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‎.editorconfig‎

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root = true
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[*]
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indent_style = space
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indent_size = 4
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end_of_line = lf
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charset = utf-8
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trim_trailing_whitespace = true
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insert_final_newline = true
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[*.{yml,yaml}]
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indent_size = 2
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[Makefile]
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indent_style = tab

‎.github/pull_request_template.md‎

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<!--
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To add a new package to the list, please add a `meta.yaml` file to the `packages` directory and
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copy the checklist from the README here and fill it out.
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-->

‎.github/workflows/make-json.yml‎

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name: Make JSON
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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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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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mkjson:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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- uses: astral-sh/setup-uv@v7
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- name: Execute validation script and create output directory
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run: |
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uvx --from ./scripts validate-registry --registry-dir packages --outdir=build
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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FORCE_COLOR: "1"
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COLUMNS: "150"
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- name: Upload GitHub Pages artifact
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uses: actions/upload-pages-artifact@v4
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with:
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path: "build"
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deploy:
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runs-on: ubuntu-latest
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needs: mkjson
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# Grant GITHUB_TOKEN the permissions required to make a Pages deployment
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permissions:
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pages: write # to deploy to Pages
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id-token: write
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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if: github.ref == 'refs/heads/main'
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4
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- name: Trigger website build
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run: |
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curl -XPOST \
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-u "scverse-bot:${{ secrets.BOT_GH_TOKEN }}" \
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-H "Accept: application/vnd.github.everest-preview+json" \
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-H "Content-Type: application/json" \
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https://api.github.com/repos/scverse/scverse.github.io/actions/workflows/gh-pages.yml/dispatches \
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--data '{"ref": "main"}'

‎.github/workflows/register-template-repos.yml‎

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name: Register template repos
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on:
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schedule:
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# Twice a month: https://crontab.guru/#0_5_1,15_*_*
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- cron: "0 5 1,15 * *"
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workflow_dispatch:
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jobs:
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register-template-repos:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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with:
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token: ${{ secrets.BOT_GH_TOKEN }}
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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- name: Update template repo registry
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run: uvx --from ./scripts register-template-repos template-repos.yml
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env:
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GITHUB_TOKEN: "${{ secrets.BOT_GH_TOKEN }}"
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FORCE_COLOR: "1"
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COLUMNS: "150"
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- uses: EndBug/add-and-commit@v9
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with:
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add: ./template-repos.yml
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author_name: scverse-bot
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author_email: core-team@scverse.org
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message: "Updated template-repos.yml"
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push: true
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- name: Show diff
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run: git diff HEAD~1

‎.gitignore‎

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.DS_STORE
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__pycache__/
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.*cache/
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/.vscode/
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.venv
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schema.pyi

‎.pre-commit-config.yaml‎

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fail_fast: false
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default_language_version:
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python: python3
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default_stages:
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- pre-commit
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- pre-push
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minimum_pre_commit_version: 2.16.0
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repos:
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# all files
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v6.0.0
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hooks:
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- id: detect-private-key
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- id: check-ast
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- id: end-of-file-fixer
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- id: mixed-line-ending
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args: [--fix=lf]
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- id: trailing-whitespace
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- id: check-case-conflict
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- repo: https://github.com/rbubley/mirrors-prettier
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rev: v3.7.4
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hooks:
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- id: prettier
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# package metadata
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- repo: https://github.com/python-jsonschema/check-jsonschema
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rev: 0.36.0
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hooks:
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- id: check-jsonschema
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files: "scripts/src/ecosystem_scripts/schema.json"
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args: ["--check-metaschema"]
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- repo: https://github.com/python-jsonschema/check-jsonschema
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rev: 0.36.0
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hooks:
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- id: check-jsonschema
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files: "packages/.*/meta.yaml"
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args: ["--schemafile", "scripts/src/ecosystem_scripts/schema.json"]
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- repo: local
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hooks:
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- id: forbid-to-commit
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name: Check files in `packages` directory
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entry: |
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Only `meta.yaml` and logo files are permitted in the packages directory
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language: fail
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files: "^packages/.*$"
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exclude: "^packages/.*/(meta.yaml|logo\\..*)$"
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# scripts
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.14.10
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hooks:
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- id: ruff-check
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args: [--fix, --exit-non-zero-on-fix]
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files: ^scripts/.*$
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- id: ruff-format
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files: ^scripts/.*$
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- repo: https://github.com/tox-dev/pyproject-fmt
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rev: v2.11.1
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hooks:
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- id: pyproject-fmt
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- repo: https://github.com/camptocamp/jsonschema-gentypes
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rev: "2.13.0"
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hooks:
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- id: jsonschema-gentypes
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args:
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- --json-schema=scripts/src/ecosystem_scripts/schema.json
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- --python=scripts/src/ecosystem_scripts/schema.pyi
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files: ^scripts/.*/schema.json$
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v1.19.1
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hooks:
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- id: mypy
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args: [--config-file=scripts/pyproject.toml, scripts]
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pass_filenames: false
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additional_dependencies:
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- httpx
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- httpx-retries
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- types-jsonschema
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- pillow
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- pygithub
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- types-PyYAML
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- rich
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files: ^scripts/.*$

