Releases: cryoem-uoft/cryosparc-tools
Releases · cryoem-uoft/cryosparc-tools
v4.6.1
What's Changed
New
- Python 3.13 support
Fixed
- Disallow non-URL-encodable characters when creating external job inputs and outputs
- Prevent queuing and killing external jobs (must use
job.start/job.stop()
orwith job.run()
)
Full Changelog: v4.6.0...v4.6.1
v4.6.0
What's Changed
New
Dataset.is_equivalent
method to check if two datasets have identical fields, but in a different orderDataset.inspect
class method which accepts a path to a dataset and returns its header without loading the entire dataset from disk- Load a subset of dataset fields with
Dataset.load
by specifyingprefixes
orfields
keyword arguments - Support for uploading job assets in
bild
format
Updated
ExternalJob.add_output
method now expectsalloc
argument to be specified as a keyword arg- Dataset methods which accept a
copy
argument now expect it to be specified as a keyword arg
Fixed
- Significantly reduced memory usage when loading large datasets with
Dataset.load
Full Changelog: v4.5.1...v4.6.0
v4.5.1
What's Changed
New
- Numpy 2.0 support
Fixed
- Add missing result data types added in CryoSPARC v4.5
Full Changelog: v4.5.0...v4.5.1
v4.5.0
What's Changed
New
- New
cluster_vars
argument forJob.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 inDataset.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
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 ofAssertionError
when a CryoSPARC command server request fails - Raise
cryosparc.errors.DatasetLoadError
to show target file path whenDataset.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
methodlane
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
fromException
- Correctly catch command request timeout
Docs
- Added T20S workflow example
Full Changelog: v4.2.0...v4.3.0