anyvar 1.0.0__tar.gz

anyvar-1.0.0/.dockerignore

@@ -0,0 +1,33 @@
+# Bytecode files
+__pycache__/
+*.pyc
+*.pyo
+
+# Virtual environment
+venv/
+.venv/
+
+# Debug and log files
+*.log
+debug*.txt
+
+# Data and media
+data/
+media/
+
+# Temporary files and directories
+tmp/
+temp/
+*.swp
+
+# IDE and OS files
+.idea/
+.vscode/
+.DS_Store
+
+# Distribution files
+dist/
+build/
+*.egg-info/
+
+.env

anyvar-1.0.0/.env.example

@@ -0,0 +1,42 @@
+###############
+# BASIC SETUP #
+###############
+
+# Data resources -- see "Getting Started" -> "Manual Setup" in the docs
+UTA_DB_URL=postgresql://anonymous@localhost:5432/uta/uta_20241220
+SEQREPO_DATAPROXY_URI=seqrepo+file:///usr/local/share/seqrepo/2024-12-20
+
+# Storage configuration -- see "Configuration" -> "Object Storage" in the docs
+ANYVAR_STORAGE_URI=postgresql://anyvar:anyvar-pw@localhost:5432/anyvar
+
+############
+# OPTIONAL #
+############
+
+## Service info definition -- see "Configuration" -> "Service-Info" in the docs
+ANYVAR_SERVICE_INFO=./.service_info_example.yaml
+
+## Logging - see "Configuration" -> "Logging" in the docs
+ANYVAR_LOGGING_CONFIG=path/to/logging/config/file.yaml
+
+## Celery - See "Configuration" -> "Asynchronous Processing" in the docs
+CELERY_BROKER_URL=redis://localhost:6379/0
+CELERY_BACKEND_URL=redis://localhost:6379/0
+ANYVAR_VCF_ASYNC_WORK_DIR=/path/to/shared/file/system
+ANYVAR_VCF_ASYNC_FAILURE_STATUS_CODE=500
+CELERY_TASK_DEFAULT_QUEUE=anyvar_q
+CELERY_EVENT_QUEUE_PREFIX=anyvar_ev
+CELERY_TIMEZONE=UTC
+CELERY_RESULT_EXPIRES=7200
+CELERY_TASK_ACKS_LATE=true
+CELERY_TASK_REJECT_ON_WORKER_LOST=false
+CELERY_WORKER_PREFETCH_MULTIPLIER=1
+CELERY_TASK_TIME_LIMIT=3900
+CELERY_SOFT_TIME_LIMIT=3600
+CELERY_WORKER_SEND_TASK_EVENTS=false
+
+## Testing - see "Contributing" -> "Testing" in the docs
+ANYVAR_TEST_STORAGE_URI=postgresql://postgres:postgres@localhost/anyvar_test
+
+# for Docker-based SeqRepo install
+SEQREPO_INSTANCE_DIR="/usr/local/share/seqrepo/2024-12-20"

anyvar-1.0.0/.git-blame-ignore-revs

@@ -0,0 +1,3 @@
+# .git-blame-ignore-revs
+# Initial linting
+1c01e4880f1973bfad61b7c591508e96e99fe6bc

