CoreMS 2.2.0__tar.gz → 3.0.0__tar.gz

{corems-2.2.0 → CoreMS-3.0.0}/CoreMS.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CoreMS
-Version: 2.2.0
+Version: 3.0.0
 Summary: Mass Spectrometry Framework for Small Molecules Analysis
 Home-page: https://github.com/EMSL-Computing/CoreMS
 Author: Corilo, Yuri
@@ -13,29 +13,8 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Development Status :: 4 - Beta
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: beautifulsoup4~=4.12.0
-Requires-Dist: chardet~=5.1.0
-Requires-Dist: h5py~=3.8.0
-Requires-Dist: IsoSpecPy~=2.2.2
-Requires-Dist: lmfit~=1.1.0
-Requires-Dist: lxml~=4.9.3
-Requires-Dist: matplotlib~=3.7.0
-Requires-Dist: netCDF4~=1.6.3
-Requires-Dist: numpy~=1.24.2
-Requires-Dist: openpyxl~=3.1.1
-Requires-Dist: pandas~=1.5.3
-Requires-Dist: pyswarm~=0.6
-Requires-Dist: pythonnet~=3.0.1
-Requires-Dist: s3path~=0.4.1
-Requires-Dist: scikit_learn~=1.2.2
-Requires-Dist: scipy~=1.10.1
-Requires-Dist: seaborn~=0.12.2
-Requires-Dist: setuptools~=67.3.3
-Requires-Dist: SQLAlchemy~=1.4.47
-Requires-Dist: toml~=0.10.2
-Requires-Dist: tqdm~=4.64.1
-
-![CoreMS Logo](docs/CoreMS.COLOR_small.png?raw=true)  
+
+![CoreMS Logo](https://github.com/EMSL-Computing/CoreMS/blob/master/docs/CoreMS.COLOR_small.png?raw=true)  
 
 <div align="left">
 
@@ -50,19 +29,18 @@ Requires-Dist: tqdm~=4.64.1
   - [CoreMS](#CoreMS)  
   - [Current Version](#current-version)  
   - [Contact Information](#main-developers/contact )  
+  - [Documentation](#documentation)
   - [Contribution Information](#contributing)
   - [Data Input](#data-input-formats)  
   - [Data Output](#data-output-formats)  
   - [Data Structure](#data-structure-types)  
   - [Features](#available-features)  
-  - [Overview Slides](examples/CoreMS-Overview.pdf)
-  - [Framework Documentation](https://emsl-computing.github.io/CoreMS/)
 - Installation
   - [Installation](#corems-installation)  
   - [Thermo Raw File on Mac and Linux](#thermo-raw-file-access)  
 - Execution     
   - [Jupyter Notebook and Docker containers](#docker-stack)  
-  - [Simple Example](#simple-script-example)  
+  - [Example for FT-ICR Data Processing](#simple-script-example)  
   - [Python Examples](examples/scripts)
   - [Jupyter Notebook Examples](examples/notebooks)  
 - Sibling Projects    
@@ -87,13 +65,22 @@ CoreMS aims to provide
 
 ## Current Version
 
- `2.2.0`
+ `3.0.0`
 
 ***
 
 ## Main Developers/Contact 
 - [Yuri. E. Corilo](mailto:corilo@pnnl.gov)  
 - [William Kew](mailto:william.kew@pnnl.gov)
+- [Katherine Heal](mailto:katherine.heal@pnnl.gov)
+
+***
+
+## Documentation
+
+API documentation can be found [here](https://emsl-computing.github.io/CoreMS/corems.html).
+
+Overview slides can be found [here](https://github.com/EMSL-Computing/CoreMS/blob/master/examples/CoreMS-Overview.pdf).
 
 ***
 
@@ -112,11 +99,12 @@ As an open source project, CoreMS welcomes contributions of all forms. Before co
 - Spectroswiss signal booster data-acquisition station (.hdf5)
 - MagLab ICR data-acquisition station (FT and magnitude mode) (.dat)
 - ANDI NetCDF for GC-MS (.cdf)
+- mzml for LC-MS (.mzml)
 - Generic mass list in profile and centroid mde (include all delimiters types and Excel formats)
 - CoreMS exported processed mass list files(excel, .csv, .txt, pandas dataframe as .pkl)
 - CoreMS self-containing Hierarchical Data Format (.hdf5)
 - Pandas Dataframe
-- Support for cloud Storage using s3path.S3path(see examples of usage here: [S3 Support](tests/s3_test.py))
+- Support for cloud Storage using s3path.S3path
 
