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build: add python boilerplate
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‎.github/workflows/python-package.yaml‎

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name: Python package
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on:
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push:
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pull_request:
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permissions:
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contents: read
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jobs:
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lint:
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name: lint
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Setup Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- name: Install uv
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uses: astral-sh/setup-uv@v6
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with:
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enable-cache: true
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- name: Install dependencies
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run: uv sync --extra dev
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- name: Check style
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run: uv run ruff check && uv run ruff format --check
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precommit_hooks:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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cmd:
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- "end-of-file-fixer"
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- "trailing-whitespace"
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- "mixed-line-ending"
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python 3.12
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uses: actions/setup-python@v5
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with:
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python-version: 3.12
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- uses: pre-commit/[email protected]
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with:
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extra_args: ${{ matrix.cmd }} --all-files

‎.pre-commit-config.yaml‎

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

‎Makefile‎

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# Makefile for Python project
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.DELETE_ON_ERROR:
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.PHONY: FORCE
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.PRECIOUS:
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.SUFFIXES:
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SHELL:=/bin/bash -e -o pipefail
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SELF:=$(firstword $(MAKEFILE_LIST))
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PKG=vlm
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PKGD=$(subst .,/,${PKG})
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PYV:=3.11
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VEDIR=venv/${PYV}
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UNAME = $(shell uname)
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ifeq (${UNAME},Darwin)
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_XRM_R:=
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else
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_XRM_R:=r
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endif
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XRM=xargs -0${_XRM_R} rm
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############################################################################
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#= BASIC USAGE
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default: help
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#=> help -- display this help message
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help:
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@sbin/makefile-extract-documentation "${SELF}"
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############################################################################
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#= SETUP, INSTALLATION, PACKAGING
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#=> venv: make a Python 3 virtual environment & install basic dependencies
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.PHONY: venv/%
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venv/%:
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python$* -m venv $@; \
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. $@/bin/activate; \
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python -m ensurepip --upgrade; \
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pip install --upgrade pip setuptools; \
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pip install .
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#=> develop: install package in develop mode
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.PHONY: develop
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develop:
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pip install -e .[test]
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#=> devready: create venv, install prerequisites, install pkg in develop mode
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.PHONY: devready
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devready:
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make ${VEDIR} && source ${VEDIR}/bin/activate && make develop
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@echo '################################################################'
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@echo '### `source ${VEDIR}/bin/activate` to use this environment ###'
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@echo '################################################################'
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#=> install: install package
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#=> bdist bdist_egg bdist_wheel build sdist: distribution options
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.PHONY: bdist bdist_egg bdist_wheel build build_sphinx sdist install
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bdist bdist_egg bdist_wheel build sdist install: %:
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python setup.py $@
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############################################################################
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#= TESTING
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# see test configuration in setup.cfg
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.PHONY: testready
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testready:
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pip install -e '.[postgres,queueing,test]'
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#=> test: execute tests
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.PHONY: test
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test:
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python -m pytest tests
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#=> cqa: execute code quality tests
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cqa:
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ruff format --check
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ruff check
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#=> reformat: reformat code
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.PHONY: reformat
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reformat:
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ruff check --fix
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ruff format
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############################################################################
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#= CLEANUP
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#=> clean: remove temporary and backup files
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.PHONY: clean
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clean:
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find . \( -name \*~ -o -name \*.bak \) -print0 | ${XRM}
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#=> cleaner: remove files and directories that are easily rebuilt
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.PHONY: cleaner
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cleaner: clean
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rm -rf .cache *.egg-info .pytest_cache build dist doc/_build htmlcov
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find . \( -name \*.pyc -o -name \*.orig -o -name \*.rej \) -print0 | ${XRM} -fr
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find . -name __pycache__ -print0 | ${XRM} -fr
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rm -fvr .ruff_cache
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#=> cleanest: remove files and directories that require more time/network fetches to rebuild
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.PHONY: cleanest
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cleanest: cleaner
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rm -fr .eggs .venv

