Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nextstrain/fauna issues and pull requests

#174 - Fix H3 vaccine strains

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

#173 - Add date fix for `vdb/avian_flu_upload`

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

#172 - WIP A/H7N6

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

#171 - Pandas and numpy version incompatibilities

Issue - State: open - Opened by jameshadfield 3 months ago - 3 comments
Labels: bug

#170 - Use custom runtime

Issue - State: closed - Opened by victorlin 3 months ago - 4 comments

#169 - Support pandas version 2

Issue - State: closed - Opened by victorlin 3 months ago - 5 comments

#168 - Pylint alerts corrections as part of an intervention experiment

Issue - State: closed - Opened by evidencebp 3 months ago - 1 comment
Labels: enhancement

#167 - vidrl_upload: Update `VACCINE_MAPPING` to match proxies

Pull Request - State: closed - Opened by joverlee521 3 months ago - 1 comment

#167 - vidrl_upload: Update `VACCINE_MAPPING` to match proxies

Pull Request - State: closed - Opened by joverlee521 3 months ago - 1 comment

#166 - vidrl_upload: fix `serum_strain` used for human sera measurements

Issue - State: closed - Opened by joverlee521 3 months ago - 2 comments
Labels: bug

#164 - Update ingest for VIDRL flat files

Pull Request - State: open - Opened by joverlee521 4 months ago

#164 - Update ingest for VIDRL flat files

Pull Request - State: open - Opened by joverlee521 4 months ago

#163 - Generate list of new titers references on each new ingest

Issue - State: open - Opened by huddlej 5 months ago - 1 comment
Labels: enhancement

#163 - Generate list of new titers references on each new ingest

Issue - State: open - Opened by huddlej 5 months ago - 1 comment
Labels: enhancement

#162 - Decouple data curation and upload

Issue - State: open - Opened by joverlee521 5 months ago

#162 - Decouple data curation and upload

Issue - State: open - Opened by joverlee521 5 months ago

#161 - Revisit ingestion of VIDRL flat files

Issue - State: open - Opened by joverlee521 5 months ago - 7 comments

#161 - Revisit ingestion of VIDRL flat files

Issue - State: open - Opened by joverlee521 5 months ago - 7 comments

#160 - Ingest VIDRL human sera references

Pull Request - State: closed - Opened by joverlee521 6 months ago - 3 comments

#160 - Ingest VIDRL human sera references

Pull Request - State: closed - Opened by joverlee521 6 months ago - 3 comments

#159 - crick_upload: Skip "comments" sheets

Pull Request - State: closed - Opened by joverlee521 6 months ago - 1 comment

#159 - crick_upload: Skip "comments" sheets

Pull Request - State: closed - Opened by joverlee521 6 months ago - 1 comment

#158 - Parse VIDRL human sera pool measurements

Issue - State: open - Opened by huddlej 6 months ago - 2 comments
Labels: enhancement

#158 - Parse VIDRL human sera pool measurements

Issue - State: open - Opened by huddlej 6 months ago - 2 comments
Labels: enhancement

#157 - Refactor `vidrl_upload` to auto-detect titer info

Pull Request - State: closed - Opened by j23414 7 months ago

#157 - Refactor `vidrl_upload` to auto-detect titer info

Pull Request - State: closed - Opened by j23414 7 months ago

#156 - Publish to pypi and then bioconda

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

#156 - Publish to pypi and then bioconda

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

#155 - Update readme

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

#153 - vdb/flu_upload: parse `submitting_lab` from XLS

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

#153 - vdb/flu_upload: parse `submitting_lab` from XLS

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

#152 - Update zika instructions

Pull Request - State: closed - Opened by j23414 about 1 year ago

#151 - script/delete_records: Add option to match fields with regex pattern

Pull Request - State: open - Opened by joverlee521 about 1 year ago - 2 comments

#150 - requirements: Skip rethinkdb v2.4.10

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

#149 - Fix GISAID avian flu accessions

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

#148 - Fix GISAID flu accessions

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

#147 - Update zika instructions

Pull Request - State: closed - Opened by j23414 about 1 year ago - 2 comments

#146 - tdb/elife_upload: Update assay_date parsing

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

#145 - TLS support

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

#144 - Revisit tdb/upload's `index_fields`

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

#143 - Delete records with date intervals

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

#142 - Support ingest of individual-level human serology data for seasonal flu viruses

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

#141 - Automate backup of Fauna databases to S3

Issue - State: closed - Opened by joverlee521 over 1 year ago - 4 comments
Labels: enhancement

#140 - Gisaid clade and download changes

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

#139 - Replace nextstrain remote with aws commands

Issue - State: closed - Opened by j23414 almost 2 years ago - 1 comment

#138 - tdb/download: correct flu type in strain names

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

#136 - Avian flu upload additions

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

#135 - Geolocation assignments fail for duplicate location names

Issue - State: open - Opened by joverlee521 about 2 years ago - 2 comments
Labels: bug

#134 - Bump express from 4.16.4 to 4.17.3

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies, javascript

#133 - Bump certifi from 2020.6.20 to 2022.12.7

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies, python

#132 - Bump qs and express

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies, javascript

#131 - Fix cdc uploads

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

#130 - Assign correct host to titers from non-ferret hosts (e.g., human and mouse)

