Actually use name set/get

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/Core/Platform.py

@@ -465,7 +465,7 @@ def application_directory(self) -> Path:
         basedir = Path(os.environ["APPDATA"]) / "mdanse"
 
         # If the application directory does not exist, create it.
-        os.makedirs(basedir)
+        basedir.mkdir(parents=True, exist_ok=True)
 
         return basedir
 

MDANSE/Src/MDANSE/Framework/Converters/Gromacs.py

@@ -15,6 +15,7 @@
 #
 
 import collections
+from pathlib import Path
 
 import numpy as np
 from mdtraj.formats.xtc import XTCTrajectoryFile
@@ -77,16 +78,13 @@ def initialize(self):
 
         data_to_be_written = ["configuration", "time"]
 
+        filename = Path(self.configuration["xtc_file"]["filename"])
         # Create XTC or TRR object depending on which kind of trajectory was loaded
-        if self.configuration["xtc_file"]["filename"].suffix == ".xtc":
-            self._xdr_file = XTCTrajectoryFile(
-                self.configuration["xtc_file"]["filename"], "r"
-            )
+        if filename.suffix == ".xtc":
+            self._xdr_file = XTCTrajectoryFile(bytes(filename), "r")
             self._xtc = True
-        elif self.configuration["xtc_file"]["filename"].suffix == ".trr":
-            self._xdr_file = TRRTrajectoryFile(
-                self.configuration["xtc_file"]["filename"], "r"
-            )
+        elif filename.suffix == ".trr":
+            self._xdr_file = TRRTrajectoryFile(bytes(filename), "r")
             self._xtc = False
 
             # Extract information about whether velocities and forces are present in the TRR file

MDANSE/Src/MDANSE/Framework/Formats/TextFormat.py

@@ -67,7 +67,8 @@ def write(
         :type header: str
         """
 
-        filename = Path(filename).with_suffix(".tar")
+        filename = Path(filename)
+        filename = filename.parent / (filename.stem + "_text.tar")
 
         PLATFORM.create_directory(filename.parent)
         tf = tarfile.open(filename, "w")

MDANSE/Src/MDANSE/MolecularDynamics/Trajectory.py

@@ -13,23 +13,23 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
-from typing import TYPE_CHECKING, Any, Dict, List
+import operator
+from typing import TYPE_CHECKING, Any, Collection, Dict, List, Union
 
 if TYPE_CHECKING:
     from MDANSE.Chemistry.Databases import AtomsDatabase
 
 import math
-import operator
-from collections.abc import Collection
 from pathlib import Path
-from typing import Union
 
 import h5py
 import numpy as np
 from MDANSE import PLATFORM
 from MDANSE.Chemistry import ATOMS_DATABASE
 from MDANSE.Chemistry.ChemicalSystem import ChemicalSystem
 from MDANSE.MolecularDynamics.Configuration import RealConfiguration
+from MDANSE.Trajectory.H5MDTrajectory import H5MDTrajectory
+from MDANSE.Trajectory.MdanseTrajectory import MdanseTrajectory
 
 available_formats = {
     "MDANSE": MdanseTrajectory,

MDANSE/Src/MDANSE/Trajectory/MdanseTrajectory.py

@@ -53,7 +53,7 @@ def __init__(self, h5_filename: Union[Path, str]):
 
         # Load the chemical system
         self._chemical_system = ChemicalSystem(self._h5_filename.stem, self)
-        self._chemical_system.load(self._h5_filename)
+        self._chemical_system.load(self._h5_file)
 
         # Load all the unit cells
         self._load_unit_cells()
@@ -69,7 +69,7 @@ def file_is_right(self, filename: Union[Path, str]):
         else:
             try:
                 temp_cs = ChemicalSystem(filename.stem)
-                temp_cs.load(filename)
+                temp_cs.load(file_object)
             except Exception:
                 LOG.warning(
                     f"Could not load ChemicalSystem from {filename}. MDANSE will try to read it as H5MD next."

MDANSE/Tests/UnitTests/test_databases.py

@@ -14,6 +14,7 @@
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
 import json
+from pathlib import Path
 import unittest
 from unittest.mock import patch, mock_open, ANY
 
@@ -101,9 +102,9 @@ def test__load_user_database(self):
                 }
             ),
         ) as m:
-            with patch("Path.exists", spec=True):
+            with patch("pathlib.Path.exists", spec=True):
                 ATOMS_DATABASE._load("user.json")
-                m.assert_called_with("user.json", "r")
+                m.assert_called_with(Path("user.json"), "r")
                 self.assertDictEqual({"family": "str"}, ATOMS_DATABASE._properties)
                 self.assertDictEqual(
                     {"H": {"family": "non-metal"}}, ATOMS_DATABASE._data