Bump gsd from 2.9.0 to 3.1.0

[dependabot]

Bumps gsd from 2.9.0 to 3.1.0.

Release notes

Sourced from gsd's releases.

v3.1.0

Fixed:

• hoomd.read_log no longer triggers a numpy deprecation warning.

Added:

• HOOMDTrajectory.flush - flush buffered writes on an open HOOMDTrajectory.

v3.0.1

Fixed:

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

v3.0.0

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]{.title-ref}, 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).

Changelog

Sourced from gsd's changelog.

3.1.0 (2023-07-28) ^^^^^^^^^^^^^^^^^^

Fixed:

• hoomd.read_log no longer triggers a numpy deprecation warning.

Added:

• HOOMDTrajectory.flush - flush buffered writes on an open HOOMDTrajectory.

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.

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](https://github.com/glotzerlab/gsd/issues/237) <https://github.com/glotzerlab/gsd/pull/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](https://github.com/glotzerlab/gsd/issues/237) <https://github.com/glotzerlab/gsd/pull/237>__).
• GSDFile.index_entries_to_buffer - get/set the write buffer size (C API index_entries_to_buffer / index_entries_to_buffer) ([#237](https://github.com/glotzerlab/gsd/issues/237) <https://github.com/glotzerlab/gsd/pull/237>__).
• On importing gsd, install a SIGTERM handler that calls sys.exit(1) ([#237](https://github.com/glotzerlab/gsd/issues/237) <https://github.com/glotzerlab/gsd/pull/237>__).

Changed:

• write_chunk buffers writes across frames to increase performance ([#237](https://github.com/glotzerlab/gsd/issues/237) <https://github.com/glotzerlab/gsd/pull/237>__).
• Use Doxygen and breathe to generate C API documentation in Sphinx ([#237](https://github.com/glotzerlab/gsd/issues/237) <https://github.com/glotzerlab/gsd/pull/237>__).

Removed:

• gsd.__version__ - use gsd.version.version.
• gsd.hoomd.Snapshot - use gsd.hoomd.Frame ([#249](https://github.com/glotzerlab/gsd/issues/249) <https://github.com/glotzerlab/gsd/pull/249>__).
• gsd.hoomd.HOOMDTrajectory.read_frame - use gsd.hoomd.HOOMDTrajectory.__getitem__ ([#249](https://github.com/glotzerlab/gsd/issues/249) <https://github.com/glotzerlab/gsd/pull/249>__).

... (truncated)

Commits

• 73a64ed Merge pull request #269 from glotzerlab/release-gsd-3.1.0
• e3e19c6 Bump version to 3.1.0.
• 625823b Document 3.1.0 release date.
• d342652 Merge branch 'trunk-patch' into trunk-minor
• e254ba7 Merge pull request #267 from glotzerlab/prevent-deprecation-warning
• efeb19b Merge pull request #266 from glotzerlab/add-flush
• 0feef0a Run pre-commit.
• b759a55 Update change log.
• 528f4f0 Manually unpack scalar quantities from numpy arrays.
• 55860f3 Update change log.
• Additional commits viewable in compare view

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[tommy-waltmann]

combining this with #1133

[dependabot]

OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting @dependabot ignore this major version or @dependabot ignore this minor version. You can also ignore all major, minor, or patch releases for a dependency by adding an ignore condition with the desired update_types to your config file.

If you change your mind, just re-open this PR and I'll resolve any conflicts on it.