chore: update submodules (#320)

* Now points to vrs 2.x branch
ga4gh · Jan 9, 2024 · 6f285d9 · 6f285d9
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commit 6f285d9
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diff --git a/.gitmodules b/.gitmodules
@@ -1,4 +1,4 @@
 [submodule "submodules/vrs"]
 	path = submodules/vrs
 	url = https://github.com/ga4gh/vrs.git
-	branch = 2.0-alpha
+	branch = 2.x
diff --git a/submodules/vrs b/submodules/vrs
+3 −1		.github/workflows/tests.yml
+4 −0		.gitignore
+3 −0		.gitmodules
+5 −1		.readthedocs.yaml
+1 −1		docs/source/appendices/associating_annotations.rst
+1 −16		docs/source/appendices/design_decisions.rst
+90 −0		docs/source/datatypes_classes/base_types.rst
+437 −0		docs/source/datatypes_classes/classes.rst
+39 −0		docs/source/datatypes_classes/general_purpose.rst
+31 −0		docs/source/datatypes_classes/index.rst
+64 −0		docs/source/datatypes_classes/primitives.rst
+87 −0		docs/source/datatypes_classes/special_purpose.rst
+1 −1		docs/source/defs
+ −		docs/source/images/adoption_lifecycle.png
+ −		docs/source/images/branch_management.png
+ −		docs/source/images/ex_ambiguous_linker.png
+ −		docs/source/images/ex_precise_linker.png
+ −		docs/source/images/ex_revcomp_breakpoint.png
+ −		docs/source/images/ex_sequence_homology.png
+ −		docs/source/images/ex_simple_breakpoint.png
+ −		docs/source/images/ex_sv_haplotype.png
+ −		docs/source/images/ex_terminal_breakend.png
+ −		docs/source/images/maturity_levels.png
+2 −0		docs/source/index.rst
+253 −0		docs/source/mm_and_versioning.rst
+3 −2		docs/source/requirements.txt
+0 −1,361		docs/source/terms_and_model.rst
+16 −0		examples/SPDI_contraction.yaml
+16 −0		examples/SPDI_expansion.yaml
+18 −0		examples/ambiguous_linker.yaml
+18 −0		examples/precise_linker.yaml
+15 −0		examples/revcomp_breakpoint.yaml
+15 −0		examples/sequence_homology.yaml
+15 −0		examples/simple_breakpoint.yaml
+23 −0		examples/simple_haplotype.yaml
+40 −0		examples/sv_haplotype.yaml
+9 −0		examples/terminal_breakend.yaml
+2 −6		schema/Makefile
+0 −306		schema/core-source.yaml
+0 −616		schema/core.json
+0 −489		schema/core.yaml
+0 −3		schema/defs/core/Code.rst
+0 −32		schema/defs/core/Coding.rst
+0 −3		schema/defs/core/Condition.rst
+0 −46		schema/defs/core/Disease.rst
+0 −46		schema/defs/core/DomainEntity.rst
+0 −32		schema/defs/core/Entity.rst
+0 −28		schema/defs/core/Extension.rst
+0 −46		schema/defs/core/Gene.rst
+0 −3		schema/defs/core/IRI.rst
+0 −38		schema/defs/core/MappableEntity.rst
+0 −42		schema/defs/core/Mapping.rst
+0 −46		schema/defs/core/TherapeuticAction.rst
+0 −46		schema/defs/core/TherapeuticAgent.rst
+0 −3		schema/defs/core/TherapeuticProcedure.rst
+0 −50		schema/defs/core/TherapeuticSubstituteGroup.rst
+0 −50		schema/defs/core/TraitSet.rst
+1 −0		schema/defs/gks.common
+20 −16		schema/defs/vrs/Adjacency.rst
+3 −3		schema/defs/vrs/Allele.rst
+3 −3		schema/defs/vrs/CopyNumber.rst
+3 −3		schema/defs/vrs/CopyNumberChange.rst
+3 −3		schema/defs/vrs/CopyNumberCount.rst
+2 −2		schema/defs/vrs/Ga4ghIdentifiableObject.rst
+2 −2		schema/defs/vrs/Genotype.rst
+1 −1		schema/defs/vrs/GenotypeMember.rst
+5 −5		schema/defs/vrs/Haplotype.rst
+11 −11		schema/defs/vrs/LengthExpression.rst
+1 −1		schema/defs/vrs/LiteralSequenceExpression.rst
+1 −1		schema/defs/vrs/ReferenceLengthExpression.rst
+1 −1		schema/defs/vrs/SequenceExpression.rst
+7 −7		schema/defs/vrs/SequenceLocation.rst
+2 −2		schema/defs/vrs/SequenceReference.rst
+1 −1		schema/defs/vrs/ValueObject.rst
+2 −2		schema/defs/vrs/Variation.rst
+1 −0		schema/gks.common-source.yaml
+1 −0		schema/gks.common.json
+1 −0		schema/gks.common.yaml
+178 −34		schema/merged.json
+137 −33		schema/merged.yaml
+125 −258		schema/vrs-source.yaml
+193 −49		schema/vrs.json
+152 −48		schema/vrs.yaml
+1 −0		submodules/gks-common
+2 −0		tests/config.py
+1 −1		tests/test_basic.py
+48 −0		tests/test_definitions.yaml
+26 −0		tests/test_examples.py