oa-configurator 0.1.0__tar.gz

oa_configurator-0.1.0/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: "🐞 Bug Report"
+description: Report a bug to help us improve the project
+labels: ["bug"]
+body:
+  - type: checkboxes
+    attributes:
+      label: Is there an existing issue for this?
+      description: Please search to see if an issue already exists for the bug you encountered.
+      options:
+      - label: I have searched the existing issues
+        required: true
+  - type: textarea
+    id: summary
+    attributes:
+      label: Bug summary
+      description: 1-2 short sentences describing the bug.
+    validations:
+      required: true
+  - type: textarea
+    id: reproduction
+    attributes:
+      label: Code for reproduction
+      description: Please provide a minimal self-contained example.
+      placeholder: Your python code here
+      render: python
+    validations:
+      required: true
+  - type: textarea
+    id: logs
+    attributes:
+      label: Error messages
+      description: Paste the full error traceback here.
+      render: python-traceback

oa_configurator-0.1.0/.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: ❓ Discussions
+    url: https://github.com/AustralianCancerDataNetwork/oa-configurator/discussions
+    about: Ask questions or start a general discussion.

oa_configurator-0.1.0/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: "🚀 Feature Request"
+description: Submit a proposal for a new feature
+labels: ["enhancement"]
+body:
+  - type: textarea
+    id: motivation
+    attributes:
+      label: Motivation
+      description: Is your feature request related to a problem? (e.g., I'm always frustrated when [...])
+    validations:
+      required: true
+  - type: textarea
+    id: pitch
+    attributes:
+      label: Pitch
+      description: A clear and concise description of what you want to happen.
+    validations:
+      required: true
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives
+      description: Any alternative solutions or features you've considered.
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional context
+      description: Add any other context or screenshots here.

oa_configurator-0.1.0/.github/ISSUE_TEMPLATE/not_working.yml

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+name: "❗ Something is not working"
+description: >
+  If something is not working as expected but you're not sure if it's a bug,
+  please follow the instructions in this template.
+
+body:
+  - type: checkboxes
+    attributes:
+      label: Is there an existing issue for this?
+      description: Please search to see if an issue already exists for the problem you encountered.
+      options:
+      - label: I have searched the existing issues
+        required: true
+
+  - type: textarea
+    id: summary
+    attributes:
+      label: Problem summary
+      description: Please provide 1-2 short sentences that succinctly describe the problem.
+    validations:
+      required: true
+
+  - type: textarea
+    id: reproduction
+    attributes:
+      label: Code for reproduction
+      description: >
+        If possible, please provide a [minimum self-contained example](https://stackoverflow.com/help/minimal-reproducible-example).
+        It will be automatically formatted.
+        Here's another useful resource: [How To Ask Questions The Smart Way](http://www.catb.org/~esr/faqs/smart-questions.html).
+      placeholder: Your code here
+      render: python
+    validations:
+      required: true
+
+  - type: textarea
+    id: actual
+    attributes:
+      label: Actual outcome
+      description: Please describe the outcome of running the above code.
+    validations:
+      required: true
+
+  - type: textarea
+    id: logs
+    attributes:
+      label: Error messages
+      description: >
+        Please copy and paste any relevant log output.
+        Paste the full error traceback, not just the last error.
+        It will be automatically formatted.
+      placeholder: Your errors here
+      render: python-traceback
+
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected outcome
+      description: >
+        Please provide a description (or visual example) of the expected outcome
+        from the code snippet.
+    validations:
+      required: true

oa_configurator-0.1.0/.github/workflows/docs.yml

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+name: Deploy Docs
+
+on:
+  workflow_run:
+    workflows: ["Release"]
+    types:
+      - completed
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    if: >-
+      github.event_name == 'workflow_dispatch' ||
+      (github.event.workflow_run.conclusion == 'success' &&
+       github.event.workflow_run.event == 'push' &&
+       github.event.workflow_run.head_branch == 'main')
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+          python-version: "3.12"
+
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+
+      - name: Install dependencies
+        run: uv sync --extra dev
+
+      - name: Deploy to GitHub Pages
+        run: uv run mkdocs gh-deploy --force

oa_configurator-0.1.0/.github/workflows/lint-pr.yml

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+# Lints pull request titles to enforce semantic-versioning commit style
+name: "Lint PR"
+
+on:
+  pull_request:
+    types:
+      - opened
+      - edited
+      - synchronize
+
+jobs:
+  main:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/action-semantic-pull-request@v5
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