Issue - State: closed - Opened by huddlej over 2 years ago
Labels: bug

#128 - feat: BV-BRC support

Issue - State: closed - Opened by j23414 over 2 years ago - 2 comments
Labels: enhancement

#127 - docs: zstd

Pull Request - State: closed - Opened by j23414 over 2 years ago

#126 - Set `serum_id` to `lot_number` for CDC titer imports

Issue - State: closed - Opened by huddlej over 2 years ago - 4 comments
Labels: bug

#125 - PhantomJS not found on PATH - installation via npm install

Issue - State: closed - Opened by limh25 over 2 years ago - 2 comments
Labels: bug

#124 - Bump moment from 2.22.2 to 2.29.4

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies, javascript

#123 - Bump numpy from 1.19.4 to 1.22.0

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies, python

#122 - docs: update dengue instructions

Pull Request - State: closed - Opened by j23414 almost 3 years ago

#121 - fauna downloads fail with Python 3.10

Issue - State: closed - Opened by huddlej almost 3 years ago - 1 comment
Labels: bug

#120 - preprocess sed command

Pull Request - State: closed - Opened by j23414 almost 3 years ago

#119 - Fix min year in API call

Pull Request - State: closed - Opened by victorlin almost 3 years ago

#118 - Bump moment from 2.22.2 to 2.29.2

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies, javascript

#117 - Remove step for starting separate rethinkdb server

Pull Request - State: closed - Opened by victorlin almost 3 years ago

#116 - document ViPR API call as an alternative download

Pull Request - State: closed - Opened by j23414 almost 3 years ago

#115 - Update ZIKA.md

Pull Request - State: closed - Opened by victorlin almost 3 years ago

#114 - Revert "Compensate for automatic compression by nextstrain remote upload

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

#113 - Switch out `xlrd`

Issue - State: open - Opened by joverlee521 about 3 years ago - 1 comment
Labels: enhancement

#112 - GitHub Action to lint Python code

Pull Request - State: closed - Opened by cclauss over 3 years ago - 1 comment

#111 - Bump urllib3 from 1.25.7 to 1.26.5

Pull Request - State: open - Opened by dependabot[bot] over 3 years ago
Labels: dependencies, python

#110 - Bump urllib3 from 1.25.7 to 1.25.8

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies, python

#109 - Include a header in titer tables

Pull Request - State: closed - Opened by huddlej almost 4 years ago - 1 comment

#108 - Include assay and inclusion dates for titer data

Pull Request - State: closed - Opened by huddlej almost 4 years ago

#107 - tdb/cdc_upload: Add filter option for new titers

Pull Request - State: closed - Opened by joverlee521 about 4 years ago - 1 comment

#106 - Wip h5nx

Pull Request - State: closed - Opened by lmoncla about 4 years ago - 1 comment

#105 - GitHub Action to lint Python code

Pull Request - State: closed - Opened by cclauss about 4 years ago

#104 - Upgrade to Python 3 and RethinkDB 2.4.8

Pull Request - State: closed - Opened by trvrb about 4 years ago

#103 - VIDRL flat file

Pull Request - State: closed - Opened by joverlee521 about 4 years ago

#102 - Use print() function in both Python 2 and Python 3

Pull Request - State: closed - Opened by cclauss almost 5 years ago - 4 comments

#101 - Fauna upload and download scripts for seasonal corona viruses

Pull Request - State: open - Opened by kistlerk almost 5 years ago

#100 - Geographic error?

Issue - State: closed - Opened by boristim66 about 5 years ago - 2 comments

#99 - fauna doesn't work with rethinkdb 2.4

Issue - State: closed - Opened by rneher about 5 years ago - 4 comments

#98 - Bump urllib3 from 1.24.1 to 1.24.2

Pull Request - State: closed - Opened by dependabot[bot] about 5 years ago
Labels: dependencies, python

#97 - Wip h9n2

Pull Request - State: closed - Opened by lmoncla about 5 years ago

#96 - Move date selection function

Pull Request - State: closed - Opened by barneypotter24 over 5 years ago

#92 - Fix imports from parent modules in vdb and tdb for python 3

Pull Request - State: closed - Opened by huddlej about 6 years ago

#91 - Crick 2018 update

Pull Request - State: closed - Opened by trvrb over 6 years ago

#90 - Fix parsing of VIDRL fluB tables

Pull Request - State: closed - Opened by barneypotter24 over 6 years ago - 1 comment

#89 - Ease README.md upload directions by matching filename casing across repositories

Pull Request - State: closed - Opened by stevenweaver over 6 years ago - 1 comment

#88 - Match filename in command to match linked repository

Pull Request - State: closed - Opened by stevenweaver over 6 years ago - 2 comments

#87 - Migrate to pandas 0.17

Issue - State: closed - Opened by stevenweaver over 6 years ago - 6 comments

#86 - vdb/download.py: Let --fasta_fields take multiple values

Pull Request - State: closed - Opened by tsibley over 6 years ago