anyvar-1.0.0/.github/CODEOWNERS

@@ -0,0 +1 @@
+* @biocommons/anyvar-maintainers

anyvar-1.0.0/.github/ISSUE_TEMPLATE/bug-report.yaml

@@ -0,0 +1,93 @@
+name: Bug Report
+description: Report a bug.
+labels: ["bug"]
+body:
+  - type: textarea
+    attributes:
+      label: Describe the bug
+      description: Provide a clear and concise description of what the bug is.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Steps to reproduce
+      description: Provide detailed steps to replicate the bug.
+      placeholder: |
+        1. In this environment...
+        2. With this config...
+        3. Run '...'
+        4. See error...
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Expected behavior
+      description: What did you expect to happen?
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Current behavior
+      description: |
+        What actually happened?
+
+        Include full errors, stack traces, and/or relevant logs.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Acceptance Criteria
+      description: |
+        Provide the criteria that must be met in order for this issue to be considered fixed.
+        Be specific, and consider potential edge cases.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Possible reason(s)
+      description: Provide any insights into what might be causing the issue.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Suggested fix
+      description: Provide any suggestions on how to resolve the bug.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Branch, commit, and/or version
+      description: Provide the branch, commit, and/or version you're using.
+      placeholder: |
+        branch: issue-1
+        commit: abc123d
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Screenshots
+      description: If applicable, add screenshots with descriptions to help explain your problem.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Environment details
+      description: Provide environment details (OS name and version, etc).
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Additional details
+      description: Provide any other additional details about the problem.
+    validations:
+      required: false
+  - type: dropdown
+    attributes:
+      label: Contribution
+      description: Can you contribute to the development of this feature?
+      options:
+        - "Yes, I can create a PR for this fix."
+        - "Yes, but I can only provide ideas and feedback."
+        - "No, I cannot contribute."
+    validations:
+      required: false

anyvar-1.0.0/.github/ISSUE_TEMPLATE/feature-request.yaml

@@ -0,0 +1,68 @@
+name: Feature Request
+description: Suggest an idea for this project.
+labels: ["enhancement"]
+body:
+  - type: textarea
+    attributes:
+      label: Feature description
+      description: Provide a clear and concise description of what you want to happen.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Use case
+      description: |
+        Why do you need this feature? For example: "I'm always frustrated when..."
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Acceptance Criteria
+      description: |
+        Provide the criteria that must be met in order for this issue to be considered complete.
+        Be specific, and consider potential edge cases.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Proposed solution
+      description: Provide proposed solution.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Alternatives considered
+      description: Describe any alternative solutions you've considered.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Implementation details
+      description: Provide any technical details on how the feature might be implemented.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Potential Impact
+      description: |
+        Discuss any potential impacts of this feature on existing functionality or performance, if known.
+        Will this feature cause breaking changes?
+        What challenges might arise?
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Additional context
+      description: Provide any other context or screenshots about the feature.
+    validations:
+      required: false
+  - type: dropdown
+    attributes:
+      label: Contribution
+      description: Can you contribute to the development of this feature?
+      options:
+        - "Yes, I can create a PR for this feature."
+        - "Yes, but I can only provide ideas and feedback."
+        - "No, I cannot contribute."
+    validations:
+      required: false

anyvar-1.0.0/.github/labels.yml

@@ -0,0 +1,3 @@
+# file must contain an array, which may be empty
+
+[]

anyvar-1.0.0/.github/workflows/labels.yml

@@ -0,0 +1,29 @@
+name: Sync labels
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - 'main'
+    paths:
+      - '.github/labels.yml'
+      - '.github/workflows/labels.yml'
+
+permissions:
+  issues: write
+
+jobs:
+  labels:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          sparse-checkout: .github/labels.yml
+
+      - uses: EndBug/label-sync@v2
+        with:
+          config-file: |
+            https://raw.githubusercontent.com/biocommons/.github/main/etc/labels.yml
+            .github/labels.yml
+
+          delete-other-labels: false

