Ecosyste.ms: Issues

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GitHub / ga4gh/vrs-python issues and pull requests

#256 - Update VRS 2.0-alpha models

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: 2.0-alpha, priority:high

#255 - chore: update uta docker image to uta_20210129b

Pull Request - State: closed - Opened by korikuzma over 1 year ago

#254 - chore: update uta docker image to uta_20210129b

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: 2.0-alpha

#253 - Update uta docker version

Issue - State: closed - Opened by korikuzma over 1 year ago

#252 - build: unpin pydantic version

Pull Request - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: 2.0-alpha, build

#251 - Include `digest` field in response

Issue - State: closed - Opened by korikuzma over 1 year ago - 2 comments
Labels: Stale-exempt, 2.0-alpha, priority:medium

#250 - Add sqlite3-based object store, with tests

Pull Request - State: closed - Opened by theferrit32 over 1 year ago - 1 comment
Labels: 2.0-alpha

#249 - docs: fix UTA readme formatting and wording

Pull Request - State: closed - Opened by jsstevenson over 1 year ago - 3 comments
Labels: documentation, priority:low

#248 - fix: _to_hgvs using wrong vars for hgvs.location.Interval

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: bug, 2.0-alpha

#247 - tests: add tests for tlr._from_gnomad

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: 2.0-alpha

#246 - Add more tests for _from_beacon

Issue - State: open - Opened by korikuzma over 1 year ago - 1 comment
Labels: Stale-exempt, 2.0-alpha, test

#245 - Add more tests for _from_gnomad

Issue - State: closed - Opened by korikuzma over 1 year ago
Labels: 2.0-alpha

#244 - Implementing enref/deref for pydantic 2 models

Pull Request - State: closed - Opened by theferrit32 over 1 year ago - 1 comment
Labels: 2.0-alpha

#243 - Update references to model __fields__

Issue - State: closed - Opened by theferrit32 over 1 year ago - 3 comments

#242 - Update notebooks to for 2.x release

Issue - State: closed - Opened by korikuzma over 1 year ago - 5 comments
Labels: Stale-exempt, 2.0-alpha

#241 - feat!: Rename SL sequence to sequenceReference + update submodules

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: 2.0-alpha

#240 - Add regex pattern to IRI class

Issue - State: open - Opened by korikuzma over 1 year ago - 3 comments
Labels: bug, Stale-exempt, 2.0-alpha

#239 - Create disk-backed object store for ga4gh_enref/deref

Issue - State: closed - Opened by theferrit32 over 1 year ago - 1 comment

#238 - Fix ga4gh_enref for pydantic v2 models

Issue - State: closed - Opened by theferrit32 over 1 year ago - 1 comment
Labels: 2.0-alpha

#237 - How to handle Allele normalization for Range Locations

Issue - State: open - Opened by ahwagner over 1 year ago - 6 comments
Labels: question, Stale-exempt, 2.0-alpha

#236 - refactor: replace pkg_resources with importlib.metadata

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: 2.0-alpha, priority:low

#235 - Unpin pydantic v2.1.1

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: 2.0-alpha, build

#234 - feat: allele rle normalization + pin pydantic version

Pull Request - State: closed - Opened by korikuzma over 1 year ago - 2 comments
Labels: enhancement, 2.0-alpha, priority:high

#233 - fix: use camel case for copy change

Pull Request - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: 2.0-alpha, priority:high

#232 - Updated some tests

Pull Request - State: closed - Opened by toneillbroad over 1 year ago

#231 - Parameterize `normalize` in translate_from methods

Issue - State: closed - Opened by korikuzma over 1 year ago - 2 comments
Labels: enhancement, Stale-exempt, priority:medium

#230 - Updates for spdi and hgvs to/from

Pull Request - State: closed - Opened by theferrit32 over 1 year ago
Labels: 2.0-alpha

#229 - Minor changes to how direct and indirect ranges are serialized

Pull Request - State: closed - Opened by toneillbroad over 1 year ago

#228 - Adding haplotype and genotype tests

Pull Request - State: closed - Opened by theferrit32 over 1 year ago
Labels: 2.0-alpha

#227 - haplotype and genotype handling

Pull Request - State: closed - Opened by theferrit32 over 1 year ago
Labels: 2.0-alpha

#226 - 2.0 model changes

Pull Request - State: closed - Opened by toneillbroad over 1 year ago

#225 - Create hashable BaseModel subclass in order to enforce uniqueItems with Set annotation

Issue - State: open - Opened by theferrit32 over 1 year ago - 3 comments
Labels: 2.0-alpha