oa_configurator-0.1.0/.github/workflows/release.yml

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+name: Release
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+    inputs:
+      force_publish:
+        description: 'Force publish to PyPI without semantic-release (use after a failed release)'
+        type: boolean
+        default: false
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: uv sync --extra dev --extra postgres
+
+      - name: Lint
+        run: uv run ruff check src/ tests/
+
+      - name: Type check
+        run: uv run mypy src/
+
+      - name: Run tests
+        run: uv run pytest tests/ -v
+
+  release:
+    needs: test
+    if: github.ref == 'refs/heads/main' && github.event_name != 'pull_request'
+    runs-on: ubuntu-latest
+    concurrency: release
+    permissions:
+      id-token: write
+      contents: write
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/oa-configurator
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          python-version: "3.12"
+          enable-cache: true
+
+      - name: Semantic Release
+        id: semantic
+        uses: cycjimmy/semantic-release-action@v6
+        with:
+          extra_plugins: |
+            @semantic-release/changelog
+            @semantic-release/git
+            @semantic-release/exec
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and publish to PyPI
+        if: steps.semantic.outputs.new_release_published == 'true' || inputs.force_publish == true
+        run: |
+          uv build
+          uv publish

oa_configurator-0.1.0/.gitignore

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+# 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
+*.lcov
+.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/*
+!.pixi/config.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
+
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
+
+# 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/
+# Temporary file for partial code execution
+tempCodeRunnerFile.py
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml
+__pycache__/
+*.py[cod]
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.venv/
+*.ipynb
+_temp/

oa_configurator-0.1.0/.releaserc.json

@@ -0,0 +1,22 @@
+{
+  "branches": ["main"],
+  "plugins": [
+    "@semantic-release/commit-analyzer",
+    "@semantic-release/release-notes-generator",
+    "@semantic-release/changelog",
+    [
+      "@semantic-release/exec",
+      {
+        "prepareCmd": "sed -i 's/^version = \".*\"/version = \"${nextRelease.version}\"/' pyproject.toml && uv lock"
+      }
+    ],
+    [
+      "@semantic-release/git",
+      {
+        "assets": ["CHANGELOG.md", "pyproject.toml", "uv.lock"],
+        "message": "chore(release): ${nextRelease.version} [skip ci]\n\n${nextRelease.notes}"
+      }
+    ],
+    "@semantic-release/github"
+  ]
+}

oa_configurator-0.1.0/CHANGELOG.md

@@ -0,0 +1,6 @@
+# [0.1.0](https://github.com/AustralianCancerDataNetwork/oa-configurator/compare/v0.0.0...v0.1.0) (2026-06-15)
+
+
+### Features
+
+* Refactor of configuration utility ([#2](https://github.com/AustralianCancerDataNetwork/oa-configurator/issues/2)) ([a0b1b5e](https://github.com/AustralianCancerDataNetwork/oa-configurator/commit/a0b1b5e60b1a5e5a957dc067fff5b747bdc39b32))

