CoreMS 2.2.0__tar.gz → 2.2.1__tar.gz

{corems-2.2.0 → CoreMS-2.2.1}/CoreMS.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CoreMS
-Version: 2.2.0
+Version: 2.2.1
 Summary: Mass Spectrometry Framework for Small Molecules Analysis
 Home-page: https://github.com/EMSL-Computing/CoreMS
 Author: Corilo, Yuri
@@ -13,27 +13,6 @@ 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)  
 
@@ -87,7 +66,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `2.2.0`
+ `2.2.1`
 
 ***
 
@@ -360,7 +339,7 @@ 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 [2.2.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.2.1), 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-2.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CoreMS
-Version: 2.2.0
+Version: 2.2.1
 Summary: Mass Spectrometry Framework for Small Molecules Analysis
 Home-page: https://github.com/EMSL-Computing/CoreMS
 Author: Corilo, Yuri
@@ -13,27 +13,6 @@ 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)  
 
@@ -87,7 +66,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `2.2.0`
+ `2.2.1`
 
 ***
 
@@ -360,7 +339,7 @@ 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 [2.2.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.2.1), 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-2.2.1}/README.md

@@ -50,7 +50,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `2.2.0`
+ `2.2.1`
 
 ***
 
@@ -323,7 +323,7 @@ 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 [2.2.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.2.1), 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-2.2.1}/corems/__init__.py

@@ -1,5 +1,5 @@
 __author__ = 'Yuri E. Corilo'
-__version__ = '2.2.0'
+__version__ = '2.2.1'
 __doc__ = '''
 <div align="left">
 

