Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / cancervariants/variation-normalization issues and pull requests
#597 - build!: update ga4gh.vrs
Pull Request -
State: open - Opened by korikuzma about 1 hour ago
Labels: priority:high, build
#596 - build: update cool-seq-tool + gene-normalizer
Pull Request -
State: open - Opened by korikuzma about 4 hours ago
Labels: priority:high, build
#595 - build: pin gene-normalizer version to >=0.7.0
Pull Request -
State: closed - Opened by korikuzma 13 days ago
Labels: priority:medium, build
#594 - Add `moleculeType` to `SequenceReference`
Issue -
State: open - Opened by korikuzma 23 days ago
Labels: enhancement, priority:low
#593 - Merge staging into main
Pull Request -
State: closed - Opened by korikuzma about 1 month ago
- 1 comment
Labels: priority:high
#592 - build: update cool-seq-tool version in Pipfile
Pull Request -
State: closed - Opened by korikuzma about 1 month ago
Labels: priority:medium, build
#591 - feat!: rename residue mode to coordinate type
Pull Request -
State: closed - Opened by korikuzma about 1 month ago
Labels: enhancement, priority:medium
#590 - Rename residue mode to coordinate type
Issue -
State: closed - Opened by korikuzma about 1 month ago
- 1 comment
Labels: enhancement, priority:medium
#589 - build: pin cool-seq-tool version ~=0.9.1
Pull Request -
State: closed - Opened by korikuzma about 1 month ago
Labels: priority:medium, build
#588 - Bump cool-seq-tool version
Issue -
State: closed - Opened by korikuzma about 1 month ago
- 1 comment
Labels: priority:high, build
#587 - Merge staging into main
Pull Request -
State: closed - Opened by korikuzma about 1 month ago
- 3 comments
Labels: priority:high
#586 - build!: require python >= 3.11
Pull Request -
State: closed - Opened by korikuzma about 1 month ago
Labels: priority:high, build
#585 - docs: update readme with vrs versioning
Pull Request -
State: closed - Opened by korikuzma about 1 month ago
Labels: documentation, priority:high
#584 - fix(build): update dependency versions in Pipfile
Pull Request -
State: closed - Opened by korikuzma about 1 month ago
Labels: bug, priority:high, build
#583 - chore!: rename optional dependency
Pull Request -
State: closed - Opened by korikuzma about 1 month ago
Labels: priority:low, chore
#582 - feat!: update models to vrs 2.0.0 community review ballot
Pull Request -
State: closed - Opened by korikuzma about 2 months ago
Labels: enhancement, priority:high, build
#581 - Update models to VRS 2.0.0 Community Review Ballot
Issue -
State: closed - Opened by korikuzma about 2 months ago
Labels: enhancement, priority:high, build
#580 - cicd: check if PR to main is coming from staging
Pull Request -
State: closed - Opened by jsstevenson 3 months ago
Labels: priority:low
#579 - chore: bring back commits on `main` to `staging`
Pull Request -
State: closed - Opened by jsstevenson 3 months ago
Labels: priority:low
#578 - style: update ruff configs
Pull Request -
State: closed - Opened by jsstevenson 3 months ago
Labels: priority:low
#577 - chore: use base gitignore
Pull Request -
State: closed - Opened by jsstevenson 3 months ago
Labels: priority:low
#576 - feat: return MANE gene(s) in normalize endpoint for genomic queries
Pull Request -
State: closed - Opened by korikuzma 7 months ago
Labels: enhancement, priority:medium
#575 - build: pin cool-seq-tool~=0.6.0
Pull Request -
State: closed - Opened by korikuzma 7 months ago
Labels: priority:medium, build
#574 - Docker Changes
Pull Request -
State: open - Opened by rajatkapoordfci 7 months ago
- 3 comments
Labels: priority:medium, stale
#573 - docs: update vrs versioning
Pull Request -
State: closed - Opened by korikuzma 7 months ago
Labels: documentation, priority:low
