Releases prior to https://github.com/ga4gh/vrs-python/releases/tag/2.2.0 (ded576f) are being deprecated.

See relevant issues:
'Add RLE params to VRS-annotated VCFs' #577
'Same-as-reference Alleles should have a ReferenceLengthExpression state' #587

This will be accomplished using PyPi's 'yank' function. The packages will not be removed, and pip and uv will still be able to install them, so projects with a version pinned >=2.0.0,<2.2.0 will not break, but the installer will log a WARN message about them being deprecated. This will also happen if such a version is required as a transitive dependency. Any new installs which do not pin a version <2.2.0 will automatically receive a version >=2.2.0.

Version 2.2.0 code is backwards compatible from a code interface standpoint, so users do not need to modify their application code to incorporate the new version.

The backwards-inconsistent changes to output data are:

• Some Allele objects which previously would have come out with a .state being a LiteralSequenceExpression will now come out with a .state being a ReferenceLengthExpression.
• VCFs annotated with reference alleles included in the VRS annotations will need to re-annotate their VCFs if any variants in them (ref or alt) are reference-derived and fall under the ReferenceLengthExpression logic explained in the normalization specification. Ref alleles are always reference-derived, so if the annotation was not run with --skip-ref, those annotations will come out differently in vrs-python versions >=2.2.0. After upgrading to >=2.2.0, the VCF Annotator will include new INFO fields which contain the values necessary for re-constructing the ReferenceLengthExpression object.

Versions which will be yanked on PyPi:

• 2.0.0
• 2.0.1
• 2.1.0
• 2.1.1
• 2.1.2
• 2.1.3
• 2.1.4