 ### Data output formats
 
@@ -124,7 +112,7 @@ As an open source project, CoreMS welcomes contributions of all forms. Before co
 - Text Files (.csv, tab separated .txt, etc)
 - Microsoft Excel (xlsx)
 - Automatic JSON for metadata storage and reuse
-- Self-containing Hierarchical Data Format (.hdf5) including raw data and ime-series data-point for processed data-sets with all associated metadata stored as json attributes
+- Self-containing Hierarchical Data Format (.hdf5) including raw data and time-series data-point for processed data-sets with all associated metadata stored as json attributes
 
 ### Data structure types
 
@@ -136,12 +124,6 @@ As an open source project, CoreMS welcomes contributions of all forms. Before co
 - Mass Spectral Peak
 - Molecular Formula
 
-### In progress data structures
-- IMS-MS
-- LC-IMS-MS 
-- Collections 
-- Molecular Structure
-
 ***
 
 ## Available features
@@ -184,6 +166,15 @@ As an open source project, CoreMS welcomes contributions of all forms. Before co
 - Prediction of mass error distribution
 - Calculated ICR Resolving Power based on magnetic field (B), and transient time(T)
 
+### LC-MS Signal Processing, Molecular Formula Search and Assignment, and Spectral Similarity Searches
+- Two dimensional (m/z and retention time) peak picking using persistent homology
+- Smoothing, cetroid detection, and integration of extracted ion chromatograms
+- Peak shape metric calculations including half peak height, tailing factor, and dispersity index
+- MS1 deconvolution of mass features
+- Idenfitication of <sup>13</sup>C isotopes within the mass features
+- Compatibility with molecular formula searching on MS1 or MS2 spectra
+- Spectral search capability using entropy similarity
+
 ***
 
 ## Installation 
@@ -276,7 +267,7 @@ If you don't have docker installed, the easiest way is to [install docker for de
 
 ***
 
-## Simple Script Example
+## Example for FT-ICR Data Processing
 
 More examples can be found under the directory examples/scripts, examples/notebooks
 
@@ -360,7 +351,7 @@ UML (unified modeling language) diagrams for Direct Infusion FT-MS and GC-MS cla
 
 If you use CoreMS in your work, please use the following citation:
 
-Version [2.2.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.2.0), archived on Zenodo:  
+Version [3.0.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.0), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
 

