CHANGELOG.md

title
Changelog

version 2.24.1 - 2021/03/19

• [bugfix] Fixes a bug introduced in v2.24.0 where certain datasets wouldn't load

version 2.24.0 - 2021/03/17

• Frequencies are no longer normalized when the data is lacking. See PR 1278 for more.
• Fixed a stack size bug, which mainly affected the TB dataset on certain browsers. See PR 1293 for more.
• Root-to-tip mutations are now displayed in the tip-clicked info box. See PR 1280 for more.
• Datasets may now define the default language. See PR 1303 for more.
• Polish language added. See PR 1288 for more.
• Tips in the tree should no longer be obscured behind the legend. See PR 1302 for more.
• Dates BCE are now correctly displayed in the phylogeny axis. See PR 1297 for more.

version 2.23.0 - 2021/01/28

• [feature] Implement genotype filtering. The sidebar, typing-based filter UI now includes genotypes (for datasets which define mutations on branches). See PR 1265 for more.
• [bugfix] Update how we generate the bundle hashes as the fix introduced in v2.22.2 was insufficient. See PR 1272 for more.

version 2.22.2 - 2021/01/14

• [bugfix] Updated how we generate hashes for the transpiled, chunked client bundles. This prevents subtle bugs where bundles could have the same hash, but different contents, and thus stale (browser cached) chunks may be used in certain situations. This bug most probably arose in v2.22.0, so please update to this version if possible! See PR 1263 for more.

version 2.22.1 - 2021/01/13

• Updated package-lock JSON file

version 2.22.0 - 2021/01/11

• The address Auspice uses to fetch map tiles, including the API token, has been updated and will now only work for local installs of auspice. For help on how to specify your own address, which lets you specify custom map tile sets, see the Auspice docs. See PR 1261 for more.
• Animation controls have moved and are now in the sidebar, underneath the date-slider. See PR 1262 for more.
• The footer has been updated to streamline the Nextstrain accreditation and now displays "Powered by Nextstrain". If you are serving your own version of auspice we ask for this accreditation to remain be maintained, in keeping with the spirit of scientific citations. Please also remember that customised version of auspice must make their source code available, as per Auspice's licence. See PR 1260 for more.

version 2.21.0 - 2021/01/06

Improved Functionality

• Tree rendering and zooming has been improved.
  • A new Zoom to Selected button has been added which allows you to zoom the tree to the clade containing the currently selected tips (PR 1257).
  • Branches ancestral to the common ancestor of the currently selected tips are now correctly rendered (PR 1248).
• The Download Data functionality has been improved to export data reflecting the currently viewed subset of data. Additionally we export annotated Nexus trees which can be parsed by FigTree. See PR 1245 for more.
• The drag & drop metadata functionality has been improved to facilitate easier filtering, custom locations and colours. See PR 1244 or these docs for more.
• Tip labels are now user-selectable via a drop-down in the sidebar. See PR 1246 for more.
• Legend values now dynamically update to reflect those in the current view. See PR 1250 for more.

Other Changes

• Italian translation added. See PR 1256.
• Amino acid labels are only shown on branches leading to big clades. See PR 1249 for more.
• Colour scale generation has been refactored and a (rare) bug fixed where color-bys which defined a scale in the JSON could cause tips with no trait value set to have a colour rather than a shade of grey. See PR 1237.
• Warnings added to documentation pages which are imported into Nextstrain's (main) RTD project. See PR 1234.
• Disabled a smoke-test which was stochastically failing on GitHub Actions (but which worked locally). See PR 1258 for more.

version 2.20.1 - 2020/11/19

• Small bugfixes and performance improvements relating to to the features introduced in 2.20.0

version 2.20.0 - 2020/11/18

See PR 1200.

• Add on-hover tooltips to the sidebar to better convey the functionality available. See PR 1200.
• Improve how we space temporal grid lines (phylogeny & frequencies panels). See PR 1229.
• Fix a bug in how we detected HTTP status codes. See PR 1226.
• Auspice documentation is now switched to the Read The Docs platform, and available at https://docs.nextstrain.org/projects/auspice. Redirects have been added for the old GitHub pages site, and can be found in the redirect-documentation branch. See PR 1220.

version 2.19.0 - 2020/10/07

• The auspice client now makes a request for the root-sequence JSON, which allows colouring of the tree by genotypes where there are no mutations. See PR 1197.
• polyfill Promise to avoid crashes in old browsers. See PR 1217.

version 2.18.4 - 2020/09/28

• (Bugfix) Update dependencies to restore behavior of the leaflet-scroll overlay. See nextstrain.org PR #223 for context, implemented in PR 1214

version 2.18.3 - 2020/09/22

This version reverts the change to URL parsing introduced in 2.18.2 which broke Auspice on Safari (and perhaps other browsers).

version 2.18.2 - 2020/09/19

• (Bugfix) Ensure generated SVG ids are escaped correctly. See PR 1209.
• Improve parsing of auspice URLs with colon characters in the pathname. See PR 1210.

version 2.18.1 - 2020/08/07

• Add between-paragraph padding for text rendering in (non-mobile) narratives.

version 2.18.0 - 2020/08/03

• Parse narratives client side. See PR 1193 and PR 1172. This shifts the default client behavior to request a narrative in markdown format and parse it client-side. The server still retains the ability to parse narratives server-side and return narratives in JSON format, so there are no breaking changes.

• Narratives can now contain multiple datasets. See PR 1193, PR 1176 and PR 1164. Narrative slides may now define their own unique datasets, with datasets preemptively fetched and cached to improve performance. Invalid datasets will show an error notification and fallback to the dataset defined by the frontmatter of the narrative.

