v0.9.0

0.9.0 (2025-03-24)

Features

• landing page organism viz - data (#289) (#290) (6817ece)

Bug Fixes

• don't run deploy jobs on forks (#408) (#409) (17f317c)
• github action syntax needs single quotes, resolves deploys (d142b04)
• github action syntax needs single quotes, resolves deploys (#417) (#416) (d142b04)
• handle NCBI rate limit (df84da0)
• handle NCBI rate limit (#407) (#406) (df84da0)
• include ncbiGene.gtf.gz file if there's no refSeq gtf (#414) (#413) (89799d4)

Chores

• use requests session to reuse tcp connection (#397) (#405) (dacdbb2)

v0.8.0

0.8.0 (2025-03-20)

Features

• add realm to taxonomic lineage filters (#389) (#390) (0d96267)
• allow limiting workflows by taxonomy id (#356) (#369) (364876f)
• build catalog and add qc report (#344) (#364) (a3a70ca)
• remove retired ncbi superkingdom rank and add domain (#385) (#386) (a7af98a)
• update workflows from IWC manifest and set assembly-specific parameters (#351, #339) (#342) (f5720a8)

Bug Fixes

• avoid assembly duplication due to duplicate taxonomy ids and add checks for duplicate entity ids (#367) (#368) (e625081)
• use correct variant calling landing body even when gene model url is absent (#347) (#365) (038d76e)

Chores

• add .venv to prettier ignore list (28981f7)
• add .venv to prettier ignore list (#373) (#374) (28981f7)
• remove issue number check from commit message validation (bba7273)
• Remove issue number check from husky (#363) (#372) (bba7273)
• rename genomes.json to assemblies.json (#343) (#360) (bebcfb2)
• replace HTML scraping with API calls (#346) (#378) (6b6c3c0)
• update findable-ui to latest v22.0.0 (#391) (#395) (8ee5a6a)

Content

• explain 'free' compute at tacc (#237) (#370) (39bab23)
• remove cards from the carousel/card deck (#403) (#404) (9f4f70e)

Continuous Integration

• add github action and workflow to check pr title for commit message format (#377) (#380) (b128499)
• fix linkml checks so that they exit with failure if the check fails for any file (#341) (#376) (a450ea5)

v0.7.0

0.7.0 (2025-03-03)

Features

• add back all assemblies (#323) (#340) (6bff3c8)
• add filters for taxonomic levels to organisms list (#301) (#306) (665a20a)
• add taxonomic levels to assembly list (#312) (#316) (06bdb3c)
• added additional workflows (#322) (#335) (8cab2ad)
• allow organisms to have multiple ploidies separately matched with workflows (#334) (#338) (7ce865a)

Styles

• fix prettierignoring of catalog files (#317) (#318) (9c97653)

v0.6.0

0.6.0 (2025-02-18)

Features

• add instructions section to home page (#278) (#303) (173f3b1)
• add linkml schemas for data source files (#269, #270) (#283) (b208c53)
• create catalog build python package (#251) (#258) (c31cf6e)
• derive workflows from yaml files (#260) (#265) (0b42fd7)
• fetch raw/primary data information from sra (#295) (5ded790)
• move assembly species from breadcrumbs to subtitle (#276) (#280) (aedfc32)
• only show workflows with compatible ploidies (#297) (#299) (9e2e04c)
• support multiple analysis methods per category (#279) (#296) (57d55db)
• update workflow card for "Launch Galaxy" button (#300) (#302) (1004775)

Chores

• delete unused build-genomes-files.py (#267) (#274) (4032561)

Content

• update main page (#243) (#259) (bbdee9f)

Documentation

• add instructions for building the catalog and adding assemblies (#266) (#268) (56110b9)

Code Refactoring

• remove unused workflows from catalog (#272) (#273) (9d37334)
• reorganize catalog folders (#271) (#281) (b9e3a38)

v0.5.1

0.5.1 (2025-02-03)

Content

• cleanup NCBI icon on the assemblies page (#248) (#249) (97472c9)

v0.5.0

0.5.0 (2025-01-31)

Features

• add environment-specific galaxy urls (#239) (#241) (cf9d95d)
• remove "Preview" chip from analysis methods (#245) (#247) (d79390a)

v0.4.0

0.4.0 (2025-01-27)

Features

• add github link to header and footer (#234) (#238) (d107863)
• add organism group to entity lists and filters (#236) (#240) (79def41)
• link to organism page from assembly list and detail (#231) (#232) (15bace5)

v0.3.1

0.3.1 (2025-01-23)

Code Refactoring

• get accessions from yaml file when building catalog source (#228) (#229) (bb79f88)

v0.3.0

0.3.0 (2025-01-22)

Features

• update analysis methods heading (#225) (#226) (a1bd78f)

v0.2.0

0.2.0 (2025-01-21)

Features

• add other fields to assembly details (#213) (#219) (c53cba3)
• move resources to top of assembly side column (#222) (#224) (7cd75d2)
• rename analysis portals to resources and add ncbi links (#214) (#220) (3c12dea)
• update organism detail page (#212) (#217) (6748ee1)
• update titles on assembly detail page (#221) (#223) (076a09b)