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Merge branch '2.x' into docs-postgresql
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korikuzma committed Jan 9, 2024
2 parents 2c68560 + 5386d5c commit e6fba6c
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2 changes: 1 addition & 1 deletion .github/workflows/release.yml
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Expand Up @@ -22,7 +22,7 @@ jobs:
name: Build distribution
runs-on: ubuntu-latest
needs: get_branch
if: needs.get_branch.outputs.branch_name == '2-alpha'
if: needs.get_branch.outputs.branch_name == '2.x'
steps:
- uses: actions/checkout@v4
- name: Set up Python
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2 changes: 1 addition & 1 deletion .gitmodules
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@@ -1,4 +1,4 @@
[submodule "submodules/vrs"]
path = submodules/vrs
url = https://github.com/ga4gh/vrs.git
branch = 2.0-alpha
branch = 2.x
4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -149,7 +149,7 @@ Check that the containers are running:
$ docker ps
CONTAINER ID IMAGE // NAMES
86e872ab0c69 biocommons/seqrepo-rest-service:latest // vrs-python_seqrepo-rest-service_1
a40576b8cf1f biocommons/uta:uta_20180821 // vrs-python_uta_1
a40576b8cf1f biocommons/uta:uta_20210129b // vrs-python_uta_1

Depending on your network and host, the _first_ run is likely to take 5-15
minutes in order to download and install data. Subsequent startups should be
Expand Down Expand Up @@ -210,4 +210,4 @@ This implementation is offered as-is, and without any security guarantees. It
will need an independent security review before it can be considered ready for
use in security-critical applications. If you integrate this code into your
application it is AT YOUR OWN RISK AND RESPONSIBILITY to arrange for a security
audit.
audit.
2 changes: 1 addition & 1 deletion submodules/vrs
Submodule vrs updated 88 files
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+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
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+87 −0 docs/source/datatypes_classes/special_purpose.rst
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+ 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
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+16 −0 examples/SPDI_contraction.yaml
+16 −0 examples/SPDI_expansion.yaml
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+15 −0 examples/revcomp_breakpoint.yaml
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+2 −6 schema/Makefile
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+0 −616 schema/core.json
+0 −489 schema/core.yaml
+0 −3 schema/defs/core/Code.rst
+0 −32 schema/defs/core/Coding.rst
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+0 −42 schema/defs/core/Mapping.rst
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+0 −50 schema/defs/core/TraitSet.rst
+1 −0 schema/defs/gks.common
+20 −16 schema/defs/vrs/Adjacency.rst
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+3 −3 schema/defs/vrs/CopyNumberChange.rst
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+2 −2 schema/defs/vrs/Ga4ghIdentifiableObject.rst
+2 −2 schema/defs/vrs/Genotype.rst
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+1 −0 schema/gks.common-source.yaml
+1 −0 schema/gks.common.json
+1 −0 schema/gks.common.yaml
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+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

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