• (Bugfix) Zooming in the entropy panel by using shift/option + mouseWheel now appropriately updates the URL query. See PR 1188

• (Bugfix) The animation occuring when zooming the phylogeny is now restored. See PR 1192

version 2.17.4 - 2020/07/21

• (Bugfix) Improve parsing of narrative files where a regex on a large string (e.g. image encoded as a blob) would hang the server

version 2.17.3 - 2020/07/14

• (Bugfix) Allow auspice view to serve custom auspice client if one exists. See PR 1182.

version 2.17.2 - 2020/07/13

• (Bugfix) Send error messages in the (HTTP) response body, not the status line. See PR 1181.

version 2.17.1 - 2020/06/25

• (Bugfix) Metadata from drag-and-drop CSVs now shows up in the color-by menu. See PR 1177.

version 2.17.0 - 2020/06/19

• You can now toggle whether the data in the frequencies panel is normalized. See PR 1158.
• You can now set the starting state of the transmissions-line toggle via the JSON or a URL query. See PR 1152 and PR 1165.
• Improve the caching settings for the auspice server. See PR 1146.
• The performance of Auspice is improved when transmission lines are not rendered. See PR 1153.
• The "narratives" folder is now part of this repo and contains a number of test narratives. See PR 1170 for more details.
• A bug was fixed where narrative slides would sometimes fail to update the tree as expected. See PR 1169.
• A bug was fixed where loading a tree zoomed to a clade would prevent zooming out. See PR 1156.
• A bug was fixed where numeric branch labels couldn't be used as URL queries. See PR 1157.
• The list of allowed nodejs versions was expanded. See PR 1166.

version 2.16.0 - 2020/05/29

Features

• Drastically improve how we bundle our JavaScript to improve loading times and allow more stable caching. See PR 1126 for more.
• Add a toggle for whether or not to show transmission lines on the map. See PR 1147 and PR 1103 for more.
• Dynamically adjust deme circle size on the map when filtering. See PR 1135 for more.
• Allow the genomic diversity data (the data behind the entropy panel) to be downloaded as a TSV. See PR 1144 for more.
• When running the auspice server incomplete URLs can now be expanded by the server. See PR 1129 for more.

Other

• Temporarily disable integration tests from the GitHub CI. See PR 1148 for more.
• Add a CC-BY license for the downloaded SVG (screenshots) . See PR 1140 for more.
• Improvement in code which decides which footers to show. See PR 1118 for more.
• Documentation improvements -- see PR 1127 for more.
• Fix an error in map positioning in some narrative slides. See PR 958 for more.
• Rename test snapshots for Windows support. See PR 1122 for more.
• Certain errors preventing the server from running are now caught & helpful messages printed. See PR 1140 for more.

version 2.15.0 - 2020/05/06

• Render "nice" dates for the frequency graph. See PR 1096 for more.
• Allow SVG in narrative markdown. See PR 1087 for more.
• Arabic translation. See PR 1107 for more.
• CSS fixes. See PR 1092 and PR 1094 for more.

version 2.14.0 - 2020/04/24

Testing

• Add screenshot integration testing using puppeteer and jest-image-snapshot, and run this through the GitHub CI. See PR 1068 & PR 1084

Features

• Turkish translation. See PR 1079

Bug fixes

• Tip labels are now rendered below tips. See PR 1069
• The included server now uses the appropriate content-type for datasets returned from the getDataset API. See PR 1080

Other

• We now use git-lfs for storing large objects. Currently this is only the screenshot images used for testing. See PR 1083
• Update the datasets fetched by npm run get-data. See PR 1088

version 2.13.0 - 2020/04/20

Testing

• Add smoke-testing to check that certain URLs render by checking the presence of strings in the DOM. This is a big step towards a comprehensive testing suite in Auspice. See PR 1057
• Add GitHub CI workflow to run tests etc automatically on PRs. See PR 1046
• Add bundle size checks to the CI. See PR 1069

Features

• Allow the display of URL confidences to be set by a URL query (?ci). This will allow narratives to render slides with the CI displayed. See PR 1046
• Add the ability to export per-strain metadata of only those strains currently being displayed. See PR 1067
• Move to using react-icons which allows the removal of the font-awesome CSS. This improves ease-of-use and reduces the bundle size. See PR 1065, PR 1041 & PR 1073
• Improve rendering of the narrative cover slide and add a license field. See PR 1060 & PR 1061
• Improve error handling in the parsing of markdown in the footer. See PR 1058
• Add a dot in the progress bar & a URL query for the end-of-narrative slide. See PR 1063

Bug Fixes

• Fix a bug where the layout couldn't be changed after the animation had been paused. See PR 1062
• Reduce unnecessary (and expensive) react updates while changing the coloring. See PR 1075
• Fix a couple of cases where functions were being called with extra (unused) arguments. See PR 1078 & PR 1077

version 2.12.0 - 2020/04/08

• Add a legend to the map! See PR 935
• Improve the animation smoothness, especially for datasets with limited temporal range. See PR 920
• Add Japanese translation See PR 1045
• Reinstate the lang URL query to allow the URL to choose the language.
• Remove unnecessary lodash code from the bundles. See PR 1018
• Update how the Root component is imported. See PR 1029
• Fix errors in the sizing of the map buttons. See PR 1040
• Improve rendering of tree tip labels by only counting the selected (visible) tips. See PR 1043

version 2.11.4 - 2020/04/04

• Temporarily remove SVG gradients in the tree due to bugs in multiple browsers. See PR 1042