‎LICENSE‎

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BSD 3-Clause License
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Copyright (c) 2022, scverse
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎README.md‎

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# Scverse Ecosystem Packages
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This repository contains the list of scverse ecosystem packages that are displayed on scverse.org and are part of
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the scverse® project.
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The goal is to increase visibility of ecosystem packages and make it easier for users to find appropriate software.
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Registered ecosystem packages can also get their own tag to use on the [scverse forum](https://discourse.scverse.org) for user discussion.
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Authors of these packages can be added to the [scverse github organization](https://github.com/scverse).
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In the future, we may also test releases of core packages against the test suites of ecosystem packages.
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If a package is part of this list, it means it fulfills certain minimum requirements as outlined below.
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It **does not** imply endorsement or that an in-depth review has been performed.
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**Hint:** If you want to receive notifications about new ecosystem packages, simply use GitHub's "watch" functionality for this repository.
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## How can my package become part of the list?
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Submit a pull-request adding a `meta.yaml` file for your package to the `packages` directory.
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- Please copy the checklist from below into the pull request description and answer all questions.
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- Please refer to other entries for examples
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- The full definition of available fields is available in [`schema.json`](scripts/src/ecosystem_scripts/schema.json)
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- You can add a logo in svg/png/webp format if you like. Currently it is not used on our website, though.
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## What are the requirements for an ecosystem package?
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For a package to become an approved ecosystem package, it must fulfill all mandatory requirements from the checklist below.
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Ecosystem packages can be written in non-Python languages as long as they fulfill the above requirements.
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If you cannot or do not want to comply with these requirements, you are still free to make your package interoperable with scverse by using our datastructures, but we will not list your package on our ecosystem page.
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## Checklist for adding packages
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### Mandatory
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Name of the tool: XXX
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Short description: XXX
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How does the package use scverse data structures (please describe in a few sentences): XXX
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- [ ] The code is publicly available under an [OSI-approved](https://opensource.org/licenses/alphabetical) license
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- [ ] The package provides versioned releases
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- [ ] The package can be installed from a standard registry (e.g. PyPI, conda-forge, bioconda)
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- [ ] Automated tests cover essential functions of the package and a reasonable range of inputs and conditions [^1]
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- [ ] Continuous integration (CI) automatically executes these tests on each push or pull request [^2]
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- [ ] The package provides API documentation via a website or README[^3]
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- [ ] The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions)
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- [ ] I am an author or maintainer of the tool and agree on listing the package on the scverse website
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### Recommended
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- [ ] Please announce this package on scverse communication channels (zulip, discourse, twitter)
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- [ ] Please tag the author(s) these announcements. Handles (e.g. `@scverse_team`) to include are:
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- Zulip:
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- Discourse:
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- Mastodon:
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- Bluesky:
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- Twitter:
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- [ ] The package provides tutorials (or "vignettes") that help getting users started quickly
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- [ ] The package uses the [scverse cookiecutter template](https://github.com/scverse/cookiecutter-scverse).
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[^1]: We recommend thtat tests cover at least all user facing (public) functions. Minimal tests ensure that the function does not fail on an example data set. Ideally, tests also ensure the correctness of the results, e.g. by comparing against a snapshot.
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[^2]: Continuous integration means that software tests are automatically executed on every push to the git repository. This guarantees they are always run and that they are run in a clean environment. Scverse ecosystem packages most commonly use [GitHub Actions](https://github.com/features/actions) for CI. For an example, check out our [cookiecutter template](https://github.com/scverse/cookiecutter-scverse).
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[^3]: By API documentation, we mean an overview of _all_ public functions provided a package, with documentation of their parameters. For an example, see the [Scanpy documentation](https://scanpy.readthedocs.io/en/stable/api/preprocessing.html). In simple cases, this can be done manually in a README file. For anything more complex, we recommend the [Sphinx Autodoc plugin](https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html)

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