♻️ Refactor Packaging and CI (#366)

## Description

This PR brings a major refactoring for the overall Python packaging as
well as the CI employed in the project.

### Packaging

We are (finally) moving away from `setuptools` and towards modern
`scikit-build-core` (https://scikit-build-core.readthedocs.io/)
This brings many advantages such as 
- truly editable installs that also include the C++ part; this implies
incredibly fast rebuilds that can be further improved by installing
ccache.
- completely eliminates the `setup.py` (and the `MANIFEST.in`) file and
all custom build code that was required previously.

As part of this change, we adopt the established best practice of a
src-layout for the Python package. This implies that the Python package
no longer lives in the main package directory, but is moved to
`src/mqt/...`.
This avoids several pitfalls when working with Python packages and makes
the overall handling way easier.

This also means there is no direct build-time dependency on cmake and
ninja anymore as this is automatically handled by scikit-build-core on
demand.

As part of this rewrite, several `nox` sessions are also updated

### CI

MQT Core has introduced reusable workflows in 
- munich-quantum-toolkit/core#396

These have been further refined in 
- munich-quantum-toolkit/core#407

Overall, this allows to 
- remove almost all workflow files of this repository
- eliminate a lot of maintenance required in this repository to keep up
with the latest best practices
- rely on dependabot for workflow updates once MQT Core has settled
enough so that it follows proper versioning and we can use tags for the
workflows here instead of `@main`

while at the same time:
- having automatic change detection and only triggering jobs that are
really necessary; with a single pass check that can be used for branch
protection
- setting up ccache for all supported workflow jobs which greatly
improves compilation times
- setting up mold as a better linker under linux
- splitting jobs into as many subjobs as possible and feasible to
distribute work
- automatically creating wheels for all supported platforms (including
exotic platforms that need emulation) and Python versions using PyPI
trusted publishing
- enabling automatic retries for flaky jobs such as MSVC builds or
coverage uploads
- enabling automatic build parallelization via using Ninja wherever
suitable
- running an automatic workflow using the minimal versiosn for all
Python dependencies to guarantee compatibility

As a nice side effect, the new CI has revealed two bugs in the heuristic
mapper. One where the single-qubit gates could not be placed properly
and one where the output permutation inference accessed arrays out of
bounds. Both issues have subsequently been fixed.

