Finish 2.0.0

CONTRIBUTING.md

@@ -0,0 +1,70 @@
+# How to contribute
+
+## Please note:
+
+* (Optional) We adopt [Git Flow](https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow). Most feature branches are pushed to the repository and deleted when merged to *develop* branch.
+* (**Important**): Submit pull requests to the *develop* branch or *feature/* branches
+* Use *GitHub Issues* for feature requests and bug reports. Include as much information as possible while reporting bugs.  
+
+
+## Contributing (Step-by-step)
+
+1. [Fork the repo](http://help.github.com/fork-a-repo) and clone it to your local computer, and set up the upstream remote:
+
+        git clone https://github.com/YourGithubUsername/pyomop.git
+        cd pyomop
+        git remote add upstream https://github.com/dermatologist/pyomop.git
+
+2. Checkout out a new local branch based on your master and update it to the latest (TRUNK-123 is the branch name, You can name it whatever you want. Try to give it a meaningful name. If you are fixing an issue, please include the issue #).
+
+        git checkout -b BRANCH-123 develop
+        git clean -df
+        git pull --rebase upstream develop
+
+ > Please keep your code clean. If you find another bug, you want to fix while being in a new branch, please fix it in a separated branch instead.
+
+3. Push the branch to your fork. Treat it as a backup.
+
+        git push origin BRANCH-123
+
+4. Code
+
+  * Adhere to common conventions you see in the existing code.
+  * Include tests as much as possible, and ensure they pass.
+
+5. Commit to your branch
+
+         git commit -m "BRANCH-123: Put change summary here (can be a ticket title)"
+
+  **NEVER leave the commit message blank!** Provide a detailed, clear, and complete description of your commit!
+
+6. Update your branch to the latest code.
+
+        git pull --rebase upstream develop
+
+7. **Important** If you have made many commits, please squash them into atomic units of work. (Most Git GUIs such as sourcetree and smartgit offer a squash option)
+
+       
+        git checkout develop
+        git pull --rebase upstream develop
+        git merge --squash BRANCH-123
+        git commit -m "fix: 123"
+
+  Push changes to your fork:
+
+        git push
+
+8. Issue a Pull Request
+
+  In order to make a pull request:
+  * Click "Pull Request".
+  * Choose the develop branch
+  * Click 'Create pull request'
+  * Fill in some details about your potential patch including a meaningful title.
+  * Click "Create pull request".
+
+  Thanks for that -- we'll get to your pull request ASAP. We love pull requests!
+
+## Feedback
+
+   If you need to contact me, see my contact details on my profile page.

README.md

@@ -22,8 +22,7 @@ pip install pyomop
 ## Usage
 
 ```
-from pyomop import CdmEngineFactory
-from pyomop import metadata
+from pyomop import CdmEngineFactory, CdmVocabulary, Cohort, Vocabulary, metadata
 from sqlalchemy.sql import select
 import datetime
 
@@ -34,10 +33,9 @@ engine = cdm.engine
 metadata.create_all(engine)
 # Create vocabulary
 vocab = CdmVocabulary(cdm)
-vocab.create_vocab('/path/to/csv/files')
+# vocab.create_vocab('/path/to/csv/files')  # Uncomment to load vocabulary csv files
 
 # SQLAlchemy as ORM
-Cohort = cdm.base.cohort
 session =  cdm.session
 session.add(Cohort(cohort_definition_id=2, subject_id=100, 
             cohort_end_date=datetime.datetime.now(), 
@@ -48,6 +46,9 @@ s = select([Cohort])
 result = session.execute(s)
 for row in result:
     print(row)
+result.close()
+for v in session.query(Vocabulary).order_by(Vocabulary.vocabulary_name):
+    print(v.vocabulary_name)
 
 ```
 

notes/notes.md

@@ -1,3 +1,8 @@
+## Use sqlacodegen
+pip install sqlacodegen
+sqlacodegen sqlite:///database.db
+
+
 ## Create an _id primary key field in the autogenerated script
 
 Replace metadata, with

requirements.txt

@@ -18,4 +18,6 @@
 sqlacodegen
 sqlalchemy
 click
-pandas
+pandas
+pytest
+psycopg2

setup.cfg

@@ -34,7 +34,7 @@ package_dir =
 # DON'T CHANGE THE FOLLOWING LINE! IT WILL BE UPDATED BY PYSCAFFOLD!
 setup_requires = pyscaffold>=3.2a0,<3.3a0
 # Add here dependencies of your project (semicolon/line-separated), e.g.
-install_requires = sqlalchemy; click
+install_requires = sqlalchemy; click; pandas; psycopg2
 # The usage of test_requires is discouraged, see `Dependency Management` docs
 # tests_require = pytest; pytest-cov
 # Require a specific Python version, e.g. Python 2.7 or >= 3.4

src/pyomop/__init__.py

@@ -5,6 +5,51 @@
 from .cdm6_tables import metadata
 from .vocabulary import CdmVocabulary
 
+from .cdm6_tables import AttributeDefinition
+from .cdm6_tables import CareSite
+from .cdm6_tables import CdmSource
+from .cdm6_tables import Cohort
+from .cdm6_tables import CohortAttribute
+from .cdm6_tables import CohortDefinition
+from .cdm6_tables import Concept
+from .cdm6_tables import ConceptAncestor
+from .cdm6_tables import ConceptClass
+from .cdm6_tables import ConceptRelationship
+from .cdm6_tables import ConceptSynonym
+from .cdm6_tables import ConditionEra
+from .cdm6_tables import ConditionOccurrence
+from .cdm6_tables import Death
+from .cdm6_tables import DeviceCost
+
+from .cdm6_tables import DeviceExposure
+from .cdm6_tables import Domain
+from .cdm6_tables import DoseEra
+from .cdm6_tables import DrugCost
+from .cdm6_tables import DrugEra
+
+from .cdm6_tables import DrugExposure
+from .cdm6_tables import DrugStrength
+from .cdm6_tables import FactRelationship
+from .cdm6_tables import Location
+from .cdm6_tables import Measurement
+
+from .cdm6_tables import Note
+from .cdm6_tables import Observation
+from .cdm6_tables import ObservationPeriod
+from .cdm6_tables import PayerPlanPeriod
+from .cdm6_tables import Person
+
+from .cdm6_tables import ProcedureCost
+from .cdm6_tables import ProcedureOccurrence
+from .cdm6_tables import Provider
+from .cdm6_tables import Relationship
+from .cdm6_tables import SourceToConceptMap
+
+from .cdm6_tables import Speciman
+from .cdm6_tables import VisitCost
+from .cdm6_tables import VisitOccurrence
+from .cdm6_tables import Vocabulary
+
 try:
     # Change here if project is renamed and does not equal the package name
     dist_name = __name__