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Merge branch 'master' of github.com:KarrLab/datanator
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lzy7071 committed Jan 10, 2020
2 parents dd93b5e + faee98d commit 19ef862
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Showing 4 changed files with 11 additions and 13 deletions.
16 changes: 9 additions & 7 deletions .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
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5 changes: 2 additions & 3 deletions requirements.txt
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Expand Up @@ -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
Expand All @@ -33,7 +33,6 @@ xmltodict
ftputil
elasticsearch
genson
quilt
jsonpickle
datanator_query_python
karr_lab_aws_manager
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2 changes: 0 additions & 2 deletions tests/data_source/test_sabio_rk.py
Original file line number Diff line number Diff line change
Expand Up @@ -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()

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1 change: 0 additions & 1 deletion tests/requirements.txt
Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,3 @@ attrdict
capturer
flask_testing
mock
quilt

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