Merge pull request #2 from OHDSI/dev

Dev

.devcontainer/devcontainer.json

@@ -0,0 +1,33 @@
+{
+    "name": "Python 3.11 & Jupyter with Ruff",
+    "image": "mcr.microsoft.com/vscode/devcontainers/python:3.11",
+    "settings": {
+        "terminal.integrated.shell.linux": "/bin/bash",
+        "python.pythonPath": "/usr/local/bin/python",
+        "python.linting.enabled": true,
+        // Disable other linters to ensure ruff is the primary linter
+        "python.linting.pylintEnabled": false,
+        "python.linting.flake8Enabled": false,
+        // Configure ruff settings
+        "python.linting.ruffEnabled": true,
+        "python.linting.ruffPath": "/usr/local/bin/ruff",
+        "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.sortImports.path": "/usr/local/py-utils/bin/isort",
+        "[python]": {
+            "editor.codeActionsOnSave": {
+                "source.organizeImports": true
+            }
+        }
+    },
+    "extensions": [
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "ms-toolsai.jupyter",
+        "charliermarsh.ruff"
+    ],
+    "forwardPorts": [8888],
+    "postCreateCommand": "pip install -r requirements.txt && pip install ruff",
+    "remoteUser": "vscode"
+}

.github/CODEOWNERS

@@ -1,8 +1,8 @@
-# Code owners file.
-# This file controls who is tagged for review for any given pull request.
-#
-# For syntax see:
-# https://help.github.com/en/github/creating-cloning-and-archiving-repositories/about-code-owners#codeowners-syntax
-#
-# default owners for changes in this repo
+# Code owners file.
+# This file controls who is tagged for review for any given pull request.
+#
+# For syntax see:
+# https://help.github.com/en/github/creating-cloning-and-archiving-repositories/about-code-owners#codeowners-syntax
+#
+# default owners for changes in this repo
 *     @haydenbspence

.github/CONTRIBUTING.md

@@ -0,0 +1,49 @@
+# Contributing to HESTIA
+
+We welcome contributions to HESTIA! Whether you're interested in fixing bugs, adding new features, or helping with documentation, your contributions are greatly appreciated.
+
+## Code of Conduct
+This project and everyone participating in it is governed by OHDSI's [Community Guidelines](https://forums.ohdsi.org/faq). By participating, you are expected to adhere to these guidelines.
+
+## How to Contribute
+There are many ways to contribute to the OHDSI project, and we value all forms of contributions. Here are some ways you can help:
+
+### Reporting Issues
+- Before submitting an issue, please check the issue tracker to avoid duplicates.
+- Use the issue templates to provide as much information as possible.
+- Describe the issue clearly and provide steps to reproduce if possible.
+
+### Submitting Changes
+1. **Fork the Repository**: Start by forking the repository and cloning your fork to your local machine.
+2. **Create a Branch**: Create a branch in your fork for your changes. Use a clear and descriptive name for your branch.
+3. **Make Your Changes**: Make the necessary changes. Keep your changes as focused as possible; if you find multiple issues or improvements, consider submitting them as separate pull requests.
+4. **Commit Your Changes**: Commit your changes using the [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0-beta.2/) format. This standardizes commit messages and facilitates the automatic generation of changelogs.
+5. **Push to Your Fork**: Push your changes to your fork on GitHub.
+6. **Submit a Pull Request (PR)**: Go to the original OHDSI repository, and you should see a prompt to submit a pull request from your new branch. Provide as much information as possible in the pull request template.
+
+## Coding Standards
+
+### OHDSI Alignment
+- Implementations should be guided by the [Book of OHDSI](https://ohdsi.github.io/TheBookOfOhdsi/) and [OMOP Common Data Model v5.4](https://ohdsi.github.io/CommonDataModel/index.html)
+
+### Pull Request Guidelines
+- Ensure your code adheres to the project's coding standards.
+- Write tests for your changes when applicable.
+- Document your changes in the project's documentation if your changes introduce new features or changes in behavior.
+- Pull requests undergo a review process, so be open to feedback and be prepared to make adjustments.
+- The project uses [release-please](https://github.com/googleapis/release-please) to automate the generation of changelogs based on commit messages. Ensure your commit messages are clear and follow the Conventional Commits format to aid in this process.
+
+### Documentation
+Improving documentation, tutorials, or examples is a valuable way to contribute. You can submit changes to documentation the same way as code changes through pull requests.
+
+## Setting Up Your Development Environment
+
+A devcontainter.json is included for VSCode / Docker users. This is the easiest way to get started on a local machine.
+
+## Community
+Please [Introduce Yourself](https://forums.ohdsi.org/t/welcome-to-ohdsi-please-introduce-yourself/704/932) and join the community! [Join the OHDSI community forums](https://forums.ohdsi.org/) and to discuss with other contributors and the OHDSI team. This is a great place to ask questions, propose ideas, and connect with the community.
+
+## Acknowledgements
+Your contributions are acknowledged in the project's documentation and releases. We value your efforts to improve health data science and informatics through open-source collaboration.
+
+Thank you for your interest in contributing to the OHDSI Open Source Project! Together, we can make a significant impact on healthcare research and outcomes.

.github/SECURITY.md

@@ -0,0 +1 @@
+To report a security vulnerability to Hestia, please DO NOT post it as a GitHub Issue or othewise public forum. Email [email protected] directly.

.github/workflows/release-please.yml

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+on:
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: write
+  pull-requests: write
+
+name: release-please
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: google-github-actions/release-please-action@v4
+        with:
+          # this assumes that you have created a personal access token
+          # (PAT) and configured it as a GitHub action secret named
+          # `MY_RELEASE_PLEASE_TOKEN` (this secret name is not important).
+          token: ${{ secrets.MY_RELEASE_PLEASE_TOKEN }}
+          # this is a built-in strategy in release-please, see "Action Inputs"
+          # for more options
+          release-type: python

.gitignore

@@ -0,0 +1,163 @@
+
+.ruff_cache
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/