{corems-2.2.0 → CoreMS-2.2.1}/ext_lib/ChemstationMSFileReader.xml

@@ -1,126 +1,126 @@
-<?xml version="1.0"?>
-<doc>
-<assembly>
-<name>
-ChemstationMSFileReader
-</name>
-</assembly>
-<members>
-<member name="M:ChemstationMSFileReader.clsChemstationDataMSFileReader.#ctor(System.String)">
-	<summary>
- Open the specified data file and read the data headers
- </summary>
-	<param name="sDatafilePath">Path to the file to read</param>
-	<remarks></remarks>
-</member><member name="M:ChemstationMSFileReader.clsChemstationDataMSFileReader.GetSpectrum(System.Int32,ChemstationMSFileReader.clsSpectralRecord@,System.Int32@)">
-	<summary>
-  Returns the mass spectrum at the specified index
- </summary>
-	<param name="intSpectrumIndex">0-based spectrum index</param>
-	<param name="oSpectrum">Spectrum object (output)</param>
-	<param name="intTotalSignalRawFromIndex">TIC value as reported by the Index; this value has been scaled down by some sort of polynomial transformation</param>
-	<returns>True if success, false if an error</returns>
-</member><member name="M:ChemstationMSFileReader.clsChemstationDataMSFileReader.ReadHeaders(System.String)">
-	<summary>
- Open the data file and read the header sections from the data file
- </summary>
-	<param name="sDataFilePath">Path to the file to read</param>
-	<returns>True if success, false if an error</returns>
-	<remarks>The file handle will remain open until this class is disposed of</remarks>
-</member><member name="M:ChemstationMSFileReader.clsChemstationDataMSFileReader.ReadIndexRecords(System.IO.FileStream@)">
-	<summary>
- Reads the index entries (aka directory records)
- </summary>
-	<param name="fsDatafile"></param>
-	<returns>True if success, false if an error</returns>
-</member><member name="M:ChemstationMSFileReader.clsChemstationDataMSFileReader.ReadNormalizationRecords(System.IO.FileStream@)">
-	<summary>
- Reads the 10 normalization records from the data file
- </summary>
-	<param name="fsDatafile"></param>
-	<returns>True if success, false if an error</returns>
-</member><member name="M:ChemstationMSFileReader.clsSpectralRecord.#ctor">
-	<summary>
- Instantiate a new spectrum object
- </summary>
-	<remarks></remarks>
-</member><member name="M:ChemstationMSFileReader.clsSpectralRecord.#ctor(System.IO.FileStream@,System.Int32)">
-	<summary>
- Populate a spectrum object with the data at the specified byte offset
- </summary>
-</member><member name="M:ChemstationMSFileReader.clsSpectralRecord.Clear">
-	<summary>
- Initialize the variables and data structures
- </summary>
-	<remarks></remarks>
-</member><member name="M:ChemstationMSFileReader.clsSpectralRecord.ReadFromFile(System.IO.FileStream@,System.Int32)">
-	<summary>
- Read the spectrum at the specified byte offset
- </summary>
-	<param name="fsDatafile"></param>
-	<param name="intByteOffsetStart"></param>
-	<remarks></remarks>
-</member><member name="M:ChemstationMSFileReader.clsSpectralRecord.ReadPackedAbundance(System.IO.FileStream@)">
-	<summary>
- Read packed abundance stored as 2-bit scale with 14 bit mantissa
- </summary>
-	<param name="fs">FileStream object</param>
-	<returns>Unpacked abundance</returns>
-</member><member name="M:ChemstationMSFileReader.clsByteConverter.ReadInt16SwapBytes(System.IO.FileStream@)">
-	<summary>
- Reads an Int16 from the filestream
- Swaps bytes prior to converting
- </summary>
-	<param name="fs">FileStream object</param>
-	<returns>The value, as an Int16 number</returns>
-</member><member name="M:ChemstationMSFileReader.clsByteConverter.ReadUInt16SwapBytes(System.IO.FileStream@)">
-	<summary>
- Reads an UInt16 from the filestream
- Swaps bytes prior to converting
- </summary>
-	<param name="fs">FileStream object</param>
-	<returns>The value, as an Int32 number</returns>
-</member><member name="M:ChemstationMSFileReader.clsByteConverter.ReadInt32SwapBytes(System.IO.FileStream@)">
-	<summary>
- Reads an Int32 from the filestream
- Swaps bytes prior to converting
- </summary>
-	<param name="fs">FileStream object</param>
-	<returns>The value, as an Int32 number</returns>
-</member><member name="M:ChemstationMSFileReader.clsByteConverter.ReadSingleSwapBytes(System.IO.FileStream@)">
-	<summary>
- Reads a 4-byte single (real) from the filestream
- Swaps bytes prior to converting
- </summary>
-	<param name="fs">FileStream object</param>
-	<returns>The value, as a single-precision number</returns>
-</member><member name="M:ChemstationMSFileReader.clsByteConverter.ReadString(System.IO.FileStream@,System.Int32,System.Boolean)">
-	<summary>
- Reads a fixed-length string from the filestream
- Optionally advances the reader one byte after reading the string
- </summary>
-	<param name="fs">FileStream object</param>
-	<param name="iStringLength">String length</param>
-	<param name="bAdvanceExtraByte">If true, then advances the read an extra byte after reading the string</param>
-	<returns>The string read</returns>
-</member><member name="M:ChemstationMSFileReader.clsByteConverter.WordOffsetToBytes(System.Int32)">
-	<summary>
- Convert byte-offset stored in words into bytes
- </summary>
-	<param name="iOffsetWords"></param>
-	<returns>The byte offset, in bytes</returns>
-</member><member name="M:ChemstationMSFileReader.clsDataHeader.#ctor(System.IO.FileStream@)">
-	<summary>
- Read header from the specified file
- </summary>
-	<param name="fsDatafile"></param>
-	<remarks></remarks>
-</member><member name="M:ChemstationMSFileReader.clsDataHeader.ReadFromFile(System.IO.FileStream@)">
-	<summary>
- Read header from the specified file
- </summary>
-	<param name="fs">Input file stream</param>
-	<returns>True if success, false if an error</returns>
