feat(nix): Build documentation and Python bindings in Nix

.editorconfig

@@ -13,5 +13,5 @@ trim_trailing_whitespace = true
 [*.{md,toml,yml,yaml,nix,html,css}]
 indent_size = 2
 
-[{Makefile,**/CMakeLists.txt}]
+[{**/Makefile,**/CMakeLists.txt}]
 indent_style = tab

.github/workflows/actions/docs/action.yml

@@ -0,0 +1,31 @@
+name: Build Documentation
+description: Build the documentation for Mata.
+inputs:
+  os:
+    description: "Operating system to run on"
+    required: false
+    default: ubuntu-latest
+  python-version:
+    description: "Python version to use"
+    required: false
+    default: "3.13"
+runs:
+  using: "composite"
+  steps:
+    - name: Setup Python environment
+      uses: ./.github/workflows/actions/setup-python
+      with:
+        os: ${{ inputs.os }}
+        python-version: ${{ inputs.python-version }}
+    - name: Install Python Dependencies for documentation build
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        make -C docs init
+    - uses: ssciwr/doxygen-install@v1
+    - name: Compile the documentation
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        make docs
+        make -C docs/ html

.github/workflows/actions/setup-python/action.yml

@@ -1,27 +1,36 @@
 name: Setup Python environment
 description: Setup Python environment for running workflows.
 inputs:
+  os:
+    description: "Operating system to run on"
+    required: false
+    default: ubuntu-latest
   python-version:
     description: "Python version to run"
     required: true
 runs:
   using: "composite"
   steps:
     - name: Add some version to VERSION file (since it cannot be inferred from git)
-      shell: sh
+      shell: bash
       run: echo "0.0.0" > VERSION
     - name: Set up Python ${{ inputs.python-version }}
       uses: actions/setup-python@v5
       with:
         python-version: ${{ inputs.python-version }}
         cache: "pip"
     - name: Install Python Dependencies
-      shell: sh
+      shell: bash
       run: |
         python -m pip install --upgrade pip
         make -C bindings/python init
-    - name: Install Unix dependencies
-      shell: sh
+    - name: Building MacOS dependencies
+      if: ${{ inputs.os == 'macos-latest' }}
+      shell: bash
+      run: brew install graphviz
+    - name: Building Unix dependencies
+      if: ${{ inputs.os == 'ubuntu-latest' }}
+      shell: bash
       run: |
-        sudo apt-get -qq update
-        sudo apt-get -qq install -y graphviz graphviz-dev
+        sudo apt -qq update
+        sudo apt -qq install -y graphviz graphviz-dev

.github/workflows/actions/setup/action.yml

@@ -15,4 +15,4 @@ runs:
     - name: Building Unix dependencies
       if: ${{ inputs.os == 'ubuntu-latest' }}
       shell: sh
-      run: sudo apt-get install -y build-essential lcov gcovr xdg-utils
+      run: sudo apt install -y build-essential lcov gcovr xdg-utils

