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Merge pull request #4 from rachis-org/pypi-rachis
MAINT: update to Rachis and add nox matrix
2 parents 6a4e6ec + ccb39c0 commit f1b2be0

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‎.github/workflows/ci-cron.yml‎

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name: "ci-cron"
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on:
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schedule:
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# At 01:05 AM UTC, every 3 days, starting on day of the month
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- cron: '05 01 1/3 * *'
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workflow_dispatch: {}
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jobs:
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setup-matrix:
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runs-on: ubuntu-latest
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outputs:
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session: ${{ steps.set-matrix.outputs.session }}
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steps:
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- uses: actions/checkout@v6
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- uses: astral-sh/setup-uv@v7
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- id: set-matrix
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shell: bash
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run: echo session=$(uv run --only-dev nox -k 'test' --json -l | jq -c '[.[].session]') | tee --append $GITHUB_OUTPUT
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tests:
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name: "${{ matrix.session }} [${{ matrix.os }}]"
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needs: [setup-matrix]
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strategy:
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fail-fast: false
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matrix:
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session: ${{ fromJson(needs.setup-matrix.outputs.session) }}
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os: ['macos-latest', 'macos-15-intel', 'ubuntu-latest']
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runs-on: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v6
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with:
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fetch-depth: 0
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fetch-tags: true
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- uses: astral-sh/setup-uv@v7
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- run: uv run nox -s "${{ matrix.session }}"

‎.github/workflows/ci-dev.yml‎

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name: ci-dev
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on:
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pull_request:
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branches: ["main"]
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push:
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branches: ["main"]
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jobs:
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setup-matrix:
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runs-on: ubuntu-latest
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outputs:
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tests: ${{ steps.set-matrix.outputs.tests }}
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misc: ${{ steps.set-matrix.outputs.misc }}
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steps:
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- uses: actions/checkout@v6
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- uses: astral-sh/setup-uv@v7
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- id: set-matrix
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shell: bash
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run: |
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echo tests=$(uv run --only-dev nox -t pr-matrix --json -l | jq -c '[.[].session]') | tee --append $GITHUB_OUTPUT
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echo misc=$(uv run --only-dev nox -t pr --json -l | jq -c '[.[].session]') | tee --append $GITHUB_OUTPUT
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misc:
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name: "${{ matrix.session }}"
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needs: [setup-matrix]
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strategy:
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fail-fast: false
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matrix:
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session: ${{ fromJson(needs.setup-matrix.outputs.misc) }}
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v6
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- uses: astral-sh/setup-uv@v7
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- run: uv run nox -s "${{ matrix.session }}"
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tests:
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name: "${{ matrix.session }} [${{ matrix.os }}]"
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needs: [setup-matrix]
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strategy:
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fail-fast: false
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matrix:
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session: ${{ fromJson(needs.setup-matrix.outputs.tests) }}
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os: ['macos-latest', 'ubuntu-latest']
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runs-on: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v6
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with:
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fetch-depth: 0
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fetch-tags: true
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- uses: astral-sh/setup-uv@v7
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- run: TMPDIR=$RUNNER_TEMP uv run nox -s "${{ matrix.session }}"

‎.github/workflows/ci.yml‎

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This file was deleted.

‎.github/workflows/pypi-publish.yml‎

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name: pypi-publish
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on:
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release:
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types: [published]
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jobs:
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build:
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name: Build Package
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runs-on: ubuntu-latest
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steps:
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- name: Install uv
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uses: astral-sh/setup-uv@61cb8a9741eeb8a550a1b8544337180c0fc8476b # v7.2.0
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- name: Checkout release
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uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v.6.0.2
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with:
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fetch-depth: 0
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fetch-tags: true
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- name: Build package
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run: uv build
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- name: Store dist/*
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uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6.0.0
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with:
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name: dist
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path: dist
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test:
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needs: [build]
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name: Test Wheels
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strategy:
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fail-fast: false
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matrix:
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os: ['macos-latest', 'ubuntu-latest']
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runs-on: ${{ matrix.os }}
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steps:
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- name: Install uv
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uses: astral-sh/setup-uv@61cb8a9741eeb8a550a1b8544337180c0fc8476b # v7.2.0
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- name: Fetch dist/*
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uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
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with:
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name: dist
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path: dist
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- name: Test package
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run: uv run --isolated --no-project --with dist/*.whl artifinder --help
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pypi:
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needs: [build, test]
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name: Publish to PyPI
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runs-on: ubuntu-latest
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# Environment and permissions for trusted publishing via PyPI
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environment:
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name: pypi
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permissions:
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id-token: write
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contents: read
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steps:
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- name: Install uv
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uses: astral-sh/setup-uv@61cb8a9741eeb8a550a1b8544337180c0fc8476b # v7.2.0
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- name: Fetch dist/*
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uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
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with:
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name: dist
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path: dist
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- name: Publish
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run: uv publish

