🚸 Make reusable workflows more generic (#407)

## Description

This PR tries to make the reusable workflows from the repository truly
reusable in our top-level projects; at least in the top-priority ones.
This includes:
- passing additional CMake arguments to the configure calls
- potentially setting up Z3
- running mypy in GitHub CI instead of pre-commit.ci (frequently runs
out of memory if you add to many dependencies to the mypy job)
- eliminates the need for a CodeQL configuration file
- adding retry jobs on coverage uploads
- a minimal versions Python test with coverage that makes sure
everything works with all the lower caps
- automatically setting the `DEPLOY` CMake variable in CI systems

## Checklist:

<!---
This checklist serves as a reminder of a couple of things that ensure
your pull request will be merged swiftly.
-->

- [x] The pull request only contains commits that are related to it.
- [x] I have added appropriate tests and documentation.
- [x] I have made sure that all CI jobs on GitHub pass.
- [x] The pull request introduces no new warnings and follows the
project's style guidelines.

.cirrus.yml

@@ -61,8 +61,6 @@ linux_aarch64_wheels_task:
     architecture: arm64
     platform: linux
     cpu: 8
-  env:
-    CIBW_SKIP: "*-musllinux_*"
   setup_pyhton_script:
     - apt-get install -y python3-venv python-is-python3
   <<: *BUILD_AND_STORE_WHEELS

.github/codecov.yml

@@ -1,7 +1,6 @@
 ignore:
   - "extern/**/*"
-  - "include/python/**/*"
-  - "src/python/**/*"
+  - "**/python"
   - "test/**/*"
 
 coverage:
@@ -27,12 +26,11 @@ flag_management:
       paths:
         - "include"
         - "src"
-        - "!src/mqt/**/*"
       after_n_builds: 1
     - name: python
       paths:
         - "src/mqt/**/*.py"
-      after_n_builds: 2
+      after_n_builds: 3
       statuses:
         - type: project
           threshold: 0.5%

.github/dependabot.yml

@@ -2,16 +2,35 @@ version: 2
 updates:
   - package-ecosystem: "gitsubmodule"
     directory: "/"
+    groups:
+      submodules:
+        patterns:
+          - "*"
     schedule:
       interval: "monthly"
-      day: "wednesday"
       time: "06:00"
       timezone: "Europe/Vienna"
 
   - package-ecosystem: "github-actions"
     directory: "/"
+    groups:
+      github-actions:
+        patterns:
+          - "*"
     schedule:
       interval: "weekly"
       day: "wednesday"
       time: "06:00"
       timezone: "Europe/Vienna"
+
+  - package-ecosystem: "pip"
+    directory: "/"
+    groups:
+      python-dependencies:
+        patterns:
+          - "*"
+    schedule:
+      interval: "weekly"
+      day: "friday"
+      time: "06:00"
+      timezone: "Europe/Vienna"

.github/workflows/release-drafter.yml

@@ -1,4 +1,4 @@
-name: 📝 • Release Drafter
+name: Release Drafter
 
 on:
   push:
@@ -20,4 +20,4 @@ jobs:
     steps:
       - uses: release-drafter/release-drafter@v5
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ github.token }}

.github/workflows/reusable-change-detection.yml

@@ -72,6 +72,7 @@ jobs:
             !test/python/**
             .clang-tidy
             .github/workflows/reusable-cpp-linter.yml
+            .github/workflows/ci.yml
       - name: Set a flag for running the C++ linter
         if: >-
           github.event_name != 'pull_request'
@@ -98,6 +99,7 @@ jobs:
             .github/workflows/reusable-python-tests.yml
             .github/workflows/reusable-python-coverage.yml
             .github/workflows/reusable-python-ci.yml
+            .github/workflows/ci.yml
       - name: Set a flag for running the Python tests
         if: >-
           github.event_name != 'pull_request'
@@ -122,6 +124,7 @@ jobs:
             .github/workflows/reusable-code-ql-cpp.yml
             .github/workflows/reusable-code-ql-python.yml
             .github/workflows/reusable-code-ql.yml
+            .github/workflows/ci.yml
       - name: Set a flag for running CodeQL
         if: >-
           github.event_name != 'pull_request'

