Merge branch 'release/1.0.0'

README.md

@@ -2,15 +2,15 @@
 
 OMOP CDM utils
 
-
 ## Description
 
-A longer description of your project goes here...
+A python library for using the OMOP Common Data Model.
 
 ## Installation
 
 ```
-pip install pyomop
+pip install https://github.com/dermatologist/pyomop/releases/download/1.0.0/pyomop-1.0.0-py2.py3-none-any.whl
+
 ```
 
 ## Usage
@@ -41,7 +41,3 @@ for row in result:
 
 ```
 
-## Note
-
-This project has been set up using PyScaffold 3.2.3. For details and usage
-information on PyScaffold see https://pyscaffold.org/.

setup.cfg

@@ -64,8 +64,8 @@ testing =
 # And any other entry points, for example:
 # pyscaffold.cli =
 #     awesome = pyscaffoldext.awesome.extension:AwesomeExtension
-[console_scripts]
-pyomop = pyomop.main:main_routine
+console_scripts =
+    pyomop = pyomop.main:main_routine
 
 [test]
 # py.test options when running `python setup.py test`
@@ -78,7 +78,7 @@ extras = True
 # e.g. --cov-report html (or xml) for html/xml output or --junitxml junit.xml
 # in order to write a coverage file that can be read by Jenkins.
 addopts =
-    --cov pyomop --cov-report term-missing
+    #--cov pyomop --cov-report term-missing
     --verbose
 norecursedirs =
     dist

src/pyomop/__init__.py

@@ -1,8 +1,8 @@
 # -*- coding: utf-8 -*-
 from pkg_resources import get_distribution, DistributionNotFound
 
-from engine_factory import CdmEngineFactory
-from cdm6_tables import metadata
+from .engine_factory import CdmEngineFactory
+from .cdm6_tables import metadata
 
 try:
     # Change here if project is renamed and does not equal the package name

tests/test_pyomop.py

@@ -0,0 +1,30 @@
+import pytest
+
+@pytest.fixture
+def pyomop_fixture():
+    from src.pyomop import CdmEngineFactory
+    cdm = CdmEngineFactory()
+    return cdm
+
+@pytest.fixture
+def metadata_fixture():
+    from src.pyomop import metadata
+    return metadata
+
+def test_create_db(pyomop_fixture, metadata_fixture, capsys):
+    import datetime
+    from sqlalchemy.sql import select
+    engine = pyomop_fixture.engine
+    metadata_fixture.create_all(engine)
+    Cohort = pyomop_fixture.base.cohort
+    session =  pyomop_fixture.session
+    session.add(Cohort(cohort_definition_id=2, subject_id=100, 
+            cohort_end_date=datetime.datetime.now(), 
+            cohort_start_date=datetime.datetime.now()))
+    session.commit()
+
+    s = select([Cohort])
+    result = session.execute(s)
+    for row in result:
+        print(row)
+    assert row['subject_id'] == 100