ga4gh/vrs-python issues and pull requests

#471 - feat!: update models to vrs 2.0.0 community review ballot

Pull Request - State: closed - Opened by korikuzma about 1 month ago - 1 comment
Labels: enhancement, priority:high

#470 - Remove `ga4gh:` prefix from VCF annotations?

Issue - State: open - Opened by jsstevenson about 2 months ago - 5 comments
Labels: enhancement, question

#469 - Update models to VRS 2.0.0 Community Review Ballot

Issue - State: closed - Opened by korikuzma about 2 months ago
Labels: enhancement, priority:high

#468 - docs: add doi badge to readme

Pull Request - State: closed - Opened by korikuzma about 2 months ago
Labels: documentation, priority:low

#467 - feat: make VRS schema release info accessible in VRS-Python

Pull Request - State: open - Opened by jsstevenson 2 months ago
Labels: priority:low

#466 - Provide maturity annotation for classes and fields

Issue - State: open - Opened by jsstevenson 3 months ago
Labels: enhancement

#465 - docs: clarify python 3.12 requirement for contributors

Pull Request - State: closed - Opened by korikuzma 3 months ago - 1 comment
Labels: documentation, priority:low, Product Review

#461 - fix: don't write digest property when `in_place=False`

Pull Request - State: open - Opened by jsstevenson 3 months ago

#458 - docs: clarify fork procedure for devs

Pull Request - State: open - Opened by jsstevenson 3 months ago - 1 comment
Labels: Product Review

#456 - Documentation: Note that "python3.12" is required for development

Issue - State: closed - Opened by melissacline 3 months ago
Labels: documentation, Product Review

#455 - cicd: fix action caching key

Pull Request - State: closed - Opened by jsstevenson 3 months ago
Labels: priority:low

#454 - cicd: add basic precommit hooks

Pull Request - State: closed - Opened by jsstevenson 3 months ago

#453 - feat!: update gks-common / vrs models

Pull Request - State: closed - Opened by korikuzma 3 months ago - 1 comment
Labels: enhancement, priority:medium

#452 - Update core + vrs models

Issue - State: closed - Opened by korikuzma 4 months ago
Labels: priority:high

#451 - fix param typo in vcf annotator

Pull Request - State: closed - Opened by quinnwai 4 months ago

#450 - feat: enable logging in annotator CLI

Pull Request - State: closed - Opened by jsstevenson 5 months ago
Labels: priority:low

#449 - feat!: enhance annotator CLI options

Pull Request - State: closed - Opened by jsstevenson 5 months ago
Labels: priority:low

#448 - docs: update VCF module docstrings

Pull Request - State: closed - Opened by jsstevenson 5 months ago

#447 - feat!: declare annotator CLI as console entrypoint

Pull Request - State: closed - Opened by jsstevenson 5 months ago - 1 comment
Labels: priority:low

#446 - feat!: enhance annotator CLI options

Pull Request - State: closed - Opened by jsstevenson 5 months ago

#445 - feat: optionally suppress console output

Pull Request - State: closed - Opened by jsstevenson 5 months ago
Labels: priority:low

#444 - chore: update VCF annotator type annotations for 3.10-12

Pull Request - State: closed - Opened by jsstevenson 5 months ago
Labels: priority:low

#443 - fix: do not allow `SequenceLocation` to have negative `start`/`end` v…

Pull Request - State: closed - Opened by korikuzma 5 months ago - 1 comment
Labels: bug, priority:medium

#442 - SequenceLocation allows for negative start/end coordinates

Issue - State: closed - Opened by korikuzma 5 months ago
Labels: bug, priority:high

#441 - sync with root-inheritance-fix from VRS

Pull Request - State: closed - Opened by larrybabb 6 months ago - 3 comments

#440 - `ga4gh_identify` adds `digest` properties in-place regardless of `in_place` argument

Issue - State: open - Opened by jsstevenson 6 months ago - 1 comment
Labels: bug, question

#439 - AlleleTranslator import error

Issue - State: closed - Opened by smoudour 6 months ago - 8 comments
Labels: bug

#438 - docs: fix alt text for github contributors

Pull Request - State: closed - Opened by korikuzma 6 months ago
Labels: documentation, priority:low

