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‎.dockerignore

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‎.gitattributes

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# singularity containers
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*.sif filter=lfs diff=lfs merge=lfs -tex
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# plink files
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*.fam filter=lfs diff=lfs merge=lfs -text
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*.bim filter=lfs diff=lfs merge=lfs -text
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*.bed filter=lfs diff=lfs merge=lfs -text
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*.frq filter=lfs diff=lfs merge=lfs -text
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# general archives
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*.bz2 filter=lfs diff=lfs merge=lfs -text
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*.gz filter=lfs diff=lfs merge=lfs -text
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*.zip filter=lfs diff=lfs merge=lfs -text
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*.tar filter=lfs diff=lfs merge=lfs -text
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# matlab files
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*.mat filter=lfs diff=lfs merge=lfs -text
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# specific files
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reference/dummybinary filter=lfs diff=lfs merge=lfs -text

‎.github/ISSUE_TEMPLATE/bug_report.md

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---
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name: Bug report
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about: Create a report to help us improve
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title: ''
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labels: ''
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assignees: ''
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---
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**Describe the bug**
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A clear and concise description of what the bug is.
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**To Reproduce**
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Steps to reproduce the behavior:
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1. Go to '...'
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2. Click on '....'
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3. Scroll down to '....'
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4. See error
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**Expected behavior**
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A clear and concise description of what you expected to happen.
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**Screenshots**
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If applicable, add screenshots to help explain your problem.
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**Setup (please complete the following information - if applicable):**
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- OS: [e.g. iOS]
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- Docker version (e.g., `Docker version 20.10.17, build 100c701`)
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- Singularity version [e.g. `singularity version 3.7.4`]
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- Container file and version [e.g. `base.sif`]
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**Additional context**
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Add any other context about the problem here.

‎.github/ISSUE_TEMPLATE/documentation_issue.md

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---
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name: Documentation issue
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about: Suggest improvements to the documentation
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title: ''
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labels: ''
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assignees: ''
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---
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**The documentation issue**
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A clear and concise description of what could be improved in the documentation and/or README files.

‎.github/ISSUE_TEMPLATE/feature_request.md

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---
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name: Feature request
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about: Suggest an idea for this project
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title: ''
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labels: ''
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assignees: ''
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---
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**Is your feature request related to a problem? Please describe.**
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A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen.
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**Describe alternatives you've considered**
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A clear and concise description of any alternative solutions or features you've considered.
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**Additional context**
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Add any other context or screenshots about the feature request here.

‎.github/pull_request_template.md

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<!-- To ensure we can review your pull request promptly please complete this template entirely. -->
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<!-- Please reference the issue number here. You can replace "Fixes" with "Closes" if it makes more sense. -->
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Fixes #
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Changes proposed in this pull request:
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<!-- Please list all changes/additions here. -->
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-
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## Before submitting
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<!-- Please complete this checklist BEFORE submitting your PR to speed along the review process. -->
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- [ ] I've read and followed all steps in the [Making a pull request](https://github.com/precimed/container_template/blob/main/CONTRIBUTING.md#making-a-pull-request)
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section of the `CONTRIBUTING` docs.
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- [ ] I've updated or added any relevant docstrings following the syntax described in the
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[Writing docstrings](https://github.com/precimed/container_template/blob/main/CONTRIBUTING.md#writing-docstrings) section of the `CONTRIBUTING` docs.
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- [ ] If this PR fixes a bug, I've added a test that will fail without my fix.
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- [ ] If this PR adds a new feature, I've added tests that sufficiently cover my new functionality.

‎.github/workflows/docker.yml

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name: Dockerfile Linter
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on: [push, pull_request]
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jobs:
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hadolint:
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name: runner / hadolint
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runs-on: ubuntu-latest
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steps:
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- name: Check out code
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uses: actions/checkout@v1
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- name: hadolint
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uses: reviewdog/action-hadolint@v1
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with:
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reporter: github-pr-review # Default is github-pr-check
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fail_on_error: true

‎.github/workflows/greetings.yml

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name: Greetings
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on: [pull_request, issues]
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jobs:
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greeting:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/first-interaction@v1
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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issue-message: 'Hello @${{ github.actor }} , thank you for submitting an issue!'
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pr-message: 'Hello @${{ github.actor }} , thank you submitting a pull request!'

‎.github/workflows/python.yml

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name: Flake8 Linter
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on: [push, pull_request]
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jobs:
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flake8-lint:
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runs-on: ubuntu-latest
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name: Lint
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steps:
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- name: Check out source repository
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uses: actions/checkout@v2
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- name: Set up Python environment
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uses: actions/setup-python@v2
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with:
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python-version: "3.10"
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- name: flake8 Lint
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uses: reviewdog/action-flake8@v3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/stale.yml

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name: Label stale issues and PRs
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on:
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schedule:
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- cron: '30 1 * * *'
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jobs:
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stale:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/stale@v3
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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stale-issue-message: 'This issue appears to be stale due to non-activity'
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stale-pr-message: 'This pull request appears to be stale due to non-activity'
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stale-issue-label: 'no-issue-activity'
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stale-pr-label: 'no-pr-activity'
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days-before-stale: 90
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days-before-close: -1

