PROTON release

Author: ayushnoori

.Rprofile

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+source("renv/activate.R")

.env.example

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+AZURE_OPENAI_ENDPOINT=
+AZURE_OPENAI_API_KEY=
+PQA_API_KEY=

.gitattributes

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+*.ipynb	diff=jupyternotebook
+*.ipynb	merge=jupyternotebook

.github/actions/setup-python-env/action.yml

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+name: "Setup Python Environment"
+description: "Set up Python environment for the given Python version"
+
+inputs:
+  python-version:
+    description: "Python version to use"
+    required: true
+    default: "3.11"
+  uv-version:
+    description: "uv version to use"
+    required: true
+    default: "0.7.0"
+
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        version: ${{ inputs.uv-version }}
+        enable-cache: 'true'
+        cache-suffix: ${{ matrix.python-version }}
+
+    - name: Install Python dependencies
+      run: make install
+      shell: bash

.github/workflows/main.yml

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+name: Main
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+
+jobs:
+  quality:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - uses: actions/cache@v4
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-python-env
+
+      - name: Run checks
+        run: make check
+
+  type-check:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+      fail-fast: false
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-python-env
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Check typing
+        run: uv run ty check --exclude "notebooks/**"

.gitignore

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+# ========== MacOS ==========
+# General
+.DS_Store
+__MACOSX/
+.AppleDouble
+.LSOverride
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+
+# ========== Windows ==========
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+
+# ========== Python ==========
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+# uv.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
+# poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+secrets.env
+.env
+.envrc
+.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/
+
+# Abstra
+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
+#   Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer,
+#   you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml
+
+
+# ========== Template ==========
+docs/source
+
+# Jupyter notebooks
+notebooks/**
+!notebooks/**.ipynb
+
+# Data
+data/**
+
+# Exceptions
+!data/.gitkeep
+!data/neurokg/
+!data/neurokg/2_enrich_kg/
+!data/mappings/
+!data/images/
+
+!data/neurokg/2_enrich_kg/roi_to_label_mapping.csv
+!data/mappings/README.md
+
+!data/images/header.png
+!data/images/figure_1a.png