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‎.devcontainer/Dockerfile‎

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FROM mcr.microsoft.com/devcontainers/python:1-3.12-bullseye
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RUN pip3 --disable-pip-version-check --no-cache-dir install \
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"matplotlib==3.8.3" \
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"numpy==1.26.4" \
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"scipy==1.12.0" \
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"scikit-image==0.22.0" \
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"scikit-learn==1.5.2" \
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"tifffile==2024.2.12" \
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"pillow==10.2.0" \
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"ipykernel==6.29.2"

‎.devcontainer/devcontainer.json‎

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// For format details, see https://aka.ms/devcontainer.json. For config options, see the
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// README at: https://github.com/devcontainers/templates/tree/main/src/python
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{
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"name": "Python Learning Codespace",
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"hostRequirements": {
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"cpus": 2
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},
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// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
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"build": {
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"dockerfile": "Dockerfile"
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},
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// Features to add to the dev container. More info: https://containers.dev/features.
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// "features": {},
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// Use 'forwardPorts' to make a list of ports inside the container available locally.
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// "forwardPorts": [],
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// Configure tool-specific properties.
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"customizations": {
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"vscode": {
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"extensions": [
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"ms-toolsai.jupyter"
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],
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"settings": {
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"python.linting.enabled": false,
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"python.languageServer": "None",
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"notebook.kernelPicker.type": "all",
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"jupyter.kernels.filter": [
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// This is a list of kernels to be filtered out, not included:
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{
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"path": "/usr/bin/python3",
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"type": "pythonEnvironment"
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}
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],
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"files.exclude": {
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"**/.*": true,
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"**/*.md": true,
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"**/LICENSE": true,
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"**/requirements.txt": true
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},
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"chat.disableAIFeatures": true
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}
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},
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"codespaces": {
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"openFiles": []
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}
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}
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// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
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// "remoteUser": "root"
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}

‎.github/ISSUE_TEMPLATE/help-wanted.yml‎

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name: Help wanted
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description: Things aren't working and I'm stuck!
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title: Things aren't working and I'm stuck!
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labels: ['help wanted']
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body:
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- type: input
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id: repository
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attributes:
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label: Repository
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description: Paste a link to your GitHub repository.
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placeholder: mobi-fs3-python
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validations:
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required: true
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- type: checkboxes
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id: confirmation_of_accessibility
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attributes:
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label: Access rights
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description: Please confirm that your GitHub repository is public, or you have [granted access](https://docs.github.com/de/account-and-profile/setting-up-and-managing-your-personal-account-on-github/managing-access-to-your-personal-repositories/inviting-collaborators-to-a-personal-repository) to the [course supervisors](https://github.com/BMCV/mobi-fs3-python/blob/master/SUPERVISORS.md).
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options:
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- label: I hereby confirm that the supervisors can access my GitHub repository.
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required: true
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- type: checkboxes
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id: confirmation_of_having_pushed
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attributes:
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label: Git commit and push
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description: Please confirm that you have pushed the work which is relevant to this issue to your GitHub repository.
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options:
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- label: I hereby confirm that I have committed and pushed to my GitHub repository.
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required: true
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- type: input
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id: task
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attributes:
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label: Task
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description: The task number(s) at which you need help.
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validations:
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required: true
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- type: textarea
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id: info
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attributes:
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label: Describe the problem (if possible)
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description: Give some context about the problem.
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validations:
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required: false

‎.github/ISSUE_TEMPLATE/organization.md‎

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---
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name: Organization
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about: Discussions regarding the course organization
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title: ''
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labels: organization
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assignees: ''
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---
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‎.github/ISSUE_TEMPLATE/review-request.yml‎

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name: Review request
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description: Things seem to work but I want comments on my solution!
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title: Things seem to work but I want comments on my solution!
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labels: ['review request']
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body:
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- type: input
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id: repository
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attributes:
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label: Repository
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description: Paste a link to your GitHub repository.
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validations:
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required: true
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- type: checkboxes
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id: confirmation_of_accessibility
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attributes:
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label: Access rights
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description: Please confirm that your GitHub repository is public, or you have [granted access](https://docs.github.com/de/account-and-profile/setting-up-and-managing-your-personal-account-on-github/managing-access-to-your-personal-repositories/inviting-collaborators-to-a-personal-repository) to the [course supervisors](https://github.com/BMCV/mobi-fs3-python/blob/master/SUPERVISORS.md).
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options:
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- label: I hereby confirm that the supervisors can access my GitHub repository.
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required: true
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- type: checkboxes
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id: confirmation_of_having_pushed
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attributes:
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label: Git commit and push
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description: Please confirm that you have pushed the work which is relevant to this issue to your GitHub repository.
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options:
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- label: I hereby confirm that I have committed and pushed to my GitHub repository.
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required: true
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- type: input
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id: task
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attributes:
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label: Task
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description: The task number(s) for which you want comments.
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validations:
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required: true
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- type: textarea
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id: info
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attributes:
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label: Additional context for the comments
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description: Give some context, if applicable.
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validations:
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required: false

‎.github/ISSUE_TEMPLATE/volunteer-presentation.yml‎

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name: Volunteer for presentation
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description: I'd like to present my solutions and discuss with the course!
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title: I'd like to present my solutions and discuss with the course!
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labels: ['volunteer for presentation']
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body:
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- type: input
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id: repository
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attributes:
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label: Repository
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description: Paste a link to your GitHub repository.
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validations:
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required: true
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- type: checkboxes
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id: confirmation_of_accessibility
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attributes:
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label: Access rights
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description: Please confirm that your GitHub repository is public, or you have [granted access](https://docs.github.com/de/account-and-profile/setting-up-and-managing-your-personal-account-on-github/managing-access-to-your-personal-repositories/inviting-collaborators-to-a-personal-repository) to the [course supervisors](https://github.com/BMCV/mobi-fs3-python/blob/master/SUPERVISORS.md).
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options:
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- label: I hereby confirm that the supervisors can access my GitHub repository.
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required: true
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- type: checkboxes
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id: confirmation_of_having_pushed
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attributes:
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label: Git commit and push
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description: Please confirm that you have pushed the work which is relevant to this issue to your GitHub repository.
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options:
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- label: I hereby confirm that I have committed and pushed to my GitHub repository.
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required: true
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- type: dropdown
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id: labsession
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attributes:
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label: Lab session
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description: The lab session for which you volunteer to present your solution.
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options:
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- Introduction (Cheat Sheet)
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- Lab Session 1
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- Lab Session 2
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- Lab Session 3
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- Lab Session 4
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- Bonus Tasks
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validations:
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required: true
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- type: textarea
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id: info
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attributes:
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label: Additional context for the comments
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description: Give some context, if applicable.
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validations:
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required: false

‎.github/workflows/label_issue.yml‎

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name: Assign semester labels to new issues
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on:
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issues:
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types: [opened]
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jobs:
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build:
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runs-on: ubuntu-latest
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permissions:
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issues: write
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steps:
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- uses: kostrykin/[email protected]
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with:
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floor: ws

‎.gitignore‎

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/#use-with-ide
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.pdm.toml
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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.DS_Store
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*.swp

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