{corems-2.2.0 → CoreMS-3.0.0}/CoreMS.egg-info/SOURCES.txt

@@ -14,12 +14,8 @@ corems/__init__.py
 corems/chroma_peak/__init__.py
 corems/chroma_peak/calc/ChromaPeakCalc.py
 corems/chroma_peak/calc/__init__.py
-corems/chroma_peak/factory/ChromaPeakClasses.py
 corems/chroma_peak/factory/__init__.py
-corems/collection/__init__.py
-corems/collection/factory/__init__.py
-corems/collection/input/__init__.py
-corems/collection/output/__init__.py
+corems/chroma_peak/factory/chroma_peak_classes.py
 corems/encapsulation/__init__.py
 corems/encapsulation/constant.py
 corems/encapsulation/factory/__init__.py
@@ -35,22 +31,24 @@ corems/mass_spectra/calc/GC_Calc.py
 corems/mass_spectra/calc/GC_Deconvolution.py
 corems/mass_spectra/calc/GC_RI_Calibration.py
 corems/mass_spectra/calc/LC_Calc.py
-corems/mass_spectra/calc/LF_Targeted.py
 corems/mass_spectra/calc/MZSearch.py
 corems/mass_spectra/calc/SignalProcessing.py
 corems/mass_spectra/calc/__init__.py
+corems/mass_spectra/calc/lc_calc.py
 corems/mass_spectra/factory/GC_Class.py
 corems/mass_spectra/factory/LC_Class.py
-corems/mass_spectra/factory/LC_Temp.py
 corems/mass_spectra/factory/__init__.py
+corems/mass_spectra/factory/chromat_data.py
+corems/mass_spectra/factory/lc_class.py
 corems/mass_spectra/input/__init__.py
 corems/mass_spectra/input/andiNetCDF.py
 corems/mass_spectra/input/boosterHDF5.py
 corems/mass_spectra/input/brukerSolarix.py
-corems/mass_spectra/input/coremsHDF5.py
+corems/mass_spectra/input/corems_hdf5.py
 corems/mass_spectra/input/massList.py
+corems/mass_spectra/input/mzml.py
+corems/mass_spectra/input/parserbase.py
 corems/mass_spectra/input/rawFileReader.py
-corems/mass_spectra/input/win_only/__init__.py
 corems/mass_spectra/output/__init__.py
 corems/mass_spectra/output/export.py
 corems/mass_spectrum/__init__.py
@@ -73,7 +71,6 @@ corems/mass_spectrum/input/boosterHDF5.py
 corems/mass_spectrum/input/coremsHDF5.py
 corems/mass_spectrum/input/massList.py
 corems/mass_spectrum/input/numpyArray.py
-corems/mass_spectrum/input/win_only/__init__.py
 corems/mass_spectrum/output/__init__.py
 corems/mass_spectrum/output/export.py
 corems/molecular_formula/__init__.py
@@ -85,7 +82,6 @@ corems/molecular_formula/input/__init__.py
 corems/molecular_formula/input/masslist_ref.py
 corems/molecular_id/__init__.py
 corems/molecular_id/calc/ClusterFilter.py
-corems/molecular_id/calc/KendrickGroup.py
 corems/molecular_id/calc/MolecularFilter.py
 corems/molecular_id/calc/SpectralSimilarity.py
 corems/molecular_id/calc/__init__.py
@@ -94,12 +90,16 @@ corems/molecular_id/factory/EI_SQL.py
 corems/molecular_id/factory/MolecularLookupTable.py
 corems/molecular_id/factory/__init__.py
 corems/molecular_id/factory/classification.py
+corems/molecular_id/factory/lipid_molecular_metadata.py
 corems/molecular_id/factory/molecularSQL.py
+corems/molecular_id/factory/spectrum_search_results.py
 corems/molecular_id/input/__init__.py
 corems/molecular_id/input/nistMSI.py
 corems/molecular_id/search/__init__.py
 corems/molecular_id/search/compoundSearch.py
+corems/molecular_id/search/database_interfaces.py
 corems/molecular_id/search/findOxygenPeaks.py
+corems/molecular_id/search/lcms_spectral_search.py
 corems/molecular_id/search/molecularFormulaSearch.py
 corems/molecular_id/search/priorityAssignment.py
 corems/ms_peak/__init__.py
@@ -145,20 +145,17 @@ ext_lib/dotnet/ThermoFisher.CommonCore.MassPrecisionEstimator.dll
 ext_lib/dotnet/ThermoFisher.CommonCore.MassPrecisionEstimator.xml
 ext_lib/dotnet/ThermoFisher.CommonCore.RawFileReader.dll
 ext_lib/dotnet/ThermoFisher.CommonCore.RawFileReader.xml
-tests/test_LossFinder.py
-tests/test_assembly_identification.py
 tests/test_calibration.py
 tests/test_classification.py
 tests/test_gcms.py
 tests/test_input.py
-tests/test_massErrorPrediction.py
 tests/test_mass_spectrum.py
 tests/test_mass_spectrum_export_import.py
 tests/test_molecular_formula.py
 tests/test_molecular_formula_db_factory.py
 tests/test_molecular_formula_search.py
 tests/test_mspeak.py
-tests/test_mz_search.py
 tests/test_output.py
 tests/test_search_mass_list.py
-tests/test_setting_settings.py
+tests/test_setting_settings.py
+tests/test_wf_lipidomics.py

{corems-2.2.0 → CoreMS-3.0.0}/CoreMS.egg-info/requires.txt

@@ -5,12 +5,16 @@ IsoSpecPy~=2.2.2
 lmfit~=1.1.0
 lxml~=4.9.3
 matplotlib~=3.7.0
+ms-entropy~=1.1.2
 netCDF4~=1.6.3
 numpy~=1.24.2
 openpyxl~=3.1.1
 pandas~=1.5.3
 pyswarm~=0.6
 pythonnet~=3.0.1
+pymzml~=2.5.2
+requests~=2.31.0
+ripser==0.6.4
 s3path~=0.4.1
 scikit_learn~=1.2.2
 scipy~=1.10.1

