Update cd-hit and mmseq installation6

.github/workflows/main.yml

@@ -54,17 +54,23 @@ jobs:
       if: runner.os == 'Windows'
       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
-        mkdir $Env:USERPROFILE\cdhit
+        New-Item -ItemType Directory -Force -Path $Env:USERPROFILE\cdhit
         tar -xzf cd-hit.tar.gz -C $Env:USERPROFILE\cdhit
-        echo "$Env:USERPROFILE\cdhit\cd-hit-v4.8.1-2019-0228\bin" | Out-File -FilePath $Env:GITHUB_PATH -Append
+        echo "$Env:USERPROFILE\cdhit\cd-hit-v4.8.1-2019-0228\bin" >> $Env:GITHUB_PATH
 
     - name: Install mmseqs2 (Windows)
       if: runner.os == 'Windows'
       run: |
         curl -L -o mmseqs2.zip https://mmseqs.com/latest/mmseqs-win64.zip
         New-Item -ItemType Directory -Force -Path $Env:USERPROFILE\mmseqs
         Expand-Archive -Path mmseqs2.zip -DestinationPath $Env:USERPROFILE\mmseqs
-        echo "$Env:USERPROFILE\mmseqs\mmseqs-win64" | Out-File -FilePath $Env:GITHUB_PATH -Append
+        echo "$Env:USERPROFILE\mmseqs\mmseqs-win64" >> $Env:GITHUB_PATH
+
+    - name: Update PATH
+      if: runner.os == 'Windows'
+      run: |
+        $env:Path += ";$Env:USERPROFILE\cdhit\cd-hit-v4.8.1-2019-0228\bin;$Env:USERPROFILE\mmseqs\mmseqs-win64"
+        [System.Environment]::SetEnvironmentVariable('PATH', $env:Path, [System.EnvironmentVariableTarget]::Process)
 
     - name: Run Tests
       run: pytest tests

aaanalysis/data_handling/_seq_preproc.py

@@ -25,28 +25,39 @@ class SequencePreprocessor:
     """
 
     @staticmethod
-    def encode_one_hot(sequence: List[str],
+    def encode_one_hot(list_seq: Union[List[str], str] = None,
                        alphabet: str = "ARNDCEQGHILKMFPSTWYV",
-                       gap: str = "_"
+                       gap: str = "_",
+                       pad_at: Literal["C", "N"] = "C",
                        ) -> np.ndarray:
         """
-        One-hot encodes a list of protein sequences into a feature matrix.
+        One-hot-encode a list of protein sequences into a feature matrix.
+
+        Padding of shorter sequences with gaps represented as zero vectors.
 
         Parameters
         ----------
-        sequence : List[str]
+        list_seq : list of str or str
             List of protein sequences to encode.
         alphabet : str, default='ARNDCEQGHILKMFPSTWYV'
             The alphabet of amino acids used for encoding.
         gap : str, default='_'
             The character used to represent gaps in sequences.
+        pad_at : str, default='C'
+            Specifies where to add the padding:
+            'N' for N-terminus (beginning of the sequence),
+            'C' for C-terminus (end of the sequence).
 
         Returns
         -------
         np.ndarray
             A numpy array where each row represents an encoded sequence.
         """
-        return encode_one_hot(sequence, alphabet, gap)
+        # Check input
+        list_str = ut.check_list_like(name="list_seq", val=list_seq, check_all_str_or_convertible=True,
+                                      accept_none=False, accept_str=True)
+        #
+        return encode_one_hot(list_seq, alphabet, gap)
 
     @staticmethod
     def encode_integer(list_seq: List[str], alphabet: str = "ARNDCEQGHILKMFPSTWYV", gap: str = "_", pad_at: Literal["C", "N"] = "C") -> np.ndarray: