nextstrain/forecasts-ncov issues and pull requests

#116 - Revert "run-models.yaml: Pin docker-base image"

Pull Request - State: closed - Opened by joverlee521 about 2 months ago

#115 - Properly handle CSV-like TSVs

Issue - State: open - Opened by joverlee521 2 months ago

#114 - run-models.yaml: Pin docker-base image

Pull Request - State: closed - Opened by joverlee521 2 months ago

#113 - Failure in run-models workflows

Issue - State: closed - Opened by joverlee521 2 months ago - 4 comments
Labels: bug

#112 - Add clades 24H, 24I

Pull Request - State: open - Opened by corneliusroemer 3 months ago - 2 comments

#111 - Add new colors for new clades

Issue - State: closed - Opened by corneliusroemer 4 months ago - 1 comment
Labels: enhancement

#110 - dev: Stop using Mambaforge in CI; the Miniforge3 installer is now equivalent

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

#109 - Adding time-varying hierarchical model

Pull Request - State: open - Opened by marlinfiggins 4 months ago - 1 comment

#108 - Update clade definitions

Pull Request - State: closed - Opened by trvrb 5 months ago - 1 comment

#107 - Failure in genbank/clade-counts

Issue - State: open - Opened by joverlee521 7 months ago - 1 comment

#106 - Add clade definition for 24C

Pull Request - State: closed - Opened by joverlee521 7 months ago - 1 comment

#105 - Add .gitattributes file

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

#104 - Model workflow failing

Issue - State: closed - Opened by joverlee521 7 months ago - 4 comments
Labels: bug

#103 - ingest: Update vendored scripts

Issue - State: open - Opened by joverlee521 7 months ago

#102 - Refactor case counts workflow

Pull Request - State: closed - Opened by joverlee521 8 months ago

#101 - Switch AWS credentials from a long-lived IAM user to short-lived role sessions

Pull Request - State: closed - Opened by tsibley 8 months ago

#100 - Add QC for clade sequence counts

Issue - State: open - Opened by joverlee521 8 months ago
Labels: enhancement

#99 - Reduce location count thresholds

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

#98 - Reduce clade count threshold

Pull Request - State: closed - Opened by trvrb 9 months ago - 1 comment

#97 - Revisit sequence data inclusion thresholds

Issue - State: closed - Opened by joverlee521 9 months ago - 2 comments

#96 - Update viz library

Pull Request - State: closed - Opened by joverlee521 10 months ago

#95 - update-ncov-case-counts: Use GitHub org variable for AWS region

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

#94 - Add clade definitions for 24A and 24B

Pull Request - State: closed - Opened by joverlee521 10 months ago - 4 comments

#93 - Bump actions/configure-pages from 4 to 5

Pull Request - State: open - Opened by dependabot[bot] 10 months ago
Labels: dependencies

#92 - Stream metadata from S3, filter, and compress

Pull Request - State: closed - Opened by huddlej 11 months ago - 3 comments

#91 - update-ncov-gisaid-clade-counts: Bump memory

Pull Request - State: closed - Opened by joverlee521 11 months ago

#90 - viz: Add growth advantage scatterplots

Issue - State: open - Opened by joverlee521 12 months ago
Labels: enhancement

#89 - Update Pango lineage pivots to JN.1

Pull Request - State: closed - Opened by joverlee521 12 months ago - 5 comments

#88 - Bump actions/checkout from 2 to 4

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 1 comment
Labels: dependencies

#87 - Pin pandas<2.2.0

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

#86 - Bump actions/upload-pages-artifact from 1 to 3

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#85 - Bump actions/deploy-pages from 1 to 4

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#84 - Bump conda-incubator/setup-miniconda from 2 to 3

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

#83 - Bump actions/configure-pages from 3 to 4

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

#82 - Bump actions/setup-node from 3 to 4

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

#81 - ingest: restore CloudFront invalidation in upload

Pull Request - State: closed - Opened by joverlee521 about 1 year ago - 1 comment

#80 - Reduce disk write of 20+GB metadata file by filtering on the fly

Issue - State: closed - Opened by corneliusroemer about 1 year ago - 2 comments
Labels: enhancement

#79 - fix: lineage_to_clade missed a `.`

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

#78 - Add provisional colors for new clades 23G/H/I

Pull Request - State: closed - Opened by corneliusroemer about 1 year ago - 4 comments

#77 - Sync location threshold text with values in config

Pull Request - State: open - Opened by corneliusroemer about 1 year ago

#76 - Country include description out of sync?

Issue - State: open - Opened by corneliusroemer about 1 year ago - 2 comments
Labels: bug

#75 - Add new Nextstrain clade definitions

Issue - State: closed - Opened by joverlee521 about 1 year ago - 1 comment

#74 - Send Slack notifications for clades without definition

Issue - State: open - Opened by joverlee521 about 1 year ago
Labels: enhancement

#73 - Add default clade color

Pull Request - State: closed - Opened by joverlee521 about 1 year ago - 1 comment

#72 - Simplify viz for local files

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

#71 - Flag potential lineages for new Nextstrain clades

Issue - State: open - Opened by joverlee521 over 1 year ago - 1 comment
Labels: enhancement