#224 - Fix localizer.py on 2-alpha

Issue - State: closed - Opened by theferrit32 over 1 year ago - 1 comment
Labels: 2.0-alpha

#223 - Repo cleanup

Issue - State: closed - Opened by jsstevenson over 1 year ago - 4 comments
Labels: Stale-exempt

#222 - Refactor ga4gh_digest to return full tree of identified objects

Issue - State: closed - Opened by theferrit32 over 1 year ago - 1 comment
Labels: 2.0-alpha

#221 - Generated and modified pydantic 2.0 based models.py

Pull Request - State: closed - Opened by toneillbroad over 1 year ago

#220 - Update models and serialization to use Pydantic and VRS 2.x

Issue - State: closed - Opened by theferrit32 over 1 year ago - 1 comment
Labels: Epic

#219 - Update Translator class to and from methods to work for VRS 2.x

Issue - State: closed - Opened by theferrit32 over 1 year ago - 2 comments
Labels: 2.0-alpha

#218 - Reimplement serialize/digest functions to use Pydantic classes and handle deeply nested structures

Issue - State: closed - Opened by theferrit32 over 1 year ago - 5 comments
Labels: 2.0-alpha

#217 - Update initial pydantic model classes to pydantic 2.x

Issue - State: closed - Opened by theferrit32 over 1 year ago - 1 comment
Labels: 2.0-alpha

#216 - Update to VRS 2.0, with pydantic classes, without python jsonschema objects

Pull Request - State: closed - Opened by theferrit32 over 1 year ago - 2 comments

#215 - Add pydantic classes, not yet integrated as ga4gh.vrs.models

Pull Request - State: closed - Opened by theferrit32 over 1 year ago - 1 comment

#214 - Pass Translator `default_assembly_name` as a method parameter

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment

#213 - test: update cassettes for variation normalizer rest dp

Pull Request - State: closed - Opened by korikuzma over 1 year ago

#212 - Fix test for variation normalizer rest dp in metaschema

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment

#211 - Update VCF Annotator for 2-alpha

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: enhancement, Stale, 2.0-alpha

#210 - cleanup: add pre-commit + resolve pylint warnings

Pull Request - State: closed - Opened by korikuzma over 1 year ago - 2 comments

#209 - docs: update pip installation + fix typos (#207)

Pull Request - State: closed - Opened by korikuzma over 1 year ago

#208 - docs: update pip installation + fix typos (#207)

Pull Request - State: closed - Opened by korikuzma over 1 year ago

#207 - docs: update pip installation + fix typos

Pull Request - State: closed - Opened by korikuzma over 1 year ago - 1 comment

#206 - Update `ga4gh_serialize` to account for new definitional array

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: enhancement, 2.0-alpha

#205 - Remove python-jsonschema-objects and use Pydantic classes

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: enhancement, 2.0-alpha

#204 - Support RLE normalization

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: enhancement, 2.0-alpha

#203 - pkg_resources is deprecated as an API

Issue - State: closed - Opened by korikuzma over 1 year ago - 4 comments
Labels: Stale-exempt

#202 - build: support python >= 3.8

Pull Request - State: closed - Opened by korikuzma over 1 year ago

#201 - build: support python >= 3.8

Pull Request - State: closed - Opened by korikuzma over 1 year ago

#200 - build: support python >= 3.8

Pull Request - State: closed - Opened by korikuzma over 1 year ago

#199 - Python versions to support

Issue - State: closed - Opened by korikuzma over 1 year ago - 7 comments

#198 - (issue#183)Updated Python-version in python-cqa.yml to 3.10

Pull Request - State: closed - Opened by aniketh3014 over 1 year ago - 2 comments

#197 - Annotation Data

Issue - State: closed - Opened by Nitram36 over 1 year ago - 4 comments
Labels: Stale

#196 - feat: include VRS location digest if identify is True (0.9 branch)

Pull Request - State: closed - Opened by korikuzma over 1 year ago

#195 - Upgrade digester logic to use new schema 'ga4gh.defs' approach

Issue - State: closed - Opened by larrybabb over 1 year ago - 1 comment
Labels: enhancement, 2.0-alpha

#194 - Replace vrs models with pydantic generated models

Issue - State: closed - Opened by larrybabb over 1 year ago - 3 comments

#192 - Initial upgrade to VRS 2.0alpha model

Issue - State: closed - Opened by larrybabb over 1 year ago - 3 comments
Labels: epic, 2.0-alpha

