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docs: 📝 update README (#129)
# Description This PR updates the (non-template) README to match the latest version. This PR needs a medium-depth review. ## Checklist - [x] Added or updated tests - [x] Updated documentation - [x] Ran `just run-all` --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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‎README.md

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# Template for Seedcase Python packages
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# Template Python Package: An opinionated setup for making Python packages
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This repository contains a template for setting up new Python package
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projects in Seedcase. The first step is to create a new repository using
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this template. This can easily be done by clicking the “Use this
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template” button on the repository page or by using the GitHub CLI:
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<!-- [![DOI]()]() -->
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``` bash
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# NAME is the name to give the new repository
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gh repo create NAME --template seedcase-project/template-python-project
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```
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[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-teal.json?raw=true)](https://github.com/copier-org/copier)
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[![GitHub
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License](https://img.shields.io/github/license/seedcase-project/template-python-package.svg)](https://github.com/seedcase-project/template-python-package/blob/main/LICENSE.md)
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[![GitHub
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Release](https://img.shields.io/github/v/release/seedcase-project/template-python-package.svg)](https://github.com/seedcase-project/template-python-package/releases/latest)
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[![Build
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website](https://github.com/seedcase-project/template-python-package/actions/workflows/build-website.yml/badge.svg)](https://github.com/seedcase-project/template-python-package/actions/workflows/build-website.yml)
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[![CodeQL](https://github.com/seedcase-project/template-python-package/actions/workflows/github-code-scanning/codeql/badge.svg?branch=main)](https://github.com/seedcase-project/template-python-package/actions/workflows/github-code-scanning/codeql)
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[![pre-commit.ci
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status](https://results.pre-commit.ci/badge/github/seedcase-project/template-python-package/main.svg)](https://results.pre-commit.ci/latest/github/seedcase-project/template-python-package/main)
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[![lifecycle](https://lifecycle.r-lib.org/articles/figures/lifecycle-experimental.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
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[![Project Status: Active – The project has reached a stable, usable
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state and is being actively
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developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
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## Setting things up after cloning
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This repository contains a [copier](https://copier.readthedocs.io/)
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template for setting up a new repository for a Python package. Along
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with a structured directory layout, this template includes configured
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development tools, CI configuration, and supporting files for package
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setup, publishing, and maintenance.
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Search for `NAME` and `REPO` and replace them with the name of your
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project and the repository name. Then look for any `TODO` items.
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Check out our
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[website](https://template-python-package.seedcase-project.org/) for
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more information, such as the features it provides and a
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[guide](https://template-python-package.seedcase-project.org/docs/guide/)
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to using the template. For a list of changes, see our
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[changelog](https://template-python-package.seedcase-project.org/docs/releases/)
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page.
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## Setting things up
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## Contributing
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Use the commands found in
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[`spaid`](https://github.com/seedcase-project/spaid) repo to run the
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next setup steps.
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Check out our [contributing
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page](https://template-python-package.seedcase-project.org/contributing/)
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for information on how to contribute to the project, including how to
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set up your development environment.
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Need to install these packages after:
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Please note that this project is released with a [Contributor Code of
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Conduct](https://github.com/seedcase-project/.github/blob/main/CODE_OF_CONDUCT.md).
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By participating in this project you agree to abide by its terms.
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``` bash
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uv add --dev pre-commit ruff typos pytest bandit commitizen \
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genbadge jupyter pytest-cov quartodoc
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```
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## Licensing
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This project is licensed under the [MIT
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License](https://github.com/seedcase-project/template-python-package/blob/main/LICENSE.md).
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## Citing
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This project is part of the Seedcase Project, which is a collaborative
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effort to create a framework for data management and analysis in
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research. If you use this project in your work, please cite it as
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follows:
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Johnston L.W., Brødbæk S.K., Beicher K., Vago M. Template Python
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Package: An opinionated setup for making Python packages URL:
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https://template-python-package.seedcase-project.org
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Or as a BibTeX entry:
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@misc{YourReferenceHere,
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author = {Johnston, Luke William and Brødbæk, Signe Kirk and Beicher, Kristiane and Vago, Marton},
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title = {Template Python Package: An opinionated setup for making Python packages},
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url = {https://template-python-package.seedcase-project.org}
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}