.github/workflows/reusable-code-ql-cpp.yml

@@ -1,6 +1,19 @@
 name: 📝 • CodeQL • C++
 on:
   workflow_call:
+    inputs:
+      cmake-args:
+        description: "Additional arguments to pass to CMake"
+        default: ""
+        type: string
+      setup-z3:
+        description: "Whether to set up Z3"
+        default: false
+        type: boolean
+      z3-version:
+        description: "The version of Z3 to set up"
+        default: "4.11.2"
+        type: string
 
 jobs:
   analyze:
@@ -16,6 +29,13 @@ jobs:
         with:
           submodules: recursive
           fetch-depth: 0
+      - if: ${{ inputs.setup-z3 }}
+        name: Setup Z3
+        uses: cda-tum/setup-z3@v1
+        with:
+          version: ${{ inputs.z3-version }}
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
       - name: Setup ccache
         uses: Chocobo1/setup-ccache-action@v1
         with:
@@ -29,8 +49,11 @@ jobs:
           languages: cpp
           config-file: .github/codeql-config.yml
           setup-python-dependencies: false
+          config: |
+            queries:
+              - uses: security-and-quality
       - name: Configure CMake
-        run: cmake -S . -B build -DCMAKE_BUILD_TYPE=Debug
+        run: cmake -S . -B build -DCMAKE_BUILD_TYPE=Debug ${{ inputs.cmake-args }}
       - name: Build
         run: cmake --build build
       - name: Perform CodeQL Analysis

.github/workflows/reusable-code-ql-python.yml

@@ -1,6 +1,19 @@
 name: 📝 • CodeQL • Python
 on:
   workflow_call:
+    inputs:
+      setup-z3:
+        description: "Whether to set up Z3"
+        default: false
+        type: boolean
+      z3-version:
+        description: "The version of Z3 to set up"
+        default: "4.11.2"
+        type: string
+      build-time-dependencies:
+        description: "The build-time dependencies to install"
+        default: "nanobind scikit-build-core[pyproject] setuptools_scm pybind11"
+        type: string
 
 jobs:
   analyze:
@@ -16,6 +29,13 @@ jobs:
         with:
           submodules: recursive
           fetch-depth: 0
+      - if: ${{ inputs.setup-z3 }}
+        name: Setup Z3
+        uses: cda-tum/setup-z3@v1
+        with:
+          version: ${{ inputs.z3-version }}
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
       - name: Setup ccache
         uses: Chocobo1/setup-ccache-action@v1
         with:
@@ -30,8 +50,8 @@ jobs:
           cache: "pip"
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip wheel
-          pip install nanobind scikit-build-core[pyproject] setuptools_scm pybind11
+          python -m pip install --upgrade pip wheel setuptools
+          pip install ${{ inputs.build-time-dependencies }}
           pip install --no-build-isolation -ve .
           echo "CODEQL_PYTHON=$(which python)" >> $GITHUB_ENV
       - name: Initialize CodeQL
@@ -40,6 +60,9 @@ jobs:
           languages: python
           config-file: .github/codeql-config.yml
           setup-python-dependencies: false
+          config: |
+            queries:
+            - uses: security-and-quality
       - name: Perform CodeQL Analysis
         uses: github/codeql-action/analyze@v2
         with:

.github/workflows/reusable-code-ql.yml

@@ -2,12 +2,47 @@ name: 📝 • CodeQL
 
 on:
   workflow_call:
+    inputs:
+      cmake-args:
+        description: "Additional arguments to pass to CMake"
+        default: ""
+        type: string
+      setup-z3:
+        description: "Whether to set up Z3"
+        default: false
+        type: boolean
+      z3-version:
+        description: "The version of Z3 to set up"
+        default: "4.11.2"
+        type: string
+      build-time-dependencies:
+        description: "The build-time dependencies to install"
+        default: "nanobind scikit-build-core[pyproject] setuptools_scm pybind11"
+        type: string
+      enable-cpp:
+        description: "Whether to enable C++ analysis"
+        default: true
+        type: boolean
+      enable-python:
+        description: "Whether to enable Python analysis"
+        default: true
+        type: boolean
 
 jobs:
   analyze-cpp:
+    if: ${{ inputs.enable-cpp }}
     name: 🇨‌
     uses: ./.github/workflows/reusable-code-ql-cpp.yml
+    with:
+      cmake-args: ${{ inputs.cmake-args }}
+      setup-z3: ${{ inputs.setup-z3 }}
+      z3-version: ${{ inputs.z3-version }}
 
   analyze-python:
+    if: ${{ inputs.enable-python }}
     name: 🐍
     uses: ./.github/workflows/reusable-code-ql-python.yml
+    with:
+      setup-z3: ${{ inputs.setup-z3 }}
+      z3-version: ${{ inputs.z3-version }}
+      build-time-dependencies: ${{ inputs.build-time-dependencies }}

