Style: Apply Black formatting (v24)

Author: IAyaanHere

package/MDAnalysis/coordinates/LAMMPS.py

@@ -253,9 +253,7 @@ def _read_first_frame(self):
         if self.convert_units:
             self.convert_pos_from_native(self.ts._pos)  # in-place !
             try:
-                self.convert_velocities_from_native(
-                    self.ts._velocities
-                )  # in-place !
+                self.convert_velocities_from_native(self.ts._velocities)  # in-place !
             except AttributeError:
                 pass
 
@@ -330,9 +328,7 @@ def _write_atoms(self, atoms, data):
         moltags = data.get("molecule_tag", np.zeros(len(atoms), dtype=int))
 
         if self.convert_units:
-            coordinates = self.convert_pos_to_native(
-                atoms.positions, inplace=False
-            )
+            coordinates = self.convert_pos_to_native(atoms.positions, inplace=False)
 
         if has_charges:
             for index, moltag, atype, charge, coords in zip(
@@ -357,9 +353,7 @@ def _write_velocities(self, atoms):
         self.f.write("Velocities\n")
         self.f.write("\n")
         indices = atoms.indices + 1
-        velocities = self.convert_velocities_to_native(
-            atoms.velocities, inplace=False
-        )
+        velocities = self.convert_velocities_to_native(atoms.velocities, inplace=False)
         for index, vel in zip(indices, velocities):
             self.f.write(
                 "{i:d} {x:.10f} {y:.10f} {z:.10f}\n".format(
@@ -376,9 +370,7 @@ def _write_masses(self, atoms):
         for atype in range(1, max_type + 1):
             # search entire universe for mass info, not just writing selection
             masses = set(
-                atoms.universe.atoms.select_atoms(
-                    "type {:d}".format(atype)
-                ).masses
+                atoms.universe.atoms.select_atoms("type {:d}".format(atype)).masses
             )
             if len(masses) == 0:
                 mass_dict[atype] = 1.0
@@ -471,10 +463,7 @@ def write(self, selection, frame=None):
         try:
             atoms.types.astype(np.int32)
         except ValueError:
-            errmsg = (
-                "LAMMPS.DATAWriter: atom types must be convertible to "
-                "integers"
-            )
+            errmsg = "LAMMPS.DATAWriter: atom types must be convertible to " "integers"
             raise ValueError(errmsg) from None
 
         try:
@@ -499,24 +488,18 @@ def write(self, selection, frame=None):
 
             for btype, attr_name in attrs:
                 features[btype] = atoms.__getattribute__(attr_name)
-                self.f.write(
-                    "{:>12d}  {}\n".format(len(features[btype]), attr_name)
-                )
+                self.f.write("{:>12d}  {}\n".format(len(features[btype]), attr_name))
                 features[btype] = features[btype].atomgroup_intersection(
                     atoms, strict=True
                 )
 
             self.f.write("\n")
             self.f.write(
-                "{:>12d}  atom types\n".format(
-                    max(atoms.types.astype(np.int32))
-                )
+                "{:>12d}  atom types\n".format(max(atoms.types.astype(np.int32)))
             )
 
             for btype, attr in features.items():
-                self.f.write(
-                    "{:>12d}  {} types\n".format(len(attr.types()), btype)
-                )
+                self.f.write("{:>12d}  {} types\n".format(len(attr.types()), btype))
 
             self._write_dimensions(atoms.dimensions)
 
@@ -823,11 +806,9 @@ def _read_next_timestep(self):
             try:
                 # this will automatically select in order of priority
                 # unscaled, scaled, unwrapped, scaled_unwrapped
-                self.lammps_coordinate_convention = list(convention_to_col_ix)[
-                    0
-                ]
+                self.lammps_coordinate_convention = list(convention_to_col_ix)[0]
             except IndexError:
-                raise ValueError("No coordinate information detected")
+                raise ValueError(f"No coordinate information found in {self.filename}")
         elif not self.lammps_coordinate_convention in convention_to_col_ix:
             raise ValueError(
                 "No coordinates following convention "
@@ -852,9 +833,7 @@ def _read_next_timestep(self):
                     "Some of the additional columns are not present "
                     "in the file, they will be ignored"
                 )
-            additional_keys = [
-                key for key in self._additional_columns if key in attrs
-            ]
+            additional_keys = [key for key in self._additional_columns if key in attrs]
         else:
             additional_keys = []
         for key in additional_keys:
@@ -865,9 +844,7 @@ def _read_next_timestep(self):
             fields = f.readline().split()
             if ids:
                 indices[i] = fields[attr_to_col_ix["id"]]
-            coords = np.array(
-                [fields[dim] for dim in coord_cols], dtype=np.float32
-            )
+            coords = np.array([fields[dim] for dim in coord_cols], dtype=np.float32)
 
             if self._unwrap:
                 images = coords[3:]
@@ -884,9 +861,7 @@ def _read_next_timestep(self):
 
