CHANGELOG.rst

Change Log

GSD releases follow semantic versioning.

3.x

3.4.2 (2024-11-13)

Fixed:

• Make NumPy 2.0 requirement optional (#405).

3.4.1 (2024-10-21)

Fixed:

• Prevent downgrading file versions when opening in write mode.

3.4.0 (2024-10-18)

Added:

• GSD_TYPE_CHARACTER chunk type for string data - valid in file layer versions 2.1 and later (#391).

Changed:

• The log dictionary in a hoomd frame now accepts string values. read_log correspondingly produces a NumPy array of variable length strings (#391).
• Require NumPy >= 2.0 (#391).

3.3.2 (2024-09-06)

Added:

• Support Python 3.13 (#388).

Removed:

• Support for Python 3.9 (#388).

3.3.1 (2024-08-19)

Changed:

• Improved build instructions (#376).

3.3.0 (2024-05-29)

Added:

• Support numpy 2.0 (#367).

Changed:

• Navigate the documentation with arrow keys (#365).
• Add button to copy code snippets from the documentation (#365).
• Remove singularity reference from the documentation (#365).

Removed:

• Support for Python 3.8 (#367).

3.2.1 (2024-01-22)

Fixed:

• Write all pending index entries to the file when gsd_flush() is called after gsd_write_chunk() and before gsd_end_frame() (#319).
• Readthedocs builds with pandas 2.2.0 (#322).
• Import without seg fault when built with CMake on macOS (#323).
• Internal cached data remains valid when users modify frames obtained by indexing trajectories (#324).

Changed:

• Provide support via GitHub discussions (#308).
• Use ruff (#317).
• Perform fewer implicit flushes when using the gsd.hoomd python API (#325).

3.2.0 (2023-09-27)

Added:

• Support Python 3.12 (#283).

3.1.1 (2023-08-03)

Fixed:

• Raise a FileExistsError when opening a file that already exists with mode = 'x' (#270).

3.1.0 (2023-07-28)

Fixed:

• hoomd.read_log no longer triggers a numpy deprecation warning (#267).

Added:

• HOOMDTrajectory.flush - flush buffered writes on an open HOOMDTrajectory (#266).

3.0.1 (2023-06-20)

Fixed:

• Prevent ValueError: signal only works in main thread of the main interpreter when importing gsd in a non-main thread (#257).

3.0.0 (2023-06-16)

Added:

• gsd.version.version - version string identifier. PEP8 compliant name replaces __version__.
• GSDFile.flush - flush write buffers (C API gsd_flush) (#237).
• GSDFile.maximum_write_buffer_size - get/set the write buffer size (C API gsd_get_maximum_write_buffer_size / gsd_set_maximum_write_buffer_size) (#237).
• GSDFile.index_entries_to_buffer - get/set the write buffer size (C API index_entries_to_buffer / index_entries_to_buffer) (#237).
• On importing gsd, install a SIGTERM handler that calls sys.exit(1) (#237).

Changed:

• write_chunk buffers writes across frames to increase performance (#237).
• Use Doxygen and breathe to generate C API documentation in Sphinx (#237).

Removed:

• gsd.__version__ - use gsd.version.version.
• gsd.hoomd.Snapshot - use gsd.hoomd.Frame (#249).
• gsd.hoomd.HOOMDTrajectory.read_frame - use gsd.hoomd.HOOMDTrajectory.__getitem__ (#249).
• The file modes 'wb', 'wb+', 'rb', 'rb+', 'ab', 'xb', and 'xb+'. Use 'r', 'r+', 'w', 'x', or 'a' (#249).

2.x

2.9.0 (2023-05-19)

Added:

• File modes 'r', 'r+', 'w', 'x', and 'a' (#238).

Changed:

• Test on gcc9, clang10, and newer (#235).
• Test and provide binary wheels on Python 3.8 and newer (#235).

Deprecated:

• File modes 'wb', 'wb+', 'rb', 'rb+', 'ab', 'xb', and 'xb+' (#238).
• [C API] GSD_APPEND file open mode (#238).

v2.8.1 (2023-03-13)

Fixed:

• Reduce memory usage in most use cases.
• Reduce likelihood of data corruption when writing GSD files.

v2.8.0 (2023-02-24)

Added:

• gsd.hoomd.read_log - Read log quantities from a GSD file.
• gsd.hoomd.Frame class to replace gsd.hoomd.Snapshot.

Changed:

• Improved documentation.

Deprecated:

• gsd.hoomd.Snapshot.

v2.7.0 (2022-11-30)

Added

• Support Python 3.11.

v2.6.1 (2022-11-04)

Fixed:

• Default values are now written to frame N (N != 0) when non-default values exist in frame 0.
• Data chunks can now be read from files opened in 'wb', 'xb', and 'ab' modes.

v2.6.0 (2022-08-19)

Changed:

• Raise an error when writing a frame with duplicate types.

v2.5.3 (2022-06-22)

Fixed

• Support Python >=3.6.

v2.5.2 (2022-04-15)

Fixed

• Correctly handle non-ASCII characters on Windows.
• Document that the fname argument to gsd_ C API functions is UTF-8 encoded.

v2.5.1 (2021-11-17)

Added

• Support for Python 3.10.
• Support for clang 13.

v2.5.0 (2021-10-13)

Changed

• Improved documentation.

Deprecated

• HOOMDTrajectory.read_frame - use indexing (trajectory[index]) to access frames from a trajectory.

v2.4.2 (2021-04-14)

Added

• MacOS and Windows wheels on PyPI.

Fixed

• Documented array shapes for angles, dihedrals, and impropers.

v2.4.1 (2021-03-11)

Added

• Support macos-arm64.