{corems-2.2.0 → CoreMS-3.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CoreMS
-Version: 2.2.0
+Version: 3.0.0
 Summary: Mass Spectrometry Framework for Small Molecules Analysis
 Home-page: https://github.com/EMSL-Computing/CoreMS
 Author: Corilo, Yuri
@@ -13,29 +13,8 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Development Status :: 4 - Beta
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: beautifulsoup4~=4.12.0
-Requires-Dist: chardet~=5.1.0
-Requires-Dist: h5py~=3.8.0
-Requires-Dist: IsoSpecPy~=2.2.2
-Requires-Dist: lmfit~=1.1.0
-Requires-Dist: lxml~=4.9.3
-Requires-Dist: matplotlib~=3.7.0
-Requires-Dist: netCDF4~=1.6.3
-Requires-Dist: numpy~=1.24.2
-Requires-Dist: openpyxl~=3.1.1
-Requires-Dist: pandas~=1.5.3
-Requires-Dist: pyswarm~=0.6
-Requires-Dist: pythonnet~=3.0.1
-Requires-Dist: s3path~=0.4.1
-Requires-Dist: scikit_learn~=1.2.2
-Requires-Dist: scipy~=1.10.1
-Requires-Dist: seaborn~=0.12.2
-Requires-Dist: setuptools~=67.3.3
-Requires-Dist: SQLAlchemy~=1.4.47
-Requires-Dist: toml~=0.10.2
-Requires-Dist: tqdm~=4.64.1
-
-![CoreMS Logo](docs/CoreMS.COLOR_small.png?raw=true)  
+
+![CoreMS Logo](https://github.com/EMSL-Computing/CoreMS/blob/master/docs/CoreMS.COLOR_small.png?raw=true)  
 
 <div align="left">
 
@@ -50,19 +29,18 @@ Requires-Dist: tqdm~=4.64.1
   - [CoreMS](#CoreMS)  
   - [Current Version](#current-version)  
   - [Contact Information](#main-developers/contact )  
+  - [Documentation](#documentation)
   - [Contribution Information](#contributing)
   - [Data Input](#data-input-formats)  
   - [Data Output](#data-output-formats)  
   - [Data Structure](#data-structure-types)  
   - [Features](#available-features)  
-  - [Overview Slides](examples/CoreMS-Overview.pdf)
-  - [Framework Documentation](https://emsl-computing.github.io/CoreMS/)
 - Installation
   - [Installation](#corems-installation)  
   - [Thermo Raw File on Mac and Linux](#thermo-raw-file-access)  
 - Execution     
   - [Jupyter Notebook and Docker containers](#docker-stack)  
-  - [Simple Example](#simple-script-example)  
+  - [Example for FT-ICR Data Processing](#simple-script-example)  
   - [Python Examples](examples/scripts)
   - [Jupyter Notebook Examples](examples/notebooks)  
 - Sibling Projects    
@@ -87,13 +65,22 @@ CoreMS aims to provide
 
 ## Current Version
 
- `2.2.0`
+ `3.0.0`
 
 ***
 
 ## Main Developers/Contact 
 - [Yuri. E. Corilo](mailto:corilo@pnnl.gov)  
 - [William Kew](mailto:william.kew@pnnl.gov)
+- [Katherine Heal](mailto:katherine.heal@pnnl.gov)
+
+***
+
+## Documentation
+
+API documentation can be found [here](https://emsl-computing.github.io/CoreMS/corems.html).
+
+Overview slides can be found [here](https://github.com/EMSL-Computing/CoreMS/blob/master/examples/CoreMS-Overview.pdf).
 
 ***
 
@@ -112,11 +99,12 @@ As an open source project, CoreMS welcomes contributions of all forms. Before co
 - Spectroswiss signal booster data-acquisition station (.hdf5)
 - MagLab ICR data-acquisition station (FT and magnitude mode) (.dat)
 - ANDI NetCDF for GC-MS (.cdf)
+- mzml for LC-MS (.mzml)
 - Generic mass list in profile and centroid mde (include all delimiters types and Excel formats)
 - CoreMS exported processed mass list files(excel, .csv, .txt, pandas dataframe as .pkl)
 - CoreMS self-containing Hierarchical Data Format (.hdf5)
 - Pandas Dataframe
-- Support for cloud Storage using s3path.S3path(see examples of usage here: [S3 Support](tests/s3_test.py))
+- Support for cloud Storage using s3path.S3path
 
 ### Data output formats
 
@@ -124,7 +112,7 @@ As an open source project, CoreMS welcomes contributions of all forms. Before co
 - Text Files (.csv, tab separated .txt, etc)
 - Microsoft Excel (xlsx)
 - Automatic JSON for metadata storage and reuse
-- Self-containing Hierarchical Data Format (.hdf5) including raw data and ime-series data-point for processed data-sets with all associated metadata stored as json attributes
+- Self-containing Hierarchical Data Format (.hdf5) including raw data and time-series data-point for processed data-sets with all associated metadata stored as json attributes
 