#437 - setup a list of unique variant examples for the basis of testing

Issue - State: open - Opened by larrybabb 7 months ago - 1 comment

#436 - cicd: update actions revs

Pull Request - State: closed - Opened by jsstevenson 7 months ago
Labels: priority:low

#435 - fix: revert Pydantic custom serializer

Pull Request - State: closed - Opened by korikuzma 7 months ago - 6 comments
Labels: bug, priority:high

#434 - fix: ensure Entity objects return type as str

Pull Request - State: closed - Opened by korikuzma 7 months ago - 1 comment
Labels: bug, priority:high

#433 - Object types return ENUM instead of ENUM.value

Issue - State: closed - Opened by ahwagner 7 months ago - 2 comments
Labels: bug, priority:high

#426 - fix: remove domain models from entity models

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: bug, priority:high

#425 - refactor: rename VrsTypes enum to VrsType

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: priority:high, technical debt

#424 - chore!: update vrs/gks-common submodules

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: priority:high, chore

#423 - refactor: remove _internal directories

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: priority:high, technical debt

#422 - refactor!: split gks-common module into domain + entity

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: priority:medium, technical debt

#421 - refactor: remove _internal directories

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: priority:high, technical debt

#420 - feat: create enum for gks-common + vrs types

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: enhancement, priority:high

#419 - feat: add make command (`nbready`) to create jupyter notebook venv

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: enhancement, priority:low

#418 - build: update SeqRepo collection to 2024-02-20

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: priority:low, build

#417 - feat!: update vrs/common models

Pull Request - State: closed - Opened by korikuzma 7 months ago - 1 comment
Labels: enhancement, priority:high

#416 - build!: remove support for python 3.9 and make 3.12 the dev default

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: priority:medium, build

#415 - update to python >= 3.10 and change default to 3.12

Issue - State: closed - Opened by korikuzma 7 months ago
Labels: priority:medium, build

#414 - chore: Pydantic fields -> model_fields

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: priority:low, chore

#413 - feat!: rename core_models to common_models

Pull Request - State: closed - Opened by korikuzma 8 months ago
Labels: enhancement, priority:medium

#412 - Rename core to common

Issue - State: closed - Opened by korikuzma 8 months ago
Labels: enhancement, priority:medium

#411 - pylint/yapf -> ruff

Issue - State: open - Opened by jsstevenson 8 months ago
Labels: priority:low, chore

#410 - Implement cat-vrs (?)

Issue - State: closed - Opened by theferrit32 8 months ago - 3 comments

#409 - Implement CisPhasedBlock

Issue - State: closed - Opened by theferrit32 8 months ago - 1 comment

#407 - Do away with "private" modules

Issue - State: closed - Opened by jsstevenson 9 months ago - 1 comment
Labels: enhancement, priority:low

#406 - docs: update readme (install seqrepo, psql cmd, + submodules)

Pull Request - State: closed - Opened by korikuzma 9 months ago
Labels: documentation, priority:low

#405 - fix: add password to docker-compose.yml for uta service

Pull Request - State: closed - Opened by korikuzma 9 months ago
Labels: bug, priority:medium

#404 - docker compose up failed for uta

Issue - State: closed - Opened by korikuzma 9 months ago
Labels: bug, priority:medium

#403 - add make notebooks command

Issue - State: closed - Opened by korikuzma 10 months ago
Labels: enhancement, priority:low

#402 - Adding the getting_started notebooks and removing the rest.

Pull Request - State: closed - Opened by toneillbroad 10 months ago - 1 comment

#401 - Only attempt to create allele if values were extracted

Pull Request - State: closed - Opened by ehclark 10 months ago

#400 - Passing an invalid variant description to AlleleTranslator.translate_from() throws TypeError

Issue - State: closed - Opened by ehclark 10 months ago
Labels: bug, 2.0-alpha

#399 - build: update supported python versions

Pull Request - State: closed - Opened by korikuzma 10 months ago - 1 comment
Labels: priority:medium, build

#398 - Only support 4 most recent python releases

Issue - State: closed - Opened by korikuzma 10 months ago - 1 comment
Labels: priority:medium, build

#397 - Provide way to stop normalization if the expression is obviously problematic (such as deletions in large gap/unknown regions)

Issue - State: open - Opened by larrybabb 10 months ago - 5 comments

GitHub / ga4gh/vrs-python issues and pull requests