Update github action; import future annotations in test scripts

.github/workflows/build-aster.yml

@@ -10,7 +10,7 @@ jobs:
     steps:
       - name: Cache ASTER
         id: cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.local/bin/astral
           key: ${{ runner.os }}-ASTER

.github/workflows/build-fasttree.yml

@@ -10,7 +10,7 @@ jobs:
     steps:
       - name: Cache FastTree
         id: cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.local/bin/FastTree
           key: ${{ runner.os }}-FastTree

.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@v4
+        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@v4
+        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@v4
+        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/conda-build.yml

@@ -10,14 +10,9 @@ on:
   workflow_dispatch:
 
 jobs:
-  call-build-aster:
-    uses: ./.github/workflows/build-aster.yml
-
   build-conda:
     runs-on: ubuntu-latest
 
-    needs: call-build-aster
-
     steps:
       - uses: actions/checkout@v3
 
@@ -31,7 +26,6 @@ jobs:
 
       - name: Lint with flake8
         run: |
-          # stop the build if there are Python syntax errors or undefined names
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=130 --statistics
         shell: micromamba-shell {0}
@@ -40,12 +34,6 @@ jobs:
         run: pip install .
         shell: micromamba-shell {0}
 
-      - name: Cache ASTER
-        uses: actions/cache@v3
-        with:
-          path: ~/.local/bin/astral
-          key: ${{ runner.os }}-ASTER
-
       - name: Test with pytest
         run: pytest --runslow
         shell: micromamba-shell {0}

.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:
@@ -29,7 +45,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Cache Python packages
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
@@ -53,17 +69,44 @@ jobs:
       - name: Install package
         run: pip install .
 
+      - name: Cache muscle
+        uses: actions/cache@v4
+        with:
+          path: ~/.local/bin/muscle
+          key: ${{ runner.os }}-muscle
+
       - name: Cache ASTER
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.local/bin/astral
           key: ${{ runner.os }}-ASTER
 
       - name: Cache FastTree
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.local/bin/FastTree
           key: ${{ runner.os }}-FastTree
 
+      - name: Cache RAxML
+        uses: actions/cache@v4
+        with:
+          path: ~/.local/bin/raxmlHPC-PTHREADS-AVX2
+          key: ${{ runner.os }}-RAxML
+
+      - name: Cache IQTree
+        uses: actions/cache@v4
+        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

@@ -4,6 +4,7 @@ channels:
   - bioconda
   - defaults
 dependencies:
+  - aster>=1.16
   - biopython>=1.81
   - clipkit>=2.1.1
   - fasttree>=2.1.11
@@ -13,5 +14,5 @@ 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

src/phyling/phylotree.py

@@ -220,7 +220,7 @@ def _with_FastTree(self, *, verbose: bool) -> Tree:
 
         if not fasttree:
             raise exception.BinaryNotFoundError(
-                'FastTree not found. Please install it through "conda install -c bioconda fasttree"'
+                'FastTree not found. Please install it through "conda install bioconda::fasttree"'
             )
 
         cmd = [fasttree, "-gamma", str(self.path)]
@@ -260,7 +260,7 @@ def _with_RAxML(self, output: Path, *, threads: int, verbose: bool) -> Tree:
                 break
 
         if not raxml:
-            raise exception.BinaryNotFoundError('RAxML not found. Please install it through "conda install -c bioconda raxml"')
+            raise exception.BinaryNotFoundError('RAxML not found. Please install it through "conda install bioconda::raxml"')
 
         if output is None:
             tempdir = Path(tempfile.mkdtemp())
@@ -322,7 +322,7 @@ def _with_IQTree(self, output: Path, *, threads: int, verbose: bool) -> Tree:
                 break
 
         if not iqtree:
-            raise exception.BinaryNotFoundError('IQTree not found. Please install it through "conda install -c bioconda iqtree"')
+            raise exception.BinaryNotFoundError('IQTree not found. Please install it through "conda install bioconda::iqtree"')
 
         if output is None:
             tempdir = Path(tempfile.mkdtemp())
@@ -508,7 +508,8 @@ def get_consensus_tree(self) -> Tree:
         if not shutil.which("astral"):
             raise exception.BinaryNotFoundError(
                 "ASTRAL not found. "
-                "Please build the C++ version from the source following the instruction on https://github.com/chaoszhang/ASTER"
+                'Please install it through "conda install bioconda::aster" '
+                "or build the source following the instruction on https://github.com/chaoszhang/ASTER"
             )
 
         logging.info("Run ASTRAL to resolve consensus among multiple trees.")

tests/conftest.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import shutil
 import tarfile
 

tests/libphyling_test.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 import shutil
 from copy import deepcopy

tests/phylotree_test.py

@@ -1,8 +1,10 @@
+from __future__ import annotations
+
 import logging
+import shutil
 from copy import deepcopy
 from itertools import permutations, product
 from pathlib import Path
-import shutil
 
 import pytest
 from Bio.AlignIO import MultipleSeqAlignment

tests/pipeline_test.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 from itertools import product
 from pathlib import Path