anyvar-1.0.0/.github/workflows/python-package.yml

@@ -0,0 +1,133 @@
+name: Python package
+
+on:
+  push:
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  lint:
+    name: lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --extra dev
+
+      - name: Check style
+        run: uv run ruff check && uv run ruff format --check
+  test:
+    name: test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+    services:
+      postgres:
+        image: postgres:17
+        env:
+          POSTGRES_PASSWORD: postgres
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 5432:5432
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Wait for Postgres
+        run: |
+          for i in {1..30}; do
+            pg_isready -h localhost -p 5432 -U postgres && exit 0
+            sleep 1
+          done
+          exit 1
+
+      - name: Initialize GiST extension
+        env:
+          PGPASSWORD: postgres
+        run: |
+          psql -h localhost -p 5432 -U postgres -d postgres \
+            -c "CREATE EXTENSION IF NOT EXISTS btree_gist;"
+
+      - name: Cache chainfiles for liftover
+        uses: actions/cache@v4
+        with:
+          path: ~/.local/share/wags_tails
+          key: ${{ runner.os }}-test-${{ hashFiles('pyproject.toml') }}
+
+      - name: Setup Python
+        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: Install dependencies
+        run: uv sync --extra test --extra queueing
+
+      - name: Run tests
+        run: uv run pytest -vv -m "ci_ok"
+        env:
+          ANYVAR_TEST_STORAGE_URI: postgresql://postgres:postgres@localhost:5432/postgres
+
+  precommit_hooks:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        cmd:
+          - "end-of-file-fixer"
+          - "trailing-whitespace"
+          - "mixed-line-ending"
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: ${{ matrix.cmd }} --all-files
+  docs:
+    runs-on: ubuntu-latest
+    env:
+      SPHINX_GITHUB_CHANGELOG_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --extra docs
+
+      - name: Attempt docs build
+        working-directory: ./docs
+        run: source ../.venv/bin/activate && make html

anyvar-1.0.0/.github/workflows/release.yml

@@ -0,0 +1,102 @@
+# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+name: Publish Python distribution to PyPI
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - 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
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/anyvar
+    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
+
+  build-and-push-image:
+    # https://docs.github.com/en/packages/managing-github-packages-using-github-actions-workflows/publishing-and-installing-a-package-with-github-actions#publishing-a-package-using-an-action
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: write
+      attestations: write
+      id-token: write
+
+    env:
+      REGISTRY: ghcr.io
+      IMAGE_NAME: ${{ github.repository }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Log in to GHCR
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=raw,value=latest,enable=${{ !github.event.release.prerelease }}
+            type=semver,pattern={{version}}
+
+      - name: Build and push Docker image
+        id: push
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v3
+        with:
+          subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}}
+          subject-digest: ${{ steps.push.outputs.digest }}
+          push-to-registry: true

anyvar-1.0.0/.github/workflows/stale.yml

@@ -0,0 +1,11 @@
+# https://github.com/actions/stale
+
+name: 'Close stale issues and PRs'
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '1 1 * * *'
+
+jobs:
+  stale:
+    uses: biocommons/.github/.github/workflows/stale.yml@main

anyvar-1.0.0/.gitignore

@@ -0,0 +1,126 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# IDEs and editors
+.vscode/
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+*.DS_Store
+eggs/
+.eggs/
+.idea/
+lib/
+lib64/
+parts/
+sdist/
+var/
+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
+
+# Testing stuff and coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+anyvar-test.duckdb
+tests/tmp_async_work_dir
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Lockfiles
+Pipfile.lock
+uv.lock
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+*~
+*.orig
+archive
+
+# local dev tooling
+.justfile
+
+docker/data*
+
+# logging configs
+logging.yaml

anyvar-1.0.0/.pre-commit-config.yaml

@@ -0,0 +1,21 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0  # pre-commit-hooks version
+    hooks:
+      - id: check-added-large-files
+      - id: detect-private-key
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+        exclude: "^docs/source/_templates/.*\\.rst"
+      - id: check-merge-conflict
+      - id: detect-aws-credentials
+        args: [ --allow-missing-credentials ]
+      - id: mixed-line-ending
+        args: [ --fix=lf ]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.12.8  # ruff version
+    hooks:
+      - id: ruff-format
+      - id: ruff
+        args: [ --fix, --exit-non-zero-on-fix ]
+minimum_pre_commit_version: 4.2.0

anyvar-1.0.0/.readthedocs.yaml

@@ -0,0 +1,16 @@
+version: 2
+
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "3.11"
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+sphinx:
+  configuration: docs/source/conf.py