Merge branch 'release/4.0.0'

.devcontainer/Dockerfile

@@ -1,5 +1,5 @@
 # [Choice] Python version: 3, 3.9, 3.8, 3.7, 3.6
-ARG VARIANT=3.7
+ARG VARIANT=3.10
 FROM mcr.microsoft.com/vscode/devcontainers/python:${VARIANT}
 
 # [Option] Install Node.js

.devcontainer/devcontainer.json

@@ -5,7 +5,7 @@
         "context": "..",
         "args": {
             // Update 'VARIANT' to pick a Python version: 3, 3.6, 3.7, 3.8, 3.9
-            "VARIANT": "3.7",
+            "VARIANT": "3.10",
             // Options
             "INSTALL_NODE": "false",
             "NODE_VERSION": "lts/*"

.github/workflows/docs.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Set up Python
       uses: actions/[email protected]
       with:
-        python-version: '3.8'
+        python-version: '3.10.13'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -24,7 +24,7 @@ jobs:
         make -C docs/ html
         cp docs/_config.yml docs/_build/html/_config.yml
     - name: Deploy Docs 🚀
-      uses: JamesIves/github-pages-deploy-action@4.1.5
+      uses: JamesIves/github-pages-deploy-action@v4
       with:
         branch: gh-pages # The branch the action should deploy to.
         folder: docs/_build/html # The folder the action should deploy.

.github/workflows/publish.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Set up Python
       uses: actions/[email protected]
       with:
-        python-version: '3.8'
+        python-version: '3.10.13'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/pytest.yml

@@ -13,10 +13,11 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.7]
+        python-version: [3.10.13]
 
     steps:
     - uses: actions/checkout@v3

.github/workflows/tox.yml

@@ -9,10 +9,11 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.8]
+        python-version: [3.10.13]
 
     steps:
     - uses: actions/checkout@v3

.readthedocs.yml

@@ -17,6 +17,6 @@ formats:
   - pdf
 
 python:
-  version: 3.8
+  version: 3.10
   install:
     - requirements: docs/requirements.txt

CHANGELOG.md

@@ -1,5 +1,17 @@
 # Changelog
 
+## [Unreleased](https://github.com/dermatologist/pyomop/tree/HEAD)
+
+[Full Changelog](https://github.com/dermatologist/pyomop/compare/3.2.0...HEAD)
+
+**Closed issues:**
+
+- SQLAlchemy 1.4 raises error [\#6](https://github.com/dermatologist/pyomop/issues/6)
+
+## [3.2.0](https://github.com/dermatologist/pyomop/tree/3.2.0) (2023-01-20)
+
+[Full Changelog](https://github.com/dermatologist/pyomop/compare/3.1.0...3.2.0)
+
 ## [3.1.0](https://github.com/dermatologist/pyomop/tree/3.1.0) (2021-09-17)
 
 [Full Changelog](https://github.com/dermatologist/pyomop/compare/3.0.0...3.1.0)

README.md

@@ -27,7 +27,67 @@ pip install pyomop
 pip install -e .
 ```
 
-## Usage
+## Usage >= 4.0.0 (Async)
+```
+from pyomop import CdmEngineFactory, CdmVocabulary, CdmVector, Cohort, Vocabulary, metadata
+from sqlalchemy.future import select
+import datetime
+import asyncio
+
+cdm = CdmEngineFactory()  # Creates SQLite database by default
+# Postgres example (db='mysql' also supported)
+# cdm = CdmEngineFactory(db='pgsql', host='', port=5432,
+#                       user='', pw='',
+#                       name='', schema='cdm6')
+
+engine = cdm.engine
+# Create Tables if required
+asyncio.run(cdm.init_models(metadata))
+# Create vocabulary if required
+vocab = CdmVocabulary(cdm)
+# vocab.create_vocab('/path/to/csv/files')  # Uncomment to load vocabulary csv files
+
+# Add a cohort
+async with cdm.session() as session:
+    async with session.begin():
+        session.add(Cohort(cohort_definition_id=2, subject_id=100,
+            cohort_end_date=datetime.datetime.now(),
+            cohort_start_date=datetime.datetime.now()))
+    await session.commit()
+
+# Query the cohort
+stmt = select(Cohort).where(Cohort.subject_id == 100)
+result = await session.execute(stmt)
+for row in result.scalars():
+    print(row)
+    assert row.subject_id == 100
+
+# Query the cohort pattern 2
+cohort = await session.get(Cohort, 1)
+print(cohort)
+assert cohort.subject_id == 100
+
+# Close session
+await session.close()
+await engine.dispose()
+
+# Convert result to a pandas dataframe
+vec = CdmVector()
+vec.result = result
+print(vec.df.dtypes)
+
+# Execute SQL statetements
+result = await vec.sql_df(cdm, 'TEST') # TEST is defined in sqldict.py
+for row in result:
+    print(row)
+
+result = await vec.sql_df(cdm, query='SELECT * from cohort')
+for row in result:
+    print(row)
+
+```
+
+## Usage <=3.2.0
 
