Add CziShrink

.github/actions/cmake-build/action.yml

@@ -20,6 +20,9 @@ inputs:
   platform:
     description: 'OS platform'
     required: true
+  src-dir:
+    description: 'The directory with the sources'
+    required: true
 runs:
   using: "composite"
   steps:
@@ -33,18 +36,21 @@ runs:
 
     - name: Set toolchain path
       shell: bash
+      working-directory: ${{inputs.src-dir}}
       run: echo "TOOLCHAIN_PATH=${{inputs.path-toolchain}}" >> "$GITHUB_ENV"
 
     - name: Install dependencies
       if: inputs.package == 'ON'
       shell: bash
+      working-directory: ${{inputs.src-dir}}
       run: |
          # We install the following packages: eigen3, catch2, cli11. Installing them with vcpkg (and caching them)
          # is faster than downloading and building them from source (which is the default behavior of the CZICompress-build-system).
          vcpkg install --triplet ${{inputs.platform}} eigen3 catch2 cli11
 
     - name: Configure CMake
       shell: bash
+      working-directory: ${{inputs.src-dir}}
       # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
       # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
       #
@@ -53,5 +59,6 @@ runs:
 
     - name: Build software
       shell: bash
+      working-directory: ${{inputs.src-dir}}
       # Build your program with the given configuration
       run: cmake --build build --config ${{inputs.build-type}}

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# yamllint disable rule:document-start
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "nuget"
+    directory: "/czishrink"
+    schedule:
+      interval: "weekly"
+      day: "wednesday"

.github/workflows/cmake.yml → .github/workflows/czicompress_cmake.yml

@@ -1,11 +1,14 @@
 ---
-name: CMake Build
+name: CMake Build (czicompress)
 
 on:
   push:
     branches: ["main"]  # run only when merge with main branch
+    paths: ["czicompress/**"]
   pull_request:
     branches: ["main"]  # run only when merge with main branch
+    paths: ["czicompress/**"]
+  workflow_dispatch: {}
 
 permissions:
   contents: read
@@ -17,6 +20,9 @@ env:
 
 jobs:
   build-tests:
+    defaults:
+      run:
+        working-directory: ${{github.workspace}}/czicompress
     name: ${{matrix.config.name}}
     runs-on: ${{matrix.config.os}}
 
@@ -46,16 +52,16 @@ jobs:
             package: ON,
             path-cache: '${{ github.workspace }}\vcpkg\installed',
             path-toolchain: 'C:/vcpkg/scripts/buildsystems/vcpkg.cmake',
-            os-id: 'windows'
+            os-id: 'windows',
           }
           - {
             name: ubuntu-release-package-on,
             os: ubuntu-20.04,   # we want to use an older version in order to increase likelihood that binaries work on other distros
             platform: x64-linux,
-            package: ON,
+            package: OFF,
             path-cache: '/usr/local/share/vcpkg/installed',
             path-toolchain: '/usr/local/share/vcpkg/scripts/buildsystems/vcpkg.cmake',
-            os-id: 'linux'
+            os-id: 'linux',
           }
 
     steps:
@@ -71,32 +77,31 @@ jobs:
           build-type: ${{env.BUILD_TYPE}}
           package: ${{matrix.config.package}}
           platform: ${{matrix.config.platform}}
+          src-dir: '${{github.workspace}}/czicompress'
 
       - name: Run unit tests
-        working-directory: ${{github.workspace}}/build
+        working-directory: ${{github.workspace}}/czicompress/build
         # Execute tests defined by the CMake configuration.
         # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
         run: ctest -C ${{env.BUILD_TYPE}}
 
       - name: Prepare licenses
-        working-directory: ${{github.workspace}}
         shell: bash
         run: |
+            set -e
             mkdir ./czicompress-${{matrix.config.name}}
             cp -R ./THIRD_PARTY_LICENSES_ARTIFACT_DISTRIBUTION.txt ./czicompress-${{matrix.config.name}}/
             cp -R ./build/app/THIRD_PARTY_LICENSES.txt ./czicompress-${{matrix.config.name}}/
 
       # gather the binaries
       - name: Prepare Linux binaries
         if: matrix.config.os == 'ubuntu-20.04'
-        working-directory: ${{github.workspace}}
         shell: bash
         run: |
             cp ./build/app/czicompress ./build/capi/libczicompressc.so ./czicompress-${{matrix.config.name}}/
 