#572 - docs: update vrs versioning
Pull Request -
State: closed - Opened by korikuzma 7 months ago
Labels: documentation, priority:medium
#571 - fix: update ga4gh.vrs + add back response_model configs for FastAPI
Pull Request -
State: closed - Opened by korikuzma 7 months ago
Labels: bug, priority:medium, build
#570 - feat!: add `sequence` to `SequenceLocation`
Pull Request -
State: closed - Opened by korikuzma 7 months ago
Labels: enhancement, priority:medium
#569 - cicd: allow missing credentials in aws creds detection
Pull Request -
State: closed - Opened by jsstevenson 7 months ago
Labels: priority:low
#568 - chore: remove unused files
Pull Request -
State: closed - Opened by korikuzma 7 months ago
Labels: priority:low, chore
#567 - style: ruff format
Pull Request -
State: closed - Opened by korikuzma 7 months ago
Labels: cleanup, priority:high
#566 - fix: TypeError for params that accept union of enums
Pull Request -
State: closed - Opened by korikuzma 7 months ago
Labels: bug, priority:high
#565 - fix: __version__ imports
Pull Request -
State: closed - Opened by korikuzma 7 months ago
- 1 comment
Labels: bug, priority:high
#564 - chore: update ebextensions for downloading latest seqrepo instance
Pull Request -
State: closed - Opened by korikuzma 7 months ago
- 2 comments
Labels: priority:high, chore
#563 - fix(cicd): add reference to stalebot
Pull Request -
State: closed - Opened by korikuzma 7 months ago
- 2 comments
Labels: bug, priority:low, ci/cd
#562 - docs: update seqrepo version to 2024-02-20
Pull Request -
State: closed - Opened by korikuzma 7 months ago
Labels: documentation, priority:low
#561 - build!: update ga4gh.vrs, cool-seq-tool, + gene-normalizer
Pull Request -
State: closed - Opened by korikuzma 7 months ago
Labels: priority:medium, build
#560 - cicd: update precommit dependency in pipfile
Pull Request -
State: closed - Opened by jsstevenson 7 months ago
Labels: priority:low
#559 - feat: enable more precise logging configuration
Pull Request -
State: closed - Opened by jsstevenson 7 months ago
Labels: priority:low
#558 - cicd: update precommit
Pull Request -
State: closed - Opened by jsstevenson 7 months ago
Labels: priority:low
#557 - style: update ruff
Pull Request -
State: closed - Opened by jsstevenson 7 months ago
- 1 comment
Labels: priority:low
#556 - cicd: update workflows/templates from template repo
Pull Request -
State: closed - Opened by jsstevenson 7 months ago
Labels: priority:low
#555 - build: update requirements and build system
Pull Request -
State: closed - Opened by jsstevenson 7 months ago
Labels: priority:low
#554 - issue in normalizer behavior for transcript sequence location
Issue -
State: closed - Opened by ahwagner 8 months ago
- 1 comment
#553 - Docker vn
Pull Request -
State: open - Opened by rajatkapoordfci 10 months ago
- 6 comments
#552 - Add back `vrs_ref_allele_seq` to response
Issue -
State: closed - Opened by korikuzma 10 months ago
- 2 comments
Labels: enhancement, priority:high
#551 - return gene context info for genomic queries
Issue -
State: open - Opened by katiestahl 11 months ago
- 10 comments
Labels: enhancement, priority:low
#550 - build: reorganize build metadata (#549)
Pull Request -
State: closed - Opened by jsstevenson 11 months ago
#549 - build: reorganize build metadata
Pull Request -
State: closed - Opened by jsstevenson 11 months ago
#548 - docs: readme glow-up
Pull Request -
State: closed - Opened by jsstevenson 11 months ago
- 1 comment
Labels: priority:low
#547 - chore: update license
Pull Request -
State: closed - Opened by jsstevenson 11 months ago
#546 - cicd: require priority label on PRs
Pull Request -
State: closed - Opened by jsstevenson 11 months ago
