wadoh-subtyping 0.3.3__tar.gz

wadoh_subtyping-0.3.3/.github/workflows/release.yml

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+name: Build, Test, Changelog, and Release Python Package
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+
+jobs:
+  unit-tests:
+    name: Test Python Package
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "0.8.13" # pin a specific version is best practice
+          enable-cache: true
+
+      # install python in 
+      - name: "Set up Python"
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: "pyproject.toml"
+
+      - name: Run tests
+        # For example, using `pytest`
+        run: uv run pytest tests
+
+  build-and-release:
+    name: Generate Changelog, build, and release
+    runs-on: ubuntu-latest
+    needs: unit-tests  # This makes sure the build job runs first
+
+    outputs:
+      released: ${{ steps.changelog.outputs.skipped == 'false' }}
+
+    steps:
+      # Checkout the code
+      - uses: actions/checkout@v4
+
+      # Generate changelog
+      - name: Conventional Changelog Action
+        id: changelog
+        uses: TriPSs/conventional-changelog-action@v3
+        with:
+          github-token: ${{ secrets.github_token }}
+          create-summary: true
+
+      - name: Set up uv
+        if: ${{ steps.changelog.outputs.skipped == 'false' }}
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh
+
+      - name: Build package
+        if: ${{ steps.changelog.outputs.skipped == 'false' }}
+        run: |
+          # VERSION=$(uvx dunamai from any --no-metadata --style pep440)
+          VERSION=$(uvx dunamai from any --no-metadata --style pep440 | sed -E 's/\.post[0-9]+\.dev[0-9]+//')
+          echo $VERSION
+          uvx --from=toml-cli toml set --toml-path=pyproject.toml project.version $VERSION
+          uv build
+
+      # Attach the build assets to the GitHub release (only if changelog creation was successful)
+      - name: Create GitHub release and discussion
+        if: ${{ steps.changelog.outputs.skipped == 'false' }}
+        run: |
+          gh release create $TAG $FILES \
+            --title "$TAG" \
+            --notes "$CHANGELOG" \
+            --discussion-category "Announcements"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          TAG: ${{ steps.changelog.outputs.tag }}
+          CHANGELOG: ${{ steps.changelog.outputs.clean_changelog }}
+          FILES: dist/*.tar.gz dist/*.whl
+
+      - name: Upload dist artifacts
+        if: ${{ steps.changelog.outputs.skipped == 'false' }}
+        uses: actions/upload-artifact@v6
+        with:
+          name: dist
+          path: dist/
+          
+      - name: Push Files for GitHub Action
+        if: ${{ steps.changelog.outputs.skipped == 'false' }}
+        run: |
+          git config user.name "Your GitHub Actions Bot"
+          git config user.email "your-email@example.com"
+          git add .
+          git commit -m "Build package and update version"
+          git push
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  publish:
+    name: publish to pypi
+    needs: build-and-release
+    if: >
+      needs.build-and-release.result == 'success' &&
+      needs.build-and-release.outputs.released == 'true'
+
+    runs-on: ubuntu-latest
+
+    environment: 
+      name: pypi-env
+
+    permissions: 
+      id-token: write
+      contents: read
+
+    steps:
+    - uses: actions/checkout@v6
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
+
+    - name: Set up Python
+      run: uv python install 3.11
+
+    - name: Download dist artifacts
+      uses: actions/download-artifact@v7
+      with:
+        name: dist
+        path: dist
+
+    - name: Smoke test (wheel)
+      run: uv run --isolated --no-project --with dist/*.whl tests/smoke_test.py
+
+    - name: Smoke test (source distribution)
+      run: uv run --isolated --no-project --with dist/*.tar.gz tests/smoke_test.py
+
+    - name: Publish
+      run: uv publish

wadoh_subtyping-0.3.3/.gitignore

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+docs/_site
+
+# 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.lock
+#   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
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.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__/

wadoh_subtyping-0.3.3/.python-version

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+3.11

wadoh_subtyping-0.3.3/CHANGELOG.md

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+## [0.3.3](https://github.com/WA-EIP/wadoh_subtyping/compare/v0.3.2...v0.3.3) (2026-06-03)
+
+
+### Bug Fixes
+
+* add pyyaml ([7c12ea5](https://github.com/WA-EIP/wadoh_subtyping/commit/7c12ea58cda2fb46827524c323369c5a510b83ba))
+
+
+
+## [0.3.2](https://github.com/WA-EIP/wadoh_subtyping/compare/v0.3.1...v0.3.2) (2026-06-03)
+
+
+### Bug Fixes
+
+* trigger pkg build ([e1a5bf2](https://github.com/WA-EIP/wadoh_subtyping/commit/e1a5bf2aa1a702b318e065927a6d1f0ebed649d4))
+
+
+
+## [0.3.1](https://github.com/WA-EIP/wadoh_subtyping/compare/v0.3.0...v0.3.1) (2026-06-03)
+
+
+### Bug Fixes
+
+* trigger pkg build ([ad64b5f](https://github.com/WA-EIP/wadoh_subtyping/commit/ad64b5f811861d7158c8a82c33d4f3962040ea07))
+
+
+
+# [0.3.0](https://github.com/WA-EIP/wadoh_subtyping/compare/v0.2.0...v0.3.0) (2026-06-03)
+
+
+### Features
+
+* modularize functions ([4296a45](https://github.com/WA-EIP/wadoh_subtyping/commit/4296a452d8e270dbe793e28ed38afca03a3e8a68))
+
+
+
+# [0.2.0](https://github.com/WA-EIP/wadoh_subtyping/compare/v0.1.2...v0.2.0) (2025-12-02)
+
+
+### Features
+
+* use sparkpl to convert spark to polars and vice versa ([a614031](https://github.com/WA-EIP/wadoh_subtyping/commit/a6140315f5b126cb51d53e963f1461866642d14c))
+
+
+