oa_configurator-0.1.0/PKG-INFO

@@ -0,0 +1,99 @@
+Metadata-Version: 2.4
+Name: oa-configurator
+Version: 0.1.0
+Summary: Prototype shared configuration layer for the OMOP-oriented stack.
+Requires-Python: <3.13,>=3.12
+Requires-Dist: click>=8.0
+Requires-Dist: pydantic<3,>=2.7
+Requires-Dist: rich<15,>=13
+Requires-Dist: sqlalchemy<3,>=2.0
+Requires-Dist: tomli-w<2,>=1
+Requires-Dist: typer<1,>=0.12
+Provides-Extra: dev
+Requires-Dist: ipython>=8.0; extra == 'dev'
+Requires-Dist: mkdocs-material>=9.7.1; extra == 'dev'
+Requires-Dist: mkdocs-mermaid2-plugin; extra == 'dev'
+Requires-Dist: mkdocs>=1.6.1; extra == 'dev'
+Requires-Dist: mkdocstrings-python>=2.0.1; extra == 'dev'
+Requires-Dist: mypy>=1.8; extra == 'dev'
+Requires-Dist: pytest-cov>=4.0; extra == 'dev'
+Requires-Dist: pytest>=9.0.3; extra == 'dev'
+Requires-Dist: requests>=2.33.0; extra == 'dev'
+Requires-Dist: ruff>=0.4; extra == 'dev'
+Provides-Extra: postgres
+Requires-Dist: psycopg[binary]>=3.1; extra == 'postgres'
+Description-Content-Type: text/markdown
+
+# oa-configurator
+
+`oa-configurator` is a shared configuration layer across the OMOP-oriented public stack.
+
+## Goals
+
+- one obvious human-managed config file
+- typed config models for code usage
+- named connections and named logical resources
+- support for single-DB and split-DB deployments
+- support for local file-based artifacts like DuckDB and FAISS
+- clean migration path from today’s env-var-heavy tools
+- stable relative path semantics via one configuration base directory
+- opt-in file or env backed secret resolution for connection passwords
+
+## App Shape
+
+This folder currently includes:
+
+- a standalone package scaffold
+- typed models for config structure
+- a TOML loader
+- a simple resolver for logical resources and tool defaults
+- an example `config.toml`
+- an architecture note describing the intended evolution
+
+## Proposed Default Config Location
+
+```text
+~/.config/omop/config.toml
+```
+
+This prototype does not force that location, but it uses it as the default when no explicit path is provided.
+
+When a profile defines `resource_overrides` or `tool_overrides`, those patches
+are applied by the resolver at access time rather than mutating the raw loaded
+config object.
+
+Connection passwords may be provided inline with `password` or indirectly with
+`secret_source`. Supported secret source formats are:
+
+- `env:VARIABLE_NAME`
+- `file:relative/or/absolute/path`
+
+When `settings.secrets_dir` is configured, relative `file:` sources resolve
+from that directory. Otherwise they resolve from `configuration_base_path`.
+
+## Example
+
+```python
+from oa_configurator import load_stack_config, Resolver
+
+config = load_stack_config()
+resolver = Resolver(config)
+
+resource = resolver.resolve_resource("default")
+tool = resolver.resolve_tool("omop_emb")
+
+print(resource.database.database_name)
+print(resource.database.safe_url)
+print(resource.vocab_db_is_primary_fallback)
+print(resource.schema_translate_map())
+print(tool.backend)
+print(resolver.configuration_base_path)
+print(config.secrets_dir)
+print(resolver.active_profile_name())
+```
+
+## Notes
+
+- This is still a sketch library, not a production-ready replacement.
+- The resolver API is intentionally small for now.
+- Compatibility shims for legacy env var consumers are described in `docs/architecture.md` but not implemented yet.

oa_configurator-0.1.0/README.md

@@ -0,0 +1,73 @@
+# oa-configurator
+
+`oa-configurator` is a shared configuration layer across the OMOP-oriented public stack.
+
+## Goals
+
+- one obvious human-managed config file
+- typed config models for code usage
+- named connections and named logical resources
+- support for single-DB and split-DB deployments
+- support for local file-based artifacts like DuckDB and FAISS
+- clean migration path from today’s env-var-heavy tools
+- stable relative path semantics via one configuration base directory
+- opt-in file or env backed secret resolution for connection passwords
+
+## App Shape
+
+This folder currently includes:
+
+- a standalone package scaffold
+- typed models for config structure
+- a TOML loader
+- a simple resolver for logical resources and tool defaults
+- an example `config.toml`
+- an architecture note describing the intended evolution
+
+## Proposed Default Config Location
+
+```text
+~/.config/omop/config.toml
+```
+
+This prototype does not force that location, but it uses it as the default when no explicit path is provided.
+
+When a profile defines `resource_overrides` or `tool_overrides`, those patches
+are applied by the resolver at access time rather than mutating the raw loaded
+config object.
+
+Connection passwords may be provided inline with `password` or indirectly with
+`secret_source`. Supported secret source formats are:
+
+- `env:VARIABLE_NAME`
+- `file:relative/or/absolute/path`
+
+When `settings.secrets_dir` is configured, relative `file:` sources resolve
+from that directory. Otherwise they resolve from `configuration_base_path`.
+
+## Example
+
+```python
+from oa_configurator import load_stack_config, Resolver
+
+config = load_stack_config()
+resolver = Resolver(config)
+
+resource = resolver.resolve_resource("default")
+tool = resolver.resolve_tool("omop_emb")
+
+print(resource.database.database_name)
+print(resource.database.safe_url)
+print(resource.vocab_db_is_primary_fallback)
+print(resource.schema_translate_map())
+print(tool.backend)
+print(resolver.configuration_base_path)
+print(config.secrets_dir)
+print(resolver.active_profile_name())
+```
+
+## Notes
+
+- This is still a sketch library, not a production-ready replacement.
+- The resolver API is intentionally small for now.
+- Compatibility shims for legacy env var consumers are described in `docs/architecture.md` but not implemented yet.