Labels: priority:low
#545 - cicd: require priority label on PRs
Pull Request -
State: closed - Opened by jsstevenson 11 months ago
Labels: priority:low
#544 - cicd: test install on 3.12
Pull Request -
State: closed - Opened by jsstevenson 11 months ago
#543 - add back missing models to openapi.json
Issue -
State: closed - Opened by korikuzma 11 months ago
- 2 comments
Labels: priority:high, technical debt
#542 - build!: udpate ga4gh.vrs version
Pull Request -
State: closed - Opened by korikuzma 11 months ago
- 1 comment
Labels: priority:high, build
#541 - Update to `ga4gh.vrs[extras]` to `2.0.0a5`
Issue -
State: closed - Opened by korikuzma 12 months ago
Labels: priority:high, build
#540 - test: only check vrs ids on certain tests
Pull Request -
State: closed - Opened by korikuzma 12 months ago
Labels: priority:medium, test
#539 - build: pin ga4gh.vrs dependency
Pull Request -
State: closed - Opened by korikuzma 12 months ago
Labels: priority:high, build
#538 - Update SeqRepo collection to `2024-02-20`
Issue -
State: closed - Opened by korikuzma 12 months ago
- 2 comments
Labels: documentation, enhancement, priority:medium
#537 - cicd: fix elastic beanstalk deployment
Pull Request -
State: closed - Opened by korikuzma 12 months ago
Labels: priority:high, ci/cd
#536 - fix: handle cases where gene_context is not found
Pull Request -
State: closed - Opened by korikuzma almost 1 year ago
Labels: bug, priority:high
#535 - gnomad_vcf_to_protein handle cases where no gene is found
Issue -
State: closed - Opened by korikuzma almost 1 year ago
Labels: bug, priority:high
#534 - pytest-asyncio DeprecationWarning for event_loop
Issue -
State: open - Opened by korikuzma about 1 year ago
- 1 comment
Labels: priority:low, test
#533 - build: modernize build configs
Pull Request -
State: closed - Opened by korikuzma about 1 year ago
- 2 comments
Labels: priority:medium, build
#532 - style: replace black with ruff
Pull Request -
State: closed - Opened by korikuzma about 1 year ago
Labels: cleanup, priority:medium
#531 - Modernize build configs
Issue -
State: closed - Opened by korikuzma about 1 year ago
Labels: priority:low, chore
#530 - Remove black and update ruff config
Issue -
State: closed - Opened by korikuzma about 1 year ago
Labels: cleanup, priority:low, build
#529 - feat!: add more support for queries in gnomad_vcf_to_protein
Pull Request -
State: closed - Opened by korikuzma about 1 year ago
- 8 comments
Labels: enhancement, priority:medium
#528 - build!: update cool-seq-tool + ga4gh.vrs versions
Pull Request -
State: closed - Opened by korikuzma about 1 year ago
- 5 comments
Labels: priority:high, build
#527 - Reduce the number of tests
Issue -
State: open - Opened by korikuzma about 1 year ago
- 1 comment
Labels: priority:low, test
#526 - Use biocommons.hgvs for parsing HGVS expressions
Issue -
State: open - Opened by korikuzma about 1 year ago
- 1 comment
Labels: priority:medium, technical debt, build
#525 - fix: hgvs/free text dup/del end positions for definite ranges
Pull Request -
State: closed - Opened by korikuzma over 1 year ago
Labels: bug, priority:medium, vrs-2-alpha
#524 - Fix hgvs/free text dup/del end range positions
Issue -
State: closed - Opened by korikuzma over 1 year ago
- 1 comment
Labels: bug, priority:high, vrs-2-alpha
#523 - feat: expose cool-seq-tool feature overlap endpoint
Pull Request -
State: closed - Opened by korikuzma over 1 year ago
Labels: enhancement, priority:high
#522 - Consider lazy loading for class attributes
Issue -
State: open - Opened by korikuzma over 1 year ago
- 1 comment
Labels: priority:low, technical debt
#521 - Expose cool-seq-tool get_grch38_mane_gene_cds_overlap endpoint
Issue -
State: open - Opened by korikuzma over 1 year ago
