rempove TODOs

deeprank2/query.py

@@ -35,8 +35,6 @@
 VALID_RESOLUTIONS = ['atom', 'residue']
 
 
-# TODO: consider whether we want to use the built-in repr and eq, or define it ourselves
-# if built-in: consider which arguments to include in either.
 @dataclass(repr=False, kw_only=True)
 class Query:
     """Represents one entity of interest: a single residue variant (SRV) or a protein-protein interface (PPI).
@@ -249,7 +247,6 @@ def __post_init__(self):
         super().__post_init__()  # calls __post_init__ of parents
 
         if len(self.chain_ids) != 1:
-            # TODO: Consider throwing a warning instead of error and taking the first entry of the list anyway.
             raise ValueError("`chain_ids` must contain exactly 1 chain for `SingleResidueVariantQuery` objects, "
                             + f"but {len(self.chain_ids)} was/were given.")
         self.variant_chain_id = self.chain_ids[0]
@@ -335,7 +332,6 @@ def __post_init__(self):
         super().__post_init__()
 
         if len(self.chain_ids) != 2:
-            # TODO: Consider throwing a warning instead of error and using the first two entries of the list anyway.
             raise ValueError("`chain_ids` must contain exactly 2 chains for `ProteinProteinInterfaceQuery` objects, "
                             + f"but {len(self.chain_ids)} was/were given.")
 
@@ -462,7 +458,6 @@ def _process_one_query(self, query: Query):
         """Only one process may access an hdf5 file at a time"""
 
         try:
-            # TODO: Maybe make exception catching optional, because I think it would be good to raise the error by default.
             output_path = f"{self._prefix}-{os.getpid()}.hdf5"
             graph = query.build(self._feature_modules)
             graph.write_to_hdf5(output_path)
@@ -528,7 +523,6 @@ def process( # pylint: disable=too-many-arguments, too-many-locals, dangerous-de
         self._feature_modules = self._set_feature_modules(feature_modules)
         _log.info(f'\nSelected feature modules: {self._feature_modules}.')
 
-        #TODO: it would be nice if all of the below could be part of GridSettings object
         self._grid_settings = grid_settings
         self._grid_map_method = grid_map_method