 ### Data structure types
 
@@ -136,12 +124,6 @@ As an open source project, CoreMS welcomes contributions of all forms. Before co
 - Mass Spectral Peak
 - Molecular Formula
 
-### In progress data structures
-- IMS-MS
-- LC-IMS-MS 
-- Collections 
-- Molecular Structure
-
 ***
 
 ## Available features
@@ -184,6 +166,15 @@ As an open source project, CoreMS welcomes contributions of all forms. Before co
 - Prediction of mass error distribution
 - Calculated ICR Resolving Power based on magnetic field (B), and transient time(T)
 
+### LC-MS Signal Processing, Molecular Formula Search and Assignment, and Spectral Similarity Searches
+- Two dimensional (m/z and retention time) peak picking using persistent homology
+- Smoothing, cetroid detection, and integration of extracted ion chromatograms
+- Peak shape metric calculations including half peak height, tailing factor, and dispersity index
+- MS1 deconvolution of mass features
+- Idenfitication of <sup>13</sup>C isotopes within the mass features
+- Compatibility with molecular formula searching on MS1 or MS2 spectra
+- Spectral search capability using entropy similarity
+
 ***
 
 ## Installation 
@@ -276,7 +267,7 @@ If you don't have docker installed, the easiest way is to [install docker for de
 
 ***
 
-## Simple Script Example
+## Example for FT-ICR Data Processing
 
 More examples can be found under the directory examples/scripts, examples/notebooks
 
@@ -360,7 +351,7 @@ UML (unified modeling language) diagrams for Direct Infusion FT-MS and GC-MS cla
 
 If you use CoreMS in your work, please use the following citation:
 
-Version [2.2.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.2.0), archived on Zenodo:  
+Version [3.0.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.0), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
 

{corems-2.2.0 → CoreMS-3.0.0}/README.md

@@ -1,4 +1,4 @@
-![CoreMS Logo](docs/CoreMS.COLOR_small.png?raw=true)  
+![CoreMS Logo](https://github.com/EMSL-Computing/CoreMS/blob/master/docs/CoreMS.COLOR_small.png?raw=true)  
 
 <div align="left">
 
@@ -13,19 +13,18 @@
   - [CoreMS](#CoreMS)  
   - [Current Version](#current-version)  
   - [Contact Information](#main-developers/contact )  
+  - [Documentation](#documentation)
   - [Contribution Information](#contributing)
   - [Data Input](#data-input-formats)  
   - [Data Output](#data-output-formats)  
   - [Data Structure](#data-structure-types)  
   - [Features](#available-features)  
-  - [Overview Slides](examples/CoreMS-Overview.pdf)
-  - [Framework Documentation](https://emsl-computing.github.io/CoreMS/)
 - Installation
   - [Installation](#corems-installation)  
   - [Thermo Raw File on Mac and Linux](#thermo-raw-file-access)  
 - Execution     
   - [Jupyter Notebook and Docker containers](#docker-stack)  
-  - [Simple Example](#simple-script-example)  
+  - [Example for FT-ICR Data Processing](#simple-script-example)  
   - [Python Examples](examples/scripts)
   - [Jupyter Notebook Examples](examples/notebooks)  
 - Sibling Projects    
@@ -50,13 +49,22 @@ CoreMS aims to provide
 
 ## Current Version
 
- `2.2.0`
+ `3.0.0`
 
 ***
 
 ## Main Developers/Contact 
 - [Yuri. E. Corilo](mailto:corilo@pnnl.gov)  
 - [William Kew](mailto:william.kew@pnnl.gov)
+- [Katherine Heal](mailto:katherine.heal@pnnl.gov)
+
+***
+
+## Documentation
+
+API documentation can be found [here](https://emsl-computing.github.io/CoreMS/corems.html).
+
+Overview slides can be found [here](https://github.com/EMSL-Computing/CoreMS/blob/master/examples/CoreMS-Overview.pdf).
 