-</member>
-</members>
+<?xml version="1.0"?>
+<doc>
+<assembly>
+<name>
+ChemstationMSFileReader
+</name>
+</assembly>
+<members>
+<member name="M:ChemstationMSFileReader.clsChemstationDataMSFileReader.#ctor(System.String)">
+	<summary>
+ Open the specified data file and read the data headers
+ </summary>
+	<param name="sDatafilePath">Path to the file to read</param>
+	<remarks></remarks>
+</member><member name="M:ChemstationMSFileReader.clsChemstationDataMSFileReader.GetSpectrum(System.Int32,ChemstationMSFileReader.clsSpectralRecord@,System.Int32@)">
+	<summary>
+  Returns the mass spectrum at the specified index
+ </summary>
+	<param name="intSpectrumIndex">0-based spectrum index</param>
+	<param name="oSpectrum">Spectrum object (output)</param>
+	<param name="intTotalSignalRawFromIndex">TIC value as reported by the Index; this value has been scaled down by some sort of polynomial transformation</param>
+	<returns>True if success, false if an error</returns>
+</member><member name="M:ChemstationMSFileReader.clsChemstationDataMSFileReader.ReadHeaders(System.String)">
+	<summary>
+ Open the data file and read the header sections from the data file
+ </summary>
+	<param name="sDataFilePath">Path to the file to read</param>
+	<returns>True if success, false if an error</returns>
+	<remarks>The file handle will remain open until this class is disposed of</remarks>
+</member><member name="M:ChemstationMSFileReader.clsChemstationDataMSFileReader.ReadIndexRecords(System.IO.FileStream@)">
+	<summary>
+ Reads the index entries (aka directory records)
+ </summary>
+	<param name="fsDatafile"></param>
+	<returns>True if success, false if an error</returns>
+</member><member name="M:ChemstationMSFileReader.clsChemstationDataMSFileReader.ReadNormalizationRecords(System.IO.FileStream@)">
+	<summary>
+ Reads the 10 normalization records from the data file
+ </summary>
+	<param name="fsDatafile"></param>
+	<returns>True if success, false if an error</returns>
+</member><member name="M:ChemstationMSFileReader.clsSpectralRecord.#ctor">
+	<summary>
+ Instantiate a new spectrum object
+ </summary>
+	<remarks></remarks>
+</member><member name="M:ChemstationMSFileReader.clsSpectralRecord.#ctor(System.IO.FileStream@,System.Int32)">
+	<summary>
+ Populate a spectrum object with the data at the specified byte offset
+ </summary>
+</member><member name="M:ChemstationMSFileReader.clsSpectralRecord.Clear">
+	<summary>
+ Initialize the variables and data structures
+ </summary>
+	<remarks></remarks>
+</member><member name="M:ChemstationMSFileReader.clsSpectralRecord.ReadFromFile(System.IO.FileStream@,System.Int32)">
+	<summary>
+ Read the spectrum at the specified byte offset
+ </summary>
+	<param name="fsDatafile"></param>
+	<param name="intByteOffsetStart"></param>
+	<remarks></remarks>
+</member><member name="M:ChemstationMSFileReader.clsSpectralRecord.ReadPackedAbundance(System.IO.FileStream@)">
+	<summary>
+ Read packed abundance stored as 2-bit scale with 14 bit mantissa
+ </summary>
+	<param name="fs">FileStream object</param>
+	<returns>Unpacked abundance</returns>
+</member><member name="M:ChemstationMSFileReader.clsByteConverter.ReadInt16SwapBytes(System.IO.FileStream@)">
+	<summary>
+ Reads an Int16 from the filestream
+ Swaps bytes prior to converting
+ </summary>
+	<param name="fs">FileStream object</param>
+	<returns>The value, as an Int16 number</returns>
+</member><member name="M:ChemstationMSFileReader.clsByteConverter.ReadUInt16SwapBytes(System.IO.FileStream@)">
+	<summary>
+ Reads an UInt16 from the filestream
+ Swaps bytes prior to converting
+ </summary>
+	<param name="fs">FileStream object</param>
+	<returns>The value, as an Int32 number</returns>
+</member><member name="M:ChemstationMSFileReader.clsByteConverter.ReadInt32SwapBytes(System.IO.FileStream@)">
+	<summary>
+ Reads an Int32 from the filestream
+ Swaps bytes prior to converting
+ </summary>
+	<param name="fs">FileStream object</param>
+	<returns>The value, as an Int32 number</returns>
+</member><member name="M:ChemstationMSFileReader.clsByteConverter.ReadSingleSwapBytes(System.IO.FileStream@)">
+	<summary>
+ Reads a 4-byte single (real) from the filestream
+ Swaps bytes prior to converting
+ </summary>
+	<param name="fs">FileStream object</param>
+	<returns>The value, as a single-precision number</returns>
+</member><member name="M:ChemstationMSFileReader.clsByteConverter.ReadString(System.IO.FileStream@,System.Int32,System.Boolean)">
+	<summary>
+ Reads a fixed-length string from the filestream
+ Optionally advances the reader one byte after reading the string
+ </summary>
+	<param name="fs">FileStream object</param>
+	<param name="iStringLength">String length</param>
+	<param name="bAdvanceExtraByte">If true, then advances the read an extra byte after reading the string</param>
+	<returns>The string read</returns>
+</member><member name="M:ChemstationMSFileReader.clsByteConverter.WordOffsetToBytes(System.Int32)">
+	<summary>
+ Convert byte-offset stored in words into bytes
+ </summary>
+	<param name="iOffsetWords"></param>
+	<returns>The byte offset, in bytes</returns>
+</member><member name="M:ChemstationMSFileReader.clsDataHeader.#ctor(System.IO.FileStream@)">
+	<summary>
+ Read header from the specified file
+ </summary>
+	<param name="fsDatafile"></param>
+	<remarks></remarks>
+</member><member name="M:ChemstationMSFileReader.clsDataHeader.ReadFromFile(System.IO.FileStream@)">
+	<summary>
+ Read header from the specified file
+ </summary>
+	<param name="fs">Input file stream</param>
+	<returns>True if success, false if an error</returns>
+</member>
+</members>
 </doc>