.github/workflows/reusable-cpp-ci.yml

@@ -5,6 +5,31 @@ on:
       token:
         description: "The token to use for Codecov"
         required: true
+    inputs:
+      cmake-args:
+        description: "Additional arguments to pass to CMake on every OS"
+        default: "-G Ninja"
+        type: string
+      cmake-args-ubuntu:
+        description: "Additional arguments to pass to CMake on Ubuntu"
+        default: ""
+        type: string
+      cmake-args-macos:
+        description: "Additional arguments to pass to CMake on macOS"
+        default: ""
+        type: string
+      cmake-args-windows:
+        description: "Additional arguments to pass to CMake on Windows"
+        default: ""
+        type: string
+      setup-z3:
+        description: "Whether to set up Z3"
+        default: false
+        type: boolean
+      z3-version:
+        description: "The version of Z3 to set up"
+        default: "4.11.2"
+        type: string
 
 jobs:
   cpp-tests-ubuntu:
@@ -16,6 +41,9 @@ jobs:
     uses: ./.github/workflows/reusable-cpp-tests-ubuntu.yml
     with:
       config: ${{ matrix.config }}
+      cmake-args: ${{ inputs.cmake-args }} ${{ inputs.cmake-args-ubuntu }}
+      setup-z3: ${{ inputs.setup-z3 }}
+      z3-version: ${{ inputs.z3-version }}
 
   cpp-tests-macos:
     name: 🍎 ${{ matrix.config }}
@@ -26,6 +54,9 @@ jobs:
     uses: ./.github/workflows/reusable-cpp-tests-macos.yml
     with:
       config: ${{ matrix.config }}
+      cmake-args: ${{ inputs.cmake-args }} ${{ inputs.cmake-args-macos }}
+      setup-z3: ${{ inputs.setup-z3 }}
+      z3-version: ${{ inputs.z3-version }}
 
   cpp-tests-windows:
     name: 🏁 ${{ matrix.config }}
@@ -36,9 +67,16 @@ jobs:
     uses: ./.github/workflows/reusable-cpp-tests-windows.yml
     with:
       config: ${{ matrix.config }}
+      cmake-args: ${{ inputs.cmake-args }} ${{ inputs.cmake-args-windows }}
+      setup-z3: ${{ inputs.setup-z3 }}
+      z3-version: ${{ inputs.z3-version }}
 
   coverage:
     name: 📈
     uses: ./.github/workflows/reusable-cpp-coverage.yml
     secrets:
       token: ${{ secrets.token }}
+    with:
+      cmake-args: ${{ inputs.cmake-args }} ${{ inputs.cmake-args-ubuntu }}
+      setup-z3: ${{ inputs.setup-z3 }}
+      z3-version: ${{ inputs.z3-version }}

.github/workflows/reusable-cpp-coverage.yml

@@ -5,6 +5,19 @@ on:
       token:
         description: "The token to use for Codecov"
         required: true
+    inputs:
+      cmake-args:
+        description: "Additional arguments to pass to CMake"
+        default: "-G Ninja"
+        type: string
+      setup-z3:
+        description: "Whether to set up Z3"
+        default: false
+        type: boolean
+      z3-version:
+        description: "The version of Z3 to set up"
+        default: "4.11.2"
+        type: string
 
 jobs:
   coverage:
@@ -18,24 +31,38 @@ jobs:
       - uses: actions/checkout@v3
         with:
           submodules: recursive
+      - if: ${{ inputs.setup-z3 }}
+        name: Setup Z3
+        uses: cda-tum/setup-z3@v1
+        with:
+          version: ${{ inputs.z3-version }}
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
       - name: Setup ccache
         uses: Chocobo1/setup-ccache-action@v1
         with:
           prepend_symlinks_to_path: false
           override_cache_key: c++-coverage
       - name: Set up mold as linker
         uses: rui314/setup-mold@v1
+      - name: Install Ninja
+        run: pipx install ninja
       - name: Configure CMake
-        run: cmake -S . -B build -DCMAKE_BUILD_TYPE=Debug -DENABLE_COVERAGE=ON -DDEPLOY=ON
+        run: cmake -S . -B build -DCMAKE_BUILD_TYPE=Debug -DENABLE_COVERAGE=ON ${{ inputs.cmake-args }}
       - name: Build
         run: cmake --build build --config Debug
       - name: Test
-        run: ctest -C Debug --output-on-failure --test-dir build --repeat until-pass:3 --timeout 300
+        run: ctest -C Debug --output-on-failure --test-dir build --repeat until-pass:3 --timeout 600
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        # Coverage uploads can be flaky, so we retry them a few times.
+        uses: Wandalen/wretry.action@v1.3.0
         with:
-          fail_ci_if_error: true
-          flags: cpp
-          gcov: true
-          gcov_ignore: "extern/**/*"
-          token: ${{ secrets.token }}
+          action: codecov/codecov-action@v3
+          attempt_limit: 5
+          attempt_delay: 2000
+          with: |
+            fail_ci_if_error: true
+            flags: cpp
+            gcov: true
+            gcov_ignore: "extern/**/*"
+            token: ${{ secrets.token }}