- 1 comment
Labels: enhancement, priority:high
#520 - fix: vrs-python translator import statement
Pull Request -
State: closed - Opened by korikuzma over 1 year ago
Labels: bug, priority:high
#519 - Add basic API endpoint tests
Issue -
State: open - Opened by korikuzma over 1 year ago
- 1 comment
Labels: priority:medium, test
#518 - Update /translate_from
Issue -
State: closed - Opened by korikuzma over 1 year ago
- 1 comment
Labels: bug, priority:high, vrs-2-alpha
#517 - build!: update depdency versions
Pull Request -
State: closed - Opened by korikuzma over 1 year ago
Labels: priority:low, build
#516 - fix: pin versions + fix /translate_identifier
Pull Request -
State: closed - Opened by korikuzma over 1 year ago
Labels: bug, priority:high, build
#515 - build!: update depdency versions
Pull Request -
State: closed - Opened by korikuzma over 1 year ago
- 4 comments
Labels: priority:medium, build
#514 - cicd: update release.yml (publish python distribution to pypi)
Pull Request -
State: closed - Opened by korikuzma over 1 year ago
Labels: priority:low, ci/cd
#513 - cicd: update release.yml (publish python distribution to pypi)
Pull Request -
State: closed - Opened by korikuzma over 1 year ago
Labels: priority:low, ci/cd
#512 - feat!: update to vrs 2.0-alpha
Pull Request -
State: closed - Opened by korikuzma over 1 year ago
Labels: enhancement, priority:high
#511 - fix: catch pydantic ValidationError in parsed to cnv endpoints
Pull Request -
State: closed - Opened by korikuzma over 1 year ago
Labels: bug, priority:medium
#510 - cicd: update elastic beanstalk eb extensions for python3.11 + p7zip
Pull Request -
State: closed - Opened by korikuzma over 1 year ago
Labels: priority:low, ci/cd
#509 - Update prod AWS instance to python3.11
Issue -
State: closed - Opened by korikuzma over 1 year ago
- 1 comment
Labels: priority:medium, chore
#508 - feat!: add / update to copy number methods from metaschema branch
Pull Request -
State: closed - Opened by korikuzma over 1 year ago
Labels: enhancement, priority:high
#507 - fix: still return a result for protein/cdna with no mane data found
Pull Request -
State: closed - Opened by korikuzma over 1 year ago
- 1 comment
Labels: bug, priority:high
#506 - If genomic query fails getting liftover/mane, try using original input to return a response
Issue -
State: open - Opened by korikuzma over 1 year ago
- 2 comments
Labels: enhancement, priority:medium
#505 - refactor branch: if no mane data is found, still return a result
Issue -
State: closed - Opened by korikuzma over 1 year ago
- 2 comments
Labels: bug, priority:high
#504 - fix: _get_priority_translation_result using wrong variable
Pull Request -
State: closed - Opened by korikuzma over 1 year ago
Labels: bug, priority:high
#503 - Refactor
Pull Request -
State: closed - Opened by korikuzma over 1 year ago
- 1 comment
#502 - Investigate VRS IDs changing for protein free text queries on refactor branch using /normalize
Issue -
State: closed - Opened by korikuzma over 1 year ago
- 2 comments
Labels: bug, priority:high
#501 - fix: add condition when there are no valid results in /to_vrs
Pull Request -
State: closed - Opened by korikuzma over 1 year ago
Labels: bug, priority:medium
#500 - Add condition when there are no valid results in /to_vrs
Issue -
State: closed - Opened by korikuzma over 1 year ago
- 1 comment
Labels: bug, priority:high
#499 - Stabilize construction of required resources
Issue -
State: open - Opened by jsstevenson over 1 year ago
- 1 comment
Labels: priority:low, technical debt
#498 - Add new endpoint for lifting over SPDI + using vrs-python translate from
Issue -
State: closed - Opened by korikuzma over 1 year ago
- 1 comment
Labels: enhancement