Merge branch 'release/3.1.0'

.devcontainer/Dockerfile

@@ -0,0 +1,20 @@
+# [Choice] Python version: 3, 3.9, 3.8, 3.7, 3.6
+ARG VARIANT=3.7
+FROM mcr.microsoft.com/vscode/devcontainers/python:${VARIANT}
+
+# [Option] Install Node.js
+ARG INSTALL_NODE="true"
+ARG NODE_VERSION="lts/*"
+RUN if [ "${INSTALL_NODE}" = "true" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
+
+# [Optional] If your pip requirements rarely change, uncomment this section to add them to the image.
+# COPY requirements.txt /tmp/pip-tmp/
+# RUN pip3 --disable-pip-version-check --no-cache-dir install -r /tmp/pip-tmp/requirements.txt \
+#    && rm -rf /tmp/pip-tmp
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>
+
+# [Optional] Uncomment this line to install global node packages.
+# RUN su vscode -c "source /usr/local/share/nvm/nvm.sh && npm install -g <your-package-here>" 2>&1

.devcontainer/devcontainer.json

@@ -0,0 +1,47 @@
+{
+    "name": "Python 3",
+    "build": {
+        "dockerfile": "Dockerfile",
+        "context": "..",
+        "args": {
+            // Update 'VARIANT' to pick a Python version: 3, 3.6, 3.7, 3.8, 3.9
+            "VARIANT": "3.7",
+            // Options
+            "INSTALL_NODE": "false",
+            "NODE_VERSION": "lts/*"
+        }
+    },
+    "containerEnv": {
+        "GITHUB_TOKEN": "${localEnv:GITHUB_TOKEN}",
+        "GITHUB_USER": "${localEnv:GITHUB_USER}"
+    },
+    "workspaceFolder": "/nlp-qrmine",
+    "workspaceMount": "src=nlp-qrmine,dst=/nlp-qrmine,type=volume,volume-driver=local",
+    // Set *default* container specific settings.json values on container create.
+    "settings": {
+        "python.pythonPath": "/usr/local/bin/python",
+        "python.languageServer": "Pylance",
+        "python.linting.enabled": true,
+        "python.linting.pylintEnabled": true,
+        "python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8",
+        "python.formatting.blackPath": "/usr/local/py-utils/bin/black",
+        "python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf",
+        "python.linting.banditPath": "/usr/local/py-utils/bin/bandit",
+        "python.linting.flake8Path": "/usr/local/py-utils/bin/flake8",
+        "python.linting.mypyPath": "/usr/local/py-utils/bin/mypy",
+        "python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle",
+        "python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle",
+        "python.linting.pylintPath": "/usr/local/py-utils/bin/pylint"
+    },
+    // Add the IDs of extensions you want installed when the container is created.
+    "extensions": [
+        "ms-python.python",
+        "ms-python.vscode-pylance"
+    ],
+    // Use 'forwardPorts' to make a list of ports inside the container available locally.
+    // "forwardPorts": [],
+    // Use 'postCreateCommand' to run commands after the container is created.
+    "postCreateCommand": "pip3 install --user -r requirements.txt -r dev-requirements.txt",
+    // Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+    // "remoteUser": "vscode"
+}

.github/config.yml

@@ -0,0 +1,25 @@
+# Configurations for todo: https://probot.github.io/apps/todo/
+# Automatically add issues from @todo with @body
+# /**
+#  * @todo What needs to be done
+#  * @body How to do it.
+# */
+
+# https://github.com/behaviorbot/welcome
+newIssueWelcomeComment: >
+  Thank you for raising this issue. We will try and get back to you as soon as possible.
+
+  Be sure to star ✨ the repository for a priority response!
+
+  Please make sure you have given us as much context as possible.
+
+
+newPRWelcomeComment: >
+  Thank you for submitting a pull request.
+
+  Please make sure you have followed our contributing guidelines in CONTRIBUTING.md. We will review it as soon as possible.
+
+  Be sure to star ✨ the repository.
+
+firstPRMergeComment: >
+  Congrats on merging your first pull request! 🎉🎉🎉

.github/dependabot.yml

@@ -0,0 +1,12 @@
+version: 2
+updates:
+  - package-ecosystem: pip
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    # open-pull-requests-limit: 10
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/bump.yml

@@ -0,0 +1,27 @@
+name: Generate changelog
+
+on:
+  push:
+    branches:
+      - "release/**"
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+
+    steps:
+    - name: Checkout Latest Commit
+      uses: actions/checkout@v2
+
+    - name: Generate changelog
+      uses: charmixer/auto-changelog-action@v1
+      with:
+        token: ${{ secrets.github_token }}
+
+    - name: Commit changes
+      uses: EndBug/add-and-commit@v7
+      with:
+        default_author: github_actions
+        add: '*.md'

.github/workflows/docs.yml

@@ -0,0 +1,29 @@
+name: Generate and publish gh-pages
+# https://docs.github.com/en/actions/guides/building-and-testing-python
+# https://packaging.python.org/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+    - uses: actions/checkout@v2.3.4
+    - name: Set up Python
+      uses: actions/setup-python@v2.2.2
+      with:
+        python-version: '3.8'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt -r dev-requirements.txt
+    - name: Create docs
+      run: |
+        make -C docs/ html
+    - name: Deploy Docs 🚀
+      uses: JamesIves/github-pages-deploy-action@4.1.5
+      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

