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Reorganised everything to get into PIP!
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happykhan committed Apr 12, 2018
1 parent 90f2352 commit e53c3f4
Showing 245 changed files with 62 additions and 1,292 deletions.
4 changes: 2 additions & 2 deletions GTree
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#!/usr/bin/env python
import main
from grapetree import __main__

main.main()
__main__.main()
7 changes: 6 additions & 1 deletion MANIFEST.in
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@@ -1 +1,6 @@
include *
include binaries/*
include GT_icon*
include LICENSE
include README*
recursive-include grapetree/templates *
recursive-include grapetree/static *
1,265 changes: 0 additions & 1,265 deletions MSTree_holder.html

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27 changes: 19 additions & 8 deletions README.md
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@@ -44,7 +44,8 @@ to install these modules is with pip:
pip install -r requirements.txt
chmod +x binaries/
```
On Linux or MacOSX you need to make sure the binaries in binaries/ can be executed. To run GrapeTree;
On Linux or MacOSX you need to make sure the binaries in binaries/ can be
executed. To run GrapeTree;

1. Navigate to the directory where you installed GrapeTree.
1. Run it through python as below.
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## License
Copyright Warwick University
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
Copyright Warwick University This program is free software: you can
redistribute it and/or modify it under the terms of the GNU General Public
License as published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.
This program is distributed in the hope that it will be useful, but without
any warranty; without even the implied warranty of merchantability or fitness
for a particular purpose. See the GNU General Public License for more
details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
You should have received a copy of the GNU General Public License along with
this program. If not, see <http://www.gnu.org/licenses/>.


## Citation
EnteroMSTree - GrapeTree has not been formally published yet. If you use GrapeTree please cite the preprint: https://www.biorxiv.org/content/early/2017/11/09/216788
## Citation EnteroMSTree - GrapeTree has not been formally published yet. If
you use GrapeTree please cite the preprint:
https://www.biorxiv.org/content/early/2017/11/09/216788

An extended citation could be:
Z Zhou, NF Alikhan, MJ Sergeant, N Luhmann, C Vaz, AP Francisco, JA Carrico, M Achtman (2017) "GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens", bioRxiv 216788; doi: https://doi.org/10.1101/216788
Z Zhou, NF Alikhan, MJ Sergeant, N Luhmann, C Vaz, AP Francisco, JA Carrico,
M Achtman (2017) "GrapeTree: Visualization of core genomic relationships
among 100,000 bacterial pathogens", bioRxiv 216788; doi:
https://doi.org/10.1101/216788
4 changes: 2 additions & 2 deletions build_win.bat
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@@ -2,5 +2,5 @@ pyinstaller -n GrapeTree_win --icon=GT_icon.ico ^
--add-binary binaries/edmonds.exe;binaries/ ^
--add-binary binaries/fastme.exe;binaries/ ^
--add-data grapetree/templates/;grapetree/templates/ ^
--add-data static/;static/ ^
main.py
--add-data grapetree/static/;grapetree/static/ ^
grapetree/__main__.py
4 changes: 2 additions & 2 deletions grapetree/__init__.py
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@@ -8,8 +8,8 @@
static_folder = os.path.join(sys._MEIPASS, 'static')
app = Flask(__name__, template_folder=template_folder, static_folder=static_folder)
else:
app = Flask(__name__, static_folder='../static',template_folder='..')
app = Flask(__name__, static_folder='static/', template_folder='templates/')

app.config.from_object(config)

from grapetree import views
from grapetree import views
16 changes: 11 additions & 5 deletions main.py → grapetree/__main__.py
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@@ -13,10 +13,16 @@
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>.
"""
GrapeTree draws awesome trees
Web interface of GrapTree, which is a program for phylogenetic analysis.
TODO: Detailed description
GrapeTree is an integral part of EnteroBase and we advise that you use GrapeTree
through EnteroBase for the best results. However, many people have asked for a
stand-alone GrapeTree version that they could use offline or integrate into the
other applications.
The stand-alone version emulates the EnteroBase version through a lightweight
webserver running on your local computer. You will be interacting with the
program as you would in EnteroBase; through a web browser.
"""

import threading
@@ -31,9 +37,9 @@
import sys

__licence__ = 'GPLv3'
__author__ = 'Zhemin Zhou, Martin Sergeant, Nabil-Fareed Alikhan & Mark Achtman'
__author_email__ = ' M.J.Sergeant@warwick.ac.uk'
__version__ = '0.0.8'
__author__ = 'EnteroBase development team'
__author_email__ = 'zhemin.zhou@warwick.ac.uk'
__version__ = '1.2.0'

epi = "Licence: " + __licence__ + " by " + __author__ + \
" <" + __author_email__ + ">"
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2 changes: 2 additions & 0 deletions setup.cfg
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@@ -1,2 +1,4 @@
[metadata]
description-file = README.md
[bdist_wheel]
universal=1
25 changes: 18 additions & 7 deletions setup.py
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@@ -7,22 +7,30 @@

from setuptools import setup, find_packages
from codecs import open
from os import path
from os import path, walk
from grapetree.__main__ import __author_email__, __author__, __version__

def package_files(directory):
paths = []
for (pathz, directories, filenames) in walk(directory):
for filename in filenames:
paths.append(path.join('..', pathz, filename))
return paths

here = path.abspath(path.dirname(__file__))

with open(path.join(here, 'README.md'), encoding='utf-8') as f:
long_description = f.read()

setup(
name='grapetree',
version='1.1.8',
version= __version__,
description='Web interface of GrapTree, which is a program for phylogenetic analysis.',
long_description=long_description,
long_description_content_type='text/markdown',
url='https://github.com/martinSergeant/EnteroMSTree',
author='EnteroBase development team',
author_email='zhemin.zhou@warwick.ac.uk',
author= __author__,
author_email= __author_email__,
classifiers=[ # Optional
'Development Status :: 5 - Production/Stable',
'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
@@ -35,14 +43,17 @@
],
py_modules=['MSTrees'],
keywords='visulisation bioinformatics microbial genomics',
packages=['grapetree'],
packages = ['grapetree'],
package_data={'templates':['*'],
'static': ['*']},
install_requires=['DendroPy', 'numpy', 'Flask', 'networkx', 'numpy', 'psutil'],
entry_points={
'console_scripts': [
'grapetree=main:main',
'grapetree=grapetree.__main__:main',
],
},
scripts=['MSTrees.py'],
include_package_data=True,
project_urls={
'Bug Reports': 'https://github.com/martinSergeant/EnteroMSTree/issues',
'Source': 'https://github.com/martinSergeant/EnteroMSTree',
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