Merge 272651c into 08b3a8d

.gitignore

@@ -67,6 +67,9 @@ docs/_build/
 # PyBuilder
 target/
 
+# PyCharm
+.idea/
+
 # Jupyter Notebook
 .ipynb_checkpoints
 

.travis.yml

@@ -2,35 +2,15 @@ language: python
 python: 
   - '2.7'
 
-# commands to set up conda
 before_install:
-  - sudo apt-get update -qq
-  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
-    else
-      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    fi
-  - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - hash -r
-  - conda config --set always_yes yes --set changeps1 no
-  - conda update -q conda
-  # useful for debugging any issues with conda
-  - conda info -a
+- sudo apt-get update -qq
+- pip install toil[all]
+- pip install . --process-dependency-links
+- pip install -r dev-requirements.txt
 
-# commands to set up environment, install dependencies
-install:
-  - deps='pip pandas'
-  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION $deps
-  - source activate test-environment
-  - pip install python-coveralls
-  - pip install .
-  - pip install -r dev-requirements.txt
-
-# commands to run tests
 script:
   - python setup.py test
   - flake8 --select=E121,E123,E126,E226,E24,E704,W503,W504 --ignore=E501 synorchestrator/
 
 after_success:
-  - coveralls
+  - coveralls

dev-requirements.txt

@@ -2,4 +2,5 @@ flake8
 pytest
 pytest-cov
 pytest-runner
-mock
+mock
+python-coveralls

requirements.txt

@@ -1,7 +1,6 @@
-schema_salad
-ruamel.yaml
-cwltool
-subprocess32
 wes-service
 synapseclient
-
+pandas
+IPython==5.8.0
+future
+bravado

setup.cfg

@@ -2,4 +2,4 @@
 test = pytest
 
 [tool:pytest]
-addopts = --cov synorchestrator
+addopts = --cov synorchestrator

setup.py

@@ -1,7 +1,3 @@
-import os
-import sys
-import shutil
-
 # First, we try to use setuptools. If it's not available locally,
 # we fall back on ez_setup.
 try:

synorchestrator/__main__.py

@@ -1,27 +1,27 @@
-#!/usr/bin/env/python
+#!/usr/bin/env python
 
 import sys
-import pkg_resources
 import argparse
-import synorchestrator
+import pkg_resources  # part of setuptools
+import logging
+from synorchestrator.orchestrator import monitor
 
+logging.basicConfig(level=logging.INFO)
 
-def main(argv=sys.argv[1:]):
-
-    parser = argparse.ArgumentParser(
-        description='Synapse Workflow Orchestrator'
-    )
 
-    exgroup = parser.add_mutually_exclusive_group()
-    exgroup.add_argument("--version", action="store_true", default=False)
+def main(argv=sys.argv[1:]):
 
+    parser = argparse.ArgumentParser(description='Synapse Workflow Orchestrator')
+    parser.add_argument("--version", action="store_true", default=False)
     args = parser.parse_args(argv)
 
     if args.version:
         pkg = pkg_resources.require('synapse-orchestrator')
-        print u"%s %s" % (sys.argv[0], pkg[0].version)
+        print(u"%s %s" % (sys.argv[0], pkg[0].version))
         exit(0)
 
+    monitor()
+
 
 if __name__ == '__main__':
-    sys.exit(main(sys.argv[1:]))
+    main(sys.argv[1:])