@@ -0,0 +1,30 @@
+name: Upload Python Package to PyPi
+# https://docs.github.com/en/actions/guides/building-and-testing-python
+# https://packaging.python.org/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    steps:
+    - uses: actions/checkout@v2.3.4
+    - name: Set up Python
+      uses: actions/setup-python@v2.2.2
+      with:
+        python-version: '3.8'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r dev-requirements.txt
+    - name: Build and publish
+      run: |
+        python setup.py bdist_wheel
+    - name: Publish distribution 📦 to PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/pytest.yml

@@ -19,15 +19,15 @@ jobs:
         python-version: [3.7]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v2.3.4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v2.2.2
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
+        pip install -r dev-requirements.txt -r requirements.txt
     - name: Test with pytest
       run: |
         pytest

.github/workflows/tox.yml

@@ -12,19 +12,18 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.7]
+        python-version: [3.8]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v2.3.4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v2.2.2
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install tox
+        pip install -r dev-requirements.txt -r requirements.txt
     - name: Test with tox
       run: |
         tox

.readthedocs.yml

@@ -0,0 +1,22 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+
+python:
+  version: 3.8
+  install:
+    - requirements: docs/requirements.txt

AUTHORS.md

@@ -0,0 +1,3 @@
+# Contributors
+
+* Bell Eapen <github@gulfdoctor.net>

CHANGELOG.md

@@ -0,0 +1,42 @@
+# Changelog
+
+## [Unreleased](https://github.com/dermatologist/pyomop/tree/HEAD)
+
+[Full Changelog](https://github.com/dermatologist/pyomop/compare/3.0.0...HEAD)
+
+**Closed issues:**
+
+- Import directly \(no need for conditional\) when `python_requires = >= 3.8` [\#12](https://github.com/dermatologist/pyomop/issues/12)
+- ", [\#11](https://github.com/dermatologist/pyomop/issues/11)
+
+## [3.0.0](https://github.com/dermatologist/pyomop/tree/3.0.0) (2020-10-23)
+
+[Full Changelog](https://github.com/dermatologist/pyomop/compare/2.0.0...3.0.0)
+
+## [2.0.0](https://github.com/dermatologist/pyomop/tree/2.0.0) (2020-06-27)
+
+[Full Changelog](https://github.com/dermatologist/pyomop/compare/1.2.0...2.0.0)
+
+## [1.2.0](https://github.com/dermatologist/pyomop/tree/1.2.0) (2020-05-23)
+
+[Full Changelog](https://github.com/dermatologist/pyomop/compare/1.1.1...1.2.0)
+
+## [1.1.1](https://github.com/dermatologist/pyomop/tree/1.1.1) (2020-05-03)
+
+[Full Changelog](https://github.com/dermatologist/pyomop/compare/1.1.0...1.1.1)
+
+## [1.1.0](https://github.com/dermatologist/pyomop/tree/1.1.0) (2020-05-03)
+
+[Full Changelog](https://github.com/dermatologist/pyomop/compare/1.0.0...1.1.0)
+
+## [1.0.0](https://github.com/dermatologist/pyomop/tree/1.0.0) (2020-05-03)
+
+[Full Changelog](https://github.com/dermatologist/pyomop/compare/0.1.0...1.0.0)
+
+## [0.1.0](https://github.com/dermatologist/pyomop/tree/0.1.0) (2020-05-03)
+
+[Full Changelog](https://github.com/dermatologist/pyomop/compare/c647331d8bcb13f0353f85a49ed552294631fee3...0.1.0)
+
+
+
+\* *This Changelog was automatically generated by [github_changelog_generator](https://github.com/github-changelog-generator/github-changelog-generator)*

README.md

@@ -1,17 +1,15 @@
-# pyomop
+# :notebook: pyomop
 
-OMOP CDM utils. This repo may be similar to [@jbadger3's](https://github.com/jbadger3) [inspectomop](https://github.com/jbadger3/inspectomop), but this is not a fork.
+[![forthebadge made-with-python](http://ForTheBadge.com/images/badges/made-with-python.svg)](https://www.python.org/)
+[![PyPI download total](https://img.shields.io/pypi/dm/pyomop.svg)](https://pypi.python.org/pypi/pyomop/)
+[![Build](https://github.com/dermatologist/pyomop/workflows/Python%20Test/badge.svg)](https://nuchange.ca)
+
+* *Inspired by [@jbadger3's](https://github.com/jbadger3) [inspectomop](https://github.com/jbadger3/inspectomop)*
 
 ## Description
 
 The [OHSDI](https://www.ohdsi.org/) OMOP Common Data Model allows for the systematic analysis of healthcare observational databases. This is a python library to use the CDM v6 compliant databases using SQLAlchemy as the ORM. **pyomop** also supports converting query results to a pandas dataframe (see below) for use in machine learning pipelines. See some useful [SQL Queries here.](https://github.com/OHDSI/QueryLibrary)
 
-### Support
-* Postgres
-* MySQL
-* SqLite
-* More to follow..
-
 ## Installation
 
 ```
@@ -74,7 +72,27 @@ 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)**
+
+**Use the same functions in [.NET](https://github.com/dermatologist/omopcdm-dot-net) and [Golang](https://github.com/E-Health/gocdm)!**
+
+### Support
+* Postgres
+* MySQL
+* SqLite
+* More to follow..
+
 
 ## Contributors
 
-* [Bell Eapen](https://nuchange.ca)
+* [Bell Eapen](https://nuchange.ca) | [![Twitter Follow](https://img.shields.io/twitter/follow/beapen?style=social)](https://twitter.com/beapen)
+* PRs welcome. See CONTRIBUTING.md

dev-requirements.in

@@ -0,0 +1,10 @@
+# dev-requirements.in
+-c requirements.txt
+pytest-cov
+pytest
+recommonmark
+sphinx>=3.2.1
+setuptools
+setuptools_scm
+wheel
+tox