‎README.qmd

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# Template for Seedcase Python packages
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---
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format: gfm
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execute:
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echo: false
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jupyter: python3
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metadata-files:
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- _metadata.yml
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---
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This repository contains a template for setting up new Python package projects in Seedcase. The first step is to create a new repository using this template. This can easily be done by clicking the "Use this template" button on the repository page or by using the GitHub CLI:
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# {{< meta titles.full >}}
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``` bash
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# NAME is the name to give the new repository
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gh repo create NAME --template seedcase-project/template-python-project
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```
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{{< include /docs/includes/_badges.qmd >}}
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This repository contains a [copier](https://copier.readthedocs.io/)
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template for setting up a new repository for a Python package. Along
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with a structured directory layout, this template includes configurations
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for tools that improve developer experience, continuous integration and
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delivery workflows, and supporting files for building robust Python packages.
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Check out our
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[website](https://{{< meta gh.repo >}}.{{< meta gh.org >}}.org/) for
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more information, such as the features it provides and a
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[guide](https://{{< meta gh.repo >}}.{{< meta gh.org >}}.org/docs/guide/)
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to using the template. For a list of changes, see our
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[changelog](https://{{< meta gh.repo >}}.{{< meta gh.org >}}.org/docs/releases/)
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page.
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## Contributing
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Check out our [contributing
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page](https://{{< meta gh.repo >}}.{{< meta gh.org >}}.org/contributing/)
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for information on how to contribute to the project, including how to
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set up your development environment.
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Please note that this project is released with a [Contributor Code of
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Conduct](https://github.com/{{< meta gh.org >}}/.github/blob/main/CODE_OF_CONDUCT.md).
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By participating in this project you agree to abide by its terms.
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## Setting things up after cloning
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::: content-hidden
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<!-- TODO: Unhide after more contributors -->
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Search for `NAME` and `REPO` and replace them with the name of your project and the repository name. Then look for any `TODO` items.
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### Contributors
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## Setting things up
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{{< include /_contributors.qmd >}}
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:::
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Use the commands found in [`spaid`](https://github.com/seedcase-project/spaid) repo to run the next setup steps.
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## Licensing
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This project is licensed under the [MIT
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License](https://github.com/{{< meta gh.org >}}/{{< meta gh.repo >}}/blob/main/LICENSE.md).
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## Citing
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This project is part of the Seedcase Project, which is a collaborative
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effort to create a framework for data management and analysis in
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research. If you use this project in your work, please cite it as
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follows:
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```{python}
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#| output: asis
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!uvx --quiet cffconvert --format apalike
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```
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Need to install these packages after:
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Or as a BibTeX entry:
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``` bash
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uv add --dev pre-commit ruff typos pytest bandit commitizen \
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genbadge jupyter pytest-cov quartodoc
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```{python}
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!uvx --quiet cffconvert --format bibtex
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```

‎_contributors.qmd

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These are the people who have contributed by submitting changes through pull requests :tada:
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[\@lwjohnst86](https://github.com/lwjohnst86), [\@signekb](https://github.com/signekb), [\@martonvago](https://github.com/martonvago)

‎_metadata.yml

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gh:
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org: "seedcase-project"
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repo: "template-python-package"
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titles:
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full: "Template Python Package: An opinionated setup for making Python packages"
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short: "Template Python Package"

‎tools/get-contributors.sh

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#!/usr/bin/env bash
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# Get a list of contributors to this repository and save it to
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# _contributors.qmd.tmp file. It also:
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# _contributors.qmd file (overwritten if it exists). It also:
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#
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# - Formats users into Markdown links to their GitHub profiles.
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# - Removes any usernames with the word "bot" in them.
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# - Removes the trailing comma from the list.
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repo_spec=${1}
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echo "These are the people who have contributed by submitting changes through pull requests :tada:\n\n" > _contributors.qmd.tmp
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echo "These are the people who have contributed by submitting changes through pull requests :tada:\n\n" > _contributors.qmd
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gh api \
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-H "Accept: application/vnd.github+json" \
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-H "X-GitHub-Api-Version: 2022-11-28" \
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/repos/$repo_spec/contributors \
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--template '{{range .}} [\@{{.login}}]({{.html_url}}){{"\n"}}{{end}}' | \
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grep -v "\[bot\]" | \
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tr '\n' ', ' | \
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sed -e 's/,$//' >> _contributors.qmd.tmp
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sed -e 's/,$//' >> _contributors.qmd

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