Convert os.path to pathlib based Paths (#646)

* Convert os.path to pathlib based Paths

* Actually use name set/get

* Add custom JSONEncoder to handle Paths

MDANSE/Src/MDANSE/Chemistry/ChemicalSystem.py

@@ -36,7 +36,7 @@ def __init__(self, name: str = "", trajectory=None):
         :type name: str
         """
 
-        self._name = name
+        self.name = str(name)
         self._database = ATOMS_DATABASE
         if trajectory is not None:
             self._database = trajectory
@@ -55,7 +55,7 @@ def __init__(self, name: str = "", trajectory=None):
         self._unique_elements = set()
 
     def __str__(self):
-        return f"ChemicalSystem {self._name} consisting of {len(self._atom_types)} atoms in {len(self._clusters)} molecules"
+        return f"ChemicalSystem {self.name} consisting of {len(self._atom_types)} atoms in {len(self._clusters)} molecules"
 
     def initialise_atoms(self, element_list: List[str], name_list: List[str] = None):
         self._atom_indices = [
@@ -191,7 +191,7 @@ def copy(self) -> "ChemicalSystem":
         :return: Copy of the ChemicalSystem instance
         :rtype: MDANSE.Chemistry.ChemicalSystem.ChemicalSystem
         """
-        cs = ChemicalSystem(self._name)
+        cs = ChemicalSystem(self.name)
 
         for attribute_name, attribute_value in self.__dict__.items():
             if attribute_name in ["rdkit_mol", "_configuration"]:
@@ -248,7 +248,7 @@ def serialize(self, h5_file: h5py.File) -> None:
         string_dt = h5py.special_dtype(vlen=str)
 
         grp = h5_file.create_group("/composition")
-        grp.attrs["name"] = self._name
+        grp.attrs["name"] = self.name
 
         try:
             grp.create_dataset("atom_types", data=self._atom_types, dtype=string_dt)
@@ -292,7 +292,7 @@ def load(self, trajectory: str):
         self.rdkit_mol = Chem.RWMol()
 
         grp = source["/composition"]
-        self._name = grp.attrs["name"]
+        self.name = grp.attrs["name"]
 
         atom_types = [binary.decode("utf-8") for binary in grp["atom_types"][:]]
         atom_names = None
@@ -326,7 +326,7 @@ def legacy_load(self, trajectory: str):
         self.rdkit_mol = Chem.RWMol()
 
         grp = source["/chemical_system"]
-        self._name = grp.attrs["name"]
+        self.name = grp.attrs["name"]
         atoms = grp["atoms"]
         element_list = [line[0].decode("utf-8").strip("'") for line in atoms]
         self.initialise_atoms(element_list)

MDANSE/Src/MDANSE/Chemistry/Databases.py

@@ -15,8 +15,8 @@
 #
 
 import copy
-import os
 from typing import Union, ItemsView, Dict, Any
+from pathlib import Path
 
 import json
 
@@ -30,8 +30,8 @@ class _Database(metaclass=Singleton):
     Base class for all the databases.
     """
 
-    _DEFAULT_DATABASE: str
-    _USER_DATABASE: str
+    _DEFAULT_DATABASE: Path
+    _USER_DATABASE: Path
 
     def __init__(self):
         """
@@ -65,7 +65,11 @@ def __iter__(self):
         for v in self._data.values():
             yield copy.deepcopy(v)
 
-    def _load(self, user_database: str = None, default_database: str = None) -> None:
+    def _load(
+        self,
+        user_database: Union[Path, str, None] = None,
+        default_database: Union[Path, str, None] = None,
+    ) -> None:
         """
         Load the database. This method should never be called elsewhere than __init__ or unit testing.
 
@@ -77,10 +81,14 @@ def _load(self, user_database: str = None, default_database: str = None) -> None
         """
         if user_database is None:
             user_database = self._USER_DATABASE
+        else:
+            user_database = Path(user_database)
         if default_database is None:
             default_database = self._DEFAULT_DATABASE
+        else:
+            default_database = Path(default_database)
 
-        if os.path.exists(user_database):
+        if user_database.exists():
             database_path = user_database
         else:
             database_path = default_database
@@ -164,10 +172,10 @@ class AtomsDatabase(_Database):
     >>> atoms = ATOMS_DATABASE.atoms()
     """
 
-    _DEFAULT_DATABASE = os.path.join(os.path.dirname(__file__), "atoms.json")
+    _DEFAULT_DATABASE = Path(__file__).parent / "atoms.json"
 
     # The user path
-    _USER_DATABASE = os.path.join(PLATFORM.application_directory(), "atoms.json")
+    _USER_DATABASE = PLATFORM.application_directory() / "atoms.json"
 
     # The python types supported by the database
     _TYPES = {"str": str, "int": int, "float": float, "list": list}