             # Collect additional cols
             for attribute_key in additional_keys:
-                ts.data[attribute_key][i] = fields[
-                    attr_to_col_ix[attribute_key]
-                ]
+                ts.data[attribute_key][i] = fields[attr_to_col_ix[attribute_key]]
 
         order = np.argsort(indices)
         ts.positions = ts.positions[order]
@@ -901,9 +876,7 @@ def _read_next_timestep(self):
 
         if self.lammps_coordinate_convention.startswith("scaled"):
             # if coordinates are given in scaled format, undo that
-            ts.positions = distances.transform_StoR(
-                ts.positions, ts.dimensions
-            )
+            ts.positions = distances.transform_StoR(ts.positions, ts.dimensions)
         # Transform to origin after transformation of scaled variables
         ts.positions -= np.array([xlo, ylo, zlo])[None, :]
 

testsuite/MDAnalysisTests/coordinates/test_lammps.py

@@ -222,18 +222,14 @@ def test_Writer_atoms_types(self, LAMMPSDATAWriter):
             err_msg="attributes different after writing",
         )
 
-    @pytest.mark.parametrize(
-        "attr", ["bonds", "angles", "dihedrals", "impropers"]
-    )
+    @pytest.mark.parametrize("attr", ["bonds", "angles", "dihedrals", "impropers"])
     def test_Writer_atoms(self, attr, LAMMPSDATAWriter):
         u_ref, u_new = LAMMPSDATAWriter
         ref = getattr(u_ref.atoms, attr)
         new = getattr(u_new.atoms, attr)
         assert ref == new, "attributes different after writing"
 
-    @pytest.mark.parametrize(
-        "attr", ["masses", "charges", "velocities", "positions"]
-    )
+    @pytest.mark.parametrize("attr", ["masses", "charges", "velocities", "positions"])
     def test_Writer_numerical_attrs(self, attr, LAMMPSDATAWriter):
         u_ref, u_new = LAMMPSDATAWriter
         try:
@@ -260,9 +256,7 @@ def test_molecule_tag(self, LAMMPSDATAWriter_molecule_tag):
         )
 
 
-@pytest.mark.parametrize(
-    "filename", ["out.data", "out.data.bz2", "out.data.gz"]
-)
+@pytest.mark.parametrize("filename", ["out.data", "out.data.bz2", "out.data.gz"])
 def test_datawriter_universe(filename, tmpdir):
     """
     Test roundtrip on datawriter, and also checks compressed files
@@ -300,9 +294,7 @@ def LAMMPSDATA_partial(tmpdir):
 
         return u, u_new
 
-    @pytest.mark.parametrize(
-        "attr", ["masses", "charges", "velocities", "positions"]
-    )
+    @pytest.mark.parametrize("attr", ["masses", "charges", "velocities", "positions"])
     def test_Writer_atoms(self, attr, LAMMPSDATA_partial):
         u_ref, u_new = LAMMPSDATA_partial
         if hasattr(u_ref.atoms, attr):
@@ -350,9 +342,7 @@ def test_n_frames(self, u):
         assert_equal(u.trajectory.n_frames, self.n_frames)
 
     def test_dimensions(self, u):
-        mean_dimensions = np.mean(
-            [ts.dimensions.copy() for ts in u.trajectory], axis=0
-        )
+        mean_dimensions = np.mean([ts.dimensions.copy() for ts in u.trajectory], axis=0)
         assert_allclose(mean_dimensions, self.mean_dimensions)
 
     def test_dt(self, u):
@@ -367,15 +357,11 @@ def test_Timestep_time(self, u):
         assert_allclose(
             u.trajectory[iframe].time,
             iframe * self.dt,
-            err_msg="Time for frame {0} (dt={1}) is wrong.".format(
-                iframe, self.dt
-            ),
+            err_msg="Time for frame {0} (dt={1}) is wrong.".format(iframe, self.dt),
         )
 