version 2.11.3 - 2020/04/02

• Add Portuguese translation. See PR 1017
• Fig bug where some branches would not display on certain browsers. See PR 1022
• Fix bug with selected dates shown when no genomes were selected. See PR 1011
• Show --includeTiming argument when viewing help (--help).
• Add second node version to TravisCI. See PR 1023
• Fix docs typo. See PR 1027

version 2.11.2 - 2020/03/30

• Add French translation - See PR 1020
• Improve rendering of long strain names in strain search - See PR 1026
• Lithuanian translation fixes

version 2.11.1 - 2020/03/28

• Add Lithuanian translation
• Fig bugs in translation strings which contained : or .
• Fix syntax error in docs - See PR 1010

version 2.11.0 - 2020/03/27

• You can now zoom out to the parent clade in the tree by clicking on the basal in-view branch. See PR 1001
• Scroll gestures can now zoom the map. See PR 1002
• Which panels are displayed by default can now be defined by the dataset JSON. See PR 1006
• Mapbox attribution logo added to the map. See PR 1003
• New translations!
  • Russian -- See PR 995 & See PR 1004
  • German -- See PR 996
  • Spanish translation completed
  • Sentence structure improved to facilitate future Japanese translation. See PR 994
• Improvements to contributing documentation. See PR 1000

version 2.10.0 - 2020/03/24

• Tree branches which have an inferred state which differes between parent & child (i.e. different colours) now show a gradient across the branch. See PR 947
• Hovering on a deme in the map now emphasizes the tips in the tree which make up that deme. See PR 940
• Fix multiple bugs related to incorrect rendering of the map when downloading the SVG. See PR 925
• Fix a bug relating to the ordering of legend items. See PR 979.
• Update Spanish locale data (still in a partially complete state). See commit f9c8ad2
• Reorganisation and general improvements to documentation around contributing to auspice development. See PR 978, commit 707f563 and commit 9f002c9
• Fix a bug where the narrative table styling introduced in 2.9.0 were applied outside the narratives.
• Fix all linting errors and warnings (potentially the first time this has happened!)

version 2.9.1 - 2020/03/23

• Bugfix related to the byline for SARS-CoV-2 datasets when viewed on nextstrain.org

version 2.9.0 - 2020/03/23

• Add language support for auspice! Currently we have an incomplete translation of the strings into Spanish, but we can now begin to crowd-source translations. See PR 953
• Add shebang to shell scripts. See PR 962
• Add styling to tables in narratives. See PR 966
• Improve accessiblity of slide-dots in narratives. See PR 972
• Fix typo in readme. See PR 963
• Improve file modes in docs. See PR 964
• Fix broken links in docs. See PR 967
• Linting fixes. See PR 931

version 2.8.1 - 2020/03/20

• Fix bug in dependencies which could prevent auspice from being built

version 2.8.0 - 2020/03/20

• Allow right-to-left text in narratives See PR 960
• Introduce a testing framework. See PR 943
• Modify byline for SARS-CoV-2 datasets when viewed on nextstrain.org

version 2.7.0 - 2020/03/15

• Add axis labels to the tree. See PR 942
• Fix a bug where the map would jump to an incorrect view position in narratives. See PR 950
• Do not display "github.com" in the built-by byline (link is unchanged). See PR 949
• Improve the REAMDE.
• Allow translators to be specified in narratives & translators and authors (and their links) can be set as arrays. See PR 937
• Add documentation about CSV/TSV drag-and-drop functionality

version 2.6.0 - 2020/03/09

• Highlight tips which (partially) match strain search. See PR 930
• Allow HTML tables in narratives (main-auspice-display-markdown). See PR 924
• Add hidden URL query to force open / close state of legend. See PR 923
• Make tree-text unselectable. See PR 922

version 2.5.7 - 2020/03/09

• Allow lat-longs for locations only set on internal nodes.

version 2.5.6 - 2020/03/09

• Fig bug in legend for numerical values (introduced in 2.5.5). See PR 927
• Improve documentation. See PR 919

version 2.5.5 - 2020/03/04

• Improve legend display for long names. See PR 914
• Fix a bug which prevented CSV drag&drop working on Windows machines. See PR 913
• Better display clades with extremely low divergence (i.e. polytomies) See PR 909
• Improved branch labeling display. See PR 908

version 2.5.4 - 2020/02/26

• Improve entropy blending on branches. See PR 898
• Bugfix: temporal scale was poorly displayed when a second tree was displayed ("tangletrees"). See PR 910
• Bugfix: CSV drag-and-drop now works again. See PR 904

version 2.5.3 - 2020/02/12

• Improve how we display mutations to distinguish between gaps & Ns, and to not show undetermined AAs. See PR 895
• Improve mapbox attribution. See PR 894
• Add windows-specific documentation See PR 893

version 2.5.2 - 2020/02/11

• Allow npm scripts to run on windows. See PR 868
• Improve the zoom level for the map when automatically zooming to one (or very few) demes. See PR 891

version 2.5.1 - 2020/02/07

• Allow narrative markdown files to have CRLF line endings.

version 2.5.0 - 2020/02/05

• Add URL query options to facilitate embedding nextstrain via an iframe. See PR 884
  • Sidebar state can be set via JSON & URL query.
  • A special URL query will disable rendering of the footer & header.
• Improve tree & map zooming. See PR 886
  • The map will now automatically zoom upon changes in tree visibility (e.g. filters, time scrubbing, zoom-into-branch) or geographic resolution, unless the map has been interacted with.
  • The tree URL query for specifying which node in the tree is zoomed has been changed to ?label=<labelName>:<labelValue>, and the docs updated accordingly. The old syntax ?clade=<cladeName> will still work and automatically correct to the new syntax.
  • The set of branch labels to be displayed is now customisable.
• Add documentation surrounding auspice view-settings
• Improve text rendering in certain situations when the lato font is not available. See PR 882

version 2.4.1 - 2020/02/01

• Fix two bigs in narrative UI. See PR 881

version 2.4.0 - 2020/01/31

• Implement a new narratives view for mobile displays. See PR 857
• Subsequent map-pages in narratives will reset the zoom if the geo resolution has changed. See PR 866
• Fix narrative progress-bar styling. See PR 875

version 2.3.7 - 2020/01/30

• Fix a number of narrative bugs See PR 865

version 2.3.6 - 2020/01/30

• Improve wording related to reported mutation rates. See PR 860
• Hide tip labels when animating. See PR 859
• Improve sizing of tip-clicked infobox. See PR 862

version 2.3.5 - 2020/01/28

• Fix bug during branch-hover introduced in 2.3.3. See PR 855
• Fix bug related to back-button behavior. See PR 852

version 2.3.4 - 2020/01/28

• Reinstate width prop passed to nav-bar extensions & update documentation. See PR 853

version 2.3.3 - 2020/01/27

• Improved display of divergence values > 0.01 when hovering on a branch
• Modified behavior specifically related to display of nCoV datasets:
  • Accession display modified if the node has the field gisaid_epi_isl See PR 850
  • GISAID attribution added to byline for nextstrain.org/ncov datasets See PR 850

version 2.3.2 - 2020/01/24

• Minor styling changes to: (1) change min map zoom, (2) hide sidebar on GISAID pages and (3) show author in hover box. See PR 849

version 2.3.1 - 2020/01/24

• Improvements to narrative text styling with the intention that narratives are more functional on mobile devices.
• This version introduces experimental support for writing narratives where a page may define a section of markdown to be displayed in the main panel, instead of a tree or map. Documentation is forthcoming.

version 2.3.0 - 2020/01/23

• Improved positioning of temporal grid lines for the phylogeny See PR 846
• Improved browser title & SEO information See PR 845
• Added the nCoV dataset to the get-data script

version 2.2.4 - 2020/01/11

• Fix bug in computing state when nodes lack num_date attributes

version 2.2.3 - 2020/01/06

• Improved display of numerical values in the tip clicked modal. See PR 840
• Fix certain cases where the back button resulted in an inconsistent state being displayed. See PR 841

version 2.2.2 - 2020/01/03

• Remove unnecessary console log statements.

version 2.2.1 - 2020/01/03

• Improve conversion functions to go between numeric & calendar dates. See PR 839

version 2.2.0 - 2019/12/16

• Update datasets fetched via npm run get-data to reflect the move to v2 (unified) JSONs.
• Allow datasets to define their own footer text via a string of markdown formatted text. Harcoded footers are now only used on the nextstrain.org domain and will be removed as they are incorporated into their respective builds. See PR 834 and augur PR 423.
• Copy contributing docs into a top-level CONTRIBUTING.md file. See PR 833.
• Include fonts & other CSS assets in the auspice build to improve the behavior of auspice when offline. See PR 826.
• UI improvement: Display build source (if defined via JSON.meta.build_url), GitHub avatar (if build source is a GitHub repo) and maintainers as a byline under the title. See PR 821.
• Performance improvement: Stream (v2) datasets between auspice server & auspice client. See PR 825.

version 2.1.0 - 2019/11/15

• Added support in the narratives to navigate via arrow keys. In addition to improved UI, this allows decktape to convert narratives to PDFs, and a guide has been added to the auspice docs for this. See PR 824.
• Added GISAID and GISRS logos to the footer for flu datasets. See PR 822.
• Bugfix: Fix the broken implementation of the "serverAddress" client customisation and update the relevant documentation
• Bugfix: Colorings in v2 JSONs were not being correctly ordered. They now maintain the order specified in the JSON. The ordering of v1 JSONs is still sorted, as per auspice v1 behavior. See PR 823.
• Bugifx: The "download author data (TSV)" button no longer appears if no author information is defined in the dataset.
• Minor auspice docs improvements.

version 2.0.3 - 2019/11/06

Bugfix: Correctly handle the url and accession of strains both in the tip-clicked info box and in the strain TSV download. See PR 819.

version 2.0.2 - 2019/10/30

Bugfix: The ability to download per-strain metadata as a TSV file is now working again. See issue #816.

version 2.0.1 - 2019/10/25

Improved handling of traits associated with tips:

• Added documentation around how auspice displays missing or unknown trait values
• It a trait is defined as a coloring, then use the provided title in the tree info boxes
• Improve logic as to whether a value is inferred (i.e. display associate confidence) or known. See this issue for more details.

Fix a bug where two trees couldn't be colored by date.

version 2.0.0 - 2019/10/21

Please see the release notes for a full list of features and changes associated with auspice's v2 release. Associated with the v2 release are much improved documentation at nextstrain.github.io/auspice

Here is a summary of the main changes:

• Pie charts to represent discrete variables on a map
• New dataset JSON format:
  • Strings parsed unchanged
  • Both metadata and tree data in a single JSON
  • Gene / Genome definitions are now in GFF format
  • Changes to how node data is stored
  • Multiple maintainers
  • Continous, Categorical, Ordinal, and Boolean Color Scales
• More information in tree info boxes
• Display of second trees
• Display better dates on the tree axis
• Map "reset zoom" button zooms to include all demes
• Consistent colouring of missing data in the tree
• Removal of Twitter & Google Analytics
• Improvements in the entropy panel
• Auspice responds to server redirects for datasets
• Importing (server) code from Auspice
• New Auspice subcommand: auspice convert
• Ability to show a "build" source URL in the sidebar
• auspice view uses a custom Auspice client if present

version 1.39.1 - 2019/10/21

This release marks the final v1 release before auspice v2 is released. Auspice v1 may still receive bug-fixes, and will be npm-tagged with "version1" so that it may be installed via npm install --global auspice@version1.

• Minor dependency version upgrades.

version 1.39.0 - 2019/09/12

• Slight changes to the auspice splash page wording to remove the word "Locally".
• getDataset API calls may now return code 204 ("no content") resulting in the auspice splash page displayed without an error message.
• Default styling of narrative text much improved.

version 1.38.2 - 2019/09/06

• Fix footer for INRB Ebola builds.

version 1.38.1 - 2019/09/06

• Update footer for INRB Ebola builds. cd

version 1.38.0 - 2019/08/29

• Add support for frequency projections. See PR 777
• Local Auspice servers listen on only localhost by default instead of all interfaces. See PR 781
• update dependencies

version 1.37.5 - 2019/08/09

• Allo increased zoom levels in map. [See PR 765](nextstrain#765

version 1.37.4 - 2019/08/04

• Improved layout of unrooted trees when zoomed into a clade. See PR 754
• Remove link to "deprecated" nextflu.org site from flu page footer.

version 1.37.3 - 2019/07/29

• Reinstate github dataset link in sidebar for community builds

version 1.37.2 - 2019/07/20

• Fix two bugs related to (a) "root" appearing as the selected clade in the URL and (b) applying filtering would remove the selected clade from the URL. See issue #744 and PR 746.
• Fix bug where auspice would crash if the JSON contained an "annotation" property but not a "annotation.nuc" key. See issue #732
• The Map panel title is now "Grography" when transmissions are not inferred. See issue #743

version 1.37.1 - 2019/07/13

• Fig a bug where "unknown" values of a discrete scales (e.g. "?") could be given a colour. They are now grey.

version 1.37.0 - 2019/07/09

• Fix two bugs relating to narratives and the Map component. See PR 736
• Improve logic behind when to display tip labels on the tree

version 1.36.6 - 2019/05/18

• Improve minor axis tick spacing on tree. See PR 725
• Entropy calculations ignore ambiguous bases See PR 723

version 1.36.5 - 2019/04/17

• Fix a bug in the initial rendering of the date slider. See PR 713

version 1.36.4 - 2019/03/16

• Fix map deme border coloring.

version 1.36.3 - 2019/03/11

• Various map improvements, including transmission ribbons, improved initial map bounds and improved deme circle sizing. See PR 712
• Check mutation type against tree. (See PR 709)[nextstrain#709]

version 1.36.2 - 2019/03/04

• Update footer information. Don't display "live" footers for "community" URLs.

version 1.36.1 - 2019/02/27

• Update npm packages identified as security vulnerabilities
• Fixes a bug (only in v1.36.0) where, for some datasets, interacting with the tree would cause the app to crash. Issue 708
• auspice build now exits (with non-zero exit code) if there are errors during webpack bundling

version 1.36.0 - 2019/02/25

• Improve app load times using code splitting. See PR 701

version 1.35.5 - 2019/02/08

• Add acknowledgements to mumps page.
• Preserve URL during 404. Issue #700

version 1.35.4 - 2019/01/28

• Restore download modal functionality. Issue 699

version 1.35.3 - 2019/01/25

• Show useful help message if port is in use. See PR 694
• Fixed a bug where URL query strings may become corrupted in certain cases. See PR 695
• Restore (deprecated) "npm run {server,dev}" commands. See PR 692
• Fix broken links in documentation. See PR 690
• Update WNV footer text

version 1.35.2 - 2019/01/16

• Auspice is now extensible (at build stage), allowing customisations and serverless builds. See PR 688
• Documentation is now available via github pages -- nextstrain.github.io/auspice

version 1.34.4 - 2019/01/15

• Update mumps footer

version 1.34.3 - 2018/12/18

• Don't display deme circle if lat/long is absent

version 1.34.2 - 2018/12/05

• Update mumps footer
• Modify the casing of how labels are displayed See PR 685

version 1.34.1 - 2018/11/29

• Small change to make the 'Second Tree' option appear when virus segments are named according to "segment1", "segment2" etcetera. See PR 684

version 1.34.0 - 2018/11/19

• Community builds are now sourced from githubusercontent, which is the official source for "raw" files from GitHub. PR 682

version 1.33.0 - 2018/11/18

• Gene names can now include - and _, as well as code improvements to genotype encoding/decoding -- PR 681

version 1.32.0 - 2018/11/02

• Allow hidden property on tree nodes -- PR 676
• Update packages & package.json metadata -- PR 677 PR 678 PR 679
• Restore hot-reloading ability for development (above PRs)

version 1.31.0 - 2018/10/29

• Allow time-only trees or div-only trees -- PR 670
• Minor fixes to handle trees with missing data -- PR 673

version 1.30.3 - 2018/09/19

• Colours were sometimes inconsistent when two trees were displayed -- PR 665
• Clicking on a tip while two trees were displayed no longer causes a crash -- PR 666

version 1.30.2 - 2018/09/07

• Publish the package to the npm registry from the release branch automatically. [#660, #662]
• Fix inability to run npm locally introduced by repo's .npmrc file. [#661]

version 1.30.1 - 2018/09/05

version 1.30.0 - 2018/09/05

• Auspice is now globally installable and published as a npm package npmjs.com/package/auspice
• AA entropy calculation bug fixed - PR 657
• Narrative scroll bars are fixed for Linux & Windows browsers - PR 653
• Tree legend placement improved - PR 650
• npm run start is no longer deprecated

version 1.29.0 - 2018/08/31

• The visibility of nodes on the tree now more accurately reflects the selected date range - PR 644
• Info text is easier to read & the date range reflects the genomes in view - PR 639

Narrative improvements

• Toggle between narrative & interactive mode is much clearer - PR 648
• URL queries with no clade set zoom to the entire tree - PR 644

version 1.28.0 - 2018/08/25

• Narratives -- see nextstrain.org/docs/visualisation/narratives for documentation.
• Time slicing & non-highlighted branches are now displayed in a cleaner fashion - PR 638
• Selected clades (i.e. the tree has been zoomed) are now part of URL state - PR 633

version 1.27.1 - 2018/08/24

• Fixed broken navigation links
• Entropy zooming bug fixed - PR 637

version 1.27.0 - 2018/08/20

• Saved SVGs now include two trees (if displayed) - PR 630

version 1.26.0 - 2018/08/20

• Entropy panel zoom changes are now reflected in URL state - PR 626

version 1.25.2 - 2018/08/17

• Negative dates (BCE) are now handled correctly - PR 627
• Small entropy zooming fixes - PR 624
• Bugfix to prevent the grid being drawn over the branches / tips in some situations - PR 629
• Transmissions which involve demes without lat/longs now show an error notification - PR 608

version 1.25.1 - 2018/08/10

• Small fixes to entropy zooming behaviour
• Gaps are not counted in the entropy calculations & are not displayed in the info panel pop up

version 1.25.0 - 2018/08/09

• New Entropy panel zooming functionality - PR 609

version 1.24.1 - 2018/08/08

• Upgrade dependencies
• Bugfix when changing between staging datasets - issue 618

version 1.24.0 - 2018/08/05

• Tree grid improvements - PR 610
  • Allow negative (i.e. BCE) dates
  • Display y-dates and horizontal lines in the clock layout view
  • Improved spacing between grid points
• SVG elements in the DOM are now in named groups which improves debugging and prevents incorrect-layering bugs. PR 612
• Fixed a bug where the available datasets (dropdowns in sidebar) contained invalid values PR 614
• Community sourced datasets (nextstrain.org/community/...) display a link to the github repo in the sidebar PR 615
• Since v1.22.3 changing datasets preserved the URL queries (e.g. ?l=radial). A number of bugs relating to this have been fixed, where these queries were no longer valid for the new dataset. This also fixed potential issues related to loading datasets where the URL queries were invalid. PR 613

version 1.23.2 - 2018/07/30

• Increase the padding when displaying two panels side by side to avoid bugs on different browsers / OSs. issue 574

version 1.23.1 - 2018/07/30

• Improved the alignment of branch labels for the second tree

version 1.23.0 - 2018/07/28

• The server no longer needs to be transpiled
• The interaction between data sources (local / staging / live) has been changed.
  • The first part of the URL now defines the source, e.g. /flu is live, /local/flu is local, /staging/flu...
  • Accordingly, npm run server.js localData no longer has the effect it used to!
  • Github committed JSONs are now accessible via /community/orgName/repoName (slightly experimental and subject to change)
• JSONs are now delivered to the client using compression (when available)
• Frequency JSONs are only fetched when the frequency panel is specified (in the meta JSON)
• The server combines the tree & meta JSONs into a single "unified" JSON, in preparation for a move to v2.0 JSONs.
• Manifest files / parsing have been moved from the server
• Various improvements to the narratives (still experimental and the API is subject to change)
• Second trees are specified by /na:ha/ rather than /na/...?tt=ha. The old syntax is still supported for backwards compatibility.

version 1.22.3 - 2018/07/19

• Trigger Docker Hub automated build to rebuild via Travis CI when master branch is pushed and tests are successful
• Simplify counting of traits across tree
• Improve README
• Remove Electron
• Restored the ability to run the non-dev server with local data PR 589

version 1.22.2 - 2018/07/10

• Bugfix in tip attribute counting algorithm

version 1.22.1 - 2018/07/09

• Legend items no longer include duplicates, and include month for dates within the past 10 years - thanks @emmahodcroftPR 592
• Bugfix related to colorBy values only specified on internal nodes issue 593

version 1.22.0 - 2018/07/03

• Auspice can now run with an incomplete metadata file, or even without a metadata file at all! PR 586
• Download modal reinstated PR 587
  • Improved styling
  • All panes now saved to a single SVG
  • Map panning SVG-save bugs (mostly) fixed
  • TSV used instead of CSV
• Fix WNV colorBy link in footer -- issue 590

version 1.21.3 - 2018/06/27

• Show tree titles (e.g. NA) when two trees are displayed
• Multi-part datasets (e.g. flu/seasonal/h3n2...) which are not in the manifest file can now be loaded; various bugs fixed for running locally without a manifest file.
• Other minor bugfixes & package upgrades

version 1.21.2 - 2018/06/07

• Disable Untangling

version 1.21.1 - 2018/06/04

• Narratives are now sourced from the static github repo

version 1.21.0 - 2018/06/01

• Untangling via a simple algorithm upon 2nd tree load
• Segment names displayed above trees (if 2 trees)
• Fix hover-info-box date bug -- issue 572

version 1.20.3 - 2018/05/30

• Narratives now accessed via /narratives/... URLs
• App now works without needing a manifest file (but the datasets dropdown needs it)
• Initial load simplified
• Sidebar doesn't appear until the data is ready to be displayed

version 1.20.2 - 2018/05/21

• Changes to the frequencies threshold

version 1.20.1 - 2018/05/21

• Changes to the frequencies threshold
• Narratives restored

version 1.20.0 - 2018/05/15

Auspice is now served via the nextstrain.org server together with the static (gatsbyjs) site

• Changes to the server code organisation
• Static content removed
• New splash page listing the (should only be accessed from local instances or 404s, live site splash is via the static site)
• Improved page navigation API
• Travis CI 🎉
• Auspice version is displayed in the footer
• Release script modified (Travis CI listens to release and pushes a successful build to S3 which is fetched by the live server)

version 1.19.1 - 2018/05/09

• Fixed a bug where proteins starting with a number (e.g. 2K) were assumed to be nucleotide genotypes.

version 1.19.0 - 2018/05/09

• Improved sidebar styling on both mobile & desktop
• Reset layout button doesn't re-instantiate the PhyloTree object, rather it resets the branch thicknesses & sets the whole tree to be in view
• Padding improvements - tip labels are now visible, and small clades render better.
• Tip names now shown for up to 100 taxa
• Branch thickness restored -- issue 544
• Tree panning has been removed (we no longer use react-svg-pan-zoom)

version 1.18.10 - 2018/05/07

• Separate Nucleotide mutations from gaps / Ns in info-box - thanks @emmahodcroft PR 552
• Frequencies y-axis is no longer rounded to the nearest 0.05

version 1.18.9 - 2018/05/03

• update flu footer
• start using travis CI

version 1.18.8 - 2018/05/02

• temporary fix for map transmissionIndices errors (bug still exists, issue 547)

version 1.18.7 - 2018/05/02

• Fix frequencies panel x-axis bug
• Linting
• Minor style changes

version 1.18.6 - 2018/04/30

• update WNV footer

version 1.18.5 - 2018/04/27

• update WNV footer

version 1.18.4 - 2018/04/26

• Use exponential notation for the clock rate

version 1.18.3 - 2018/04/23

• Updated the footer for LASV & WNV

version 1.18.2 - 2018/04/16

• LBI color scale domain is [0, 0.7] Issue 541
• Fix bug with antigenic advance & frequencies Issue 540
• Hovering over a tree legend value of zero now correctly highlights matching tips
• Undefined color traits are now grey on a discrete scale
• Removed all references to node.attr.strain (tree JSON) and seq_author_map (meta JSON)

version 1.18.1 - 2018/04/15

• Make date slider spacing consistent between animation and drag

version 1.18.0 - 2018/04/14

• Tanglegrams enabled! (bugfixes & reinstate controls dropdown)
• Status pages: nextstrain.org/status & nextstrain.org/status/staging
• Narrative files are sourced from nextstrain.org repository

version 1.17.4 - 2018/04/10

• Updated LASV footer

version 1.17.3 - 2018/04/04

• Allowed arbitrary user manifests to be served
• Changed how the tanglegram updates, so that it is now triggered straight after the trees update.
• Updated the files downloaded from get_data.sh
• Add lassa (LASV) footer acknowledgments.

version 1.17.2 - 2018/04/02

• Job ad on splash page.

version 1.17.1 - 2018/03/28

• Fix tree SVG bug Issue 535

version 1.17.0 - 2018/03/26

Narrative

• Now exposed via a "hidden" URL query. E.g. flu/h3n2/3y?n=1
• Frequencies added to narrative
• block in focus is part of the URL query, and can be reloaded via the URL

Second Tree / Tanglegram

• Second tree can be loaded via a URL (e.g. ?tt=na). Sidebar dropdown currently disabled.
• In this mode, trees are forced to be rectangular, and the map & frequencies are not displayed.
• Tanglegram exists, but no untangling (yet)
• Bugs still exist (which is why the sidebar has been disabled)

Internals

• All JSONs (incl. frequencies, narrative) are loaded within a single Promise & dispatch
• phylotree.change() only ever called once, and always in componentDidUpdate (fixes bugs where it fired in both CWRP and CDU)
• old & deprecated code removed

version 1.16.5 - 2018/03/26

• Authors filter is now an explicit setting in the JSONs PR 532

version 1.16.4 - 2018/03/22

• Flu footer updated
• Fix bug in genotype colouring PR 531
• Adjust vaccine cross styling & remove dashed line PR 529

version 1.16.3 - 2018/03/21

• Flu footer updated

version 1.16.2 - 2018/03/21

• Add redirect of www.nextstrain.org to nextstrain.org via express middleware PR 528

version 1.16.1 - 2018/03/16

• Fix bug in the color scales where clades were coloured white after switching trees.

version 1.16.0 - 2018/03/16

Browser support

• Now works on Internet Explorer 11 (tested on windows 7)
• Grid layout issue fixed for Firefox on linux/windows
• Embedding Nextstrain in an iFrame works - see /scripts/gisaid_iframe.html

version 1.15.1 - 2018/03/14

• Fix Firefox branch / tip hover bug Issue 525

version 1.15.0 - 2018/03/12

• Multiple genotypes (for the same amino acid) by typing in multiple comma separated AA/nuc positions. PR 523.