 ```
 
@@ -50,7 +110,7 @@ metadata.create_all(engine)
 vocab = CdmVocabulary(cdm)
 # vocab.create_vocab('/path/to/csv/files')  # Uncomment to load vocabulary csv files
 
-# SQLAlchemy as ORM
+# Create a Cohort (SQLAlchemy as ORM)
 session =  cdm.session
 session.add(Cohort(cohort_definition_id=2, subject_id=100,
             cohort_end_date=datetime.datetime.now(),
@@ -82,13 +142,6 @@ print(vec.df.dtypes) # vec.df is a pandas dataframe
 pyomop -help
 ```
 
-## Troubleshoot
-
-* sqlalchemy > 1.4 may not work. See [issue #6](https://github.com/dermatologist/pyomop/issues/6). Please downgrade sqlalchemy untill [issue #6](https://github.com/dermatologist/pyomop/issues/6) is fixed.
-```
-pip install sqlalchemy==1.3.24
-```
-
 ## Other utils
 
 **Want to convert FHIR to pandas data frame? Try [fhiry](https://github.com/dermatologist/fhiry)**

dev-requirements.txt

@@ -1,6 +1,6 @@
 #
-# This file is autogenerated by pip-compile with python 3.8
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.10
+# by the following command:
 #
 #    pip-compile dev-requirements.in
 #
@@ -10,16 +10,18 @@ attrs==21.2.0
     # via pytest
 babel==2.9.1
     # via sphinx
-backports.entry-points-selectable==1.1.0
+backports-entry-points-selectable==1.1.0
     # via virtualenv
-certifi==2021.5.30
+certifi==2022.12.7
     # via requests
 charset-normalizer==2.0.6
     # via requests
 commonmark==0.9.1
     # via recommonmark
 coverage[toml]==5.5
-    # via pytest-cov
+    # via
+    #   coverage
+    #   pytest-cov
 distlib==0.3.2
     # via virtualenv
 docutils==0.17.1
@@ -66,7 +68,7 @@ pytest==6.2.5
     #   pytest-cov
 pytest-cov==3.0.0
     # via -r dev-requirements.in
-pytz==2021.1
+pytz==2023.3.post1
     # via
     #   -c requirements.txt
     #   babel

docs/index.md

@@ -1,18 +1,7 @@
 # pyomop
 
 OMOP CDM utils in Python
-
-
-## Note
-
-> This is the main page of your project's [Sphinx] documentation. It is
-> formatted in [Markdown]. Add additional pages by creating md-files in
-> `docs` or rst-files (formated in [reStructuredText]) and adding links to
-> them in the `Contents` section below.
->
-> Please check [Sphinx], [recommonmark] and [autostructify] for more information
-> about how to document your project and how to configure your preferences.
-
+*[by Bell Eapen](https://nuchange.ca)*
 
 ## Contents
 

requirements.txt

@@ -1,28 +1,28 @@
 #
-# This file is autogenerated by pip-compile with python 3.8
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.10
+# by the following command:
 #
 #    pip-compile
 #
-click==8.0.3
+aiosqlite==0.19.0
     # via pyomop (setup.py)
-inflect==5.3.0
-    # via sqlacodegen
-numpy==1.21.4
-    # via pandas
-pandas==1.3.5
+click==8.1.7
     # via pyomop (setup.py)
-psycopg2-binary==2.9.3
+greenlet==3.0.1
+    # via sqlalchemy
+numpy==1.26.2
+    # via pandas
+pandas==2.1.3
     # via pyomop (setup.py)
 python-dateutil==2.8.2
     # via pandas
-pytz==2021.1
+pytz==2023.3.post1
     # via pandas
 six==1.16.0
     # via python-dateutil
-sqlacodegen==2.3.0
+sqlalchemy==2.0.23
     # via pyomop (setup.py)
-sqlalchemy==1.3.24
-    # via
-    #   pyomop (setup.py)
-    #   sqlacodegen
+typing-extensions==4.8.0
+    # via sqlalchemy
+tzdata==2023.3
+    # via pandas

setup.cfg

@@ -22,7 +22,7 @@ classifiers =
     Development Status :: 4 - Beta
     Operating System :: OS Independent
     Programming Language :: Python
-    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.10
     Topic :: Scientific/Engineering :: Information Analysis
 
 [options]
@@ -35,11 +35,10 @@ package_dir =
 # Add here dependencies of your project (semicolon/line-separated), e.g.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    sqlacodegen
-    sqlalchemy<1.4
+    sqlalchemy>=1.4
     click
     pandas
-    psycopg2-binary
+    aiosqlite
 # 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/cdm6_tables.py

@@ -19,7 +19,7 @@
 
 # coding: utf-8
 from sqlalchemy import BigInteger, Column, Integer, Numeric, String, Text
-from sqlalchemy.ext.declarative import declarative_base
+from sqlalchemy.orm import declarative_base
 
 Base = declarative_base()
 metadata = Base.metadata