.github/workflows/code-quality.yml

@@ -11,9 +11,12 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
-          ref: ${{ github.event.pull_request.base_ref }}
+          # fetch-depth: 0
+          # If PR, checkout the PR's repo (needed for PRs coming from forks).
+          repository: ${{ github.event.pull_request.base.repo.full_name || github.repository }}
+          ref: ${{ github.event.pull_request.base.sha || github.event.pull_request.base_ref || github.sha }}
       - uses: ./.github/workflows/actions/setup
         with:
           os: ${{ matrix.os }}
@@ -27,7 +30,12 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+        with:
+          # fetch-depth: 0
+          # If PR, checkout the PR's repo (needed for PRs coming from forks).
+          repository: ${{ github.event.pull_request.head.repo.full_name || github.repository }}
+          ref: ${{ github.event.pull_request.head.sha || github.sha }}
       - uses: ./.github/workflows/actions/setup
         with:
           os: ${{ matrix.os }}
@@ -41,7 +49,12 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+        with:
+          # fetch-depth: 0
+          # If PR, checkout the PR's repo (needed for PRs coming from forks).
+          repository: ${{ github.event.pull_request.head.repo.full_name || github.repository }}
+          ref: ${{ github.event.pull_request.head.sha || github.sha }}
       - uses: ./.github/workflows/actions/setup
         with:
           os: ${{ matrix.os }}
@@ -55,27 +68,28 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [
-          #ubuntu-latest,
-          macos-latest]
+        os: [ubuntu-latest, macos-latest]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
-          ref: ${{ github.event.pull_request.base_ref }}
+          # fetch-depth: 0
+          # If PR, checkout the PR's repo (needed for PRs coming from forks).
+          repository: ${{ github.event.pull_request.base.repo.full_name || github.repository }}
+          ref: ${{ github.event.pull_request.base.sha || github.event.pull_request.base_ref || github.sha }}
       - uses: ./.github/workflows/actions/setup
         with:
           os: ${{ matrix.os }}
       - uses: ./.github/workflows/actions/compile
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.12
+          python-version: 3.13
           cache: "pip"
       - name: Install Python Dependencies
         shell: sh
         run: |
           python -m pip install --upgrade pip
-          pip install -r tests-integration/requirements.txt
+          pip install ./tests-integration/
       - name: Test the library
         run: make test-performance
       - name: Cache performance results
@@ -90,25 +104,28 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [
-          #ubuntu-latest,
-          macos-latest]
+        os: [ubuntu-latest, macos-latest]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+        with:
+          # fetch-depth: 0
+          # If PR, checkout the PR's repo (needed for PRs coming from forks).
+          repository: ${{ github.event.pull_request.head.repo.full_name || github.repository }}
+          ref: ${{ github.event.pull_request.head.sha || github.sha }}
       - uses: ./.github/workflows/actions/setup
         with:
           os: ${{ matrix.os }}
       - uses: ./.github/workflows/actions/compile
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.12
+          python-version: 3.13
           cache: "pip"
       - name: Install Python Dependencies
         shell: sh
         run: |
           python -m pip install --upgrade pip
-          pip install -r tests-integration/requirements.txt
+          pip install ./tests-integration/
       - name: Test the library
         run: make test-performance
       - name: Cache performance results
@@ -123,16 +140,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [
-          #ubuntu-latest,
-          macos-latest]
+        os: [ubuntu-latest, macos-latest]
     needs: [run-test-performance, run-test-performance-base]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+        with:
+          # fetch-depth: 0
+          # If PR, checkout the PR's repo (needed for PRs coming from forks).
+          repository: ${{ github.event.pull_request.head.repo.full_name || github.repository }}
+          ref: ${{ github.event.pull_request.head.sha || github.sha }}
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.12
+          python-version: 3.13
           cache: "pip"
       - name: Install Python Dependencies
         shell: sh
@@ -146,17 +166,19 @@ jobs:
             ./tests-integration/results/corr-single-param-jobs.csv
             ./tests-integration/results/corr-double-param-jobs.csv
           key: performance-tests-target-${{ runner.os }}-${{ github.sha }}
-      - run: mv ./tests-integration/results/corr-single-param-jobs.csv single-param-target.csv
-      - run: mv ./tests-integration/results/corr-double-param-jobs.csv double-param-target.csv
+      - run: |
+          mv ./tests-integration/results/corr-single-param-jobs.csv single-param-target.csv
+          mv ./tests-integration/results/corr-double-param-jobs.csv double-param-target.csv
       - name: Restore baseline profiles
         uses: actions/cache/restore@v4
         with:
           path: |
             ./tests-integration/results/corr-single-param-jobs.csv
             ./tests-integration/results/corr-double-param-jobs.csv
           key: performance-tests-baseline-${{ runner.os }}-${{ github.sha }}
-      - run: mv ./tests-integration/results/corr-single-param-jobs.csv single-param-baseline.csv
-      - run: mv ./tests-integration/results/corr-double-param-jobs.csv double-param-baseline.csv
+      - run: |
+          mv ./tests-integration/results/corr-single-param-jobs.csv single-param-baseline.csv
+          mv ./tests-integration/results/corr-double-param-jobs.csv double-param-baseline.csv
       - name: LOOK HERE for Comparison of operations accepting single automaton as parameters
         run: python3 tests-integration/scripts/compare_profiles.py single-param-target.csv single-param-baseline.csv
       - name: LOOK HERE for Comparison of operations accepting two automata as parameters
@@ -200,7 +222,12 @@ jobs:
     runs-on: ubuntu-latest
     needs: run-tests
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+        with:
+          # fetch-depth: 0
+          # If PR, checkout the PR's repo (needed for PRs coming from forks).
+          repository: ${{ github.event.pull_request.head.repo.full_name || github.repository }}
+          ref: ${{ github.event.pull_request.head.sha || github.sha }}
       - uses: ./.github/workflows/actions/setup
       - name: Build library for coverage
         run: make coverage
@@ -218,7 +245,12 @@ jobs:
       - uses: cachix/install-nix-action@v31
         with:
           nix_path: nixpkgs=channel:nixos-unstable
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+        with:
+          # fetch-depth: 0
+          # If PR, checkout the PR's repo (needed for PRs coming from forks).
+          repository: ${{ github.event.pull_request.head.repo.full_name || github.repository }}
+          ref: ${{ github.event.pull_request.head.sha || github.sha }}
       - uses: ./.github/workflows/actions/setup
       - name: Check formatting using treefmt through Nix
         run: |
@@ -230,3 +262,18 @@ jobs:
           else
               echo "Code is properly formatted."
           fi
+  build-docs:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          # fetch-depth: 0
+          # If PR, checkout the PR's repo (needed for PRs coming from forks).
+          repository: ${{ github.event.pull_request.head.repo.full_name || github.repository }}
+          ref: ${{ github.event.pull_request.head.sha || github.sha }}
+      - uses: ./.github/workflows/actions/docs
+        with:
+          os: ${{ matrix.os }}

.github/workflows/python-binding.yml

@@ -14,10 +14,14 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
     steps:
-      - name: Checkout latest version
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+        with:
+          # fetch-depth: 0
+          # If PR, checkout the PR's repo (needed for PRs coming from forks).
+          repository: ${{ github.event.pull_request.head.repo.full_name || github.repository }}
+          ref: ${{ github.event.pull_request.head.sha || github.sha }}
       - name: Setup Python environment
         uses: ./.github/workflows/actions/setup-python
         with:
@@ -44,10 +48,14 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
     steps:
-      - name: Checkout latest version
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+        with:
+          # fetch-depth: 0
+          # If PR, checkout the PR's repo (needed for PRs coming from forks).
+          repository: ${{ github.event.pull_request.head.repo.full_name || github.repository }}
+          ref: ${{ github.event.pull_request.head.sha || github.sha }}
       - name: Setup Python environment
         uses: ./.github/workflows/actions/setup-python
         with: