v2.2.3

What's Changed

This version contains mainly minor changes in the dashboard. We have added a news section to inform users about upcoming data updates or new versions of the Covigator package and pipeline.

• remove titles by @priesgo in #135

• update RTFD recipe by @priesgo in #140

• 134 add news section by @johausmann in #139

• Add feature table and update dependencies to newer versions by @johausmann in #143

• Update dependencies by @johausmann in #145

Full Changelog: v2.2.2...v2.2.3

v2.2.2

What's Changed

• ENA 2023 api update by @johausmann in #128
• Updated accessor module filters in order to support other viruses
• Dashboard improvements by @johausmann in #129
• v2.2.2 release by @johausmann in #132

Full Changelog: v2.2.1...v2.2.2

v2.2.1

What's Changed

This is a minor release. It includes changes to the github release pipeline.

• Update release.yml by @johausmann in #126
• Update release pipeline to checkout submodules by @johausmann in #127

Full Changelog: v2.2.0...v2.2.1

Release v2.2.0

Changes

Major

• Added Pangolin lineage defining mutations. Add parser for the data coming from pangolin constellations, add model to hold the data in the DB, annotate the mutations tables with lineages

Minor

• Update the documentation to prepare custom references for CoVigator pipeline
• Update CoVigator paper citation
• Remove effect column from mutations tables

v2.1.0

What's Changed

• Add date selection controls and a prevalence filter for lineages plot by @johausmann in #95
• add feedback form from user report by @priesgo in #96

Full Changelog: v2.0.0...v2.1.0

v2.0.0

What's Changed

• Integrate COVID19 Data Portal FASTA sequences into CoVigator by @priesgo in #53
• Smooth lineages plot with sliding window by @priesgo in #58
• Code coverage by @priesgo in #69
• Bump numpy from 1.21.0 to 1.22.0 by @dependabot in #72
• Bump ipython from 7.27.0 to 7.31.1 in /docs by @dependabot in #71
• Introduce low quality clonal mutations (ie: VAF < 0.5) by @priesgo in #77
• Some patches to the DB + a bugfix on a date by @priesgo in #78
• Avoid error that was showing allele frequencies greater than 1.0 by @priesgo in #76
• Apply filters to obtain high quality intrahost mutation calls by @priesgo in #79
• Fix codacy style issues by @priesgo in #81
• Rollback session after error by @priesgo in #84
• Avoid SQL injection and extend mutation color palette by @johausmann in #87
• Update screenshots in documentation by @priesgo in #83
• Update documentation by @priesgo in #88
• Fix codacy issues by @priesgo in #91
• Release v2.0.0 by @priesgo in #90

New Contributors

• @dependabot made their first contribution in #72
• @johausmann made their first contribution in #87

Full Changelog: v1.1.0...v2.0.0

v1.1.0

Changes

• Move download tab to the menu buttom as now also COVID1-9 Data Portal data is available
• Update the documentation with COVID-19 Data Portal

v1.0.0

Changes

• Add support for Covid19 data portal sequences data

Release v0.9.0

Changes

• Upgrade pangolin to v4.1.2
• Remove GISAID entities from DB model

Release v0.8.2

Changes

• Fix links to imprint and data protection in the footer
• Update a figure from the manuscript