GenomicMedLab · korikuzma · May 12, 2026 · May 11, 2026
@@ -0,0 +1 @@
+* @GenomicMedLab/mci-knowledge-pilot-analysis
@@ -0,0 +1,33 @@
+name: checks
+on: [push, pull_request]
+jobs:
+  lint:
+    name: lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Setup Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.13"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --extra dev
+
+      - name: Check style
+        run: uv run ruff check && uv run ruff format --check
+
+  precommit_hooks:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: j178/prek-action@v1
+        with:
+          extra_args: '--all-files --skip "ruff-format" --skip "ruff-check"'
@@ -0,0 +1,23 @@
+name: Pull Request Has Priority Label
+on:
+  pull_request:
+    types: [opened, labeled, unlabeled, synchronize]
+jobs:
+  pr-priority-label:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    outputs:
+      status: ${{ steps.check-labels.outputs.status }}
+    steps:
+      - id: check-labels
+        uses: mheap/github-action-required-labels@v5
+        with:
+          mode: exactly
+          count: 1
+          labels: "priority:*"
+          use_regex: true
+          add_comment: true
+          message: "PRs require a priority label. Please add one."
+          exit_type: failure
@@ -0,0 +1,144 @@
+# Ignore xlsx temp file
+\~*
+
+# Ignore system files
+.DS_Store
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$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/
+docs/build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# Package/executable/environment management
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+.python-version
+Pipfile.lock
+uv.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# 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/
+
+# allow pytest override with pytest.ini
+pytest.ini
+
+# IDE materials
+.idea/
+.vim/
+*.swp
@@ -0,0 +1,28 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0  # pre-commit-hooks version
+    hooks:
+      - id: detect-aws-credentials
+        args: [ --allow-missing-credentials ]
+  - repo: builtin
+    hooks:
+      - id: trailing-whitespace
+      - id: check-added-large-files
+        args: ['--maxkb=1500']
+      - id: check-case-conflict
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
+      - id: check-json
+      - id: check-toml
+      - id: check-yaml
+      - id: mixed-line-ending
+        args: [ --fix=lf ]
+      - id: check-merge-conflict
+      - id: detect-private-key
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.10  # ruff version
+    hooks:
+      - id: ruff-format
+      - id: ruff-check
+        args: [ --fix, --exit-non-zero-on-fix ]
+minimum_prek_version: 0.2.23
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Wagner Laboratory at the Institute for Genomic Medicine
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
@@ -1,5 +1,33 @@
 # Molecular Characterization Initiative (MCI) Knowledge Pilot
 
+[![Actions status](https://github.com/genomicmedlab/mci_knowledge_pilot/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/mci_knowledge_pilot/actions/checks.yaml)
+
 This repository contains a pilot effort to transform semi-structured somatic cancer variant classification knowledge into computable clinical assertions using [GA4GH Genomic Knowledge Standards (GKS)](https://www.ga4gh.org/work_stream/genomic-knowledge-standards/).
 
 Previously captured clinical significance classifications from spreadsheets were programmatically mapped to the [GA4GH Variant Annotation Specification (VA-Spec)](https://www.ga4gh.org/product/variant-annotation/) to evaluate approaches for reducing knowledge silos and improving interoperability.
+
+---
+
+## Development
+
+Clone the repo and create a virtual environment:
+
+```shell
+git clone https://github.com/genomicmedlab/mci_knowledge_pilot
+cd mci_knowledge_pilot
+python3 -m virtualenv venv
+source venv/bin/activate
+```
+
+Install development dependencies and `prek`:
+
+```shell
+python3 -m pip install -e '.[dev]'
+prek install
+```
+
+Check style with `ruff`:
+
+```shell
+python3 -m ruff format . && python3 -m ruff check --fix .
+```
@@ -0,0 +1,105 @@
+[project]
+name = "mci_knowledge_pilot"
+version = "0.1.0"
+authors = [
+    {name = "Matthew Cannon"},
+    {name = "Anastasia Bratulin"},
+    {name = "Kori Kuzma"},
+    {name = "Daniel Puthawala"},
+    {name = "Alex Wagner"},
+]
+readme = "README.md"
+requires-python = ">=3.13,<3.14"
+description = "Transform semi-structured somatic cancer variant classification knowledge into computable clinical assertions using GA4GH GKS"
+license = "MIT"
+license-files = ["LICENSE"]
+dependencies = [
+    "ipykernel"
+]
+
+[project.optional-dependencies]
+dev = [
+    "prek>=0.2.23",
+    "ruff==0.14.10",
+]
+
+[tool.ruff]
+extend-include = ["*.ipynb"]
+
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = [
+    # unused
+    "AIR",
+    "ERA",
+    "YTT",
+    "BLE",
+    "FBT",
+    "CPY",
+    "DJ",
+    "EXE",
+    "FIX",
+    "FA",
+    "PYI",
+    "TD",
+    "C90",
+    "NPY",
+    "PD",
+    # ignore for compatibility with formatter
+    "D206",
+    "D300",
+    "W191",
+    "E111",
+    "E114",
+    "E117",
+    "E501",
+    "W191",
+    "S321",
+    "COM812",
+    "COM819",
+    "Q000",
+    "Q001",
+    "Q002",
+    "Q003",
+    # don't require types on *args, **kwargs
+    "ANN002",
+    "ANN003",
+    # subjective pylint thresholds
+    "PLR0904",
+    "PLR091",
+    "PLR1702",
+    "PLC0206",
+    # misc unnecessary stuff
+    "S321",
+    "D203",
+    "D205",
+    "D213",
+    "D400",
+    "D415",
+]
+
+[tool.ruff.lint.per-file-ignores]
+# ANN001 - missing-type-function-argument
+# ANN2 - missing-return-type
+# D100 - undocumented-public-module
+# D102 - undocumented-public-class
+# D103 - undocumented-public-function
+# S101 - assert
+# B011 - assert-false
+# INP001 - implicit-namespace-package
+# PLR2004 - magic-value-comparison
+"tests/*" = [
+    "ANN001",
+    "ANN2",
+    "D",
+    "S101",
+    "B011",
+    "INP001",
+    "PLR2004",
+]
+
+[tool.ruff.lint.flake8-annotations]
+mypy-init-return = true
+
+[tool.ruff.format]
+docstring-code-format = true