Class refactor (#2)

* beginning to refractor classes for better OO design

* Refactoring class structure. Now have something semi-working. Need to add more tests and extend functionality.

* Adding more test cases. Fixed many bugs. Class refactoring is mostly done and in a good state.

* changes to travis

* travis

* travis

* travis

* travis

* travis

* travis

* removing dependency import

* missed other dependency import

* Added cycle detection test.

Author: Landon Clipp

.travis.yml

@@ -1,5 +1,16 @@
-install: true
 sudo: required
+language: python
+python:
+    - "3.5"
+install: 
+    - pip install pyyaml
+    - pip install pytest
+    - pip install setuptools
+    - export PYTHONUSERBASE="${HOME}"
+    - export PYTHONPATH="$PYTHONPATH:/home/travis/.local/lib/python2.7/site-packages"
+    - python --version
+    - sudo python setup.py install --user
+    - python -c "import sys; print( sys.path )"
 script: 
-    - ./install.sh
+    - pytest ./tests
 

batch4py/__init__.py

@@ -1,5 +1,7 @@
-from .dependency import Dependency
-from .jobchain import JobChain
-from .job import Job
-
+from . import constants
+import yaml
+with open( constants.CONFIG_PATH, 'r' ) as f:
+    constants.CONFIG = yaml.load(f)
 
+from .job import Job
+from .jobchain import JobChain

batch4py/config.yml

@@ -1,11 +1,14 @@
 # This file describes the semantics used for various batch schedulers.
 
 torque:
-    sys_exe:    qsub
+    exe:        qsub
+    resource:   '-l'
     nodes:      '-l nodes={}:ppn={}'
-    node_type:  ':{}'
+    ppn:        'ppn={}'
+    node_type:  '{}'
     account:    '-A'
     depend:     '-W depend={}'
+    walltime:   '-l walltime={}'
     delimit:    ':'
     supported_dep: 
         - after

batch4py/constants.py

@@ -4,6 +4,8 @@
 __email__  = '[email protected]'
 
 PBS_DIR = os.path.join( os.path.dirname( __file__ ), 'pbs_files' )
+CONFIG_PATH = os.path.join( os.path.dirname( __file__ ), 'config.yml' )
+CONFIG = None
 
 max_pbs_num = 5000
 '''maximum number of PBS files to store in PBS_DIR'''