Update github action

.github/workflows/build-iqtree.yml

@@ -0,0 +1,36 @@
+name: Build IQTree
+
+on: workflow_call
+
+jobs:
+  build_IQTree:
+    name: Build IQTree
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Cache IQTree
+        id: cache
+        uses: actions/cache@v3
+        with:
+          path: ~/.local/bin/iqtree2
+          key: ${{ runner.os }}-IQTree
+
+      - name: Download IQTree executable
+        if: steps.cache.outputs.cache-hit != 'true'
+        run: |
+          sudo apt-get install wget
+          wget https://github.com/iqtree/iqtree2/releases/download/v2.3.2/iqtree-2.3.2-Linux-intel.tar.gz
+          tar zxf iqtree-2.3.2-Linux-intel.tar.gz
+
+      - name: Move executable
+        if: steps.cache.outputs.cache-hit != 'true'
+        working-directory: ${{ github.workspace }}
+        run: |
+          mkdir -p ~/.local/bin
+          cp iqtree-2.3.2-Linux-intel/bin/iqtree2 ~/.local/bin/
+          chmod +x ~/.local/bin/iqtree2
+
+      - name: Export IQTree to PATH and verify
+        run: |
+          export PATH=$PATH:$HOME/.local/bin
+          which iqtree2

.github/workflows/build-muscle.yml

@@ -0,0 +1,36 @@
+name: Build muscle
+
+on: workflow_call
+
+jobs:
+  build_muscle:
+    name: Build muscle
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Cache muscle
+        id: cache
+        uses: actions/cache@v3
+        with:
+          path: ~/.local/bin/muscle
+          key: ${{ runner.os }}-muscle
+
+      - name: Download muscle executable
+        if: steps.cache.outputs.cache-hit != 'true'
+        run: |
+          sudo apt-get install wget
+          wget https://github.com/rcedgar/muscle/releases/download/5.1.0/muscle5.1.linux_intel64
+          mv muscle5.1.linux_intel64 muscle
+
+      - name: Move executable
+        if: steps.cache.outputs.cache-hit != 'true'
+        working-directory: ${{ github.workspace }}
+        run: |
+          mkdir -p ~/.local/bin
+          cp muscle ~/.local/bin/
+          chmod +x ~/.local/bin/muscle
+
+      - name: Export muscle to PATH and verify
+        run: |
+          export PATH=$PATH:$HOME/.local/bin
+          which muscle

.github/workflows/build-raxml.yml

@@ -0,0 +1,41 @@
+name: Build RAxML
+
+on: workflow_call
+
+jobs:
+  build_RAxML:
+    name: Build RAxML
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Cache RAxML
+        id: cache
+        uses: actions/cache@v3
+        with:
+          path: ~/.local/bin/raxmlHPC-PTHREADS-AVX2
+          key: ${{ runner.os }}-RAxML
+
+      - name: Install dependencies
+        if: steps.cache.outputs.cache-hit != 'true'
+        run: sudo apt-get install build-essential g++ wget unzip
+
+      - name: Compile RAxML
+        if: steps.cache.outputs.cache-hit != 'true'
+        run: |
+          wget https://github.com/stamatak/standard-RAxML/archive/refs/tags/v8.2.13.zip
+          unzip v8.2.13.zip
+          cd standard-RAxML-8.2.13
+          make -f Makefile.AVX2.PTHREADS.gcc
+
+      - name: Move executable
+        if: steps.cache.outputs.cache-hit != 'true'
+        working-directory: ${{ github.workspace }}
+        run: |
+          mkdir -p ~/.local/bin
+          cp standard-RAxML-8.2.13/raxmlHPC-PTHREADS-AVX2 ~/.local/bin/
+          chmod +x ~/.local/bin/raxmlHPC-PTHREADS-AVX2
+
+      - name: Export RAxML to PATH and verify
+        run: |
+          export PATH=$PATH:$HOME/.local/bin
+          which raxmlHPC-PTHREADS-AVX2

.github/workflows/python-versions.yml

@@ -10,16 +10,32 @@ on:
   workflow_dispatch:
 
 jobs:
+  call-build-muscle:
+    uses: ./.github/workflows/build-muscle.yml
+
   call-build-aster:
     uses: ./.github/workflows/build-aster.yml
 
   call-build-fasttree:
     uses: ./.github/workflows/build-fasttree.yml
 
+  call-build-raxml:
+    uses: ./.github/workflows/build-raxml.yml
+
+  call-build-iqtree:
+    uses: ./.github/workflows/build-iqtree.yml
+
   test_pythons:
     name: Test on different python versions
     runs-on: ubuntu-latest
-    needs: [call-build-aster, call-build-fasttree]
+    needs:
+      [
+        call-build-muscle,
+        call-build-aster,
+        call-build-fasttree,
+        call-build-raxml,
+        call-build-iqtree,
+      ]
     strategy:
       fail-fast: false
       matrix:
@@ -53,6 +69,12 @@ jobs:
       - name: Install package
         run: pip install .
 
+      - name: Cache muscle
+        uses: actions/cache@v3
+        with:
+          path: ~/.local/bin/muscle
+          key: ${{ runner.os }}-muscle
+
       - name: Cache ASTER
         uses: actions/cache@v3
         with:
@@ -65,5 +87,26 @@ jobs:
           path: ~/.local/bin/FastTree
           key: ${{ runner.os }}-FastTree
 
+      - name: Cache RAxML
+        uses: actions/cache@v3
+        with:
+          path: ~/.local/bin/raxmlHPC-PTHREADS-AVX2
+          key: ${{ runner.os }}-RAxML
+
+      - name: Cache IQTree
+        uses: actions/cache@v3
+        with:
+          path: ~/.local/bin/iqtree2
+          key: ${{ runner.os }}-IQTree
+
+      - name: Export to PATH and verify
+        run: |
+          export PATH=$PATH:$HOME/.local/bin
+          which muscle
+          which FastTree
+          which raxmlHPC-PTHREADS-AVX2
+          which iqtree2
+          which astral
+
       - name: Test with pytest
         run: pytest --runslow

environment.yml

@@ -13,5 +13,5 @@ dependencies:
   - numpy>=1.26.0
   - phykit>=1.12.5
   - pyhmmer>=0.10.4
-  - python>=3.7.12
+  - python>=3.9
   - raxml>=8.2.12

requirements.txt

@@ -1,7 +1,6 @@
 biopython>=1.81
 clipkit>=2.1.1
-importlib-metadata; python_version<"3.8"
-phykit>=1.12.5
-pyhmmer>=0.10.2
 matplotlib>=3.5.3
-numpy
+numpy>=1.26.0
+phykit>=1.12.5
+pyhmmer>=0.10.4