Merge pull request #33 from IMSY-DKFZ/develop

v0.2.1 release

.dockerignore

@@ -557,6 +557,8 @@ migrated
 **/*.blosc
 **/*.model
 **/*.png
+!resources/icon.png
+!resources/logo.png
 **/*.pkl
 **/*.pdf
 **/*.lprof

.editorconfig

@@ -18,3 +18,6 @@ trim_trailing_whitespace = false
 
 [*.{diff,patch}]
 trim_trailing_whitespace = false
+
+[*.{yaml,yml,json}]
+indent_size = 2

.gitattributes

@@ -1,2 +0,0 @@
-*.png filter=lfs diff=lfs merge=lfs -text
-*.svg filter=lfs diff=lfs merge=lfs -text

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,39 @@
+---
+name: 🐛 Bug report
+about: If something isn't working 🔧
+title: ''
+labels: bug
+assignees:
+---
+
+## 🐛 Bug Report
+
+<!-- A clear and concise description of what the bug is. -->
+
+## 🔬 How To Reproduce
+
+Steps to reproduce the behavior:
+
+1. ...
+
+### Code sample
+
+<!-- If applicable, attach a minimal code sample to reproduce the decried issue. -->
+
+### Environment
+
+* OS: e.g. Linux / Windows / macOS
+* CMake version: e.g. 3.22.1
+* Compiler: e.g. gcc / clang
+
+### Screenshots
+
+<!-- If applicable, add screenshots to help explain your problem. -->
+
+## 📈 Expected behavior
+
+<!-- A clear and concise description of what you expected to happen. -->
+
+## 📎 Additional context
+
+<!-- Add any other context about the problem here. -->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,3 @@
+# Configuration: https://help.github.com/en/github/building-a-strong-community/configuring-issue-templates-for-your-repository
+
+blank_issues_enabled: false

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,23 @@
+---
+name: 🚀 Feature request
+about: Suggest an idea for this project 🏖
+title: ''
+labels: enhancement
+assignees:
+---
+
+## 🚀 Feature Request
+
+<!-- A clear and concise description of the feature proposal. -->
+
+## 🔈 Motivation
+
+<!-- Please describe the motivation for this proposal. -->
+
+## 🛰 Alternatives
+
+<!-- A clear and concise description of any alternative solutions or features you've considered. -->
+
+## 📎 Additional context
+
+<!-- Add any other context or screenshots about the feature request here. -->

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,27 @@
+## Description
+
+<!-- Add a more detailed description of the changes if needed. -->
+
+## Related Issue
+
+<!-- If your PR refers to a related issue, link it here. -->
+
+## Type of Change
+
+<!-- Mark with an `x` all the checkboxes that apply (like `[x]`) -->
+
+- [ ] 📚 Examples / docs / tutorials / dependencies update
+- [ ] 🔧 Bug fix (non-breaking change which fixes an issue)
+- [ ] 🥂 Improvement (non-breaking change which improves an existing feature)
+- [ ] 🚀 New feature (non-breaking change which adds functionality)
+- [ ] 💥 Breaking change (fix or feature that would cause existing functionality to change)
+- [ ] 🔐 Security fix
+
+## Checklist
+
+<!-- Mark with an `x` all the checkboxes that apply (like `[x]`) -->
+
+- [ ] I've read the `CODE_OF_CONDUCT.md` document.
+- [ ] I've updated the code style using the `pre-commit hooks`.
+- [ ] I've written tests for all new methods and classes that I created.
+- [ ] I've written the docstring for all the methods and classes that I used.

.github/release-drafter.yml

@@ -0,0 +1,32 @@
+name-template: 'v$RESOLVED_VERSION 🌈'
+tag-template: 'v$RESOLVED_VERSION'
+categories:
+  - title: '🚀 Features'
+    labels:
+      - 'feature'
+      - 'enhancement'
+      - 'documentation'
+  - title: '🐛 Bug Fixes'
+    labels:
+      - 'fix'
+      - 'bugfix'
+      - 'bug'
+  - title: '🧰 Maintenance'
+    label: 'chore'
+change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
+change-title-escapes: '\<*_&' # You can add # and @ to disable mentions, and add ` to disable code blocks.
+version-resolver:
+  major:
+    labels:
+      - 'major'
+  minor:
+    labels:
+      - 'minor'
+  patch:
+    labels:
+      - 'patch'
+  default: patch
+template: |
+  ## Changes
+
+  $CHANGES

.github/stale.yml

@@ -0,0 +1,17 @@
+# Number of days of inactivity before an issue becomes stale
+daysUntilStale: 60
+# Number of days of inactivity before a stale issue is closed
+daysUntilClose: 7
+# Issues with these labels will never be considered stale
+exemptLabels:
+  - pinned
+  - security
+# Label to use when marking an issue as stale
+staleLabel: wontfix
+# Comment to post when marking an issue as stale. Set to `false` to disable
+markComment: >
+  This issue has been automatically marked as stale because it has not had
+  recent activity. It will be closed if no further activity occurs. Thank you
+  for your contributions.
+# Comment to post when closing a stale issue. Set to `false` to disable
+closeComment: false

