DEV: Simplify Workflows (#112)

* DEV: move iq-tree building into composite action

* DEV: correctly specify composite action

* DEV: specify shell to use

* DEV: merge python setup and libiqtree fetching into composite action

* DEV: ensure dependabot updates composite actions

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

@@ -0,0 +1,37 @@
+name: Fetch or Build IQ-TREE 2 Static Library
+description: "Checks if the IQ-TREE 2 static library exists, if not then building it."
+inputs:
+  os:
+    description: "Runner OS Name."
+    required: true
+outputs:
+  iqtree2-sha:
+    description: "SHA for commit of IQ-TREE 2 static library."
+    value: ${{ steps.iqtree2-sha.outputs.iqtree2-sha }}
+runs:
+  using: "composite"
+  steps:
+    - id: iqtree2-sha
+      name: Get IQ-TREE 2 SHA
+      shell: bash
+      run: |
+        cd iqtree2
+        IQ_TREE_2_SHA=$(git rev-parse HEAD)
+        echo "iqtree2-sha=${IQ_TREE_2_SHA}" >> "$GITHUB_OUTPUT"
+
+    - uses: actions/cache@v4
+      id: cache
+      with:
+        key: libiqtree-${{ inputs.os }}-${{ steps.iqtree2-sha.outputs.iqtree2-sha }}
+        path: src/piqtree2/_libiqtree/libiqtree2.a
+        lookup-only: true
+
+    - name: Build IQ-TREE
+      shell: bash
+      if: steps.cache.outputs.cache-hit != 'true'
+      run: |
+        if [[ "${{ inputs.os }}" == "ubuntu-latest" ]]; then
+        sudo ./build_tools/before_all_linux.sh
+        else
+        ./build_tools/before_all_mac.sh
+        fi

.github/actions/setup-piqtree/action.yml

@@ -0,0 +1,21 @@
+name: Setup piqtree
+description: "Setup Python and Fetch Static Library."
+inputs:
+  python-version:
+    description: "Python version."
+    required: true
+  cache-key:
+    description: "Key for static library cache."
+    required: true
+runs:
+  using: "composite"
+  steps:
+    - uses: "actions/setup-python@v5"
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - uses: actions/cache/restore@v4
+      with:
+        key: ${{ inputs.cache-key }}
+        path: src/piqtree2/_libiqtree/libiqtree2.a
+        fail-on-cache-miss: true

.github/dependabot.yml

@@ -16,6 +16,16 @@ updates:
     schedule:
       interval: "weekly"
     open-pull-requests-limit: 10
+  - package-ecosystem: "github-actions"
+    directory: "/.github/actions/build-iqtree/"
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 10
+  - package-ecosystem: "github-actions"
+    directory: "/.github/actions/setup-piqtree/"
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 10
 
   - package-ecosystem: "gitsubmodule"
     directory: "/"

.github/workflows/build_docs.yml

@@ -1,4 +1,4 @@
-name: Build docs
+name: Build Docs
 
 on: [workflow_dispatch]
 
@@ -12,23 +12,13 @@ jobs:
           fetch-depth: 0
           submodules: recursive
 
-      - name: Get IQ-TREE 2 SHA
-        run: |
-          cd iqtree2
-          IQ_TREE_2_SHA=$(git rev-parse HEAD)
-          echo "IQ_TREE_2_SHA=${IQ_TREE_2_SHA}" >> $GITHUB_ENV
-
-      - uses: actions/cache@v4
-        id: cache
+      - id: build
+        uses: ./.github/actions/build-iqtree
         with:
-          key: libiqtree-${{ matrix.os }}-${{ env.IQ_TREE_2_SHA }}
-          path: src/piqtree2/_libiqtree/libiqtree2.a
-          lookup-only: true
-
-      - name: Build IQ-TREE
-        if: steps.cache.outputs.cache-hit != 'true'
-        run: |
-          sudo ./build_tools/before_all_linux.sh
+          os: ubuntu-latest
+
+    outputs:
+      iqtree2-sha: ${{steps.build.outputs.iqtree2-sha}}
 
   build-docs:
     runs-on: ubuntu-latest
@@ -40,16 +30,10 @@ jobs:
           fetch-depth: 0
           submodules: recursive
 
