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Changelog

v5.0.3

  • Fixed: correct session/workspace API type signatures
  • Docs: correct defaults for CryoSPARC class init

v5.0.2

  • Fixed: Correct session signatures model definition

v5.0.1

  • Fixed: Correctly use order argument when listing workspaces

v5.0.0

  • BREAKING: replaced low-level CryoSPARC.cli, CryoSPARC.rtp and CryoSPARC.vis attributes with single unified CryoSPARC.api
  • BREAKING: Can no longer add inputs or outputs when an external job has completed status, first clear the job with job.clear()
  • BREAKING: Can no longer save outputs when an external job has building or completed status, first clear the job, call job.start(), save outputs, and call job.stop()
  • BREAKING: CryoSPARC.download_asset(fileid, target) no longer accepts a directory target. Must specify a filename.
  • BREAKING: removed CryoSPARC.get_job_specs(). Use CryoSPARC.job_register instead
  • BREAKING: CryoSPARC.list_assets() and Job.list_assets() return list of models instead of list of dictionaries, accessible with dot-notation
    • OLD: job.list_assets()[0]['filename']
    • NEW: job.list_assets()[0].filename
  • BREAKING: CryoSPARC.get_lanes() now returns a list of models instead of dictionaries
    • OLD: cs.get_lanes()[0]['name']
    • NEW: cs.get_lanes()[0].name
  • BREAKING: CryoSPARC.get_targets now returns a list of models instead of dictionaries
    • OLD: cs.get_targets()[0]['hostname']
    • NEW: cs.get_targets()[0].hostname
    • Some top-level target attributes have also been moved into the .config attribute
  • BREAKING: CryoSPARC.print_job_types section argument renamed to category
    • OLD: cs.print_job_types(section=["extraction", "refinement"])
    • NEW: cs.print_job_types(category=["extraction", "refinement"])
  • BREAKING: Restructured schema for Job models, many Job.doc fields have been internally rearranged. Some fields like params_spec and output_result_groups are no longer available (replaced with a unified spec field)
  • Added: Python 3.14 support
  • Added: Secure command-line login with shell command python -m cryosparc.tools login --url <URL>, to avoid exposing login credentials in plain text
  • Added: Option to initialize CryoSPARC instance with a URL, e.g., cs = CryoSPARC("https://cryosparc.example.com:61000")
  • Added: find_projects(), find_workspaces() and find_jobs() methods to find lists of Projects, Workspaces and Jobs; filters are available for attributes like project UID and creation date
  • Added: CryoSPARC.job_register attribute
  • Added: New title and desc attributes for Project, Workspace and Job objects
  • Added: New status attribute for Job objects
  • Added: Methods to update title and description for Projects, Workspaces and Jobs
  • Added: Ability to set External job tile and output images
  • Added: job.load_input() and job.load_output() now accept "default", "passthrough" and "all" keywords for their slots argument
  • Added: job.alloc_output() now accepts dtype_params argument for fields with dynamic shapes
  • Added: CryoSPARC.print_job_types now includes a job stability column
  • Added: Job.print_output_spec now includes a passthrough indicator column for results
  • Added: Job.log() now accepts a name argument to create or update the same event log
  • Updated: Improved type definitions
  • Updated: cryosparc.mrc always converts float16 arrays to float32 before writing
  • Updated: Access to BASE_PORT + 2, BASE_PORT + 3 and BASE_PORT + 5 no longer required, only BASE_PORT or the web URL is required
  • Fixed: Prevent error on some datasets with many columns when using Numpy >= 1.24
  • Fixed: Querying a dataset with a non-existent field now correctly raises a KeyError
  • Deprecated: When adding external inputs and outputs, expanded slot definitions now expect "name" key instead of "prefix", support for which will be removed in a future release.
    • OLD: job.add_input("particle", slots=[{"prefix": "component_mode_1", "dtype": "component", "required": True}])
    • NEW: job.add_input("particle", slots=[{"name": "component_mode_1", "dtype": "component", "required": True}])
  • Deprecated: license argument no longer required when creating a CryoSPARC instance, will be removed in a future release
  • Deprecated: external_job.stop() now expects optional error string instead of boolean, support for boolean errors will be removed in a future release
  • Deprecated: CryoSPARC.get_job_sections() will be removed in a future release, use CryoSPARC.job_register instead
  • Deprecated: Most functions no longer require a refresh argument, including job.set_param(), job.connect(), job.disconnect() and external_job.save_output()
  • Deprecated: Attributes Project.doc, Workspace.doc and Job.doc will be removed in a future release, use .model attribute instead
  • Deprecated: project.dir() and job.dir() methods will be removed in a future release, use .dir attribute instead

v4.7.1

  • Added: job.connect_result and job.disconnect_result for connecting and disconnecting low-level results

v4.7.0

  • Added: Datasets appear as tables in a Jupyter notebook without requiring pandas or similar
  • Updated: Dropped official support for Python 3.7
  • Fixed: Prevent dataset load or save error when dataset is empty
  • Fixed: Prevent dataset load error on Linux when dataset file is exactly 4 kiB

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