PyPI - CoreMS - Versions diffs - 2.2.1__tar.gz → 3.0.1__tar.gz - Mend

CoreMS 2.2.1tar.gz → 3.0.1tar.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.

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{CoreMS-2.2.1 → CoreMS-3.0.1}/CoreMS.egg-info/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CoreMS
-Version: 2.2.1
+Version: 3.0.1
 Summary: Mass Spectrometry Framework for Small Molecules Analysis
 Home-page: https://github.com/EMSL-Computing/CoreMS
 Author: Corilo, Yuri
@@ -14,13 +14,13 @@ Classifier: Development Status :: 4 - Beta
 Description-Content-Type: text/markdown
 License-File: LICENSE
-![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">
 <br>
 <br>
-<a href="https://doi.org/10.5281/zenodo.4641552"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg" alt="CoreMS DOI" style="width:150px"></a>
+<a href="https://doi.org/10.5281/zenodo.14009575"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg" alt="DOI"></a>
 <br>
 </div>
@@ -29,19 +29,18 @@ License-File: LICENSE
   - [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
@@ -66,13 +65,22 @@ CoreMS aims to provide
 ## Current Version
- `2.2.1`
+ `3.0.1`
 ***
 ## 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).
 ***
@@ -91,11 +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
@@ -103,7 +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
@@ -115,12 +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
@@ -163,6 +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
@@ -255,7 +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
@@ -339,11 +351,11 @@ 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 [2.2.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.2.1), archived on Zenodo:
+Version [3.0.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.1), archived on Zenodo:
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg)](https://doi.org/10.5281/zenodo.14009575)
-Yuri E. Corilo, William R. Kew, Lee Ann McCue (2021, March 27). EMSL-Computing/CoreMS: CoreMS 2.0.1 (Version v2.0.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.4641552
+Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.0.1 (Version v3.0.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
 ```

{CoreMS-2.2.1 → CoreMS-3.0.1}/CoreMS.egg-info/SOURCES.txt RENAMED Viewed

@@ -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-2.2.1 → CoreMS-3.0.1}/CoreMS.egg-info/requires.txt RENAMED Viewed

@@ -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-2.2.1 → CoreMS-3.0.1}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CoreMS
-Version: 2.2.1
+Version: 3.0.1
 Summary: Mass Spectrometry Framework for Small Molecules Analysis
 Home-page: https://github.com/EMSL-Computing/CoreMS
 Author: Corilo, Yuri
@@ -14,13 +14,13 @@ Classifier: Development Status :: 4 - Beta
 Description-Content-Type: text/markdown
 License-File: LICENSE
-![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">
 <br>
 <br>
-<a href="https://doi.org/10.5281/zenodo.4641552"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg" alt="CoreMS DOI" style="width:150px"></a>
+<a href="https://doi.org/10.5281/zenodo.14009575"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg" alt="DOI"></a>
 <br>
 </div>
@@ -29,19 +29,18 @@ License-File: LICENSE
   - [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
@@ -66,13 +65,22 @@ CoreMS aims to provide
 ## Current Version
- `2.2.1`
+ `3.0.1`
 ***
 ## 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).
 ***
@@ -91,11 +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
@@ -103,7 +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
@@ -115,12 +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
@@ -163,6 +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
@@ -255,7 +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
@@ -339,11 +351,11 @@ 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 [2.2.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.2.1), archived on Zenodo:
+Version [3.0.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.1), archived on Zenodo:
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg)](https://doi.org/10.5281/zenodo.14009575)
-Yuri E. Corilo, William R. Kew, Lee Ann McCue (2021, March 27). EMSL-Computing/CoreMS: CoreMS 2.0.1 (Version v2.0.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.4641552
+Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.0.1 (Version v3.0.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
 ```

{CoreMS-2.2.1 → CoreMS-3.0.1}/README.md RENAMED Viewed

@@ -1,10 +1,10 @@
-![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">
 <br>
 <br>
-<a href="https://doi.org/10.5281/zenodo.4641552"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg" alt="CoreMS DOI" style="width:150px"></a>
+<a href="https://doi.org/10.5281/zenodo.14009575"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg" alt="DOI"></a>
 <br>
 </div>
@@ -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
- `2.2.1`
+ `3.0.1`
 ***
 ## 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
@@ -323,11 +335,11 @@ 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 [2.2.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.2.1), archived on Zenodo:
+Version [3.0.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.1), archived on Zenodo:
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg)](https://doi.org/10.5281/zenodo.14009575)
-Yuri E. Corilo, William R. Kew, Lee Ann McCue (2021, March 27). EMSL-Computing/CoreMS: CoreMS 2.0.1 (Version v2.0.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.4641552
+Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.0.1 (Version v3.0.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
 ```

CoreMS-3.0.1/corems/__init__.py ADDED Viewed

@@ -0,0 +1,60 @@
+__author__ = "Yuri E. Corilo"
+__version__ = "3.0.1"
+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 if it exists
+if os.path.exists(readme_path):
+    try:
+        with open(readme_path, "r", encoding="utf-8") as readme_file:
+            __doc__ = readme_file.read()
+    except Exception as e:
+        __doc__ = "CoreMS: A comprehensive mass spectrometry framework for software development and data analysis of small molecules analysis."
+        print(f"Warning: Could not read README.md file. Error: {e}")
+else:
+    __doc__ = "CoreMS: A comprehensive mass spectrometry framework for software development and data analysis of small molecules analysis."
+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)

CoreMS 2.2.1__tar.gz → 3.0.1__tar.gz

CoreMS 2.2.1tar.gz → 3.0.1tar.gz