 ***
 
@@ -75,11 +83,12 @@ As an open source project, CoreMS welcomes contributions of all forms. Before co
 - Spectroswiss signal booster data-acquisition station (.hdf5)
 - MagLab ICR data-acquisition station (FT and magnitude mode) (.dat)
 - ANDI NetCDF for GC-MS (.cdf)
+- mzml for LC-MS (.mzml)
 - Generic mass list in profile and centroid mde (include all delimiters types and Excel formats)
 - CoreMS exported processed mass list files(excel, .csv, .txt, pandas dataframe as .pkl)
 - CoreMS self-containing Hierarchical Data Format (.hdf5)
 - Pandas Dataframe
-- Support for cloud Storage using s3path.S3path(see examples of usage here: [S3 Support](tests/s3_test.py))
+- Support for cloud Storage using s3path.S3path
 
 ### Data output formats
 
@@ -87,7 +96,7 @@ As an open source project, CoreMS welcomes contributions of all forms. Before co
 - Text Files (.csv, tab separated .txt, etc)
 - Microsoft Excel (xlsx)
 - Automatic JSON for metadata storage and reuse
-- Self-containing Hierarchical Data Format (.hdf5) including raw data and ime-series data-point for processed data-sets with all associated metadata stored as json attributes
+- Self-containing Hierarchical Data Format (.hdf5) including raw data and time-series data-point for processed data-sets with all associated metadata stored as json attributes
 
 ### Data structure types
 
@@ -99,12 +108,6 @@ As an open source project, CoreMS welcomes contributions of all forms. Before co
 - Mass Spectral Peak
 - Molecular Formula
 
-### In progress data structures
-- IMS-MS
-- LC-IMS-MS 
-- Collections 
-- Molecular Structure
-
 ***
 
 ## Available features
@@ -147,6 +150,15 @@ As an open source project, CoreMS welcomes contributions of all forms. Before co
 - Prediction of mass error distribution
 - Calculated ICR Resolving Power based on magnetic field (B), and transient time(T)
 
+### LC-MS Signal Processing, Molecular Formula Search and Assignment, and Spectral Similarity Searches
+- Two dimensional (m/z and retention time) peak picking using persistent homology
+- Smoothing, cetroid detection, and integration of extracted ion chromatograms
+- Peak shape metric calculations including half peak height, tailing factor, and dispersity index
+- MS1 deconvolution of mass features
+- Idenfitication of <sup>13</sup>C isotopes within the mass features
+- Compatibility with molecular formula searching on MS1 or MS2 spectra
+- Spectral search capability using entropy similarity
+
 ***
 
 ## Installation 
@@ -239,7 +251,7 @@ If you don't have docker installed, the easiest way is to [install docker for de
 
 ***
 
-## Simple Script Example
+## Example for FT-ICR Data Processing
 
 More examples can be found under the directory examples/scripts, examples/notebooks
 
@@ -323,7 +335,7 @@ UML (unified modeling language) diagrams for Direct Infusion FT-MS and GC-MS cla
 
 If you use CoreMS in your work, please use the following citation:
 
-Version [2.2.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.2.0), archived on Zenodo:  
+Version [3.0.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.0), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
 

CoreMS-3.0.0/corems/__init__.py

@@ -0,0 +1,52 @@
+__author__ = "Yuri E. Corilo"
+__version__ = "3.0.0"
+import time
+import os
+import sys
+import hashlib
+
+# Get the path to the README file
+readme_path = os.path.join(os.path.dirname(__file__), "..", "README.md")
+
+# Read the contents of the README file
+with open(readme_path, "r", encoding="utf-8") as readme_file:
+    __doc__ = readme_file.read()
+
+
+def timeit(method):
+    def timed(*args, **kw):
+        ts = time.time()
+        result = method(*args, **kw)
+        te = time.time()
+        if "log_time" in kw:
+            name = kw.get("log_name", method.__name__.upper())
+            kw["log_time"][name] = int((te - ts) * 1000)
+        else:
+            print("%r  %2.2f ms" % (method.__name__, (te - ts) * 1000))
+        return result
+
+    return timed
+
+
+class SuppressPrints:
+    def __enter__(self):
+        self._original_stdout = sys.stdout
+        sys.stdout = open(os.devnull, "w")
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        sys.stdout.close()
+        sys.stdout = self._original_stdout
+
+
+def chunks(lst, n):
+    """Yield successive n-sized chunks from lst."""
+    for i in range(0, len(lst), n):
+        yield lst[i : i + n]
+
+
+def corems_md5(fname):
+    bytes_io = fname.open("rb").read()
+
+    md5_returned = hashlib.sha256(bytes_io).hexdigest()
+
+    return "{}:{}".format("sha256", md5_returned)