wadoh_subtyping-0.3.3/LICENSE

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+MIT License
+
+Copyright (c) 2025 Washington State - Emerging Infections Program (EIP)
+
+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.

wadoh_subtyping-0.3.3/PKG-INFO

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+Metadata-Version: 2.4
+Name: wadoh-subtyping
+Version: 0.3.3
+Summary: Add your description here
+Author-email: Frank Aragona <92396451+DOH-FAA3303@users.noreply.github.com>
+License-File: LICENSE
+Requires-Python: >=3.11
+Requires-Dist: databricks-sdk>=0.113.0
+Requires-Dist: polars>=1.32.3
+Requires-Dist: pyarrow>=21.0.0
+Requires-Dist: pycap>=2.7.0
+Requires-Dist: pyyaml>=6.0.2
+Requires-Dist: sparkpl>=2.0.1
+Requires-Dist: wadoh-raccoon>=0.4.3
+Description-Content-Type: text/markdown
+
+# wadoh_subtyping
+A Python package for transforming and processing RESPNET subtyping data

wadoh_subtyping-0.3.3/README.md

@@ -0,0 +1,2 @@
+# wadoh_subtyping
+A Python package for transforming and processing RESPNET subtyping data

wadoh_subtyping-0.3.3/docs/.gitignore

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+/.quarto/

wadoh_subtyping-0.3.3/docs/_extensions/r-wasm/live/_extension.yml

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+title: Quarto Live
+author: George Stagg
+version: 0.1.3-dev
+quarto-required: ">=1.4.0"
+contributes:
+  filters:
+    - live.lua
+  formats:
+    common:
+      ojs-engine: true
+      filters:
+        - live.lua
+    html: default
+    revealjs: default
+    dashboard: default

wadoh_subtyping-0.3.3/docs/_extensions/r-wasm/live/_gradethis.qmd

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+```{webr}
+#| edit: false
+#| output: false
+webr::install("gradethis", quiet = TRUE)
+library(gradethis)
+options(webr.exercise.checker = function(
+  label, user_code, solution_code, check_code, envir_result, evaluate_result,
+  envir_prep, last_value, engine, stage, ...
+) {
+  if (is.null(check_code)) {
+    # No grading code, so just skip grading
+    invisible(NULL)
+  } else if (is.null(label)) {
+    list(
+      correct = FALSE,
+      type = "warning",
+      message = "All exercises must have a label."
+    )
+  } else if (is.null(solution_code)) {
+    list(
+      correct = FALSE,
+      type = "warning",
+      message = htmltools::tags$div(
+        htmltools::tags$p("A problem occurred grading this exercise."),
+        htmltools::tags$p(
+          "No solution code was found. Note that grading exercises using the ",
+          htmltools::tags$code("gradethis"),
+          "package requires a model solution to be included in the document."
+        )
+      )
+    )
+  } else {
+    gradethis::gradethis_exercise_checker(
+      label = label, solution_code = solution_code, user_code = user_code,
+      check_code = check_code, envir_result = envir_result,
+      evaluate_result = evaluate_result, envir_prep = envir_prep,
+      last_value = last_value, stage = stage, engine = engine)
+  }
+})
+```

wadoh_subtyping-0.3.3/docs/_extensions/r-wasm/live/_knitr.qmd

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+```{r echo=FALSE}
+# Setup knitr for handling {webr} and {pyodide} blocks
+# TODO: With quarto-dev/quarto-cli#10169, we can implement this in a filter
+
+# We'll handle `include: false` in Lua, always include cell in knitr output
+knitr::opts_hooks$set(include = function(options) {
+  if (options$engine == "webr" || options$engine == "pyodide") {
+    options$include <- TRUE
+  }
+  options
+})
+
+# Passthrough engine for webr
+knitr::knit_engines$set(webr = function(options) {
+  knitr:::one_string(c(
+    "```{webr}",
+    options$yaml.code,
+    options$code,
+    "```"
+  ))
+})
+
+# Passthrough engine for pyodide
+knitr::knit_engines$set(pyodide = function(options) {
+  knitr:::one_string(c(
+    "```{pyodide}",
+    options$yaml.code,
+    options$code,
+    "```"
+  ))
+})
+```