## 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.

Author: burgholzer

.cirrus.yml

@@ -0,0 +1,117 @@
+.clone_script: &clone |
+  if [ -z "$CIRRUS_PR" ]; then
+    git clone --recursive --branch=$CIRRUS_BRANCH https://x-access-token:${CIRRUS_REPO_CLONE_TOKEN}@github.com/${CIRRUS_REPO_FULL_NAME}.git $CIRRUS_WORKING_DIR
+    git reset --hard $CIRRUS_CHANGE_IN_REPO
+  else
+    git clone https://x-access-token:${CIRRUS_REPO_CLONE_TOKEN}@github.com/${CIRRUS_REPO_FULL_NAME}.git $CIRRUS_WORKING_DIR
+    git fetch origin pull/$CIRRUS_PR/head:pull/$CIRRUS_PR
+    git checkout $CIRRUS_BASE_BRANCH
+    git -c user.email="you@example.com" merge --no-commit pull/$CIRRUS_PR
+    git submodule update --init --recursive
+  fi
+
+.statistics_script: &statistics |
+  ccache -s -v
+  echo $(python -m pip cache dir)
+  echo $(python -m pip cache list)
+
+macos_arm64_test_task:
+  name: 🐍 Test / 🍎 arm64
+  alias: macos_arm64_test
+  clone_script: *clone
+  macos_instance:
+    image: ghcr.io/cirruslabs/macos-monterey-xcode:latest
+  ccache_cache:
+    folder: .ccache
+    populate_script:
+      - mkdir -p .ccache
+    fingerprint_key: ccache-macosx_arm64
+  pip_cache:
+    folder: /Users/admin/Library/Caches/pip
+  prepare_env_script: |
+    brew install python@3.10 ccache pipx ninja nox z3
+    ln -s $(which python3.10) python
+    export PATH=/opt/homebrew/opt/python@3.10/libexec/bin:$PATH
+    export PATH=/opt/homebrew/opt/ccache/libexec:$PATH
+    export PATH=/opt/homebrew/opt/pipx/libexec:$PATH
+    export PATH=/opt/homebrew/opt/ninja/libexec:$PATH
+    export PATH=/opt/homebrew/opt/nox/libexec:$PATH
+    echo "PATH=$PATH" >> $CIRRUS_ENV
+    echo "CCACHE_DIR=$PWD/.ccache" >> $CIRRUS_ENV
+    echo "Z3_ROOT=/opt/homebrew/opt/z3" >> $CIRRUS_ENV
+  run_nox_script:
+    - nox -s tests-3.10 --verbose
+  statistics_script: *statistics
+
+build_and_store_wheels: &BUILD_AND_STORE_WHEELS
+  install_cibuildwheel_script:
+    - python -m pip install cibuildwheel~=2.15.0
+  run_cibuildwheel_script:
+    - cibuildwheel
+  wheels_artifacts:
+    path: "wheelhouse/*"
+
+linux_aarch64_wheels_task:
+  only_if: "$CIRRUS_RELEASE != ''"
+  name: 🐍 Packaging / 🎡 🐧 arm64
+  alias: linux_aarch64_wheels
+  clone_script: *clone
+  compute_engine_instance:
+    image_project: cirrus-images
+    image: family/docker-builder-arm64
+    architecture: arm64
+    platform: linux
+    cpu: 8
+  env:
+    CIBW_BEFORE_ALL_LINUX: /opt/python/cp311-cp311/bin/pip install z3-solver==4.11.2
+  setup_pyhton_script:
+    - apt-get install -y python3-venv python-is-python3
+  <<: *BUILD_AND_STORE_WHEELS
+
+macos_arm64_wheels_task:
+  only_if: "$CIRRUS_RELEASE != ''"
+  name: 🐍 Packaging / 🎡 🍎 arm64
+  alias: macos_arm64_wheels
+  clone_script: *clone
+  macos_instance:
+    image: ghcr.io/cirruslabs/macos-monterey-xcode:latest
+  ccache_cache:
+    folder: .ccache
+    populate_script:
+      - mkdir -p .ccache
+    fingerprint_key: ccache-macosx_arm64-wheels
+  pip_cache:
+    folder: /Users/admin/Library/Caches/pip
+  prepare_env_script: |
+    brew install python@3.10 ccache pipx ninja nox z3
+    ln -s $(which python3.10) python
+    export PATH=/opt/homebrew/opt/python@3.10/libexec/bin:$PATH
+    export PATH=/opt/homebrew/opt/ccache/libexec:$PATH
+    export PATH=/opt/homebrew/opt/pipx/libexec:$PATH
+    export PATH=/opt/homebrew/opt/ninja/libexec:$PATH
+    export PATH=/opt/homebrew/opt/nox/libexec:$PATH
+    echo "PATH=$PATH" >> $CIRRUS_ENV
+    echo "CCACHE_DIR=$PWD/.ccache" >> $CIRRUS_ENV
+    echo "Z3_ROOT=/opt/homebrew/opt/z3" >> $CIRRUS_ENV
+  <<: *BUILD_AND_STORE_WHEELS
+  statistics_script: *statistics
+
+publish_task:
+  name: 🚀 Deploy to PyPI
+  container: { image: "python:3.10-bullseye" }
+  depends_on:
+    - linux_aarch64_wheels
+    - macos_arm64_wheels
+  only_if: "$CIRRUS_RELEASE != ''"
+  env:
+    TWINE_REPOSITORY: pypi
+    TWINE_USERNAME: __token__
+    TWINE_PASSWORD: "ENCRYPTED\
+      [068b092a2dca55f5b1bc74cff487cf53b9cacb3b77bcbc74\
+      057a446c826e4265e3b46f20081ab5fe44ac5aa4bbd74ee4]"
+  install_script: pip install twine
+  publish_script:
+    - curl -L https://api.cirrus-ci.com/v1/artifact/build/$CIRRUS_BUILD_ID/wheels.zip -o wheels.zip
+    - unzip wheels.zip
+    - python -m twine check wheelhouse/*
+    - python -m twine upload wheelhouse/*

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -1,47 +1,28 @@
 name: 🐛 Bug report
 description: Something is not working correctly.
 title: "🐛 <title>"
-labels: ["bug"]
-assignees:
-  - burgholzer
 body:
   - type: markdown
     attributes:
       value: >-
         **Thank you for wanting to report a bug for this project!**
 
         ⚠
-        Verify first that your issue is not [already reported on GitHub](https://github.com/cda-tum/qmap/search?q=is%3Aissue&type=issues).
+        Verify first that your issue is not [already reported on GitHub](https://github.com/cda-tum/mqt-qmap/search?q=is%3Aissue&type=issues).
 
