add additional python version support and ci config

Author: John Ziegler

.travis.yml

@@ -3,6 +3,8 @@ python:
     - 2.7
     - 3.5
     - 3.6
+    - 3.7
+    - 3.8
 before_install:
     - sudo apt-get -y update
 install:

data/generate_vectors/create_data.py

@@ -296,7 +296,7 @@ def create_data(
             raise Exception(
                 "Label column in case list can be empty or contain one the values +1 (MSI) or -1 (MSS)."
             )
-        cases = cases.replace({pd.np.nan: None})
+        cases = cases.replace({np.nan: None})
         for index, row in cases.iterrows():
             tumor_id, normal_id, tumor_bam, normal_bam, label = map(
                 lambda x: row[x] if x in row and row[x] else None,

main/evaluate_sample.py

@@ -90,7 +90,7 @@ def sample_name_parser(sample):
         try:
             os.mkdir(save_loc)
         except OSError as e:
-            if e.errno != os.errno.EEXIST:
+            if e.errno != errno.EEXIST:
                 print("Exception when creating directory to store final results.")
                 raise
 

requirements.txt

@@ -1,13 +1,16 @@
-future==0.18.2
 nose>=1.3.7
 numpy==1.16.1
-pandas==0.24.2
-Pillow==5.3.0
+pandas==0.24.2; python_version <= '2.7'
+pandas
+pillow>=8.1.1
 pysam==0.16.0.1
 python-dateutil==2.8.1
-scikit-learn==0.20.0
-scipy==1.1.0
+scikit-learn>=0.20.0; python_version <= '2.7'
+scikit-learn
+scipy>=1.1.0; python_version <= '2.7'
+scipy
 six==1.11.0
-sklearn==0.0
+sklearn==0.0; python_version <= '2.7'
+sklearn
 torch==1.4.0
 torchvision==0.5.0

setup.py

@@ -29,7 +29,7 @@ def most_recent_tag():
 
 setup(
     name="MiMSI",
-    version=most_recent_tag(),
+    version="v.0.4.1",
     description="A deep, multiple instance learning based classifier for identifying Microsatellite Instability from NGS",
     url="https://github.com/mskcc/mimsi",
     author="John Ziegler",