Several updates and fixes for next release (#8)

* Update README.rst

* Update form (GUI)

* Update tests and test data

* Update and bump dependencies

* Fix incompatibilities

* Update configs project

* Bump version to v0.1.5 (development version)

* Update adduct and isotope libraries using nist_database.txt

* Rename beams to beamspy

Author: RJMW

.travis.yml

@@ -15,7 +15,7 @@ before_script:
   - "export DISPLAY=:99.0"
 
 script:
-  - beams --help
+  - beamspy --help
   - green -vvv --run-coverage
 
 after_script:

MANIFEST.in

@@ -5,6 +5,6 @@ include examples/*.*
 include tests/*.py
 include tests/test_data/*.*
 include tests/test_results/.gitignore
-include beams/data/*.txt
-include beams/data/databases/*.sql.gz
-include beams/data/databases/databases.txt
+include beamspy/data/*.txt
+include beamspy/data/databases/*.sql.gz
+include beamspy/data/databases/databases.txt

README.rst

@@ -1,107 +1,116 @@
-BEAMS - Birmingham mEtabolite Annotation for Mass SpectroMetry
-================================================================
+BEAMSpy - Birmingham mEtabolite Annotation for Mass Spectrometry (Python package)
+==================================================================================
 |Version| |Py versions| |Git| |Bioconda| |Build Status (Travis)| |Build Status (AppVeyor)| |License| |RTD doc| |codecov| |mybinder|
 
-BEAMS is a Python Package to annotate LC-MS and DIMS data.
+BEAMSpy (Birmingham mEtabolite Annotation for Mass Spectrometry) is a Python package that includes several automated and
+seamless computational modules that are applied to putatively annotate metabolites detected in untargeted ultra (high)
+performance liquid chromatography-mass spectrometry or untargeted direct infusion mass spectrometry metabolomic assays
+in an automated process. All reported metabolites are annotated to level 3 of the Metabolomics Standards
+Initiative (MSI) reporting standards (Metabolomics. 2007 Sep; 3(3): 211–221. `doi: 10.1007/s11306-007-0082-2 <https://doi.org/10.1007/s11306-007-0082-2>`_).
 
+The package is highly flexible to suit the diversity of sample types studied and mass spectrometers applied in
+untargeted metabolomics studies. The user can use the standard reference files included in the package or can develop
+their own reference files.
+
+
+- :ref:`Quick installation <quick_installation>`
 - |documentation|
-- |source|
 - |bug reports|
+- |License|
 
-Installation
-------------------------
+
+.. _quick_installation:
+
+Quick installation
+-------------------
 
