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CHANGELOG.md

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Changelog

v4.6.1

  • Added: Python 3.13 support
  • Fix: Disallow non-URL-encodable characters when creating external job inputs and outputs
  • Fix: Prevent queuing and killing external jobs (must use job.start/job.stop() or with job.run())

v4.6.0

  • Added: Dataset.is_equivalent method to check if two datasets have identical fields, but in a different order
  • Added: Dataset.inspect class method which accepts a path to a dataset and returns its header without loading the entire dataset from disk
  • Added: Load a subset of dataset fields with Dataset.load by specifying prefixes or fields keyword arguments
  • Added: Support for uploading job assets in bild format
  • Updated: ExternalJob.add_output method now expects alloc argument to be specified as a keyword arg
  • Updated: Dataset methods which accept a copy argument now expect it to be specified as a keyword arg
  • Fixed: Significantly reduced memory when loading large datasets with Dataset.load

v4.5.1

  • Added: Numpy 2.0 support
  • Fixed: Add missing result data types added in CryoSPARC v4.5

v4.5.0

  • Added: New cluster_vars argument for Job.queue method for queueing to clusters
  • Added: Various print methods for inspecting available job types, inputs, outputs and parameters
  • Updated: Allow copy and symlink operations from outside project directory
  • Updated: Allow larger shapes for dataset fields
  • Fixed: Always raise explicit errors when dataset allocation fails
  • Fixed: Correctly retain fields when appending or creating a union of empty datasets with non-empty fields
  • Fixed: Correctly allow excluding uid field in Dataset.descr method
  • Docs: New guide for job access and inspection
  • Docs: Fix broken code in custom latent trajectory example
  • Docs: Generalize 3D Flex custom trajectory example to >2 dimensions

v4.4.1

  • Fixed: Correct command response error data formatting

v4.4.0

  • Added: Python 3.11 and 3.12 support
  • Added: 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)
  • Added: 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
  • Updated: Raise cryosparc.errors.CommandError instead of AssertionError when a CryoSPARC command server request fails
  • Updated: Raise cryosparc.errors.DatasetLoadError to show target file path when Dataset.load encounters an exception
  • Updated: Improved server- and slot- related error messages
  • Updated: Warn when connecting to CryoSPARC version that doesn’t match cryosparc-tools version
  • Docs: Delete Rejected Exposures example
  • Docs: Instructions for plotting scale bars on 2D Classes
  • Docs: Revert downsampled, symmetry expanded particles example
  • Docs: Connect a volume series to Class3D example

v4.3.1

  • Fixed: Job.queue method lane argument is now optional when queuing directly to master
  • Fixed: Dataset memory leak due to missing reference count decrease during dataset garbage collection
  • Docs: pip update instructions
  • Docs: Recommend Python environment as a prerequisite

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
  • Fixed: Auto-exclude slots with missing metafile and better error message when output metafile is missing
  • Fixed: Extend CommandClient.Error from Exception
  • Fixed: Correctly catch command request timeout
  • Docs: Added T20S workflow example

v4.2.0

  • Support for CryoSPARC v4.2

v4.1.3

  • Fix error when creating a job with CryoSPARC.create_job
  • Fix Dataset allocation error due to slot generation overflow
  • Docs minor fixes

v4.1.2

  • Preliminary access to CryoSPARC Live via CryoSPARC.rtp command client
  • Documenation fixes

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

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