diff --git a/znh5md/__init__.py b/znh5md/__init__.py index d0afb65..6a26787 100644 --- a/znh5md/__init__.py +++ b/znh5md/__init__.py @@ -1,4 +1,5 @@ """ZnH5MD: High Performance Interface for H5MD Trajectories.""" + import contextlib import importlib.metadata diff --git a/znh5md/format/__init__.py b/znh5md/format/__init__.py index 509bb6a..fba91bf 100644 --- a/znh5md/format/__init__.py +++ b/znh5md/format/__init__.py @@ -1,4 +1,5 @@ """Format handler for h5md files.""" + import contextlib import dataclasses import typing @@ -33,16 +34,14 @@ class GRP: @staticmethod def encode_boundary(value) -> np.ndarray: - return np.array( - [ - ( - "periodic".encode(encoding="utf-8") - if x - else "none".encode(encoding="utf-8") - ) - for x in value - ] - ) + return np.array([ + ( + "periodic".encode(encoding="utf-8") + if x + else "none".encode(encoding="utf-8") + ) + for x in value + ]) @staticmethod def decode_boundary(value) -> np.ndarray: diff --git a/znh5md/io/base.py b/znh5md/io/base.py index 66a9d20..cb8d9c6 100644 --- a/znh5md/io/base.py +++ b/znh5md/io/base.py @@ -99,9 +99,9 @@ def append_to_dataset(self, dataset_group: h5py.Group): self.resize_by_particle_count(dataset_group) for key in ("value", "time", "step"): dataset_group[key].resize(n_current_frames + len(self), axis=0) - dataset_group[key][:] = np.concatenate( - [dataset_group[key][:n_current_frames], self.value] - ) + dataset_group[key][:] = np.concatenate([ + dataset_group[key][:n_current_frames], self.value + ]) @dataclasses.dataclass @@ -124,9 +124,9 @@ def append_to_dataset(self, dataset_group: h5py.Group): self.resize_by_particle_count(dataset_group) dataset_group["value"].resize(n_current_frames + len(self), axis=0) - dataset_group["value"][:] = np.concatenate( - [dataset_group["value"][:n_current_frames], self.value] - ) + dataset_group["value"][:] = np.concatenate([ + dataset_group["value"][:n_current_frames], self.value + ]) CHUNK_DICT = typing.Dict[str, ExplicitStepTimeChunk] diff --git a/znh5md/io/reader.py b/znh5md/io/reader.py index 1fb25fb..6685d9b 100644 --- a/znh5md/io/reader.py +++ b/znh5md/io/reader.py @@ -224,9 +224,9 @@ def yield_chunks(self) -> typing.Iterator[typing.Dict[str, FixedStepTimeChunk]]: if "energy" in frame.list_properties(): energy.append(np.copy(frame["energy"]).astype(float)) if "pbc" in frame.list_properties(): - pbc.append( - [True if x == "T" else False for x in frame["pbc"].split()] - ) + pbc.append([ + True if x == "T" else False for x in frame["pbc"].split() + ]) if len(positions) == self.frames_per_chunk: positions = self._fill_with_nan(positions).astype(float)