       - name: Prepare Windows binaries
         if: matrix.config.os == 'windows-latest'
-        working-directory: ${{github.workspace}}
         shell: bash
         run: |
             cp ./build/app/${{env.BUILD_TYPE}}/*.exe ./build/capi/${{env.BUILD_TYPE}}/libczicompressc.dll ./czicompress-${{matrix.config.name}}/
@@ -106,4 +111,4 @@ jobs:
         uses: actions/upload-artifact@v3
         with:
           name: czicompress-${{matrix.config.name}}
-          path: czicompress-${{matrix.config.name}}/
+          path: czicompress/czicompress-${{matrix.config.name}}/

.github/workflows/codeql.yml → .github/workflows/czicompress_codeql.yml

@@ -1,5 +1,5 @@
 ---
-name: "CodeQL"
+name: "CodeQL (czicompress)"
 
 on:
   push:
@@ -17,7 +17,10 @@ permissions:
 
 jobs:
   analyze:
-    name: Analyze
+    name: Analyze CPP
+    defaults:
+      run:
+        working-directory: ${{github.workspace}}/czicompress
     runs-on: ubuntu-latest
 
     strategy:
@@ -50,6 +53,7 @@ jobs:
           build-type: Release
           package: ON
           platform: x64-linux
+          src-dir: '${{github.workspace}}/czicompress'
 
       - name: Perform CodeQL Analysis
         uses: github/codeql-action/analyze@v2

.github/workflows/czishrink_codeql.yml

@@ -0,0 +1,60 @@
+---
+name: "CodeQL (CziShrink)"
+
+on:
+  push:
+    branches: [main]
+    paths: ["czishrink/**", ".github/workflows/czishrink_codeql.yml"]
+  pull_request:
+    branches: [main]
+    paths: ["czishrink/**", ".github/workflows/czishrink_codeql.yml"]
+  schedule:
+    #        ┌───────────── minute (0 - 59)
+    #        │  ┌───────────── hour (0 - 23)
+    #        │  │ ┌───────────── day of the month (1 - 31)
+    #        │  │ │ ┌───────────── month (1 - 12 or JAN-DEC)
+    #        │  │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
+    #        │  │ │ │ │
+    #        │  │ │ │ │
+    #        │  │ │ │ │
+    #        *  * * * *
+    - cron: '30 2 * * 2'
+  workflow_dispatch: {}
+
+permissions: read-all
+
+jobs:
+  analyze:
+    name: Analyze CziShrink
+    defaults:
+      run:
+        working-directory: czishrink
+    runs-on: ubuntu-latest
+    permissions:
+      security-events: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          lfs: true
+
+      - name: Setup .NET
+        uses: actions/setup-dotnet@v3
+        with:
+          dotnet-version: 7.0.x
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: csharp
+          queries: security-and-quality
+
+      - name: Restore dependencies
+        run: dotnet restore
+
+      - name: Build
+        run: dotnet build --no-restore -c Release
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2