Changed

• Stop testing with clang 4-5, gcc 4.8-6.

v2.4.0 (2020-11-11)

Changed

• Set gsd.hoomd.ConfigurationData.dimensions default based on box's L_z value.

Fixed

• Failure in test_fl.py when run by a user and GSD was installed by root.

v2.3.0 (2020-10-30)

Added

• Support clang 11.
• Support Python 3.9.

Changed

• Install unit tests with the Python package.

Fixed

• Compile error on macOS 10.15.

v2.2.0 (2020-08-05)

Added

• Command line convenience interface for opening a GSD file.

v2.1.2 (2020-06-26)

Fixed

• Adding missing close method to HOOMDTrajectory.
• Documentation improvements.

v2.1.1 (2020-04-20)

Fixed

• List defaults in gsd.fl.open documentation.

v2.1.0 (2020-02-27)

Added

• Shape specification for sphere unions.

v2.0.0 (2020-02-03)

Note

• This release introduces a new file storage format.
• GSD >= 2.0 can read and write to files created by GSD 1.x.
• Files created or upgraded by GSD >= 2.0 can not be opened by GSD < 1.x.

Added

• The upgrade method converts a GSD 1.0 file to a GSD 2.0 file in place.
• Support arbitrarily long chunk names (only in GSD 2.0 files).

Changed

• gsd.fl.open accepts None for application, schema, and schema_version when opening files for reading.
• Improve read latency when accessing files with thousands of chunk names in a frame (only for GSD 2.0 files).
• Buffer small writes to improve write performance.
• Improve performance and reduce memory usage in read/write modes ('rb+', 'wb+' and ('xb+').
• C API: functions return error codes from the gsd_error enum. v2.x integer error codes differ from v1.x, use the enum to check. For example: if (retval == GSD_ERROR_IO).
• Python, Cython, and C code must follow strict style guidelines.

Removed

• gsd.fl.create - use gsd.fl.open.
• gsd.hoomd.create - use gsd.hoomd.open.
• GSDFile v1.0 compatibility mode - use gsd.fl.open.
• hoomdxml2gsd.py.

Fixed

• Allow more than 127 data chunk names in a single GSD file.

v1.x

v1.10.0 (2019-11-26)

• Improve performance of first frame write.
• Allow pickling of GSD file handles opened in read only mode.
• Removed Cython-generated code from repository. fl.pyx will be cythonized during installation.

v1.9.3 (2019-10-04)

• Fixed preprocessor directive affecting Windows builds using setup.py.
• Documentation updates

v1.9.2 (2019-10-01)

• Support chunk sizes larger than 2GiB

v1.9.1 (2019-09-23)

• Support writing chunks wider than 255 from Python.

v1.9.0 (2019-09-18)

• File API: Add find_matching_chunk_names()
• HOOMD schema 1.4: Add user defined logged data.
• HOOMD schema 1.4: Add type_shapes specification.
• pytest >= 3.9.0 is required to run unit tests.
• gsd.fl.open and gsd.hoomd.open accept objects implementing os.PathLike.
• Report an error when attempting to write a chunk that fails to allocate a name.
• Reduce virtual memory usage in rb and wb open modes.
• Additional checks for corrupt GSD files on open.
• Synchronize after expanding file index.

v1.8.1 (2019-08-19)

• Correctly raise IndexError when attempting to read frames before the first frame.
• Raise RuntimeError when importing gsd in unsupported Python versions.

v1.8.0 (2019-08-05)

• Slicing a HOOMDTrajectory object returns a view that can be used to directly select frames from a subset or sliced again.
• raise IndexError when attempting to read frames before the first frame.
• Dropped support for Python 2.

v1.7.0 (2019-04-30)

• Add hpmc/sphere/orientable to HOOMD schema.
• HOOMD schema 1.3

v1.6.2 (2019-04-16)

• PyPI binary wheels now support numpy>=1.9.3,<2

v1.6.1 (2019-03-05)

• Documentation updates

v1.6.0 (2018-12-20)

• The length of sliced HOOMDTrajectory objects can be determined with the built-in len() function.

v1.5.5 (2018-11-28)

• Silence numpy deprecation warnings

v1.5.4 (2018-10-04)

• Add pyproject.toml file that defines numpy as a proper build dependency (requires pip >= 10)
• Reorganize documentation

v1.5.3 (2018-05-22)

• Revert setup.py changes in v1.5.2 - these do not work in most circumstances.
• Include sys/stat.h on all architectures.

v1.5.2 (2018-04-04)

• Close file handle on errors in gsd_open.
• Always close file handle in gsd_close.
• setup.py now correctly pulls in the numpy dependency.

v1.5.1 (2018-02-26)

• Documentation fixes.

v1.5.0 (2018-01-18)

• Read and write HPMC shape state data.

v1.4.0 (2017-12-04)

• Support reading and writing chunks with 0 length. No schema changes are necessary to support this.

v1.3.0 (2017-11-17)

• Document state entries in the HOOMD schema.
• No changes to the gsd format or reader code in v1.3.

v1.2.0 (2017-02-21)

• Add gsd.hoomd.open() method which can create and open hoomd gsd files.
• Add gsd.fl.open() method which can create and open gsd files.
• The previous create/class GSDFile instantiation is still supported for backward compatibility.

v1.1.0 (2016-10-04)

• Add special pairs section pairs/ to HOOMD schema.
• HOOMD schema version is now 1.1.

v1.0.1 (2016-06-15)

• Fix compile error on more strict POSIX systems.

v1.0.0 (2016-05-24)

Initial release.