cancervariants/therapy-normalization issues and pull requests

#431 - cicd: remove mypy checks

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

#430 - cicd: only lint in 3.11

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

#429 - cicd: add issue templates/stalebot

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

#428 - build!: use setuptools-scm to declare version

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

#427 - cicd: update precommit

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

#426 - feat: use latest VRS models

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

#425 - style: update to ruff==0.5.0

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

#424 - build: require python >= 3.10

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

#423 - fix: use enum for source name to ensure proper pydantic serialization

Pull Request - State: closed - Opened by jsstevenson 4 months ago
Labels: priority:medium, bug

#422 - feat: add progress bars/indicators to CLI ETL processes

Pull Request - State: closed - Opened by jsstevenson 6 months ago - 1 comment
Labels: priority:low

#421 - Capture "pref_name" from ChEMBL

Issue - State: open - Opened by jsstevenson 6 months ago
Labels: ChEMBL, priority:low, enhancement

#420 - Add orphan status indicator

Issue - State: open - Opened by jsstevenson 6 months ago - 1 comment
Labels: ChEMBL, priority:medium, enhancement, keep-alive

#419 - fix: prohibit xrefs from hemonc combo therapies

Pull Request - State: closed - Opened by jsstevenson 6 months ago
Labels: priority:medium

#418 - fix: handle label and order by biologic suffix in merge groups

Pull Request - State: closed - Opened by jsstevenson 6 months ago
Labels: priority:medium

#417 - Handle over-eager xrefs from combo therapies

Issue - State: closed - Opened by jsstevenson 6 months ago
Labels: bug

#416 - fix: handle multiple CHEBI IDs on a row

Pull Request - State: closed - Opened by jsstevenson 6 months ago
Labels: priority:medium, bug

#415 - GuideToPharm importer producing invalid xrefs

Issue - State: closed - Opened by jsstevenson 6 months ago - 1 comment
Labels: priority:high, bug

#414 - use `pkgutil` for relative paths to data files

Issue - State: open - Opened by jsstevenson 6 months ago
Labels: priority:low, technical debt

#413 - docs: readme glow-up

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

#412 - build: update metadata

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

#411 - chore: update license

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

#410 - cicd: test on 3.12

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

#409 - cicd: require priority label on PRs

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

#408 - style: pin ruff version to match template

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

#407 - chore: remove unused files

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

#406 - style: add ruff updates

Pull Request - State: closed - Opened by jsstevenson 8 months ago
Labels: priority:low, cleanup

#405 - build: get disease ETL dependencies

Pull Request - State: closed - Opened by jsstevenson 9 months ago

#404 - fix: handle brand name lookup KeyError

Pull Request - State: closed - Opened by jsstevenson 9 months ago - 2 comments

#403 - Hemonc ETL raises KeyError

Issue - State: closed - Opened by korikuzma 9 months ago - 1 comment
Labels: priority:medium, bug

#402 - docs: fix click option for sources to update

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

#401 - Update click option for updating sources

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

#400 - docs: fix env var name for harvard dataverse api key

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

#399 - Update Harvard Dataverse API Key Env Var in README

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

#398 - feat: set silent to False in CLI

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

#397 - docs: update hemonc instructions in readme

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

#396 - Provide link to dataverse website

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

#395 - Capture known treatment regimens

Issue - State: open - Opened by jsstevenson 10 months ago
Labels: priority:low, enhancement

#394 - feat!: remove search result formatting option

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

#393 - feat: sort everything

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

#392 - feat!: refine schemas

Pull Request - State: closed - Opened by jsstevenson 10 months ago
Labels: priority:low

#391 - perf: improve disease caching

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

#390 - chore: fix up logging

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

#389 - feat!: use wags-tails for data management

Pull Request - State: closed - Opened by jsstevenson 11 months ago
Labels: priority:low

#388 - style: fix ruff settings

Pull Request - State: closed - Opened by jsstevenson 11 months ago - 1 comment
Labels: priority:low

#387 - Add ATC-based features

Issue - State: closed - Opened by jsstevenson 11 months ago - 1 comment

#386 - test: suppress noisy boto logs by default

Pull Request - State: closed - Opened by jsstevenson 11 months ago

#385 - feat: implement latest data updates

Pull Request - State: closed - Opened by jsstevenson 11 months ago
Labels: priority:medium

#384 - fix: handle hemonc deprecated concept

Pull Request - State: closed - Opened by jsstevenson 11 months ago
Labels: priority:medium

#383 - Overhaul tests

Issue - State: open - Opened by jsstevenson 11 months ago - 2 comments
Labels: priority:medium, test

#382 - docs: add paper citation

Pull Request - State: closed - Opened by jsstevenson 11 months ago - 1 comment

#381 - style: remove unnecessary noqa: E501

Pull Request - State: closed - Opened by korikuzma 11 months ago
Labels: priority:low, cleanup

#380 - build: fix package name in pyproject.toml

Pull Request - State: closed - Opened by korikuzma 11 months ago
Labels: build, bug

