MEDS-DEV 0.0.1__tar.gz

meds_dev-0.0.1/.github/ISSUE_TEMPLATE/add-a-dataset.md

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+---
+name: Add a Dataset
+about: Request or track the addition of a new dataset to be supported by MEDS-DEV
+title: '[Dataset] Adds dataset NAME'
+labels: Datasets
+assignees: ''
+---
+
+1. What is the (unique) dataset name?
+2. Is this dataset public or private?
+3. Are there publications _about_ the dataset? If so, provide links here.
+4. Are there publications _using_ the dataset? If so, provide links here.
+5. Is there a public ETL to extract this dataset? If so, is it MEDS-compliant?
+6. Is there a demo (fully openly available for generic download) version of this data available for use in testing and CI?
+7. Who is the expected local dataset owner for this dataset? (tag their GitHub ID and/or provide contact information)
+8. Would there be interest in running MEDS-DEV experiments on this dataset to help densify the MEDS-DEV results?
+9. Are there any unique features about this dataset that are not sufficiently captured by the current [MEDS schema](https://github.com/Medical-Event-Data-Standard/meds)? If so, provide a link to the issue on the [MEDS repository](https://github.com/Medical-Event-Data-Standard/meds/issues/new?template=Blank+issue) tracking what would need to be added to MEDS to support them.
+10. Is this dataset over a general or heavily restricted population? Describe the cohort included in this dataset.

meds_dev-0.0.1/.github/ISSUE_TEMPLATE/add-a-model.md

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+---
+name: Add a Model
+about: Request or track the addition of a new model to be supported by MEDS-DEV
+title: '[Model] Add the model NAME'
+labels: Models
+assignees: ''
+---
+
+1. What is the (unique) model's name?
+2. Is there a publication about the model? If so, provide a link.
+3. Is there a codebase for the model? If so, is it MEDS-compliant?
+4. What dataset-specific variables would need to be specified to run this model?
+5. What dataset-specific features would need to be present in a dataset for this model to be appropriate on that dataset?
+6. Who is the primary author of this model? (tag their GitHub ID and/or provide contact information)
+7. Does anything about how this model is trained/used deviate from the model runtime API (see #43)?

meds_dev-0.0.1/.github/ISSUE_TEMPLATE/add-a-task.md

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+---
+name: Add a Task
+about: Request or track the addition of a new prediction task to be supported by MEDS-DEV
+title: '[Task] Add task NAME'
+labels: Tasks
+assignees: ''
+---
+
+1. What is the task's (unique) name?
+2. Are there publications about the task? If so, provide links.
+3. Are there reproducible codebases for this task in public datasets? If so, are they [ACES](https://eventstreamaces.readthedocs.io/en/latest/)-compliant?
+4. What dataset-specific predicates would need to be specified to extract this model?
+5. What dataset-specific features would need to be present in a dataset for this task to be appropriate on that dataset?
+6. If there is a primary author studying this task, provide their GitHub ID or contact info.
+7. Could this task be extracted via [ACES](https://eventstreamaces.readthedocs.io/en/latest/), or would you need to extend ACES to support this task? If so, provide a link to the [ACES](https://github.com/justin13601/ACES/issues/new?template=Blank+issue) issue detailing what changes are needed.

meds_dev-0.0.1/.github/workflows/code-quality-main.yaml

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+# 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:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install packages
+        run: |
+          pip install .[dev]
+
+      - name: Run pre-commits
+        uses: pre-commit/action@v3.0.1

meds_dev-0.0.1/.github/workflows/code-quality-pr.yaml

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+# 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:
+    branches: [main, "release/*", "dev"]
+
+jobs:
+  code-quality:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install packages
+        run: |
+          pip install .[dev]
+
+      - name: Find modified files
+        id: file_changes
+        uses: trilom/file-changes-action@v1.2.4
+        with:
+          output: " "
+
+      - name: List modified files
+        run: echo '${{ steps.file_changes.outputs.files}}'
+
+      - name: Run pre-commits
+        uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: --files ${{ steps.file_changes.outputs.files}}

meds_dev-0.0.1/.github/workflows/python-build.yaml

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+name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install pypa/build
+        run: >-
+          python3 -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: python3 -m 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/MEDS-DEV
+    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@v2.1.1
+        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 }}'

meds_dev-0.0.1/.github/workflows/tests.yaml

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+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main, "release/*", "dev"]
+
+jobs:
+  run_tests_ubuntu:
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+
+    timeout-minutes: 30
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install packages
+        run: |
+          pip install -e .[tests]
+
+      #----------------------------------------------
+      #              run test suite
+      #----------------------------------------------
+      - name: Run tests
+        run: |
+          pytest -v --doctest-modules --cov=src --junitxml=junit.xml -s --ignore=docs
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+      - name: Upload test results to Codecov
+        if: ${{ !cancelled() }}
+        uses: codecov/test-results-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

meds_dev-0.0.1/.gitignore

@@ -0,0 +1,359 @@
+# 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/
+
+.editorconfig
+
+
+# Created by https://www.toptal.com/developers/gitignore/api/macos,pycharm,visualstudiocode,windows
+# Edit at https://www.toptal.com/developers/gitignore?templates=macos,pycharm,visualstudiocode,windows
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+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
+
+### macOS Patch ###
+# iCloud generated files
+*.icloud
+
+### PyCharm ###
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# AWS User-specific
+.idea/**/aws.xml
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# SonarLint plugin
+.idea/sonarlint/
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+### PyCharm Patch ###
+# Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721
+
+# *.iml
+# modules.xml
+# .idea/misc.xml
+# *.ipr
+
+# Sonarlint plugin
+# https://plugins.jetbrains.com/plugin/7973-sonarlint
+.idea/**/sonarlint/
+
+# SonarQube Plugin
+# https://plugins.jetbrains.com/plugin/7238-sonarqube-community-plugin
+.idea/**/sonarIssues.xml
+
+# Markdown Navigator plugin
+# https://plugins.jetbrains.com/plugin/7896-markdown-navigator-enhanced
+.idea/**/markdown-navigator.xml
+.idea/**/markdown-navigator-enh.xml
+.idea/**/markdown-navigator/
+
+# Cache file creation bug
+# See https://youtrack.jetbrains.com/issue/JBR-2257
+.idea/$CACHE_FILE$
+
+# CodeStream plugin
+# https://plugins.jetbrains.com/plugin/12206-codestream
+.idea/codestream.xml
+
+# Azure Toolkit for IntelliJ plugin
+# https://plugins.jetbrains.com/plugin/8053-azure-toolkit-for-intellij
+.idea/**/azureSettings.xml
+
+### VisualStudioCode ###
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+!.vscode/*.code-snippets
+
+# Local History for Visual Studio Code
+.history/
+
+# Built Visual Studio Code Extensions
+*.vsix
+
+### VisualStudioCode Patch ###
+# Ignore all local history of files
+.history
+.ionide
+
+### 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
+
+# End of https://www.toptal.com/developers/gitignore/api/macos,pycharm,visualstudiocode,windows