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Open source the Curate, Annotate and Repair workflows from the morphology-processing-workflow package
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.auto-changelog

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{
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"output": "CHANGELOG.md",
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"template": ".auto-changelog-template.hbs",
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"commitLimit": false,
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"backfillLimit": false,
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"ignoreCommitPattern": "Release [0-9]+\\.[0-9]+\\.[0-9]+|Update CHANGELOG.*|.*\\[skip-changelog\\].*|Initial empty repository",
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"commitUrl": "https://github.com/BlueBrain/dir-content-diff/commit/{id}",
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"issueUrl": "https://github.com/BlueBrain/dir-content-diff/issues/{id}",
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"mergeUrl": "https://github.com/BlueBrain/dir-content-diff/pull/{id}",
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"compareUrl": "https://github.com/BlueBrain/dir-content-diff/compare/{from}..{to}"
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}

.auto-changelog-template.hbs

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# Changelog
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Generated by [auto-changelog](https://github.com/CookPete/auto-changelog).
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{{#each releases}}
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{{#if href}}
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#{{#unless major}}#{{/unless}} [{{title}}]({{href}})
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{{else}}
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## {{title}}
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{{/if}}
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{{#if tag}}
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> {{niceDate}}
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{{/if}}
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{{#if summary}}
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{{summary}}
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{{/if}}
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{{#each merges}}
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- {{#if commit.breaking}}**Breaking change:** {{/if}}{{message}}{{#if href}} [#{{id}}]({{href}}){{/if}}
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{{/each}}
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{{#each fixes}}
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- {{#if commit.breaking}}**Breaking change:** {{/if}}{{commit.subject}}{{#each fixes}} ({{author}}{{#if href}} - [#{{id}}]({{href}}){{/if}}){{/each}}
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{{/each}}
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{{#each commits}}
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- {{#if breaking}}**Breaking change:** {{/if}}{{subject}} ({{author}}{{#if href}} - [{{shorthash}}]({{href}}){{/if}})
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{{/each}}
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{{/each}}

.coveragerc

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[paths]
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source =
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src/morphology_workflows
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*/site-packages/morphology_workflows
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name: Publish sdist tarball to PyPi
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on:
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push:
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tags:
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- '[0-9]+.[0-9]+.[0-9]+'
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jobs:
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build-n-publish:
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name: Build and publish on PyPI
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@master
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- name: Set up Python 3.8
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uses: actions/setup-python@v2
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with:
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python-version: 3.8
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- name: Build a source tarball
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run: |
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python setup.py sdist
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- name: Publish distribution package to PyPI
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uses: pypa/gh-action-pypi-publish@master
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with:
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user: ${{ secrets.DEVPI_USER }}
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password: ${{ secrets.DEVPI_PASSWORD }}
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repository_url: ${{ secrets.DEVPI_URL }}

.github/workflows/run-tox.yml

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name: Run all tox jobs using python3
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on:
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pull_request:
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push:
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branches:
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- main
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.8, 3.9]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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sudo apt-get install -y poppler-utils imagemagick graphviz
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python -m pip install --upgrade pip setuptools
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pip install tox-gh-actions
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- name: Run tox
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run: |
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tox
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- name: Upload to codecov
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if: ${{matrix.python-version == '3.8'}}
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uses: codecov/codecov-action@v1
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with:
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fail_ci_if_error: false
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files: ./coverage-py38.xml
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flags: pytest
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name: "diameter-synthesis-py38"

.gitignore

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**/__pycache__
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*.egg-info
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*.pyc
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._.DS_Store
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.DS_Store
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*.swp
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coverage.xml
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.coverage*
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.eggs
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.tox
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build
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dist
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reports
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doc/build
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doc/source/generated/
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doc/source/autoapi/
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doc/_images

.readthedocs.yml

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# .readthedocs.yml
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# Read the Docs configuration file
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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# Required
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version: 2
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build:
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os: ubuntu-20.04
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tools:
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python: "3.8"
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sphinx:
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configuration: doc/source/conf.py
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fail_on_warning: true
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python:
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install:
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- method: pip
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path: .
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extra_requirements:
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- docs

AUTHORS.md

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Maintainer
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----------
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Alexis Arnaudon (@arnaudon)
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Contributors
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------------
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Adrien Berchet (@adrien-berchet)

CHANGELOG.md

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# Changelog
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## [morphology-curation-workflow-v0.0.1]
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> 15 October 2021
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CONTRIBUTING.md

