v4.5.0

What's Changed

New

• New cluster_vars argument for Job.queue method for queueing to clusters
• Various print methods for inspecting available job types, inputs, outputs and parameters

Updated

• Allow copy and symlink operations from outside project directory
• Allow larger shapes for dataset fields

Fixed

• Always raise explicit errors when dataset allocation fails
• Correctly retain fields when appending or creating a union of empty datasets with non-empty fields
• Correctly allow excluding uid field in Dataset.descr method

Docs

• New guide for job access and inspection
• Fix broken code in custom latent trajectory example
• Generalize 3D Flex custom trajectory example to >2 dimensions

Full Changelog: v4.4.1...v4.5.0

v4.4.1

What's Changed

Fixed

• Correct command response error data formatting

Full Changelog: v4.4.0...v4.4.1

v4.4.0

What's Changed

New

• Python 3.11 and 3.12 support
• overwrite keyword argument for file upload functions for extra confirmation when uploading project files to a path that already exist (raises error if not specified)
• Smaller and faster compressed dataset format when saving with CSDAT_FORMAT (datasets saved in this format prior to this release may no longer be readable)

Updated

• Calls to CryoSPARC’s command servers automatically retry while CryoSPARC is down for up to one minute
• Raise cryosparc.errors.CommandError instead of AssertionError when a CryoSPARC command server request fails
• Raise cryosparc.errors.DatasetLoadError to show target file path when Dataset.load encounters an exception
• Improved server- and slot- related error messages
• Warn when connecting to CryoSPARC version that doesn’t match cryosparc-tools version

Docs

• Delete Rejected Exposures example
• Instructions for plotting scale bars on 2D Classes
• Revert downsampled, symmetry expanded particles example
• Connect a volume series to Class3D example

New Contributors

• @hsnyder made their first contribution in #37
• @arulths made their first contribution in #53
• @PlethoraChutney made their first contribution in #56

Full Changelog: v4.3.1...v4.4.0

v4.3.1

Fixed

• Job.queue method lane argument is now optional when queuing directly to master
• Dataset memory leak due to missing reference count decrease during dataset garbage collection

Docs

• pip update instructions
• Recommend Python environment as a prerequisite

Full Changelog: v4.3.0...v4.3.1

v4.3.0

Added

• Updated project doc spec with updated generate intermediate results settings field

Fixed

• Allow project file retrieval from when project directory contains a symbolic link
• Auto-exclude slots with missing metafile and better error message when output metafile is missing
• Extend CommandClient.Error from Exception
• Correctly catch command request timeout

Docs

• Added T20S workflow example

Full Changelog: v4.2.0...v4.3.0

v4.2.0

What's Changed

• Support for CryoSPARC v4.2.0

Full Changelog: v4.1.3...v4.2.0

v4.1.3

What's Changed

• Fix error when creating a job with CryoSPARC.create_job by @nfrasser in #17 and #20
• Fix Dataset allocation error due to slot generation overflow by @nfrasser in #18
• Docs minor fixes by @wtempel in #13

New Contributors

• @wtempel made their first contribution in #13

Full Changelog: v4.1.2...v4.1.3

v4.1.2

What's Changed

• Preliminary access to CryoSPARC Live via CryoSPARC.rtp command client by @KiSchnelle in #12
• Documenation fixes by @mcleanm in #14

New Contributors

• @KiSchnelle made their first contribution in #12
• @mcleanm made their first contribution in #14

Full Changelog: v4.1.1...v4.1.2

v4.1.1

• Use correct numpy object type for newer versions of Numpy
• Fix limit on number of active datasets
• Use correct C types in Cython header definition

Full Changelog: v4.1.0...v4.1.1

v4.1.0

• Initial release
• Manage CryoSPARC Projects, Workspaces and Jobs from Python
• Load input and output datasets
• Read and write MRC files
• Read and write STAR files