‎README.md‎

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@@ -13,13 +13,13 @@ This can be useful when:
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If you have an existing `rachis` deployment, such as QIIME 2 2025.10, or MOSHPIT 2025.10, you can activate that environment and then install `artifinder` as follows:
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```shell
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pip install git+https://github.com/gregcaporaso/artifinder.git@main
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pip install --no-deps artifinder
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```
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If you don't have an existing deployment, you can install the tiny distribution with artifinder as follows:
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If you don't have an existing deployment, you can install via PyPI as follows:
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```shell
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conda env create -n artifinder --file https://raw.githubusercontent.com/gregcaporaso/artifinder/refs/heads/main/environment-files/artifinder-dev.yml
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pip install artifinder
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```
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## Basic usage

‎noxfile.py‎

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#!/usr/bin/env -S uv run --script
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# /// script
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# dependencies = ["nox>=2025.11.12"]
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# ///
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import nox
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# Tags:
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# test-min - for local testing of min deps
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# test-max - for local testing of max deps
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# pr - for pull-requests
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# pr-matrix - for pull-requests, will us OS matrix
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# [*((python-version, uv-resolution), [*tags])]
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MATRIX = [
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(("3.10", "lowest-direct"), ["test-min", "pr-matrix"]),
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(("3.10", "highest"), []),
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(("3.11", "highest"), []),
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(("3.12", "highest"), ["pr-matrix"]),
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(("3.13", "highest"), []),
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(("3.14", "highest"), ["test-max", "pr-matrix"]),
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]
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def setup_uv(session: nox.Session, resolution="highest") -> None:
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"""
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IMPORTANT: make sure to set `venv_backend="uv"` on @nox.session().
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"""
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session.run_install(
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"uv",
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"sync",
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f"--resolution={resolution}",
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f"--python={session.virtualenv.location}",
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env={"UV_PROJECT_ENVIRONMENT": session.virtualenv.location},
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)
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@nox.session(venv_backend="uv", tags=["pr", "lint"])
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def lint(session: nox.Session) -> None:
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"""
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Run the linters
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"""
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setup_uv(session)
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session.run("ruff", "check", *session.posargs)
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@nox.session(venv_backend="uv")
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@nox.parametrize(
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"python,resolution",
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[x[0] for x in MATRIX],
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ids=['py' + ':'.join(x[0]) for x in MATRIX],
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tags=[x[1] for x in MATRIX],
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)
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def test(session: nox.Session, resolution) -> None:
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"""
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Run the tests (can use `-t test-min` or `-t test-max` to filter)
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"""
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setup_uv(session, resolution)
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session.run("pytest", *session.posargs, '-v')

‎pyproject.toml‎

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license = "BSD-3-Clause"
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license-files = ["LICENSE"]
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dependencies = [
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"click",
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"qiime2"
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"click>=8.1.8",
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"rachis"
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]
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[dependency-groups]
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dev = [
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"nox>=2026.2.9",
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"pytest>=9.0.2",
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"ruff>=0.15.2",
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]
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[project.scripts]
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[tool.versioningit.vcs]
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method = "git-archive"
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describe-subst = "$Format:%(describe)$"
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describe-subst = "$Format:%(describe:tags)$"
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default-tag = "0.0.1"
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[tool.versioningit.next-version]

‎src/artifinder/_util.py‎

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import click
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from qiime2.sdk.result import Result
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from qiime2.core.archive.provenance_lib import ProvDAG
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try:
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from rachis.sdk.result import Result
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from rachis.core.archive.provenance_lib import ProvDAG
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except ModuleNotFoundError:
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from qiime2.sdk.result import Result
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from qiime2.core.archive.provenance_lib import ProvDAG
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from ._version import __version__ as artifinder_version
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