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# Contributing
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We would love for you to contribute to the luigi-tools package and help make it even better
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than it is today! As a contributor, here are the guidelines we would like you to follow:
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* [Issues and Bugs](#issue)
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* [Feature Requests](#feature)
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* [Submission Guidelines](#submit)
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## <a name="issue"></a> Got a question or found a bug?
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If you have a question or find a bug in the source code, you can help us by
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[submitting an issue](#submit-issue) to our [GitHub Repository][github]. Even better, you can
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[submit a Pull Request](#submit-pr) with a fix.
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## <a name="feature"></a> Missing a Feature?
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You can *request* a new feature by [submitting an issue](#submit-issue) to our
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[GitHub Repository][github]. If you would like to *implement* a new feature, please submit an
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issue with a proposal for your work first, to be sure that we can use it. Then
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[submit a Pull Request](#submit-pr) that points to this issue.
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Please consider what kind of change it is:
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* For a **Major Feature**, first open an issue and outline your proposal so that it can be
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discussed. This will also allow us to better coordinate our efforts, prevent duplication of work,
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and help you to craft the change so that it is successfully accepted into the project.
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* **Small Features** can be crafted and directly [submitted as a Pull Request](#submit-pr).
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## <a name="submit"></a> Submission Guidelines
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### <a name="submit-issue"></a> Submitting an Issue
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Before you submit an issue, please search the issue tracker, maybe an issue for your problem
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already exists and the discussion might inform you of workarounds readily available.
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We want to fix all the issues as soon as possible, but before fixing a bug we need to reproduce
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and confirm it. In order to reproduce bugs we will need as much information as possible, a
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[Minimal Working Example](https://stackoverflow.com/help/minimal-reproducible-example), and
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preferably be in touch with you to gather information.
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### <a name="submit-pr"></a> Submitting a Pull Request (PR)
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When you wish to contribute to the code base, please consider the following guidelines:
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* Make a [fork](https://guides.github.com/activities/forking/) of this repository.
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* Make your changes in your fork, in a new git branch:
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```shell
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git checkout -b my-fix-branch main
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```
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* Create your patch, **including appropriate test cases** (please note that the coverage must
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always be equal to 100%).
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* Run the full test suite, and ensure that all tests pass.
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* Commit your changes using a descriptive commit message.
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```shell
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git commit -a
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```
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Note: the optional commit `-a` command line option will automatically **add** and **rm** edited
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files.
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* Push your branch to GitHub:
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```shell
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git push origin my-fix-branch
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```
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* In GitHub, send a Pull Request to the `main` branch of the upstream repository of the relevant
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component.
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* If we suggest changes then:
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* Make the required updates.
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* Re-run the test suites to ensure tests are still passing.
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* Rebase your branch and force push to your GitHub repository (this will update your Pull Request):
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```shell
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git rebase main -i
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git push -f
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```
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That's it! Thank you for your contribution!
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#### After your pull request is merged
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After your pull request is merged, you can safely delete your branch and pull the changes from the
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main (upstream) repository:
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* Delete the remote branch on GitHub either through the GitHub web UI or your local shell as follows:
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```shell
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git push origin --delete my-fix-branch
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```
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* Check out the main branch:
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```shell
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git checkout main
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```
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* Delete the local branch:
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```shell
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git branch -D my-fix-branch
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```
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* Update your main with the latest upstream version:
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```shell
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git pull --ff upstream main
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```
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### <a name="release"></a> Releasing a new version
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Releasing a new version can only be done by the maintainers.
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The release process is the following:
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* Checkout the main branch and ensure your local version is up to date:
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```shell
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git checkout main
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git pull
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```
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* Create a new branch locally:
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```shell
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git checkout -b release_X.Y.Z
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```
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* Create a new temporary tag locally:
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```shell
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git tag X.Y.Z
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```
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* Update the CHANGELOG file using auto-changelog:
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```shell
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auto-changelog
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```
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* Commit the new changelog and remove the tag:
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```shell
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git commit -m "Release X.Y.Z"
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git tag -d X.Y.Z
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git push origin
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```
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* Open a new pull request from this branch and merge it.
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* Checkout the main branch and update it:
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```shell
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git checkout main
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git pull
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```
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* Create the final tag and push it:
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```shell
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git tag X.Y.Z
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git push origin X.Y.Z
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```
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After these steps the CI should automatically build the wheel and push it to pypi.
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[github]: https://github.com/BlueBrain/morphology-workflows

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