add version check between ppanggolin file and the installed ppanggolin

ppanggolin/formats/readBinaries.py

@@ -105,6 +105,13 @@ def get_status(pangenome: Pangenome, pangenome_file: Path):
         pangenome.status["geneFamilySequences"] = "inFile"
     if status_group._v_attrs.NeighborsGraph:
         pangenome.status["neighborsGraph"] = "inFile"
+
+    if hasattr(status_group._v_attrs, "version"):
+        pangenome.status["ppanggolin_version"] = str(status_group._v_attrs.version)
+    else:
+        logging.getLogger("PPanGGOLiN").error(f'The provided pangenome file {pangenome_file} does not have a version stored in its status.'
+                         ' This issue may indicate that the file is corrupted.')
+        pangenome.status["ppanggolin_version"] = None
 
     if status_group._v_attrs.Partitioned:
         pangenome.status["partitioned"] = "inFile"

ppanggolin/pangenome.py

@@ -66,19 +66,25 @@ def __init__(self):
         }
         self.parameters = {}
 
-    def add_file(self, pangenome_file: Path):
-        """Links an HDF5 file to the pangenome. If needed elements will be loaded from this file,
+    def add_file(self, pangenome_file: Path, check_version:bool=True):
+        """
+        Links an HDF5 file to the pangenome. If needed elements will be loaded from this file,
         and anything that is computed will be saved to this file when
         :func:`ppanggolin.formats.writeBinaries.writePangenome` is called.
 
         :param pangenome_file: A string representing filepath to hdf5 pangenome file to be either used or created
-
+        :param check_version: Check ppanggolin version of the pangenome file to be compatible with the current version of ppaggolin being used.
         :raises AssertionError: If the `pangenome_file` is not an instance of the Path class
         """
         assert isinstance(pangenome_file, Path), "pangenome file should be a Path object type"
         from ppanggolin.formats.readBinaries import get_status
+        from ppanggolin.utils import check_version_compatibility
         # importing on call instead of importing on top to avoid cross-reference problems.
+
         get_status(self, pangenome_file)
+
+        check_version_compatibility(self.status["ppanggolin_version"])
+
         self.file = pangenome_file.absolute().as_posix()
 
     """ Gene Methods"""

ppanggolin/utils.py

@@ -1065,3 +1065,41 @@ def flatten(dictionary, parent_key=''):
 
     flatten(nested_dict)
     return flat_dict
+
+def get_major_version(version: str) -> int:
+    """
+    Extracts the major version number from a version string.
+
+    :param version: A string representing the version number.
+    :return: The major version extracted from the input version string.
+    :raises ValueError: If the input version does not have the expected format.
+    """
+    try:
+        major_version = int(version.split('.')[0])
+    except ValueError:
+        raise ValueError(f"Version {version} does not have the expected format.")
+
+    return major_version
+
+
+def check_version_compatibility(file_version: str) -> None:
+    """
+    Checks the compatibility of the provided pangenome file version with the current PPanGGOLiN version.
+
+    :param file_version: A string representing the version of the pangenome file.
+    """
+    # Get the current PPanGGOLiN version
+    current_version = distribution('ppanggolin').version
+
+    current_version_major = get_major_version(current_version)
+    file_major_version = get_major_version(file_version)
+
+    # Check for compatibility issues
+    if file_major_version != current_version_major:
+        logging.getLogger("PPanGGOLiN").error('Your pangenome file has been created with a different major version '
+                                              'of PPanGGOLiN than the one installed in the system. This mismatch may lead to compatibility issues.')
+
+    if file_major_version < 2 and current_version_major >= 2:
+        raise ValueError(f'The provided pangenome file was created by PPanGGOLiN version {file_version}, which is '
+                         f'incompatible with the current PPanGGOLiN version {current_version}.')
+