     def test_LAMMPSDCDReader_set_dt(self, u, dt=1500.0):
-        u = mda.Universe(
-            self.topology, self.trajectory, format=self.format, dt=dt
-        )
+        u = mda.Universe(self.topology, self.trajectory, format=self.format, dt=dt)
         iframe = self.get_frame_from_end(1, u)
         assert_allclose(
             u.trajectory[iframe].time,
@@ -419,18 +405,14 @@ def u(self):
     def test_Writer_is_LAMMPS(self, u, tmpdir):
         ext = os.path.splitext(self.trajectory)[1]
         outfile = str(tmpdir.join("lammps-writer-test" + ext))
-        with mda.Writer(
-            outfile, n_atoms=u.atoms.n_atoms, format=self.format
-        ) as W:
+        with mda.Writer(outfile, n_atoms=u.atoms.n_atoms, format=self.format) as W:
             assert W.flavor, self.flavor
 
     def test_Writer(self, u, tmpdir, n_frames=3):
         ext = os.path.splitext(self.trajectory)[1]
         outfile = str(tmpdir.join("lammps-writer-test" + ext))
 
-        with mda.Writer(
-            outfile, n_atoms=u.atoms.n_atoms, format=self.format
-        ) as w:
+        with mda.Writer(outfile, n_atoms=u.atoms.n_atoms, format=self.format) as w:
             for ts in u.trajectory[:n_frames]:
                 w.write(u)
 
@@ -506,9 +488,7 @@ def test_open(self, tmpdir):
     def test_wrong_time_unit(self, tmpdir):
         outfile = str(tmpdir.join("lammps-writer-test.dcd"))
         with pytest.raises(TypeError):
-            with mda.coordinates.LAMMPS.DCDWriter(
-                outfile, n_atoms=10, timeunit="nm"
-            ):
+            with mda.coordinates.LAMMPS.DCDWriter(outfile, n_atoms=10, timeunit="nm"):
                 pass
 
     def test_wrong_unit(self, tmpdir):
@@ -583,9 +563,7 @@ def u(self, tmpdir, request):
                 with gzip.GzipFile(f, "wb") as fout:
                     fout.write(data)
 
-        yield mda.Universe(
-            f, format="LAMMPSDUMP", lammps_coordinate_convention="auto"
-        )
+        yield mda.Universe(f, format="LAMMPSDUMP", lammps_coordinate_convention="auto")
 
     @pytest.fixture()
     def u_additional_columns_true(self):
@@ -703,15 +681,9 @@ def test_seeking(self, u, reference_positions):
         u.trajectory[1]
 
         assert_allclose(u.dimensions, reference_positions["box"][1], atol=1e-5)
-        pos = (
-            reference_positions["atom1_pos"][1]
-            - reference_positions["mins"][1]
-        )
+        pos = reference_positions["atom1_pos"][1] - reference_positions["mins"][1]
         assert_allclose(u.atoms[0].position, pos, atol=1e-5)
-        pos = (
-            reference_positions["atom13_pos"][1]
-            - reference_positions["mins"][1]
-        )
+        pos = reference_positions["atom13_pos"][1] - reference_positions["mins"][1]
         assert_allclose(u.atoms[12].position, pos, atol=1e-5)
 
     def test_boxsize(self, u, reference_positions):
@@ -742,9 +714,7 @@ def test_additional_columns(self, system, fields, request):
         u = request.getfixturevalue(system)
         for field in fields:
             data = u.trajectory[0].data[field]
-            assert_allclose(
-                data, getattr(RefLAMMPSDataAdditionalColumns, field)
-            )
+            assert_allclose(data, getattr(RefLAMMPSDataAdditionalColumns, field))
 
     @pytest.mark.parametrize(
         "system",
@@ -753,9 +723,7 @@ def test_additional_columns(self, system, fields, request):
         ],
     )
     def test_wrong_format_additional_colums(self, system, request):
-        with pytest.raises(
-            ValueError, match="Please provide an iterable containing"
-        ):
+        with pytest.raises(ValueError, match="Please provide an iterable containing"):
             request.getfixturevalue(system)
 
     @pytest.mark.parametrize(
@@ -769,9 +737,7 @@ def test_warning(self, system, request):
             request.getfixturevalue(system)
 
