Merge branch 'lcms_dev' into 'master'

CoreMS 3.0

Closes #109, #158, and #104

See merge request mass-spectrometry/corems!101

Author: corilo

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.2.1
+current_version = 3.0.0
 commit = False
 tag = False
 

.gitignore

@@ -83,3 +83,4 @@ r00*/
 ext_lib/
 *.egg*
 config.yaml
+*.token

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
 
- `2.2.1`
+ `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).
 
 ***
 
@@ -75,19 +83,20 @@ 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
 
 - Pandas data frame (can be saved using pickle, h5, etc)
 - 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 [2.2.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.2.1), 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)