Merge pull request #130 from Franck-Dernoncourt/requirements

Add requirements, fix tests

Author: Franck-Dernoncourt

.gitignore

@@ -5,4 +5,7 @@
 *.project
 *.pydevproject
 output/*
-data/*
+data/*
+
+# OS X file
+.DS_Store

.travis.yml

@@ -4,12 +4,11 @@ os:
     - linux
 language: python
 python: 
-  - "3.5"
+  - "3.6"
 # command to install dependencies
 install:
   - bash .travis_install_ubuntu.sh
-  - pip install tensorflow
-  - pip install -U networkx matplotlib scikit-learn scipy spacy pycorenlp
+  - pip install -r requirements.txt
   - python -m spacy download en
   # ensure that NeuroNER doesn't perform too many epochs (Travis jobs are limited to 50 minutes)
   - sed -i 's/maximum_number_of_epochs = 100/maximum_number_of_epochs = 1/g' src/parameters.ini

requirements.txt

@@ -0,0 +1,8 @@
+matplotlib==3.0.2
+networkx==2.2
+pycorenlp==0.3.0
+scikit-learn==0.20.2
+scipy==1.2.0
+spacy==2.0.18
+tensorflow==1.12.0
+# tensorflow-gpu==1.1.0

src/utils_plots.py

@@ -143,7 +143,7 @@ def plot_classification_report(classification_report, title='Classification repo
     else:
         lines = classification_report.split('\n')
         for line in lines[2 : (len(lines) - 1)]:
-            t = line.strip().replace('avg / total', 'micro-avg').split()
+            t = line.strip().replace(' avg', '-avg').split()
             if len(t) < 2: continue
             classes.append(t[0])
             v = [float(x)*100 for x in t[1: len(t) - 1]]