X2IdJ-e8G_FRSla1lO0pzLj7hOtI,5373
-pycompound/plot_spectra.py,sha256=wOnf2oOAfifj7FYkTZAcIeD7dHW1aRHzmsspPpySDcY,42023
+pycompound/plot_spectra.py,sha256=9s6bDgNv_CZsgMlM_CDToJMxJCasVJbFAGoUrZPfnW8,42027
 pycompound/plot_spectra_CLI.py,sha256=ObaLad5Z5DmfQB-j0HSCg1mLORbYj2BM3hb5Yd0ZdDI,8395
 pycompound/processing.py,sha256=vqtKaZ6vot6wlnKNTYUQFX7ccPpnCAl0L6bN289vZoM,11068
 pycompound/similarity_measures.py,sha256=TuvtEXWwyxE6dfpmuAqRC6gOHvHg3Jf21099pVaNBAs,10702
 pycompound/spec_lib_matching.py,sha256=pfDPmH1aQ11_25T80U9i0OUbgjCvvkzNEcDeBrDWNtA,59962
 pycompound/spec_lib_matching_CLI.py,sha256=EdXM0dRQfwGQAK4OKxhcVytuUnX9pRyJROwC6rloZ9s,9915
 pycompound/tuning_CLI.py,sha256=lkFBRZ5VxCBteIh_KTkQFdUBVZA0dL-BLiyMZce1vzE,8539
-pycompound-0.0.7.dist-info/licenses/LICENSE,sha256=fPFFlkSGg60VQWyWqTSv8yoJnpLzppzdihVWY5NKom8,1064
-pycompound-0.0.7.dist-info/METADATA,sha256=naSYyQcQRUvWSHkmi0lg9ETBOb3sch3oKfVLQSvkwAc,1704
-pycompound-0.0.7.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-pycompound-0.0.7.dist-info/top_level.txt,sha256=wFBLVrqpC07HghIU8tsEdgdvgkdOE3GN_1Gfjk-uEUc,15
-pycompound-0.0.7.dist-info/RECORD,,
+pycompound-0.0.8.dist-info/licenses/LICENSE,sha256=fPFFlkSGg60VQWyWqTSv8yoJnpLzppzdihVWY5NKom8,1064
+pycompound-0.0.8.dist-info/METADATA,sha256=N76PE3DJwBvDV2VU4qXrbMvVQc7tTHaxZE_fpBxuC84,1706
+pycompound-0.0.8.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+pycompound-0.0.8.dist-info/top_level.txt,sha256=wFBLVrqpC07HghIU8tsEdgdvgkdOE3GN_1Gfjk-uEUc,15
+pycompound-0.0.8.dist-info/RECORD,,