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Merge branch 'main' into add-smokeshow-coverage
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‎.all-contributorsrc‎

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"profile": "https://github.com/nicoloesch",
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"contributions": [
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"code",
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"bug"
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"bug",
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"design",
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"maintenance",
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"question",
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"review"
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]
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},
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{
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"contributions": [
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"doc"
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]
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},
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{
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"login": "marius-sm",
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"name": "marius-sm",
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"avatar_url": "https://avatars.githubusercontent.com/u/40166021?v=4",
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"profile": "https://github.com/marius-sm",
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"contributions": [
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"ideas"
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]
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},
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{
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"login": "haarisr",
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"name": "haarisr",
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"avatar_url": "https://avatars.githubusercontent.com/u/122410226?v=4",
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"profile": "https://github.com/haarisr",
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"contributions": [
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"code"
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]
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},
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{
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"login": "c-winder",
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"name": "Chris Winder",
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"avatar_url": "https://avatars.githubusercontent.com/u/50587864?v=4",
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"profile": "https://github.com/c-winder",
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"contributions": [
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"bug"
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]
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},
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{
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"login": "rickymwalsh",
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"name": "Ricky Walsh",
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"avatar_url": "https://avatars.githubusercontent.com/u/70853488?v=4",
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"profile": "https://www.linkedin.com/in/ricky-walsh/",
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"contributions": [
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"code"
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]
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},
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{
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"login": "sravan953",
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"name": "Keerthi Sravan Ravi",
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"avatar_url": "https://avatars.githubusercontent.com/u/6049061?v=4",
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"profile": "https://github.com/sravan953",
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"contributions": [
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"bug"
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]
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},
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{
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"login": "RJacobArthrex",
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"name": "Rahul Kurian Jacob",
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"avatar_url": "https://avatars.githubusercontent.com/u/144900466?v=4",
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"profile": "https://github.com/RJacobArthrex",
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"contributions": [
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"doc"
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]
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},
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{
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"login": "erooke",
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"name": "Ethan Rooke",
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"avatar_url": "https://avatars.githubusercontent.com/u/46689793?v=4",
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"profile": "https://ethan.roo.ke",
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"contributions": [
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"doc"
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]
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},
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{
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"login": "mrdkucher",
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"name": "David Kucher",
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"avatar_url": "https://avatars.githubusercontent.com/u/13631603?v=4",
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"profile": "https://github.com/mrdkucher",
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"contributions": [
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"code"
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]
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},
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{
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"login": "StijnvWijn",
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"name": "StijnvWijn",
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"avatar_url": "https://avatars.githubusercontent.com/u/78531113?v=4",
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"profile": "https://github.com/StijnvWijn",
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"contributions": [
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"code"
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]
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},
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{
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"login": "toufiqmusah",
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"name": "Toufiq",
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"avatar_url": "https://avatars.githubusercontent.com/u/92761339?v=4",
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"profile": "http://toufiqmusah.github.io/toufiqmusah/",
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"contributions": [
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"code"
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]
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}
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],
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"contributorsPerLine": 7,
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"projectName": "torchio",
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"projectOwner": "fepegar",
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"projectOwner": "TorchIO-project",
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"repoType": "github",
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"repoHost": "https://github.com",
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"skipCi": true,
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"commitConvention": "angular",
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"commitConvention": "atom",
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"commitType": "docs"
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}

‎.bumpversion.cfg‎

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This file was deleted.

‎.github/ISSUE_TEMPLATE/bug_report.yml‎

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Please run this command in your console and paste the output below
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```shell
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python <(curl -s https://raw.githubusercontent.com/fepegar/torchio/main/print_system.py)
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python <(curl -s https://raw.githubusercontent.com/TorchIO-project/torchio/main/print_system.py)
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```
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placeholder: Your system info
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render: shell

‎.github/ISSUE_TEMPLATE/config.yml‎

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blank_issues_enabled: true
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contact_links:
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- name: ❓ Discussions tab
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url: https://github.com/fepegar/torchio/discussions/new
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url: https://github.com/TorchIO-project/torchio/discussions/new
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about: Ask and answer TorchIO-related questions or start a general discussion
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- name: 💬 Slack
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url: https://join.slack.com/t/torchioworkspace/shared_invite/zt-exgpd5rm-BTpxg2MazwiiMDw7X9xMFg
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about: Chat with our community in real time (if they are connected!)