#191 - Improve Terra notebooks documentation

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: Stale

#190 - pip install ga4gh.vrs[extras] returns "no matches found"

Issue - State: closed - Opened by larrybabb over 1 year ago - 3 comments
Labels: Stale

#189 - VRS-demo-notebooks on Terra not accessible

Issue - State: closed - Opened by larrybabb over 1 year ago - 8 comments

#188 - Updated Docker Documentation on Readme

Pull Request - State: closed - Opened by kehshiba over 1 year ago - 2 comments
Labels: Stale

#187 - fix: VCF Annotator VRS_Allele_Ids renamed to VRS_Allele_IDs (#186)

Pull Request - State: closed - Opened by korikuzma over 1 year ago

#186 - fix: VCF Annotator VRS_Allele_Ids renamed to VRS_Allele_IDs

Pull Request - State: closed - Opened by korikuzma over 1 year ago

#185 - refactor: pluralize VRS attrs + update descrs in VCF Annotator (#184)

Pull Request - State: closed - Opened by korikuzma over 1 year ago

#184 - refactor: pluralize VRS attrs + update descrs in VCF Annotator

Pull Request - State: closed - Opened by korikuzma over 1 year ago

#183 - Python CQA should run python 3.10

Issue - State: closed - Opened by korikuzma almost 2 years ago - 2 comments

#182 - refactor: Rename VRS Info fields + descriptions in VCF Annotator (#181)

Pull Request - State: closed - Opened by korikuzma almost 2 years ago

#181 - refactor: Rename VRS Info fields + descriptions in VCF Annotator

Pull Request - State: closed - Opened by korikuzma almost 2 years ago

#180 - Rename VRS Info fields in VCF Annotator

Issue - State: closed - Opened by korikuzma almost 2 years ago - 3 comments

#179 - docs: update readme for vrs branch tracking

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: docs

#178 - fix: mybinder build

Pull Request - State: closed - Opened by korikuzma almost 2 years ago

#177 - fix: mybinder build

Pull Request - State: closed - Opened by korikuzma almost 2 years ago

#176 - fixing mybinder build error

Pull Request - State: closed - Opened by SalemBajjali almost 2 years ago

#175 - Error when building mybinder

Issue - State: closed - Opened by SalemBajjali almost 2 years ago - 3 comments

#174 - feat: Update submodules to incorporate 1.3 CNV changes

Pull Request - State: closed - Opened by korikuzma almost 2 years ago - 1 comment

#173 - cicd: try having release run on ubuntu-latest

Pull Request - State: closed - Opened by korikuzma almost 2 years ago

#172 - Update to VRS 1.3.0 release

Pull Request - State: closed - Opened by ahwagner almost 2 years ago

#171 - merge `main` to `0.8`

Pull Request - State: closed - Opened by ahwagner almost 2 years ago

#170 - Consider expanding issue labels

Issue - State: closed - Opened by korikuzma almost 2 years ago - 4 comments
Labels: Stale-exempt

#169 - cicd: 0.8 branch should be able to make releases

Pull Request - State: closed - Opened by korikuzma almost 2 years ago

#168 - feat: add additional vrs fields to vcf annotator

Pull Request - State: closed - Opened by korikuzma almost 2 years ago

#167 - Add additional fields to info field in VCF Annotator

Issue - State: closed - Opened by korikuzma almost 2 years ago
Labels: enhancement

#166 - ci: python-cqa should run on 0.8 branch

Pull Request - State: closed - Opened by korikuzma almost 2 years ago - 1 comment

#165 - build: fix broken long_description reference

Pull Request - State: closed - Opened by jsstevenson almost 2 years ago

#164 - build: fix broken long_description reference

Pull Request - State: closed - Opened by jsstevenson almost 2 years ago

#163 - build: fix broken long_description reference

Pull Request - State: closed - Opened by jsstevenson almost 2 years ago

#162 - docs: update readme for vrs branch tracking

Pull Request - State: closed - Opened by korikuzma almost 2 years ago - 8 comments

#161 - Add support for VRS 1.3.x

Issue - State: closed - Opened by korikuzma almost 2 years ago - 2 comments
Labels: enhancement

#160 - chore: remove pylint warning for overgeneral-exceptions

Pull Request - State: closed - Opened by korikuzma almost 2 years ago

#158 - Merge main branch into 0.7 branch

Pull Request - State: closed - Opened by korikuzma almost 2 years ago

#157 - Update 0.7 branch with latest updates and make pypi release

Issue - State: closed - Opened by korikuzma almost 2 years ago - 1 comment
Labels: enhancement