-        If you are having general questions, please consider [starting a discussion](https://github.com/cda-tum/qmap/discussions).
-  - type: markdown
-    attributes:
-      value: >-
-        **Environment**
-  - type: input
-    attributes:
-      label: mqt.qmap version
-      placeholder: For example, mqt.qmap===1.11.0
-    validations:
-      required: true
-  - type: input
+        If you have general questions, please consider [starting a discussion](https://github.com/cda-tum/mqt-qmap/discussions).
+  - type: textarea
     attributes:
-      label: OS
-      placeholder: For example, Ubuntu 22.04, macOS Big Sur, Windows etc.
+      label: Environment information
+      description: >-
+        Please provide information about your environment. For example, OS, C++ compiler, mqt.core version etc.
+      placeholder: |
+        - OS:
+        - C++ compiler:
+        - mqt.core version:
+        - Additional environment information:
     validations:
       required: true
-  - type: input
-    attributes:
-      label: Python version
-      placeholder: For example, Python 3.10
-  - type: input
-    attributes:
-      label: C++ compiler
-      placeholder: For example, gcc-10
-  - type: textarea
-    attributes:
-      label: Additional environment information
-      description: Feel free to add more information about your environment here.
   - type: textarea
     attributes:
       label: Description

.github/ISSUE_TEMPLATE/feature-request.yml

@@ -1,9 +1,6 @@
 name: ✨ Feature request
 description: Suggest an idea
 title: "✨ <title>"
-labels: ["enhancement"]
-assignees:
-  - burgholzer
 body:
   - type: markdown
     attributes:

.github/codecov.yml

@@ -1,8 +1,7 @@
 ignore:
   - "extern/**/*"
-  - "apps/*"
+  - "**/python"
   - "test/**/*"
-  - "mqt/**/*.cpp"
 
 coverage:
   range: 60..90
@@ -13,10 +12,12 @@ coverage:
 
 flag_management:
   default_rules:
+    carryforward: true
     statuses:
       - type: project
         target: auto
         threshold: 0.5%
+        removed_code_behavior: adjust_base
       - type: patch
         target: 90%
         threshold: 1%
@@ -25,12 +26,15 @@ flag_management:
       paths:
         - "include"
         - "src"
+      after_n_builds: 1
     - name: python
       paths:
-        - "mqt/**/*.py"
+        - "src/mqt/**/*.py"
+      after_n_builds: 3
       statuses:
         - type: project
           threshold: 0.5%
+          removed_code_behavior: adjust_base
         - type: patch
           target: 95%
           threshold: 1%
@@ -41,6 +45,7 @@ parsers:
       conditional: no
       loop: no
 
-codecov:
-  notify:
-    after_n_builds: 4
+comment:
+  layout: "reach, diff, flags, files"
+  require_changes: true
+  show_carryforward_flags: true

.github/codeql-config.yml

@@ -2,14 +2,21 @@ version: 2
 updates:
   - package-ecosystem: "gitsubmodule"
     directory: "/"
+    groups:
+      submodules:
+        patterns:
+          - "*"
     schedule:
-      interval: "weekly"
-      day: "friday"
+      interval: "monthly"
       time: "06:00"
       timezone: "Europe/Vienna"
 
   - package-ecosystem: "github-actions"
     directory: "/"
+    groups:
+      github-actions:
+        patterns:
+          - "*"
     schedule:
       interval: "weekly"
       day: "friday"
@@ -18,6 +25,10 @@ updates:
 
   - package-ecosystem: "pip"
     directory: "/"
+    groups:
+      python-dependencies:
+        patterns:
+          - "*"
     schedule:
       interval: "weekly"
       day: "friday"

.github/dependabot.yml

@@ -0,0 +1,32 @@
+{
+  "problemMatcher": [
+    {
+      "severity": "warning",
+      "pattern": [
+        {
+          "regexp": "^([^:]+):(\\d+):(\\d+): ([A-DF-Z]\\d+): \\033\\[[\\d;]+m([^\\033]+).*$",
+          "file": 1,
+          "line": 2,
+          "column": 3,
+          "code": 4,
+          "message": 5
+        }
+      ],
+      "owner": "pylint-warning"
+    },
+    {
+      "severity": "error",
+      "pattern": [
+        {
+          "regexp": "^([^:]+):(\\d+):(\\d+): (E\\d+): \\033\\[[\\d;]+m([^\\033]+).*$",
+          "file": 1,
+          "line": 2,
+          "column": 3,
+          "code": 4,
+          "message": 5
+        }
+      ],
+      "owner": "pylint-error"
+    }
+  ]
+}

.github/matchers/pylint.json

@@ -0,0 +1,29 @@
+name: CD
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  python-packaging:
+    name: 🐍 Packaging
+    uses: cda-tum/mqt-core/.github/workflows/reusable-python-packaging.yml@main
+    with:
+      setup-z3: true
+
+  deploy:
+    if: github.event_name == 'release' && github.event.action == 'published'
+    name: 🚀 Deploy to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/mqt.qmap
+    permissions:
+      id-token: write
+    needs: [python-packaging]
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1