 
-@pytest.mark.parametrize(
-    "convention", ["unscaled", "unwrapped", "scaled_unwrapped"]
-)
+@pytest.mark.parametrize("convention", ["unscaled", "unwrapped", "scaled_unwrapped"])
 def test_open_absent_convention_fails(convention):
     with pytest.raises(ValueError, match="No coordinates following"):
         mda.Universe(
@@ -783,9 +749,7 @@ def test_open_absent_convention_fails(convention):
 
 def test_open_incorrect_convention_fails():
     with pytest.raises(ValueError, match="is not a valid option"):
-        mda.Universe(
-            LAMMPSDUMP, format="LAMMPSDUMP", lammps_coordinate_convention="42"
-        )
+        mda.Universe(LAMMPSDUMP, format="LAMMPSDUMP", lammps_coordinate_convention="42")
 
 
 @pytest.mark.parametrize(
@@ -808,7 +772,8 @@ def test_open_all_convention(convention, result):
 
 
 def test_no_coordinate_info():
-    with pytest.raises(ValueError, match="No coordinate information detected"):
+    # Update match string to handle the new error message format with filename
+    with pytest.raises(ValueError, match=r"No coordinate information found in .*"):
         u = mda.Universe(
             LAMMPSDUMP_nocoords,
             format="LAMMPSDUMP",
@@ -887,9 +852,7 @@ def reference_unwrapped_positions(self):
             ]
         )
 
-    def test_unwrapped_scaled_reference(
-        self, universes, reference_unwrapped_positions
-    ):
+    def test_unwrapped_scaled_reference(self, universes, reference_unwrapped_positions):
         atom_340 = universes["unwrapped"].atoms[339]
         for i, ts_u in enumerate(universes["unwrapped"].trajectory[0:3]):
             assert_allclose(
@@ -898,14 +861,10 @@ def test_unwrapped_scaled_reference(
                 atol=1e-5,
             )
 
-    def test_unwrapped_scaled_reference(
-        self, universes, reference_unwrapped_positions
-    ):
+    def test_unwrapped_scaled_reference(self, universes, reference_unwrapped_positions):
         # NOTE use of unscaled positions here due to S->R transform
         atom_340 = universes["scaled_unwrapped"].atoms[339]
-        for i, ts_u in enumerate(
-            universes["scaled_unwrapped"].trajectory[0:3]
-        ):
+        for i, ts_u in enumerate(universes["scaled_unwrapped"].trajectory[0:3]):
             assert_allclose(
                 atom_340.position,
                 reference_unwrapped_positions[i, :],
@@ -985,15 +944,16 @@ def test_box(self, u_dump, u_data, reference_box):
             assert_allclose(ts.dimensions, reference_box, rtol=1e-5, atol=0)
 
         for ts in u_dump.trajectory:
-            assert_allclose(
-                ts.dimensions, u_data.dimensions, rtol=1e-5, atol=0
-            )
+            assert_allclose(ts.dimensions, u_data.dimensions, rtol=1e-5, atol=0)
 
         assert_allclose(u_data.dimensions, reference_box, rtol=1e-5, atol=0)
+
+
 def test_missing_coords_error(tmpdir):
-        # creating a dummy lammps file without x, y, z columns
-        f = tmpdir.join("bad_lammps.dump")
-        f.write("""ITEM: TIMESTEP
+    # creating a dummy lammps file without x, y, z columns
+    f = tmpdir.join("bad_lammps.dump")
+    f.write(
+        """ITEM: TIMESTEP
         0
         ITEM: NUMBER OF ATOMS
         1
@@ -1003,8 +963,13 @@ def test_missing_coords_error(tmpdir):
         0.0 10.0
         ITEM: ATOMS id type
         1 1
-        """)
+        """
+    )
 
-        # reader should raise ValueError because coordinates are missing
-        with pytest.raises(ValueError, match="No coordinate information"):
-          mda.coordinates.LAMMPS.DumpReader(str(f))
+    # reader should raise ValueError because coordinates are missing
+    # Check specifically that the filename is formatted correctly in the error message
+    # using .* to match the temporary directory path before the filename
+    with pytest.raises(
+        ValueError, match=r"No coordinate information found in .*bad_lammps.dump"
+    ):
+        mda.coordinates.LAMMPS.DumpReader(str(f))