‎pyproject.toml‎

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[project]
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name = "vlm"
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authors = [
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{ name="biocommons contributors", email="[email protected]" },
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]
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description = "Off-the-shelf solution for adding local aggregate-level variant information to a VLM network"
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readme = "README.md"
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license = { file="LICENSE" }
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requires-python = ">=3.11"
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classifiers = [
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Programming Language :: Python :: 3.13",
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"Programming Language :: Python :: 3.14",
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"License :: OSI Approved :: MIT License",
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"Operating System :: OS Independent",
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]
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dependencies = [
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"fastapi>=0.95.0",
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"python-multipart", # required for fastapi file uploads
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"uvicorn",
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"python-dotenv",
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"anyio",
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]
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dynamic = ["version"]
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[project.optional-dependencies]
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test = [
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"pytest",
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"pytest-cov",
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"httpx",
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"jsonschema",
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"pyyaml",
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]
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dev = [
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"ruff==0.12.8",
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"pre-commit>=4.2.0",
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"ipykernel",
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]
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[project.urls]
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Homepage = "https://github.com/genomicmedlab/vlm_in_a_box"
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Documentation = "https://github.com/genomicmedlab/vlm_in_a_box/"
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Changelog = "https://github.com/genomicmedlab/vlm_in_a_box/releases"
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Source = "https://github.com/genomicmedlab/vlm_in_a_box/"
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"Bug Tracker" = "https://github.com/genomicmedlab/vlm_in_a_box/issues"
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[build-system]
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requires = [
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"setuptools >= 65.3",
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"setuptools_scm >= 8"
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]
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build-backend = "setuptools.build_meta"
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[tool.setuptools_scm]
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[tool.pytest.ini_options]
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addopts = "--cov=anyvar --cov-report term-missing"
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testpaths = ["tests"]
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pythonpath = ["src"]
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[tool.coverage.run]
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branch = true
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source = ["biocommons.example"]
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omit = ["*_test.py", "*/test/*", "*/tests/*"]
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[tool.coverage.report]
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show_missing = true
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exclude_lines = [
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# Have to re-enable the standard pragma
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"pragma: no cover",
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# Don't complain about missing debug-only code:
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"def __repr__",
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"if self.debug",
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# Don't complain if tests don't hit defensive assertion code:
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"raise AssertionError",
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"raise NotImplementedError",
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# Don't complain if non-runnable code isn't run:
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"if __name__ == .__main__.:",
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]
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[tool.ruff]
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src = ["src"]
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include = ["src/**/*.py", "tests/**/*.py"]
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[tool.ruff.lint]
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select = ["ALL"]
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ignore = [
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# not used
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"AIR",
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"ERA",
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"FAST",
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"YTT",
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"FBT",
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"CPY",
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"DJ",
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"EM",
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"EXE",
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"FIX",
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"FA",
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"INT",
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"PYI",
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"TID",
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"TD",
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"TC",
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"C90",
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"NPY",
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"PD",
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# ignore for compatibility with formatter
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"D206",
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"D300",
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"W191",
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"E111",
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"E114",
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"E117",
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"E501",
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"W191",
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"S321",
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"COM812",
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# don't require types on *args, **kwargs
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"ANN002",
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"ANN003",
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# subjective pylint thresholds
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"PLR0904",
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"PLR091",
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"PLR1702",
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# excessive docstring requirements
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"D105",
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"D205",
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"D203",
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"D213", # conflicts with D212
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"D400",
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"D401",
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"D403",
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"D415",
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# excessive exception message requirements
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"TRY003",
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# excessive type ignore requirements
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"PGH003",
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# misc unnecessary readability requirements
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"RET504",
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]
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[tool.ruff.lint.flake8-unused-arguments]
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ignore-variadic-names = true
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[tool.ruff.lint.per-file-ignores]
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"__init__.py" = ["F401", "E402"]
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"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011", "INP001", "D", "C400", "PLR2004"]
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[tool.ruff.format]
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docstring-code-format = true

‎src/vlm/__init__.py‎

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