Merge 5f20345 into 51856d0

.travis.yml

@@ -1,38 +1,5 @@
 matrix:
     include:
-        - name: "Python 3.5"
-          language: python
-          sudo: required
-          dist: xenial
-          python: 
-            - 3.5
-          before_install:
-            - sudo apt-get -qq update
-            - sudo apt-get install -y ghostscript
-            - sudo apt-get install -y gcc
-          install:
-            - pip install Cython
-            - pip install swagger-spec-validator==2.1.0
-            - pip install connexion==1.4.2
-            - pip install bokeh==0.13.0
-            - pip install tornado==5.0.2
-            - pip install jsonschema==2.6.0
-            - pip install mhcnuggets==2.3.3
-            - pip install mhcflurry==2.0.1
-            - pip install tensorflow==2.2.1
-            - pip install keras==2.3.1
-            - pip install Werkzeug==0.16.1
-            - pip install biopython==1.76
-            - pip install watchdog==0.9.0
-            - pip install coveralls
-            - pip install -e .
-            - mhcflurry-downloads fetch
-          services:
-            - postgresql
-          script:
-            - TEST_FLAG=1 coverage run --source=lib,tools -m unittest discover -v
-          after_success:
-            - coveralls
         - name: "Python 3.6"
           language: python
           sudo: required
@@ -48,9 +15,6 @@ matrix:
             - pip install bokeh==0.13.0
             - pip install tornado==5.0.2
             - pip install jsonschema==2.6.0
-            - pip install mhcnuggets==2.3.3
-            - pip install mhcflurry==2.0.1
-            - pip install tensorflow==2.2.1
             - pip install keras==2.3.1
             - pip install pandas==0.25.2
             - pip install Werkzeug==0.16.1
@@ -78,9 +42,6 @@ matrix:
             - pip install bokeh==0.13.0
             - pip install tornado==5.0.2
             - pip install jsonschema==2.6.0
-            - pip install mhcnuggets==2.3.3
-            - pip install mhcflurry==2.0.1
-            - pip install tensorflow==2.2.1
             - pip install keras==2.3.1
             - pip install pandas==0.25.2
             - pip install Werkzeug==0.16.1
@@ -108,9 +69,6 @@ matrix:
             - pip install bokeh==0.13.0
             - pip install tornado==5.0.2
             - pip install jsonschema==2.6.0
-            - pip install mhcnuggets==2.3.3
-            - pip install mhcflurry==2.0.1
-            - pip install tensorflow==2.2.1
             - pip install keras==2.3.1
             - pip install pandas==0.25.2
             - pip install Werkzeug==0.16.1

docs/install.rst

@@ -5,7 +5,7 @@ Installation
 
 pVACtools is written for Linux but some users have been able to run it successfully on Mac OS X. If you are using Windows you will need to set up a Linux environment, for example by setting up a virtual machine.
 
-pVACtools requires Python 3.5 or above. Before running any installation steps, check the Python version installed on your system:
+pVACtools requires Python 3.6 or above. Before running any installation steps, check the Python version installed on your system:
 
 .. code-block:: none
 

setup.py

@@ -2,10 +2,10 @@
 import os
 
 import sys
-if sys.version_info < (3,5):
+if sys.version_info < (3,6):
     print("This python version is not supported:")
     print(sys.version)
-    print("pVACtools requires python 3.5 or greater")
+    print("pVACtools requires python 3.6 or greater")
     sys.exit(1)
 
 pvacseq_data_files = []
@@ -109,6 +109,9 @@
         'jsonschema==2.6.0',
         'mock',
         'vaxrank>=1.1.0',
+        'tensorflow==2.2.2',
+        'mhcnuggets==2.3.3',
+        'mhcflurry==2.0.1',
     ],
     package_data={
         'tools.pvacseq': pvacseq_data_files,
@@ -124,7 +127,7 @@
         'Intended Audience :: Science/Research',
         'Topic :: Scientific/Engineering :: Bio-Informatics',
 
-        "Programming Language :: Python :: 3.5"
+        "Programming Language :: Python :: 3.6"
     ],
 
     author = "Jasreet Hundal, Susanna Kiwala, Joshua McMichael, Yang-Yang Feng, Christopher A. Miller, Aaron Graubert, Amber Wollam, Connor Liu, Jonas Neichin, Megan Neveau, Jason Walker, Elaine R. Mardis, Obi L. Griffith, Malachi Griffith",