EveryQuery 0.1.0__tar.gz

everyquery-0.1.0/.github/actions/setup/action.yaml

@@ -0,0 +1,28 @@
+name: Setup Package
+description: This workflow sets up the package for other workflows.
+inputs:
+  python-version:
+    description: The Python version to use for the setup.
+    required: true
+    default: "3.11"
+  group:
+    description: The dependency group to install (benchmarks, dev, docs)
+    required: false
+    default: "dev"
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "${{ inputs.python-version }}"
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        enable-cache: true
+        cache-suffix: "py${{ inputs.python-version }}"
+
+    - name: Install packages
+      shell: bash
+      run: |
+        uv sync --locked --group ${{ inputs.group }}

everyquery-0.1.0/.github/workflows/code-quality-main.yaml

@@ -0,0 +1,23 @@
+# Same as `code-quality-pr.yaml` but triggered on commit to main branch
+# and runs on all files (instead of only the changed ones)
+
+name: Code Quality Main
+
+on:
+  push:
+    branches: [main]
+
+jobs:
+  code-quality:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup package
+        uses: ./.github/actions/setup
+        with:
+          python-version: "3.12"
+
+      - name: Run pre-commits
+        run: uv run pre-commit run --all-files --show-diff-on-failure

everyquery-0.1.0/.github/workflows/code-quality-pr.yaml

@@ -0,0 +1,34 @@
+# This workflow finds which files were changed, prints them,
+# and runs `pre-commit` on those files.
+
+# Inspired by the sktime library:
+# https://github.com/alan-turing-institute/sktime/blob/main/.github/workflows/test.yml
+
+name: Code Quality PR
+
+on:
+  pull_request:
+
+jobs:
+  code-quality:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup package
+        uses: ./.github/actions/setup
+        with:
+          python-version: "3.12"
+
+      - name: Find modified files
+        id: file_changes
+        uses: tj-actions/changed-files@v46.0.5
+
+      - name: List all changed files
+        run: echo '${{ steps.file_changes.outputs.all_changed_files }}'
+
+      - name: Run pre-commits
+        run: >
+          uv run pre-commit run --show-diff-on-failure
+          --files ${{ steps.file_changes.outputs.all_changed_files}}

everyquery-0.1.0/.github/workflows/python-build.yaml

@@ -0,0 +1,100 @@
+name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
+      - name: Build
+        run: uv build
+
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    name: Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/EveryQuery
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to GitHub Release
+    needs:
+      - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write # IMPORTANT: mandatory for sigstore
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Sign the dists with Sigstore
+        uses: sigstore/gh-action-sigstore-python@v3.0.0
+        with:
+          inputs: >-
+            ./dist/*.tar.gz
+            ./dist/*.whl
+      - name: Create GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: >-
+          gh release create
+          '${{ github.ref_name }}'
+          --repo '${{ github.repository }}'
+          --notes ""
+      - name: Upload artifact signatures to GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        # Upload to GitHub Release using the `gh` CLI.
+        # `dist/` contains the built packages, and the
+        # sigstore-produced signatures and certificates.
+        run: >-
+          gh release upload
+          '${{ github.ref_name }}' dist/**
+          --repo '${{ github.repository }}'

everyquery-0.1.0/.github/workflows/tests.yaml

@@ -0,0 +1,47 @@
+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  run_tests_ubuntu:
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+
+    timeout-minutes: 30
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup package
+        uses: ./.github/actions/setup
+        with:
+          python-version: "3.12"
+
+      - name: Run tests
+        run: >
+          uv run pytest -v
+          --ignore=docs
+          --cov=src
+          --cov-report=xml:coverage.xml
+          --cov-report=term
+          --junitxml=junit.xml
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.xml
+          fail_ci_if_error: true
+          verbose: true
+
+      - name: Upload test results to Codecov
+        if: ${{ !cancelled() }}
+        uses: codecov/test-results-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: junit.xml

everyquery-0.1.0/.gitignore

@@ -0,0 +1,184 @@
+mgb_lvef/
+mgb_lvef_pt/
+mgb_ecg_pt/
+mgb/
+mimic/
+results/
+meds-torch/
+data-test/
+figures/
+logs/*
+MEDS_EIC_AR/
+*.png
+*.pkl
+experiment_registry.pkl
+outputs/
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+core*
+
+# 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/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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/
+
+src/every_query/eval_suite/conf/eval_codes/
+src/every_query/aces_to_eq/query_codes/
+
+# Generated train code YAMLs
+src/every_query/train_codes/

