Commit 23b56d85 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 3.0.0

parent b2ab29e8

.gitignore

+1 −0
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@@ -63,6 +63,7 @@ docs/_build/ 
**/doc/_build/



#Data files

/data/

*.wig

*.dat

*.png

CHANGELOG.md

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# Change log

All notable changes to this project will be documented in this file.



## Version 3.0.0 2019-07-18

#### TRANSIT:

 - TRANSIT now supports python 3. (To use with python 2, use releases < 3.0.0)

 - Improved speed of GSEA in Pathway Enrichment analysis.



## Version 2.5.2 2019-05-16

#### TRANSIT:

README.md

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# TRANSIT 2.5.1



[![Build Status](https://travis-ci.org/mad-lab/transit.svg?branch=master)](https://travis-ci.org/mad-lab/transit)   [![Documentation Status](https://readthedocs.org/projects/transit/badge/?version=latest)](http://transit.readthedocs.io/en/latest/?badge=latest)   [![Downloads](https://pepy.tech/badge/tnseq-transit)](https://pepy.tech/project/tnseq-transit)

# TRANSIT



[![Version](https://img.shields.io/github/tag/mad-lab/transit.svg)](https://github.com/mad-lab/transit)   [![Build Status](https://travis-ci.org/mad-lab/transit.svg?branch=master)](https://travis-ci.org/mad-lab/transit)   [![Documentation Status](https://readthedocs.org/projects/transit/badge/?version=latest)](http://transit.readthedocs.io/en/latest/?badge=latest)   [![Downloads](https://pepy.tech/badge/tnseq-transit)](https://pepy.tech/project/tnseq-transit)

=======



Welcome! This is the distribution for the TRANSIT and TPP tools developed by the [Ioerger Lab](http://orca2.tamu.edu/tom/iLab.html) at Texas A&M University.

setup.py

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@@ -61,6 +61,7 @@ class UploadCommand(Command): 
        if not self.yes_or_no("Have you done the following? \n" +

                    "- Updated README/Documentation?\n"

                    "- Are in the master branch, and have you merged version branch into master?\n"

                    "- Have you run the tests ('pytest tests/')?\n"

                    "- Have you updated CHANGELOG?\n"

                    "- Have you updated Transit Essentiality page?\n"

                    "- Updated version in src/pytransit/__init__.py (used to set git tag)?\n"
@@ -111,12 +112,14 @@ setup( 


    # Choose your license

    license='GNU GPL',



    python_requires='>=3.6',

    # See https://pypi.python.org/pypi?%3Aaction=list_classifiers



    classifiers=[

        #'Development Status :: 3 - Alpha',

        'Development Status :: 5 - Production/Stable',

        'Programming Language :: Python :: 2.7',

        'Programming Language :: Python',

        'Programming Language :: Python :: 3',

        'Intended Audience :: Science/Research',

        'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',

        'Operating System :: OS Independent',
@@ -144,7 +147,7 @@ setup( 
    # your project is installed. For an analysis of "install_requires" vs pip's

    # requirements files see:

    # https://packaging.python.org/en/latest/requirements.html

    install_requires=['setuptools', 'numpy~=1.15', 'scipy~=1.2', 'matplotlib~=2.2', 'pillow~=5.0', 'statsmodels~=0.9'],

    install_requires=['setuptools', 'numpy~=1.16', 'scipy~=1.2', 'matplotlib~=3.0', 'pillow~=6.0', 'statsmodels~=0.9'],



    #dependency_links = [

    #	"git+https://github.com/wxWidgets/wxPython.git#egg=wxPython"

src/pytpp/__main__.py

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@@ -30,8 +30,8 @@ import shutil 
import platform

import gzip



from tpp_tools import *

from tpp_gui import *

from pytpp.tpp_tools import *

from pytpp.tpp_gui import *





def run_main():
@@ -67,9 +67,9 @@ def main(*args, **kwargs): 
            pass



    elif not args and not kwargs and not hasWx:

        print "Please install wxPython to run in GUI Mode."

        print "To run in Console Mode please follow these instructions:"

        print ""

        print("Please install wxPython to run in GUI Mode.")

        print("To run in Console Mode please follow these instructions:")

        print("")

        show_help()



    else:
@@ -85,7 +85,7 @@ def main(*args, **kwargs): 
                           "window-size", "bwa-alg", "replicon-ids","primer-start-window"])

        unknown_flags = set(kwargs.keys()) - known_flags

        if unknown_flags:

            print "error: unrecognized flags:", ", ".join(unknown_flags)

            print("error: unrecognized flags:", ", ".join(unknown_flags))

            show_help()

            sys.exit()