.github/workflows/czishrink_dotnet.yml

@@ -0,0 +1,136 @@
+---
+# This workflow will build a .NET project
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-net
+permissions:
+  pull-requests: write
+  contents: read
+
+name: .NET Build (CziShrink)
+
+on:
+  push:
+    branches: ["main"]
+    paths: ["czishrink/**"]
+  pull_request:
+    branches: ["main"]
+    paths: ["czishrink/**"]
+  workflow_dispatch: {}
+
+jobs:
+  build:
+    defaults:
+      run:
+        working-directory: czishrink
+    name: ${{matrix.config.name}}
+    runs-on: ${{matrix.config.os}}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {
+            name: windows,
+            os: windows-latest,
+            osfamily: win,
+          }
+          - {
+            name: ubuntu,
+            os: ubuntu-latest,
+            osfamily: linux,
+          }
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          lfs: true
+
+      - name: Setup .NET
+        uses: actions/setup-dotnet@v3
+        with:
+          dotnet-version: 7.0.x
+
+      - name: Get Version from Directory.Build.props
+        id: getversion
+        uses: m-ringler/get-xpath@v3
+        with:
+          xml-file: czishrink/Directory.Build.props
+          xpath: 'concat(//VersionPrefix/text(), "-", //VersionSuffix/text())'
+
+      - name: Add build ID to version
+        run: |
+          Write-Output "Add build ID ${{ github.run_id }} to VersionSuffix in Directory.Build.props"
+          $file = Get-Item "Directory.Build.props"
+          $xml = [xml](Get-Content -Path $file.FullName)
+          $versionElement = $xml.SelectSingleNode('//VersionSuffix')
+          $versionElement.'#text' += '+${{ github.run_id }}'
+          $xml.Save($file.FullName)
+        shell: pwsh
+
+      - name: Restore dependencies
+        run: dotnet restore
+
+      - name: Build
+        run: dotnet build --no-restore -c Release
+
+      - name: Test
+        run: >
+          dotnet test
+          -c Release
+          --no-build
+          --verbosity normal
+          --logger trx
+          --results-directory "TestResults"
+          -p:CollectCoverage=true
+          -p:CoverletOutputFormat=cobertura
+          -p:CoverletOutput=${{ github.workspace }}/TestResults/coverage.cobertura.xml
+          -p:ExcludeByAttribute=GeneratedCodeAttribute%2cObsoleteAttribute
+          -p:ExcludeByFile=**/*.axaml%2c**/*.g.cs
+          -p:Exclude='[netczicompress]netczicompress.Views.*'
+
+      - name: Upload dotnet test results
+        uses: actions/upload-artifact@v3
+        with:
+          name: dotnet-results-${{ matrix.config.name }}
+          path: TestResults
+        # Use always() to also publish test results when there are test failures
+        if: ${{ always() }}
+
+      - name: Code Coverage Report
+        uses: irongut/[email protected]
+        if: matrix.config.name == 'ubuntu'
+        with:
+          filename: TestResults/coverage.cobertura.xml
+          badge: true
+          fail_below_min: false
+          format: markdown
+          hide_branch_rate: false
+          hide_complexity: false
+          indicators: true
+          output: both
+          thresholds: '60 80'
+
+      - name: Add Coverage PR Comment
+        uses: marocchino/sticky-pull-request-comment@v2
+        if: github.event_name == 'pull_request' && matrix.config.name == 'ubuntu'
+        with:
+          recreate: true
+          path: code-coverage-results.md
+
+      - name: Publish
+        if: github.event_name == 'push'
+        run: >
+          dotnet publish netczicompress.Desktop/netczicompress.Desktop.csproj
+          -c Release
+          -a x64
+          --self-contained
+          -p:PublishSingleFile=true
+          -p:PublishReadyToRun=true
+          -p:PublishReadyToRunShowWarnings=true
+          -o ${{ github.workspace }}/publish
+
+      - name: Upload published binaries
+        uses: actions/upload-artifact@v3
+        if: github.event_name == 'push'
+        with:
+          name: CziShrink_${{ steps.getversion.outputs.info }}_${{ matrix.config.osfamily}}-x64
+          path: publish

.jsonlintrc.yml

@@ -0,0 +1,5 @@
+# SPDX-FileCopyrightText: 2023 Carl Zeiss Microscopy GmbH
+#
+# SPDX-License-Identifier: MIT
+---
+comments: true

.reuse/dep5

@@ -3,10 +3,18 @@ Upstream-Name: czicompress
 Upstream-Contact: Carl Zeiss Microscopy GmbH <[email protected]>
 Source: https://github.com/ZEISS/czicompress
 
-Files: cla_*.txt CMakeSettings.json CODE_OF_CONDUCT.md CONTRIBUTING.md README.md SECURITY.md THIRD_PARTY_LICENSES*.txt
+Files: cla_*.txt czicompress/CMakeSettings.json CODE_OF_CONDUCT.md CONTRIBUTING.md README.md SECURITY.md czicompress/THIRD_PARTY_LICENSES*.txt czicompress/README.md
 Copyright: 2023 Carl Zeiss Microscopy GmbH
 License: MIT
 
-Files: .github/* .gitignore .editorconfig .runsettings CPPLINT.cfg .clang-format
+Files: .github/* .gitignore czicompress/.editorconfig czicompress/.gitignore czicompress/.runsettings czicompress/CPPLINT.cfg czicompress/.clang-format
 Copyright: 2023 Carl Zeiss Microscopy GmbH
 License: CC0-1.0
+
+Files: czishrink/*.axaml czishrink/.gitignore czishrink/*/.gitignore czishrink/*.json czishrink/*.nuspec czishrink/*.txt czishrink/*.ico czishrink/*.png czishrink/*.props czishrink/*.targets czishrink/*.sh czishrink/*.svg czishrink/*.csproj czishrink/*.gitattributes czishrink/*.nupkg czishrink/*.md czishrink/*.pdf czishrink/*.config czishrink/*.ruleset czishrink/*.ps1 czishrink/*.czi czishrink/*.xml czishrink/*.sln czishrink/*.manifest README.md
+Copyright: 2023 Carl Zeiss Microscopy GmbH
+License: GPL-3.0-or-later
+
+Files: czishrink/*/mandelbrot.czi
+Copyright: 2023 Carl Zeiss Microscopy GmbH
+License: CC0-1.0