Changelog¶

v4.0.0¶

The v4.0.0 release of the Python API was paired with the v3 release of the Client. A summary of the changes between Client v2 and Client v3 is below along with some migration notes, including a list of new API classes.

Client V2 Field	Client V3 Field
`Annotation.files`	`Annotation.annotation_shapes[*].annotation_files`
`Annotation.tomogram_voxel_spacing`	`Annotation.annotation_shapes[].annotation_files[].tomogram_voxel_spacing`
`AnnotationFile.annotation`	`AnnotationFile.annotation_shape.annotation`
`AnnotationFile.shape_type`	`AnnotationFile.annotation_shape.shape_type`
`AnnotationAuthor.primary_annotator_status`	removed
`Dataset.dataset_citations`	removed
`Dataset.organism_taxid`	Converted from str -> int
`Dataset.related_database_links`	`Dataset.related_database_entries`
`TiltSeries.frames_count`	`TiltSeries.tiltseries_frames_count`
`TiltSeries.https_mrc_bin1`	`TiltSeries.https_mrc_file`
`TiltSeries.s3_mrc_bin1`	`TiltSeries.s3_mrc_file`
`TiltSeries.s3_alignment_file`	`TiltSeries.alignments[*].download_alignment_file(FORMAT)`
`TiltSeries.https_alignment_file`	`TiltSeries.alignments[*].download_alignment_file(FORMAT)`
`Tomogram.https_mrc_scale0`	`Tomogram.https_mrc_file`
`Tomogram.s3_mrc_scale0`	`Tomogram.s3_mrc_file`
`Tomogram.type`	Replaced with `Tomogram.is_canonical` and `Tomogram.is_standardized`
`Tomogram.affine_transformation_matrix`	`Tomogram.alignment.affine_transformation_matrix`
`Deposition.dataset`	`Deposition.datasets`
`Deposition.deposition_types`	`Deposition.deposition_types[*].type`
`Deposition.https_prefix`	removed
`TomogramVoxelSpacing.annotations`	`TomogramVoxelSpacing.annotation_files[*].annotation_shape.annotations`
`Tiltseries.download_collection_metadata()`	removed

Migration Notes:¶

8 new classes were added to the API:

Class name	Description
`Alignment`	Tilt series alignment
`AnnotationMethodLink`	A set of links to models, source code, documentation, etc referenced by annotation method
`AnnotationShape`	Shapes associated with an annotation
`DepositionType`	The type of data submitted as a part of a deposition (e.g. annotation, dataset, tomogram)
`Frame`	Raw frames used for generating tilt series
`FrameAcquisitionFile`	References to files containing more information about frame acquisition
`GainFile`	Gain values for frames in this run
`PerSectionAlignmentParameters`	Map alignment parameters to tilt series frames