.github/workflows/build.yml

@@ -0,0 +1,95 @@
+name: Build, Test & Install
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    types: [ opened, reopened, synchronize ]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [ ubuntu-22.04, ubuntu-24.04 ]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Checkout project
+        uses: actions/[email protected]
+      - name: Install apt dependencies
+        run: |
+          sudo apt install xvfb libgl1-mesa-dev -y
+          chmod +x install_dependencies.sh
+          sudo ./install_dependencies.sh
+      - name: Build project
+        run: |
+          mkdir build
+          cd build
+          cmake -DCMAKE_INSTALL_PREFIX=/usr ..
+          xvfb-run -a --server-args="-screen 0 1024x768x24" make all -j
+      - name: Run tests
+        run: |
+          cd build
+          CTEST_OUTPUT_ON_FAILURE=1 xvfb-run -a --server-args="-screen 0 1024x768x24" make test -j
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Build and install DEB package
+        run: |
+          cd build
+          xvfb-run -a --server-args="-screen 0 1024x768x24" make package -j
+          sudo apt install ./xilens*.deb
+      - name: Upload DEB package artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: xilens_deb-${{ matrix.os }}
+          path: build/xilens*.deb
+      - name: Install application
+        run: |
+          cd build
+          sudo make install
+  install_deb:
+    needs: build
+    strategy:
+      matrix:
+        os: [ ubuntu-22.04, ubuntu-24.04 ]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Download DEB package
+        uses: actions/download-artifact@v4
+        with:
+          name: xilens_deb-${{ matrix.os }}
+      - name: Install DEB package
+        run: |
+          sudo apt install ./xilens*.deb
+      - name: Install non-apt dependencies
+        run: |
+          wget --progress=bar:force:noscroll https://www.ximea.com/downloads/recent/XIMEA_Linux_SP.tgz
+          tar xzf XIMEA_Linux_SP.tgz
+          cd package
+          sed -i '/^[^#]/ s/\(^.*udevadm control --reload.*$\)/#\ \1/' scripts/install_steps
+          sudo ./install
+          cd ..
+          git clone https://github.com/Blosc/c-blosc2.git
+          cd c-blosc2
+          git checkout v2.15.1
+          mkdir build
+          cd build
+          cmake -DCMAKE_INSTALL_PREFIX=/usr ..
+          sudo make install -j
+      - name: Check app installation
+        run: |
+          xilens --version
+  documentation:
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Checkout project
+        uses: actions/[email protected]
+      - name: Documentation
+        run: |
+          sudo apt install doxygen graphviz
+          sudo pip3 install -U sphinx furo breathe
+          cd docs
+          doxygen Doxyfile
+          make html

.github/workflows/codeql.yml

@@ -0,0 +1,62 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "develop", "main" ]
+  pull_request:
+    branches: [ "develop", "main" ]
+  schedule:
+    - cron: '31 12 * * 6'
+
+jobs:
+  analyze:
+    name: Analyze (${{ matrix.language }})
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # required to fetch internal or private CodeQL packs
+      packages: read
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - language: c-cpp
+            build-mode: manual
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          sudo apt install xvfb libgl1-mesa-dev -y
+          chmod +x install_dependencies.sh
+          sudo ./install_dependencies.sh
+
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        with:
+          languages: ${{ matrix.language }}
+          build-mode: ${{ matrix.build-mode }}
+
+      # Build xilens manually
+      - if: matrix.build-mode == 'manual'
+        shell: bash
+        run: |
+          mkdir build
+          cd build
+          cmake -DCMAKE_INSTALL_PREFIX=/usr ..
+          xvfb-run -a --server-args="-screen 0 1024x768x24" make all -j
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3
+        with:
+          category: "/language:${{matrix.language}}"

.github/workflows/greetings.yml

@@ -0,0 +1,16 @@
+name: Greetings
+
+on: [ pull_request, issues ]
+
+jobs:
+  greeting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/first-interaction@v1
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          pr-message: 'Hello @${{ github.actor }}, thank you for submitting a PR! We will respond as soon as possible.'
+          issue-message: |
+            Hello @${{ github.actor }}, thank you for your interest in our work!
+
+            If this is a bug report, please provide screenshots and **minimum viable code to reproduce your issue**, otherwise we can not help you.

.github/workflows/release-drafter.yml

@@ -0,0 +1,41 @@
+name: Release Drafter
+
+on:
+  push:
+    # branches to consider in the event; optional, defaults to all
+    branches:
+      - main
+  # pull_request event is required only for autolabeler
+#  pull_request:
+    # Only following types are handled by the action, but one can default to all as well
+#    types: [ opened, reopened, synchronize ]
+  # pull_request_target event is required for autolabeler to support PRs from forks
+  # pull_request_target:
+  #   types: [opened, reopened, synchronize]
+
+permissions:
+  contents: read
+
+jobs:
+  update_release_draft:
+    permissions:
+      # write permission is required to create a github release
+      contents: write
+      # write permission is required for autolabeler
+      # otherwise, read permission is required at least
+      pull-requests: read
+    runs-on: ubuntu-latest
+    steps:
+      # (Optional) GitHub Enterprise requires GHE_HOST variable set
+      #- name: Set GHE_HOST
+      #  run: |
+      #    echo "GHE_HOST=${GITHUB_SERVER_URL##https:\/\/}" >> $GITHUB_ENV
+
+      # Drafts your next Release notes as Pull Requests are merged into "main"
+      - uses: release-drafter/release-drafter@v6
+        # (Optional) specify config name to use, relative to .github/. Default: release-drafter.yml
+        # with:
+        #   config-name: my-config.yml
+        #   disable-autolabeler: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}