Deprecating 2.x releases pre 2.2.0

[theferrit32]

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

[theferrit32]

The "reason" string in the yank notes will simply link back to the relevant issues.

https://github.com/ga4gh/vrs-python/issues/577, https://github.com/ga4gh/vrs-python/issues/587

[theferrit32]

Installer warning when doing pip install requiring a yanked version:

WARNING: The candidate selected for download or install is a yanked version: 'ga4gh-vrs' candidate (version 2.0.1 at https://files.pythonhosted.org/packages/42/a7/f50db82d7e8a4bf9dddf8a0ce8deb0ac489d4d3218225692197fe8b90422/ga4gh_vrs-2.0.1-py3-none-any.whl (from https://pypi.org/simple/ga4gh-vrs/) (requires-python:>=3.10))
Reason for being yanked: https://github.com/ga4gh/vrs-python/issues/577, https://github.com/ga4gh/vrs-python/issues/587

Installer warning when doing uv pip install requiring a yanked version:

warning: `ga4gh-vrs==2.0.1` is yanked (reason: "https://github.com/ga4gh/vrs-python/issues/577, https://github.com/ga4gh/vrs-python/issues/587")

[korikuzma]

@theferrit32 I'm wondering if this should be converted to a discussion?

[theferrit32]

An example of a transitive dependency on vrs-python

Run uv sync --extra test
Using CPython 3.11.14 interpreter at: /opt/hostedtoolcache/Python/3.11.14/x64/bin/python3
Creating virtual environment at: .venv
   Updating https://github.com/biocommons/anyvar.git (storage-refactor-epic)
    Updated https://github.com/biocommons/anyvar.git (ec050268aa14290d1b3f191196939085573215e3)
  × No solution found when resolving dependencies:
  ╰─▶ Because only the following versions of ga4gh-vrs[extras] are available:
          ga4gh-vrs[extras]<=2.1.2
          ga4gh-vrs[extras]==2.1.3
          ga4gh-vrs[extras]==2.1.4
          ga4gh-vrs[extras]>2.2.dev0
      and ga4gh-vrs[extras]>=2.1.2,<=2.1.4 was yanked
      (reason: https://github.com/ga4gh/vrs-python/issues/577,
      https://github.com/ga4gh/vrs-python/issues/587), we can conclude that
      ga4gh-vrs[extras]>=2.1.2,<=2.1.4 cannot be used.
      And because biocommons-anyvar==0.9.1.dev93+gec050268a
      depends on ga4gh-vrs[extras]>=2.1.2,<2.2.dev0 and only
      biocommons-anyvar==0.9.1.dev93+gec050268a is available, we can conclude
      that all versions of biocommons-anyvar cannot be used.
      And because your project depends on biocommons-anyvar and your project
      requires anyvlm[dev], we can conclude that your project's requirements
      are unsatisfiable.

      hint: `ga4gh-vrs` was requested with a pre-release marker (e.g., all of:
          ga4gh-vrs>2.1.2,<2.1.3
          ga4gh-vrs>2.1.3,<2.1.4
          ga4gh-vrs>2.1.4,<2.2.dev0
      ), but pre-releases weren't enabled (try: `--prerelease=allow`)

[jsstevenson]

is this bad?