Skip tests for filtering on windows

.github/workflows/main.yml

@@ -50,62 +50,6 @@ jobs:
         sudo apt-get update
         sudo apt-get install -y mmseqs2
 
-    - name: Install cd-hit (Windows)
-      if: matrix.os == 'windows-latest'
-      shell: pwsh
-      run: |
-        curl -L -o cd-hit.tar.gz https://github.com/weizhongli/cdhit/releases/download/V4.8.1/cd-hit-v4.8.1-2019-0228.tar.gz
-        $cdhitDir = "$Env:USERPROFILE\cdhit"
-        New-Item -ItemType Directory -Force -Path $cdhitDir
-        tar -xzf cd-hit.tar.gz -C $cdhitDir
-        $cdhitBinPath = "$cdhitDir\cd-hit-v4.8.1-2019-0228\bin"
-        Write-Host "cd-hit binary path: $cdhitBinPath"
-        [Environment]::SetEnvironmentVariable("PATH", "$Env:PATH;$cdhitBinPath", [System.EnvironmentVariableTarget]::Machine)
-        Write-Host "Contents of cd-hit bin directory:"
-        Get-ChildItem $cdhitBinPath
-
-    - name: Install mmseqs2 (Windows)
-      if: matrix.os == 'windows-latest'
-      shell: pwsh
-      run: |
-        curl -L -o mmseqs2.zip https://mmseqs.com/latest/mmseqs-win64.zip
-        $mmseqsDir = "$Env:USERPROFILE\mmseqs"
-        New-Item -ItemType Directory -Force -Path $mmseqsDir
-        Expand-Archive -Path mmseqs2.zip -DestinationPath $mmseqsDir
-        $mmseqsBinPath = "$mmseqsDir\mmseqs-win64"
-        Write-Host "mmseqs2 binary path: $mmseqsBinPath"
-        [Environment]::SetEnvironmentVariable("PATH", "$Env:PATH;$mmseqsBinPath", [System.EnvironmentVariableTarget]::Machine)
-        Write-Host "Contents of mmseqs2 directory:"
-        Get-ChildItem $mmseqsBinPath
-
-    - name: Verify mmseqs2 installation
-      if: matrix.os == 'windows-latest'
-      shell: pwsh
-      run: |
-        $mmseqsBinPath = "$Env:USERPROFILE\mmseqs\mmseqs-win64"
-        $env:Path += ";$mmseqsBinPath"
-        Write-Host "Updated PATH: $env:Path"
-        Write-Host "Checking mmseqs binary in PATH:"
-        if (-Not (Get-Command mmseqs -ErrorAction SilentlyContinue)) {
-          Write-Error "mmseqs not found in PATH"
-        } else {
-          Write-Host "mmseqs found in PATH"
-          mmseqs --version
-
-    - name: Verify cd-hit installation
-      if: matrix.os == 'windows-latest'
-      shell: pwsh
-      run: |
-        $cdhitBinPath = "$Env:USERPROFILE\cdhit\cd-hit-v4.8.1-2019-0228\bin"
-        $env:Path += ";$cdhitBinPath"
-        Write-Host "Updated PATH: $env:Path"
-        Write-Host "Checking cd-hit binary in PATH:"
-        if (-Not (Get-Command cd-hit -ErrorAction SilentlyContinue)) {
-          Write-Error "cd-hit not found in PATH"
-        } else {
-          Write-Host "cd-hit found in PATH"
-          cd-hit --version
-
     - name: Run Tests
       run: pytest tests
       env:

tests/unit/data_handling_tests/test_filter_seq.py

@@ -1,19 +1,23 @@
-"""This is a script to test the filter_seq() function."""
+"""This is a script to test the filter_seq() function.
+Will only be tested for Linux since CD-HIT not installable on windows"""
 import pandas as pd
 from hypothesis import given, settings
 import hypothesis.strategies as st
 import aaanalysis as aa
 import pytest
-import random
+import platform
 
 aa.options["verbose"] = False
 
 # Set default deadline from 200 to 20000
 settings.register_profile("ci", deadline=20000)
 settings.load_profile("ci")
 
+is_windows = platform.system() == "Windows"
+
 
 # Normal Cases
+@pytest.mark.skipif(is_windows, reason="Skipping tests on Windows")
 class TestFilterSeq:
     """Test filter_seq function."""
 
@@ -157,8 +161,8 @@ def test_invalid_sort_clusters(self):
             with pytest.raises(ValueError):
                 aa.filter_seq(df_seq=df_seq, sort_clusters=sort_cluster, method="mmseqs")
 
-
 # Complex Cases
+@pytest.mark.skipif(is_windows, reason="Skipping tests on Windows")
 class TestFilterSeqComplex:
     """Test filter_seq function for complex cases."""