‎.gitignore

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# misc
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.DS_Store
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# bash
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.bash_history
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# Python
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*.pyc
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.pytest_cache
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__pycache__
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# R
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.rda
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# Sphinx
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_build

‎.readthedocs.yml

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version: 2
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sphinx:
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configuration: docs/source/conf.py
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formats: all
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build:
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image: latest
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conda:
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environment: docs/source/environment.yml
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python:
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version: "3.8"

‎CHANGELOG.md

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# Changelog
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All notable changes to the container-template project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [Unreleased]
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### Added
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- additions goes here
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### Updated
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- updates goes here
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### Fixed
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- fixes goes here
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### Removed
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- removals goes here
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## [MAJOR.MINOR.PATCH] - YYYY-MM-DD
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### Added
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- additions goes here
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### Updated
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- updates goes here
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### Fixed
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- fixes goes here
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### Removed
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- removals goes here

‎CONTRIBUTING.md

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# Contributing
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Thanks for considering contributing! Please read this document to learn the various ways you can contribute to this project and how to go about doing it.
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## Bug reports and feature requests
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### Did you find a bug?
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First, do [a quick search](https://github.com/precimed/container_template/issues) to see whether your issue has already been reported.
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If your issue has already been reported, please comment on the existing issue.
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Otherwise, open [a new GitHub issue](https://github.com/precimed/container_template/issues). Be sure to include a clear title
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and description. The description should include as much relevant information as possible. The description should
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explain how to reproduce the erroneous behavior as well as the behavior you expect to see. Ideally you would include a
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code sample or an executable test case demonstrating the expected behavior.
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### Do you have a suggestion for an enhancement or new feature?
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We use GitHub issues to track feature requests. Before you create a feature request:
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* Make sure you have a clear idea of the enhancement you would like. If you have a vague idea, consider discussing
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it first on a GitHub issue.
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* Check the documentation to make sure your feature does not already exist.
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* Do [a quick search](https://github.com/precimed/container_template/issues) to see whether your feature has already been suggested.
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When creating your request, please:
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* Provide a clear title and description.
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* Explain why the enhancement would be useful. It may be helpful to highlight the feature in other libraries.
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* Include code examples to demonstrate how the enhancement would be used.
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## Making a pull request
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When you're ready to contribute code to address an open issue, please follow these guidelines to help us be able to review your pull request (PR) quickly.
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1. **Initial setup** (only do this once)
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<details><summary>Expand details 👇</summary><br/>
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If you haven't already done so, please [fork](https://help.github.com/en/enterprise/2.13/user/articles/fork-a-repo) this repository on GitHub.
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Then clone your fork locally with
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git clone https://github.com/USERNAME/container_template.git
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or
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git clone [email protected]:USERNAME/container_template.git
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At this point the local clone of your fork only knows that it came from *your* repo, github.com/USERNAME/container_template.git, but doesn't know anything the *main* repo, [https://github.com/precimed/container_template.git](https://github.com/precimed/container_template). You can see this by running
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git remote -v
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which will output something like this:
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origin https://github.com/USERNAME/container_template.git (fetch)
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origin https://github.com/USERNAME/container_template.git (push)
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This means that your local clone can only track changes from your fork, but not from the main repo, and so you won't be able to keep your fork up-to-date with the main repo over time. Therefore you'll need to add another "remote" to your clone that points to [https://github.com/precimed/container_template.git](https://github.com/precimed/container_template). To do this, run the following:
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git remote add upstream https://github.com/precimed/container_template.git
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Now if you do `git remote -v` again, you'll see
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origin https://github.com/USERNAME/container_template.git (fetch)
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origin https://github.com/USERNAME/container_template.git (push)
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upstream https://github.com/precimed/container_template.git (fetch)
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upstream https://github.com/precimed/container_template.git (push)
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2. **Ensure your fork is up-to-date**
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<details><summary>Expand details 👇</summary><br/>
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Once you've added an "upstream" remote pointing to [https://github.com/precimed/container_template.git](https://github.com/precimed/container_template), keeping your fork up-to-date is easy:
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git checkout main # if not already on main
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git pull --rebase upstream main
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git push
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</details>
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3. **Create a new branch to work on your fix or enhancement**
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<details><summary>Expand details 👇</summary><br/>
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Committing directly to the main branch of your fork is not recommended. It will be easier to keep your fork clean if you work on a separate branch for each contribution you intend to make.
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You can create a new branch with
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# replace BRANCH with whatever name you want to give it
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git checkout -b BRANCH
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git push -u origin BRANCH
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</details>
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4. **Test your changes**
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<details><summary>Expand details 👇</summary><br/>
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Our continuous integration (CI) testing runs [a number of checks](https://github.com/precimed/container_template/actions) for each pull request on [GitHub Actions](https://github.com/features/actions).
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You can run most of these tests locally, which is something you should do *before* opening a PR to help speed up the review process and make it easier for us.
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And finally, please update the [CHANGELOG](https://github.com/precimed/container_template/blob/main/CHANGELOG.md) with notes on your contribution in the "Unreleased" section at the top.
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After all of the above checks have passed, you can now open [a new GitHub pull request](https://github.com/precimed/container_template/pulls).
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Make sure you have a clear description of the problem and the solution, and include a link to relevant issues.
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We look forward to reviewing your PR!
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</details>

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