version 1.14.4 - 2018/03/05

• Restore staging server toggle issue 514

version 1.14.3 - 2018/03/01

• Bug fix where tip colours reverted to their initial colours after a layout change. issue 519

version 1.14.2 - 2018/02/28

• PR 518
  • Frequency y-axis is now dynamic
  • Frequency text box is more readable
  • Frequency normalisation has been removed

version 1.14.1 - 2018/02/27

• Style tip stroke separately from branch stroke (node.stroke replaced with node.branchStroke & node.tipStroke)

version 1.14.0 - 2018/02/27

Features

• Strain search (using awesomplete). This highlights the path to a single tip and increases the tip radius. Strain is stored in the URL query (s=...) and can be restored via URL. Selected strain also appears in the info panel (top of screen).
• Amino acid branch labels (for every tree) as well as clade labels if specified by the clade_annotation attribute. AA labels are shown where the descendent visible tips account for more than 5% of the total visible tips (same as nextflu). Clade labels are always displayed.
• Default geneotype gene is now HA1 if available (previously nucleotide).
• ColorBy ordering (sidebar dropdown) is now ordered (via an array in globals.js)

Internals

• The JSON processing on initial load has been shifted from the reducers to a single action - fewer dispatches, fewer potential bugs, faster code.
• Frequencies are initialised in a single action (previously 2).
• tip-frequencies are now downloaded via get_data.sh
• Frequency actions are not dispatched unless the frequency panel is loaded.

version 1.13.2 - 2018/02/26

• Improve consistency of panel controls
• Show unassigned in tree legend (if applicable)

version 1.13.1 - 2018/02/26

• Tree button "reset layout" now at top right

version 1.13.0 - 2018/02/26

Features

• Frequencies are now displayed via a stream graph panel - see PR 497. These require the fetching of a separate tip-frequencies JSON, and must be specified in the panels array of the meta.JSON.
• "Panels To Display" toggles in the sidebar allow customisation of the display, and this is reflected in the URL.
• The + - buttons in the tree have been replaced by a "reset tree" button. This resets the bounds to the entire tree & completely re-renders the tree (filters are maintained). Pan behaviour is unchanged.

Internals

• React-PhyloTree interface is completely rewritten to use phylotree.change() - see PR 501 for the API. The new interface is both easier to understand and quicker.
• changePageQuery (used for changing narrative blocks) is now a single action
• Ongoing narrative work (still disabled).
• React sidebar has been removed (no UI changes).

version 1.12.0 - 2018/02/14

Features

• Vaccine strains are shown at their use date (in temporal trees), with dotted lines connecting them to their tips (representing collection date) (PR 498)

Internals

• updateGeometryFade uses counters to know when transitions are finished rather than setTimeout

version 1.11.0 - 2018/02/05

Features

• Vaccine strains are now displayed if they are specified in metaJSON.vaccine_choices (PR 490)

Internals

• Tree components and PhyloTree have been reorganized (in src/components/tree) and the syntax improved (PR 493)
• Upgraded to React 16, as well as upgrading redux & react-svg-pan-zoom (PR 494)

version 1.10.0 - 2018/02/05

Features

• Local Branching Index (LBI) coloring can be calculated in Auspice (code identical to nextflu) if specified in color_options (meta JSON) (PR 491)

Internals

• get_data.sh script updated to no longer download sequences & entropy JSONs
• action logging middleware available for debugging / development

version 1.9.0 - 2018/01/30

Animation

• Animations can now loop! This is selected via a toggle in the sidebar.
• While animating, the URL displays information which defines the animation (bounds, looping, cumulative, speed). This allows the animation to start automatically by linking to this URL.
• The code for the animation (i.e. the setInterval code) has been moved out of Map and into a separate AnimationController component.
• Animation is stopped & started by examining redux state, rather than with imperative controls.

misc

• The narrative machinery has been moved forward, but this functionality is still disabled and not present in production code.
• The (rather expensive) calendarToNumeric calculations have become part of state.controls so that components no longer have to calculate them from the string form.

version 1.8.0 - 2018/01/18

entropy calculated via tree

• The entropy panel data is now computed within Auspice by examining mutations throughout the tree, and is throttled to improve speed under load.
• Both entropy and number of mutations are available via a toggle similar to AA/NT
• This results in entropy.JSON no longer being fetched.
• The entropy data is stored in redux state rather than the react component
• The D3 code has been reorganised
• Note that the entropy values are slightly different to those exported by Augur in some situations - see nextstrain#478 (comment)

genotype calculated via tree

• This results in sequences.JSON no longer being fetched.
• Augur was updated to export annotations which are needed for entropy gene display.

middleware / react router

• All changes to the URL are now performed via middleware rather than side-effects within the action definition.
• React router has been removed
• Browser back/forward is detected via window.addEventListener('popstate', this.onURLChanged) which also fires on initial page load.
• Pages are selected via the <PageSelect> component.

other

• The number of proteins displayed while hovering over a branch has been limited to 7 (issue #484)
• The presence of author data is checked before display (issue #488)
• This changelog has been created and a step in the releaseNewVersion script added to prepend the version number upon release.

version 1.7.2 - 2018/1/4

Narrative / situational report

• Functionality has been added, but is currently disabled via a flag in globals.js.
• This is currently rendered in a right-hand sidebar. This feature is not yet complete.

URL queries

• The following state has been added to the URL query:
  • filters, e.g. f_authors=Tong_et_al,Capobianchi_et_al&f_division=kerouane
  • genotype URLs (these were previously set as the URL but not parsed)
  • panel layout (grid/full)
• A number of bugs regarding URL query state parsing (esp with genotype colorBys) have been fixed.

version 1.7.1 - 2017/10/31

• Added mumps acknowledgment

version 1.7.0 - 2017/10/17

version - 2018/01/18