everyquery-0.1.0/.pre-commit-config.yaml

@@ -0,0 +1,95 @@
+default_language_version:
+  python: python3.12
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      # list of supported hooks: https://pre-commit.com/hooks.html
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-docstring-first
+      - id: check-yaml
+      - id: debug-statements
+      - id: detect-private-key
+      - id: check-executables-have-shebangs
+      - id: check-toml
+      - id: check-json
+      - id: check-xml
+      - id: check-merge-conflict
+      - id: check-case-conflict
+      - id: check-added-large-files
+        args: [--maxkb, "800"]
+
+  # python code formatting, linting, and import sorting using ruff
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.12.10
+    hooks:
+      # Run the formatter
+      - id: ruff-format
+      # Run the linter
+      - id: ruff
+        args: ["--fix", "--exit-non-zero-on-fix"]
+
+  # python docstring formatting
+  - repo: https://github.com/myint/docformatter
+    rev: v1.7.7
+    hooks:
+      - id: docformatter
+        args: [--in-place, --wrap-summaries=110, --wrap-descriptions=110]
+
+  # yaml formatting
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        types: [yaml]
+        exclude: "environment.yaml"
+
+  # shell scripts linter
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.11.0.1
+    hooks:
+      - id: shellcheck
+
+  # md formatting
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.22
+    hooks:
+      - id: mdformat
+        args: ["--number"]
+        additional_dependencies:
+          - mdformat-ruff
+          - mdformat-gfm
+          - mdformat-gfm-alerts
+          - mdformat-tables
+          - mdformat_frontmatter
+          - mdformat-black
+          - mdformat-config
+          - mdformat-shfmt
+          - mdformat-mkdocs
+          - mdformat-toc
+
+  # word spelling linter
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.1
+    hooks:
+      - id: codespell
+        args:
+          - --skip=*.ipynb,*.bib,*.svg,pyproject.toml
+          - --ignore-words-list=ehr,crate
+
+  # jupyter notebook cell output clearing
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.8.1
+    hooks:
+      - id: nbstripout
+
+  # jupyter notebook linting with ruff
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.9.1
+    hooks:
+      - id: nbqa-ruff
+        args: ["--fix"]
+      - id: nbqa-ruff-format
+        args: ["--line-length=110"]

everyquery-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Payal Chandak
+
+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.

everyquery-0.1.0/PKG-INFO

@@ -0,0 +1,53 @@
+Metadata-Version: 2.4
+Name: EveryQuery
+Version: 0.1.0
+Summary: A framework for training and evaluating foundation models, using the MEDS ecosystem for data processing and PyTorch Lightning for training.
+Author-email: Payal Chandak <payal.chandak@gmail.com>, Matthew McDermott <mattmcdermott8@gmail.com>, Gregory Kondas <gregkondas9@gmail.com>
+Project-URL: Homepage, https://github.com/payalchandak/EveryQuery
+Project-URL: Issues, https://github.com/payalchandak/EveryQuery/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: polars~=1.30.0
+Requires-Dist: pyarrow
+Requires-Dist: hydra-core
+Requires-Dist: numpy
+Requires-Dist: meds~=0.4.0
+Requires-Dist: filelock
+Requires-Dist: pytest
+Requires-Dist: MEDS-transforms~=0.5.2
+Requires-Dist: meds-torch-data[lightning]~=0.6.3
+Requires-Dist: transformers
+Requires-Dist: torch
+Requires-Dist: torchmetrics
+Requires-Dist: lightning~=2.5.1
+Requires-Dist: dotenv>=0.9.9
+Dynamic: license-file
+
+# EveryQuery
+
+.env
+
+```
+PROJECT_DIR="/home/pac4279/EveryQuery"
+DATA_DIR="/n/data1/hms/dbmi/zaklab/payal/mimic"
+SAVE_DIR="/n/data1/hms/dbmi/zaklab/payal/EveryQuery/results"
+RAW="${DATA_DIR}/raw"
+INTERMEDIATE="${DATA_DIR}/intermediate"
+PROCESSED="${DATA_DIR}/processed"
+```
+
+run for processing data
+
+```
+MEICAR_process_data input_dir="$RAW" intermediate_dir="$INTERMEDIATE" output_dir="$PROCESSED"
+```
+
+run for training
+
+```
+source .env; set -a; . ./.env; set +a; python source/train.py
+```

everyquery-0.1.0/README.md

@@ -0,0 +1,24 @@
+# EveryQuery
+
+.env
+
+```
+PROJECT_DIR="/home/pac4279/EveryQuery"
+DATA_DIR="/n/data1/hms/dbmi/zaklab/payal/mimic"
+SAVE_DIR="/n/data1/hms/dbmi/zaklab/payal/EveryQuery/results"
+RAW="${DATA_DIR}/raw"
+INTERMEDIATE="${DATA_DIR}/intermediate"
+PROCESSED="${DATA_DIR}/processed"
+```
+
+run for processing data
+
+```
+MEICAR_process_data input_dir="$RAW" intermediate_dir="$INTERMEDIATE" output_dir="$PROCESSED"
+```
+
+run for training
+
+```
+source .env; set -a; . ./.env; set +a; python source/train.py
+```