Merge branch 'master' of github.com:KarrLab/datanator

.circleci/config.yml

@@ -17,13 +17,13 @@ jobs:
       # Python 3 installation tasks
       - run:
           name: Install pkg_utils (Python 3)
-          command: pip3 install -U git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils
+          command: python3 -m pip install -U git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils
       - run:
           name: Install karr_lab_build_utils (Python 3)
           command: |
-            pip3 install -U git+https://github.com/KarrLab/sphinxcontrib-googleanalytics.git#egg=sphinxcontrib_googleanalytics
-            pip3 install -U git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils[all]
-            pip3 install -U git+https://github.com/KarrLab/karr_lab_build_utils.git#egg=karr_lab_build_utils[all]
+            python3 -m pip install -U git+https://github.com/KarrLab/sphinxcontrib-googleanalytics.git#egg=sphinxcontrib_googleanalytics
+            python3 -m pip install -U git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils[all]
+            python3 -m pip install -U git+https://github.com/KarrLab/karr_lab_build_utils.git#egg=karr_lab_build_utils[all]
       - run:
           name: Install package configuration files including credentials
           command: karr_lab_build_utils3 download-install-package-config-files
@@ -33,23 +33,25 @@ jobs:
             if [[ -f .circleci/requirements.txt ]]; then
               while IFS="" read -r line || [ -n "$line" ]; do
                 if [[ ! -z "$line" ]] && [[ ! "$line" =~ ^# ]]; then
-                  pip3 install -U "$line"
+                  python3 -m pip install -U "$line"
                 fi
               done < .circleci/requirements.txt
             fi
       - run:
           name: Install package (Python 3)
-          command: pip3 install -U -e .
+          command: python3 -m pip install -U -e .
 
       # Save packages to cache
       - save_cache:
           key: v4-{{ arch }}-{{ .Branch }}-{{ checksum "/etc/docker-image-tag" }}-{{ checksum "requirements.txt" }}
           paths:
-            - /usr/local/lib/python3.6/site-packages
+            - /usr/local/lib/python3.7/site-packages
 
       # Test code
       - run:
           name: Test code
+          environment:
+            PYTHONFAULTHANDLER: 1
           command: |
             set +e
 

requirements.txt

@@ -5,15 +5,15 @@ bioservices >= 1.5.0
 cement >= 3.0.0
 configobj
 ete3
+flask_migrate
 jxmlease
 marshmallow_sqlalchemy
 numpy
 obj_tables
 openbabel
 openpyxl
 pandas
-pint >= 0.9
-pronto
+pint >= 0.10
 psycopg2_binary
 pubchempy
 python_dateutil
@@ -33,7 +33,6 @@ xmltodict
 ftputil
 elasticsearch
 genson
-quilt
 jsonpickle
 datanator_query_python
 karr_lab_aws_manager

tests/data_source/test_sabio_rk.py

@@ -20,15 +20,13 @@
 import mock
 import numpy
 import os
-import quilt
 import scipy.constants
 import shutil
 import sqlalchemy
 import sys
 import tempfile
 import unittest
 import wc_utils.config
-import wc_utils.quilt
 
 warning_util.disable_warnings()
 

tests/requirements.txt

@@ -2,4 +2,3 @@ attrdict
 capturer
 flask_testing
 mock
-quilt