‎.github/ISSUE_TEMPLATE/not_working.yml‎

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Please run this command in your console and paste the output below
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```shell
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python <(curl -s https://raw.githubusercontent.com/fepegar/torchio/main/print_system.py)
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python <(curl -s https://raw.githubusercontent.com/TorchIO-project/torchio/main/print_system.py)
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```
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placeholder: Your system info
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render: shell

‎.github/dependabot.yml‎

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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/" # Location of package manifests
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directory: "/"
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schedule:
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interval: "weekly"
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interval: "monthly"
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- package-ecosystem: "pip"
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directory: "/"
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schedule:
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interval: "monthly"

‎.github/pull_request_template.md‎

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<!-- You do not need to complete all the items by the time you submit the pull
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request, but most likely the changes will only be merged if all the tasks are
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done. See more information about the submission process in the
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CONTRIBUTING (https://github.com/fepegar/torchio/blob/main/CONTRIBUTING.rst) docs. -->
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CONTRIBUTING (https://github.com/TorchIO-project/torchio/blob/main/CONTRIBUTING.rst) docs. -->
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<!-- Write an `x` in all the boxes that apply -->
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- [ ] I have read the [`CONTRIBUTING`](https://github.com/fepegar/torchio/blob/main/CONTRIBUTING.rst) docs and have a developer setup (especially important are `pre-commit`and `pytest`)
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- [ ] Non-breaking change (would not break existing functionality)
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- [ ] Breaking change (would cause existing functionality to change)
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- [ ] I have read the [`CONTRIBUTING`](https://github.com/TorchIO-project/torchio/blob/main/CONTRIBUTING.rst) docs and have a developer setup ready
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- Changes are
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- [ ] Non-breaking (would not break existing functionality)
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- [ ] Breaking (would cause existing functionality to change)
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- [ ] Tests added or modified to cover the changes
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- [ ] Integration tests passed locally by running `pytest`
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- [ ] In-line docstrings updated
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- [ ] Documentation updated, tested running `make html` inside the `docs/` folder
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- [ ] Documentation updated
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- [ ] This pull request is ready to be reviewed

‎.github/workflows/check_pull_request_title.yml‎

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name: 'Check PR title'
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name: "Check PR title"
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on:
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pull_request:
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types: [edited, opened, synchronize, reopened]
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# Echo the user's login
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- name: Echo user login
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run: echo ${{ github.event.pull_request.user.login }}
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- uses: naveenk1223/action-pr-title@master
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with:
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# Valid titles: "Do something"
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# ^ Start of string
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# [A-Z] First character must be an uppercase ASCII letter
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# [a-zA-Z]* Followed by zero or more ASCII letters
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# (?<![^s]s) Negative lookbehind: disallow a single 's' at the end of the first word
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# ( .+)+ At least one space and one or more characters (requires more words)
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# [^.] Final character must not be a period
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# $ End of string
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regex: "^[A-Z][a-zA-Z]*(?<![^s]s)( .+)+[^.]$"
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# Valid titles:
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# - "Do something"
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# - "Address something"
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# Invalid title:
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# - "do something"
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# - "Do something."
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# - "Does something"
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# - "Do"
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regex: '^[A-Z][a-zA-Z]*(?<!s)( .+)+[^.]$' # Thanks, ChatGPT
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# - "Addresses something"
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min_length: 10
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max_length: 72

‎.github/workflows/code_quality.yml‎

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on:
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push:
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branches: [main]
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branches:
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- main
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pull_request:
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branches: [main]
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workflow_dispatch:
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schedule:
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- cron: "0 4 * * *"
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jobs:
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mypy:
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name: Type checks
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runs-on: ubuntu-latest
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steps:
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Install tox
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run: pip install tox
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- name: Run mypy
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run: tox -e mypy
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flake8:
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name: Code style
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runs-on: ubuntu-latest
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steps:
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Install pre-commit
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run: pip install pre-commit
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- name: Run flake8 hooks
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run: pre-commit run --all-files flake8
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black:
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name: Code formatting
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runs-on: ubuntu-latest
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steps:
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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env:
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FORCE_COLOR: 1
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Install black
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run: pip install black
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- name: Run black
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run: black --check --diff .
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docs:
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name: Documentation
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jobs:
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check:
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name: tox env ${{ matrix.tox_env }}
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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tox_env:
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- format
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- lint
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- types
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steps:
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- name: Checkout repository
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fetch-depth: 0
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- name: Install pre-commit
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run: pip install pre-commit
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- name: Install the latest version of uv
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uses: astral-sh/setup-uv@v6
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- name: Run doc8 hook
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run: pre-commit run --all-files doc8
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- name: Run check for tox env "${{ matrix.tox_env }}"
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run: uvx --with tox-uv -- tox -e ${{ matrix.tox_env }}

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