#379 - feat!: use wags-tails to manage data

Pull Request - State: closed - Opened by jsstevenson 11 months ago

#378 - feat!: use abstract interface for DB

Pull Request - State: closed - Opened by jsstevenson 11 months ago
Labels: priority:low

#377 - build: use pyproject.toml for build configuration

Pull Request - State: closed - Opened by jsstevenson 11 months ago
Labels: priority:low

#376 - cicd: add Ruff linting and formatting

Pull Request - State: closed - Opened by jsstevenson 12 months ago - 1 comment

#375 - Handle hemonc deprecated conditions

Issue - State: closed - Opened by jsstevenson 12 months ago
Labels: data-cleaning, priority:high, bug

#374 - merge concepts + metadata tables

Issue - State: closed - Opened by korikuzma 12 months ago - 1 comment
Labels: priority:low, technical debt

#373 - cicd: add python3.11 to python-version matrix

Pull Request - State: closed - Opened by korikuzma 12 months ago
Labels: priority:low, ci/cd

#372 - chore: remove unused makefile

Pull Request - State: closed - Opened by jsstevenson 12 months ago

#371 - chore: remove unused makefile

Pull Request - State: closed - Opened by jsstevenson 12 months ago
Labels: priority:high

#370 - fix: handle chembl approval enum oddities

Pull Request - State: closed - Opened by jsstevenson 12 months ago

#369 - style: resolve mypy errors

Pull Request - State: closed - Opened by korikuzma 12 months ago - 1 comment
Labels: priority:low, cleanup

#368 - style: resolve mypy errors

Pull Request - State: closed - Opened by korikuzma 12 months ago
Labels: priority:low, cleanup

#367 - cicd: update release.yml (publish python distribution to pypi)

Pull Request - State: closed - Opened by korikuzma 12 months ago
Labels: priority:low, ci/cd

#366 - cicd: update release.yml (publish python distribution to pypi)

Pull Request - State: closed - Opened by korikuzma 12 months ago
Labels: priority:low, ci/cd

#365 - Capture class hierarchies

Issue - State: open - Opened by jsstevenson about 1 year ago - 1 comment

#364 - feat!: use vrs 2.0-alpha models in /normalize

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

#363 - Update pydantic to v2 + remove ga4gh.vrsatile.pydantic dependency

Issue - State: closed - Opened by korikuzma about 1 year ago
Labels: build, priority:high

#362 - style: use Ruff and Black

Pull Request - State: closed - Opened by jsstevenson about 1 year ago
Labels: priority:low

#361 - feat: implement latest data updates

Pull Request - State: closed - Opened by jsstevenson about 1 year ago
Labels: priority:low

#360 - feat: update wikidata data import

Pull Request - State: closed - Opened by jsstevenson about 1 year ago
Labels: priority:low

#359 - feat: add download progress bar

Pull Request - State: closed - Opened by jsstevenson about 1 year ago

#358 - build: remove requirements.txt files

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

#357 - build: remove requirements.txt files

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

#356 - build(deps-dev): bump tornado from 6.2 to 6.3.2

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#355 - feat!: improve interface wording

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

#354 - build(deps): bump starlette from 0.25.0 to 0.27.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#353 - fix: expand wikidata SPARQL query

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

#352 - fix: expand wikidata SPARQL query

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

#351 - Update wikidata query

Issue - State: closed - Opened by jsstevenson over 1 year ago - 1 comment
Labels: Wikidata, bug

#350 - feat!: support PostgreSQL as optional storage backend

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

#349 - Consider removing alias count limit

Issue - State: open - Opened by jsstevenson over 1 year ago
Labels: enhancement

#348 - Don't provide RxNorm brand linkages for combo therapies

Issue - State: open - Opened by jsstevenson over 1 year ago
Labels: bug

#347 - build(deps): resolve ipython and starlette vulnerabilities

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

#346 - build(deps): resolve ipython and starlette vulnerabilities

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

#345 - build(deps): bump starlette from 0.22.0 to 0.25.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#344 - build(deps-dev): bump ipython from 8.8.0 to 8.10.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#343 - Database naming updates

Issue - State: closed - Opened by jsstevenson over 1 year ago
Labels: enhancement, data-structure

#342 - test: Add test for DiseaseIndicationBase

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

#341 - fix: Add test for DiseaseIndicationBase

Pull Request - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: priority:medium, bug, test

#340 - Add test for DiseaseIndicationBase

Issue - State: closed - Opened by korikuzma over 1 year ago
Labels: priority:medium, bug, test

#339 - build: update disease normalizer to ~0.2.19

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: build, priority:medium

#338 - build: update disease normalizer to >=0.3.1

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: build, priority:medium

#337 - fix: pypi package should include all files in etl/ (staging)

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

#336 - fix: pypi package should include all files in etl/

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

#335 - FileNotFoundError for `therapy/etl/rules.csv`

Issue - State: closed - Opened by korikuzma over 1 year ago
Labels: priority:medium, bug

#334 - Update ncit license

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

#333 - fix: remove script tags from gtop therapy names

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

#332 - feat: use new RxNorm download method

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

GitHub / cancervariants/therapy-normalization issues and pull requests