-      - uses: actions/cache/restore@v4
-        with:
-          key: libiqtree-ubuntu-latest-${{ env.IQ_TREE_2_SHA }}
-          path: src/piqtree2/_libiqtree/libiqtree2.a
-          fail-on-cache-miss: true
-
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - uses: ./.github/actions/setup-piqtree
         with:
           python-version: "3.12"
+          cache-key: libiqtree-ubuntu-latest-${{ needs.build-iqtree.outputs.iqtree2-sha }}
 
       - name: Install Docs Dependencies
         run: |

.github/workflows/ci.yml

@@ -21,27 +21,13 @@ jobs:
           fetch-depth: 0
           submodules: recursive
 
-      - name: Get IQ-TREE 2 SHA
-        run: |
-          cd iqtree2
-          IQ_TREE_2_SHA=$(git rev-parse HEAD)
-          echo "IQ_TREE_2_SHA=${IQ_TREE_2_SHA}" >> $GITHUB_ENV
-
-      - uses: actions/cache@v4
-        id: cache
+      - id: build
+        uses: ./.github/actions/build-iqtree
         with:
-          key: libiqtree-${{ matrix.os }}-${{ env.IQ_TREE_2_SHA }}
-          path: src/piqtree2/_libiqtree/libiqtree2.a
-          lookup-only: true
-
-      - name: Build IQ-TREE
-        if: steps.cache.outputs.cache-hit != 'true'
-        run: |
-          if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
-            sudo ./build_tools/before_all_linux.sh
-          else
-            ./build_tools/before_all_mac.sh
-          fi
+          os: ${{ matrix.os }}
+
+    outputs:
+      iqtree2-sha: ${{steps.build.outputs.iqtree2-sha}}
 
   tests:
     name: Run Tests with Python ${{matrix.python-version}} on ${{matrix.os}}
@@ -57,15 +43,10 @@ jobs:
           fetch-depth: 0
           submodules: recursive
 
-      - uses: "actions/setup-python@v5"
-        with:
-            python-version: "${{ matrix.python-version }}"
-
-      - uses: actions/cache/restore@v4
+      - uses: ./.github/actions/setup-piqtree
         with:
-          key: libiqtree-${{ matrix.os }}-${{ env.IQ_TREE_2_SHA }}
-          path: src/piqtree2/_libiqtree/libiqtree2.a
-          fail-on-cache-miss: true
+          python-version: ${{ matrix.python-version }}
+          cache-key: libiqtree-${{ matrix.os }}-${{ needs.build-iqtree.outputs.iqtree2-sha }}
 
       - name: Run Nox Testing
         run: |
@@ -107,20 +88,15 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: "actions/setup-python@v5"
+      - uses: ./.github/actions/setup-piqtree
         with:
-            python-version: "${{ matrix.python-version }}"          
-
-      - uses: actions/cache/restore@v4
-        with:
-            key: libiqtree-${{ matrix.os }}-${{ env.IQ_TREE_2_SHA }}
-            path: src/piqtree2/_libiqtree/libiqtree2.a
-            fail-on-cache-miss: true
+          python-version: ${{ matrix.python-version }}
+          cache-key: libiqtree-${{ matrix.os }}-${{ needs.build-iqtree.outputs.iqtree2-sha }}
 
       - name: "Run Type Checking for ${{ matrix.python-version }}" 
         run: |
-            pip install nox
-            nox -s type_check-${{ matrix.python-version }}
+          pip install nox
+          nox -s type_check-${{ matrix.python-version }}
 
   lint:
     name: "Linting"
@@ -137,17 +113,12 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: "actions/setup-python@v5"
+      - uses: ./.github/actions/setup-piqtree
         with:
-            python-version: "${{ matrix.python-version }}"          
-
-      - uses: actions/cache/restore@v4
-        with:
-            key: libiqtree-${{ matrix.os }}-${{ env.IQ_TREE_2_SHA }}
-            path: src/piqtree2/_libiqtree/libiqtree2.a
-            fail-on-cache-miss: true
+          python-version: ${{ matrix.python-version }}
+          cache-key: libiqtree-${{ matrix.os }}-${{ needs.build-iqtree.outputs.iqtree2-sha }}
 
       - name: "Run Type Checking for ${{ matrix.python-version }}" 
         run: |
-            pip install nox
-            nox -s ruff-${{ matrix.python-version }}
+          pip install nox
+          nox -s ruff-${{ matrix.python-version }}