 Conda_
 ~~~~~~~
 
 1. Install |miniconda|. Follow the steps described |conda_install|.
-2. Run the following commands to install BEAMS.
+2. Run the following commands to install BEAMSpy.
 
 Windows-64, Linux-64 and OSx
 
 ::
 
-    $ conda create -n beams beams -c conda-forge -c bioconda -c computational-metabolomics
-    $ activate beams
+    $ conda create -n beamspy beamspy -c conda-forge -c bioconda -c computational-metabolomics
+    $ activate beamspy
 
 Linux-64 and OSx
 
 ::
 
-    $ conda create -n beams beams -c conda-forge -c bioconda -c computational-metabolomics
-    $ source activate beams
+    $ conda create -n beamspy beamspy -c conda-forge -c bioconda -c computational-metabolomics
+    $ source activate beamspy
 
 
 Usage
 ------------------------
 
-Command line
-~~~~~~~~~~~~~
+Command line interface (CLI)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 ::
 
-    $ beams --help
+    $ beamspy --help
 
-GUI
-~~~~~~~~~~~~~
+Graphical user interface (GUI)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 ::
 
-    $ beams start-gui
+    $ beamspy start-gui
 
-Bugs
+Bug reports
 ------------------------
 
-Please report any bugs that you find `here <https://github.com/computational-metabolomics/beams/issues>`_.
-Or fork the repository on `GitHub <https://github.com/computational-metabolomics/beams/>`_
+Please report any bugs that you find `here <https://github.com/computational-metabolomics/beamspy/issues>`_.
+Or fork the repository on `GitHub <https://github.com/computational-metabolomics/beamspy/>`_
 and create a pull request (PR). We welcome all contributions, and we will help you to make the PR if you are new to `git <https://guides.github.com/activities/hello-world/>`_.
 
 License
 ------------------------
 
 Released under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/beams/LICENSE>`_)
 
-.. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/beams.svg?branch=dev&style=flat&maxAge=3600&label=Travis-CI
-   :target: https://travis-ci.com/computational-metabolomics/beams
+.. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/beamspy.svg?branch=dev&style=flat&maxAge=3600&label=Travis-CI
+   :target: https://travis-ci.com/computational-metabolomics/beamspy
 
-.. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/RJMW/beams.svg?style=flat&maxAge=3600&label=AppVeyor
-   :target: https://ci.appveyor.com/project/RJMW/beams
+.. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/RJMW/beamspy.svg?style=flat&maxAge=3600&label=AppVeyor
+   :target: https://ci.appveyor.com/project/RJMW/beamspy
 
-.. |Py versions| image:: https://img.shields.io/pypi/pyversions/beams.svg?style=flat&maxAge=3600
-   :target: https://pypi.python.org/pypi/beams/
+.. |Py versions| image:: https://img.shields.io/pypi/pyversions/beamspy.svg?style=flat&maxAge=3600
+   :target: https://pypi.python.org/pypi/beamspy/
 
-.. |Version| image:: https://img.shields.io/pypi/v/beams.svg?style=flat&maxAge=3600
-   :target: https://pypi.python.org/pypi/beams/
+.. |Version| image:: https://img.shields.io/pypi/v/beamspy.svg?style=flat&maxAge=3600
+   :target: https://pypi.python.org/pypi/beamspy/
 
 .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
-   :target: https://github.com/computational-metabolomics/beams
+   :target: https://github.com/computational-metabolomics/beamspy
 
 .. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600
-   :target: http://bioconda.github.io/recipes/beams/README.html
+   :target: http://bioconda.github.io/recipes/beamspy/README.html
 
-.. |License| image:: https://img.shields.io/pypi/l/beams.svg?style=flat&maxAge=3600
+.. |License| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
    :target: https://www.gnu.org/licenses/gpl-3.0.html
 
 .. |RTD doc| image:: https://img.shields.io/badge/documentation-RTD-71B360.svg?style=flat&maxAge=3600
-   :target: http://beams.readthedocs.io/en/latest/beams/index.html
+   :target: https://beamspy.readthedocs.io/en/latest/
 
-.. |codecov| image:: https://codecov.io/gh/computational-metabolomics/beams/branch/master/graph/badge.svg
-   :target: https://codecov.io/gh/computational-metabolomics/beams
+.. |codecov| image:: https://codecov.io/gh/computational-metabolomics/beamspy/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/computational-metabolomics/beamspy
 
 .. |mybinder| image:: https://mybinder.org/badge_logo.svg
-   :target: https://mybinder.org/v2/gh/computational-metabolomics/beams/master?filepath=notebooks
+   :target: https://mybinder.org/v2/gh/computational-metabolomics/beamspy/master?filepath=notebooks
 
 .. |documentation| raw:: html
 
-   <a href="http://beams.readthedocs.io/en/latest/beams/index.html" target="_blank">Documentation</a>
-
-.. |source| raw:: html
-
-   <a href="https://github.com/computational-metabolomics/beams/tree/dev/beams" target="_blank">Source</a>
+   <a href="https://beamspy.readthedocs.io/en/latest/" target="_blank">Documentation</a>
 
 .. |bug reports| raw:: html
 
-   <a href="https://github.com/computational-metabolomics/beams/issues" target="_blank">Bug reports</a>
+   <a href="https://github.com/computational-metabolomics/beamspy/issues" target="_blank">Bug reports</a>
 
 .. |conda_install| raw:: html
 
@@ -113,4 +122,3 @@ Released under the GNU General Public License v3.0 (see `LICENSE file <https://g
 
 .. _pip: https://pip.pypa.io/
 .. _Conda: http://conda.pydata.org/docs/
-

beams/__init__.py

@@ -0,0 +1,4 @@
+__author__ = '[email protected]'
+__credits__ = '[email protected]'
+__version__ = '0.1.5'
+__license__ = 'GPLv3'

beams/data/BEAMS_DB.sqlite

@@ -1,15 +1,15 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from beams import __version__
+from beamspy import __version__
 import argparse
 import sys
 import os
 import networkx as nx
-from beams import in_out
-from beams import grouping
-from beams import annotation
-from beams import plots
+from beamspy import in_out
+from beamspy import grouping
+from beamspy import annotation
+from beamspy import plots
 
 
 def map_delimiter(delimiter):
@@ -21,7 +21,7 @@ def map_delimiter(delimiter):
 
 
 def main():
-    print("Executing BEAMS version {}.".format(__version__))
+    print("Executing BEAMSpy version {}.".format(__version__))
 
     parser = argparse.ArgumentParser(description='Annotation package of LC-MS and DIMS data',
                                      formatter_class=argparse.ArgumentDefaultsHelpFormatter)
@@ -137,7 +137,7 @@ def main():
     parser_amf.add_argument('-d', '--db', type=str, required=True,
                             help="Sqlite database to write results.")
 
-    parser_amf.add_argument('-c', '--db-mf', type=str, required=True, default="http://mfdb.bham.ac.uk",
+    parser_amf.add_argument('-c', '--db-mf', type=str, default="http://mfdb.bham.ac.uk",
                             help="Molecular formulae database (reference).")
 
     parser_amf.add_argument('-a', '--adducts-library', type=str, default=None, required=False,
@@ -334,7 +334,7 @@ def main():
 
     if args.step == "start-gui":
         from PySide2 import QtWidgets
-        from beams.gui import BeamsApp
+        from beamspy.gui import BeamsApp
         app = QtWidgets.QApplication(sys.argv)
         app.setStyle("Fusion")
         form = BeamsApp()