#70 - Allow force include of Pango lineages that might not meet threshold

Issue - State: open - Opened by joverlee521 over 1 year ago
Labels: enhancement

#69 - Add recombinant clade definition

Pull Request - State: closed - Opened by joverlee521 over 1 year ago - 1 comment

#68 - ingest/fetch-ncov-global-case-counts: follow redirection

Pull Request - State: closed - Opened by joverlee521 over 1 year ago

#67 - Unify colour & display name setting for all models

Pull Request - State: closed - Opened by jameshadfield over 1 year ago - 4 comments

#66 - Update lineage colour definitions

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

#65 - workflows/run-models: Unpin nextstrain-base image

Pull Request - State: closed - Opened by joverlee521 over 1 year ago - 1 comment

#64 - Force include locations

Pull Request - State: open - Opened by corneliusroemer over 1 year ago - 1 comment

#63 - Document which `geo_resolution`'s are available

Issue - State: closed - Opened by corneliusroemer over 1 year ago
Labels: documentation

#63 - Document which `geo_resolution`'s are available

Issue - State: closed - Opened by corneliusroemer over 1 year ago
Labels: documentation

#62 - Clean up workflows

Pull Request - State: closed - Opened by joverlee521 over 1 year ago - 2 comments

#61 - .github/workflows: use vars.SLACK_CHANNELS as default

Pull Request - State: closed - Opened by joverlee521 over 1 year ago - 1 comment

#60 - Seq counts workflow

Pull Request - State: closed - Opened by joverlee521 over 1 year ago - 4 comments

#59 - Update viz library

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

#58 - Calculate weekly frequencies

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

#57 - Unpin nextstrain/base image once evofr has been updated

Issue - State: closed - Opened by joverlee521 over 1 year ago

#56 - workflow/run-models: pin nextstrain/base image

Pull Request - State: closed - Opened by joverlee521 over 1 year ago - 1 comment

#55 - Update viz library to use JSON-defined colours

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

#54 - Post process model JSONs

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

#53 - deploy-viz-app workflow: update path pattern

Pull Request - State: closed - Opened by joverlee521 over 1 year ago

#52 - bugfix - fix lineages locations

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

#51 - Remove hierarchical location from frequency panel

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

#50 - Adding raw frequencies to JSON

Pull Request - State: closed - Opened by marlinfiggins over 1 year ago - 9 comments

#49 - ingest: remove US case count scripts/steps

Pull Request - State: closed - Opened by joverlee521 over 1 year ago

#48 - Prepare data error

Pull Request - State: closed - Opened by joverlee521 over 1 year ago

#47 - Update viz library

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

#46 - Remove static image generation steps/workflow

Pull Request - State: closed - Opened by joverlee521 over 1 year ago

#45 - Replace "recombinant" clade with label "other"

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

#44 - Include model run date in abstract

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

#43 - Support hierarchical models

Pull Request - State: closed - Opened by marlinfiggins over 1 year ago - 14 comments

#42 - Update viz to replace renewal panels with MLR lineage panels

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

#41 - Update README files

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

#40 - chore: replace snakemake message directive with comment

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

#39 - Simplify pango collapsing by using pango_aliasor package

Pull Request - State: closed - Opened by corneliusroemer almost 2 years ago - 6 comments

#38 - TypeError: Object of type ArrayImpl is not JSON serializable

Issue - State: open - Opened by corneliusroemer almost 2 years ago - 5 comments
Labels: bug

#37 - Fix trigger for static images

Pull Request - State: closed - Opened by joverlee521 almost 2 years ago

#36 - Update viz library

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

#35 - Collapse rare Pango lineages

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

#34 - Include MLR estimates for Pango lineages

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

#33 - Switch to 22B (BA.5) baseline and force inclusion of 23B

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

#32 - Counts update doesn't invalidate CloudFront

Issue - State: closed - Opened by trvrb almost 2 years ago
Labels: bug

#31 - Update viz library

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

#30 - Summarize lineage counts

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

#29 - Add workflow to deploy viz app to GH pages

Pull Request - State: closed - Opened by joverlee521 almost 2 years ago - 1 comment

#28 - Add 23B (Omicron) variant

Pull Request - State: closed - Opened by joverlee521 almost 2 years ago - 3 comments

#27 - Update viz library

Pull Request - State: closed - Opened by joverlee521 almost 2 years ago

#26 - Forcing mlr models to forecast until `forecast_L` days from present.

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

#25 - fix: Add `--cores` to gh actions nextstrain build

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

#24 - Import viz code as a library

Pull Request - State: closed - Opened by jameshadfield almost 2 years ago - 4 comments

#23 - Adding forecast capabilities for MLR and Renewal equation model

Pull Request - State: closed - Opened by marlinfiggins about 2 years ago - 7 comments

#22 - Import viz code as a library

Pull Request - State: closed - Opened by jameshadfield about 2 years ago - 3 comments

#21 - Update uses of conda-incubator/setup-miniconda@v2 (part 2)

Pull Request - State: closed - Opened by victorlin about 2 years ago

#20 - Update uses of conda-incubator/setup-miniconda@v2

Pull Request - State: closed - Opened by joverlee521 about 2 years ago

#19 - Update US case counts source

Pull Request - State: closed - Opened by joverlee521 about 2 years ago - 1 comment

#18 - update-*-clade-counts: use `--freeze-installed`

Pull Request - State: closed - Opened by joverlee521 about 2 years ago - 1 comment

GitHub / nextstrain/forecasts-ncov issues and pull requests