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.devcontainer/Dockerfile

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+FROM mcr.microsoft.com/devcontainers/python:1-3.12-bullseye
+
+RUN pip3 --disable-pip-version-check --no-cache-dir install \
+    "matplotlib==3.8.3" \
+    "numpy==1.26.4" \
+    "scipy==1.12.0" \
+    "scikit-image==0.22.0" \
+    "tifffile==2024.2.12" \
+    "pillow==10.2.0" \
+    "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
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
+{
+	"name": "Python Learning Codespace",
+	"hostRequirements": {
+		"cpus": 2
+	},
+
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"build": {
+		"dockerfile": "Dockerfile"
+	},
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Configure tool-specific properties.
+	"customizations": {
+		"vscode": {
+			"extensions": [
+			  "ms-toolsai.jupyter"
+			],
+			"settings": { 
+				"python.linting.enabled": false,
+				"python.languageServer": "None",
+
+				"notebook.kernelPicker.type": "all",
+				"jupyter.kernels.filter": [
+					// This is a list of kernels to be filtered out, not included:
+					{
+						"path": "/usr/bin/python3",
+						"type": "pythonEnvironment"
+					}
+				],
+
+				"files.exclude": {
+					"images": true,
+					"**/.*": true,
+					"**/*.md": true,
+					"**/LICENSE": true,
+					"**/requirements.txt": true
+				}
+			}
+		},
+		"codespaces": {
+			"openFiles": []
+		}
+	}
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.github/ISSUE_TEMPLATE/help-wanted.yml

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+name: Help wanted
+description: Things aren't working and I'm stuck!
+title: Things aren't working and I'm stuck!
+labels: ['help wanted']
+body:
+  - type: input
+    id: repository
+    attributes:
+      label: Repository
+      description: Paste a link to your GitHub repository.
+      placeholder: mobi-fs3-python
+    validations:
+      required: true
+  - type: checkboxes
+    id: confirmation_of_accessibility
+    attributes:
+      label: Access rights
+      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).
+      options:
+        - label: I hereby confirm that the supervisors can access my GitHub repository.
+          required: true
+  - type: checkboxes
+    id: confirmation_of_having_pushed
+    attributes:
+      label: Git commit and push
+      description: Please confirm that you have pushed the work which is relevant to this issue to your GitHub repository.
+      options:
+        - label: I hereby confirm that I have committed and pushed to my GitHub repository.
+          required: true
+  - type: input
+    id: task
+    attributes:
+      label: Task
+      description: The task number(s) at which you need help.
+    validations:
+      required: true
+  - type: textarea
+    id: info
+    attributes:
+      label: Describe the problem (if possible)
+      description: Give some context about the problem.
+    validations:
+      required: false

.github/ISSUE_TEMPLATE/organization.md

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+---
+name: Organization
+about: Discussions regarding the course organization
+title: ''
+labels: organization
+assignees: ''
+
+---
+
+

.github/ISSUE_TEMPLATE/review-request.yml

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+name: Review request
+description: Things seem to work but I want comments on my solution!
+title: Things seem to work but I want comments on my solution!
+labels: ['review request']
+body:
+  - type: input
+    id: repository
+    attributes:
+      label: Repository
+      description: Paste a link to your GitHub repository.
+    validations:
+      required: true
+  - type: checkboxes
+    id: confirmation_of_accessibility
+    attributes:
+      label: Access rights
+      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).
+      options:
+        - label: I hereby confirm that the supervisors can access my GitHub repository.
+          required: true
+  - type: checkboxes
+    id: confirmation_of_having_pushed
+    attributes:
+      label: Git commit and push
+      description: Please confirm that you have pushed the work which is relevant to this issue to your GitHub repository.
+      options:
+        - label: I hereby confirm that I have committed and pushed to my GitHub repository.
+          required: true
+  - type: input
+    id: task
+    attributes:
+      label: Task
+      description: The task number(s) for which you want comments.
+    validations:
+      required: true
+  - type: textarea
+    id: info
+    attributes:
+      label: Additional context for the comments
+      description: Give some context, if applicable.
+    validations:
+      required: false

.github/ISSUE_TEMPLATE/volunteer-presentation.yml

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+name: Volunteer for presentation
+description: I'd like to present my solutions and discuss with the course!
+title: I'd like to present my solutions and discuss with the course!
+labels: ['volunteer for presentation']
+body:
+  - type: input
+    id: repository
+    attributes:
+      label: Repository
+      description: Paste a link to your GitHub repository.
+    validations:
+      required: true
+  - type: checkboxes
+    id: confirmation_of_accessibility
+    attributes:
+      label: Access rights
+      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).
+      options:
+        - label: I hereby confirm that the supervisors can access my GitHub repository.
+          required: true
+  - type: checkboxes
+    id: confirmation_of_having_pushed
+    attributes:
+      label: Git commit and push
+      description: Please confirm that you have pushed the work which is relevant to this issue to your GitHub repository.
+      options:
+        - label: I hereby confirm that I have committed and pushed to my GitHub repository.
+          required: true
+  - type: dropdown
+    id: labsession
+    attributes:
+      label: Lab session
+      description: The lab session for which you volunteer to present your solution.
+      options:
+        - Lab Session 1
+        - Lab Session 2
+        - Lab Session 3
+        - Lab Session 4
+    validations:
+      required: true
+  - type: textarea
+    id: info
+    attributes:
+      label: Additional context for the comments
+      description: Give some context, if applicable.
+    validations:
+      required: false

.github/workflows/create_future_branch.yml

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+name: Create future branch
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 0 1 9 *'
+
+jobs:
+
+  create_future_branch:
+
+    name: Create future branch
+    runs-on: ubuntu-latest
+    if: github.repository == 'BMCV/mobi-fs3-python-dev'
+
+    permissions:
+      contents: write
+
+    steps:
+
+      - name: Initialize
+        uses: actions/checkout@v4
+
+      - name: Create and initialize future branch
+        uses: kostrykin/create-future-branch-action@master
+

.github/workflows/deploy.yml

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+name: Deploy to target repository
+
+on:
+  workflow_dispatch:
+  push:
+    branches: ['master']
+
+jobs:
+
+  deploy:
+    uses: BMCV/github-workflows/.github/workflows/deploy-notebooks.yml@main
+    name: Deploy
+    if: github.repository == 'BMCV/mobi-fs3-python-dev'
+    with:
+      target-repository: BMCV/mobi-fs3-python
+      exclude: '[".github/workflows/deploy.yml"]'
+    secrets:
+      target_repo_private_key: ${{ secrets.TARGET_REPOSITORY_PRIVATE_KEY }}

.github/workflows/label_issue.yml

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