1 | ---
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2 | title: Changelog
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3 | ---
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4 |
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5 | ## version 2.5.5 - 2020/03/04
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6 |
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7 |
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8 | * Improve legend display for long names. [See PR 914](https://github.com/nextstrain/auspice/pull/914)
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9 | * Fix a bug which prevented CSV drag&drop working on Windows machines. [See PR 913](https://github.com/nextstrain/auspice/pull/913)
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10 | * Better display clades with extremely low divergence (i.e. polytomies) [See PR 909](https://github.com/nextstrain/auspice/pull/909)
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11 | * Improved branch labeling display. [See PR 908](https://github.com/nextstrain/auspice/pull/908)
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12 |
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13 |
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14 | ## version 2.5.4 - 2020/02/26
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15 | * Improve entropy blending on branches. [See PR 898](https://github.com/nextstrain/auspice/pull/898)
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16 | * Bugfix: temporal scale was poorly displayed when a second tree was displayed ("tangletrees"). [See PR 910](https://github.com/nextstrain/auspice/pull/910)
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17 | * Bugfix: CSV drag-and-drop now works again. [See PR 904](https://github.com/nextstrain/auspice/pull/904)
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18 |
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19 |
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20 | ## version 2.5.3 - 2020/02/12
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21 | * Improve how we display mutations to distinguish between gaps & Ns, and to not show undetermined AAs. [See PR 895](https://github.com/nextstrain/auspice/pull/895)
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22 | * Improve mapbox attribution. [See PR 894](https://github.com/nextstrain/auspice/pull/894)
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23 | * Add windows-specific documentation [See PR 893](https://github.com/nextstrain/auspice/pull/893)
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24 |
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25 | ## version 2.5.2 - 2020/02/11
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26 | * Allow npm scripts to run on windows. [See PR 868](https://github.com/nextstrain/auspice/pull/868)
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27 | * Improve the zoom level for the map when automatically zooming to one (or very few) demes. [See PR 891](https://github.com/nextstrain/auspice/pull/891)
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28 |
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29 | ## version 2.5.1 - 2020/02/07
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30 | * Allow narrative markdown files to have CRLF line endings.
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31 |
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32 | ## version 2.5.0 - 2020/02/05
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33 | * Add URL query options to facilitate embedding nextstrain via an iframe. [See PR 884](https://github.com/nextstrain/auspice/pull/884)
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34 | * Sidebar state can be set via JSON & URL query.
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35 | * A special URL query will disable rendering of the footer & header.
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36 | * Improve tree & map zooming. [See PR 886](https://github.com/nextstrain/auspice/pull/886)
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37 | * 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.
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38 | * 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.
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39 | * The set of branch labels to be displayed is now customisable.
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40 | * Add documentation surrounding auspice view-settings
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41 | * Improve text rendering in certain situations when the lato font is not available. [See PR 882](https://github.com/nextstrain/auspice/pull/882)
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42 |
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43 | ## version 2.4.1 - 2020/02/01
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44 | * Fix two bigs in narrative UI. [See PR 881](https://github.com/nextstrain/auspice/pull/881)
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45 |
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46 | ## version 2.4.0 - 2020/01/31
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47 | * Implement a new narratives view for mobile displays. [See PR 857](https://github.com/nextstrain/auspice/pull/857)
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48 | * Subsequent map-pages in narratives will reset the zoom if the geo resolution has changed. [See PR 866](https://github.com/nextstrain/auspice/pull/866)
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49 | * Fix narrative progress-bar styling. [See PR 875](https://github.com/nextstrain/auspice/pull/875)
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50 |
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51 | ## version 2.3.7 - 2020/01/30
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52 | * Fix a number of narrative bugs [See PR 865](https://github.com/nextstrain/auspice/pull/865)
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53 |
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54 | ## version 2.3.6 - 2020/01/30
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55 | * Improve wording related to reported mutation rates. [See PR 860](https://github.com/nextstrain/auspice/pull/860)
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56 | * Hide tip labels when animating. [See PR 859](https://github.com/nextstrain/auspice/pull/859)
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57 | * Improve sizing of tip-clicked infobox. [See PR 862](https://github.com/nextstrain/auspice/pull/862)
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58 |
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59 | ## version 2.3.5 - 2020/01/28
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60 | * Fix bug during branch-hover introduced in 2.3.3. [See PR 855](https://github.com/nextstrain/auspice/pull/855)
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61 | * Fix bug related to back-button behavior. [See PR 852](https://github.com/nextstrain/auspice/pull/852)
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62 |
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63 | ## version 2.3.4 - 2020/01/28
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64 | * Reinstate `width` prop passed to nav-bar extensions & update documentation. [See PR 853](https://github.com/nextstrain/auspice/pull/853)
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65 |
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66 | ## version 2.3.3 - 2020/01/27
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67 | * Improved display of divergence values > 0.01 when hovering on a branch
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68 | * Modified behavior specifically related to display of nCoV datasets:
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69 | * Accession display modified if the node has the field `gisaid_epi_isl` [See PR 850](https://github.com/nextstrain/auspice/pull/850)
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70 | * GISAID attribution added to byline for nextstrain.org/ncov datasets [See PR 850](https://github.com/nextstrain/auspice/pull/850)
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71 |
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72 | ## version 2.3.2 - 2020/01/24
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73 | * 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](https://github.com/nextstrain/auspice/pull/849)
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74 |
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75 | ## version 2.3.1 - 2020/01/24
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76 | * Improvements to narrative text styling with the intention that narratives are more functional on mobile devices.
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77 | * 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.
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78 |
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79 | ## version 2.3.0 - 2020/01/23
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80 | * Improved positioning of temporal grid lines for the phylogeny [See PR 846](https://github.com/nextstrain/auspice/pull/846)
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81 | * Improved browser title & SEO information [See PR 845](https://github.com/nextstrain/auspice/pull/845)
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82 | * Added the nCoV dataset to the get-data script
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83 |
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84 | ## version 2.2.4 - 2020/01/11
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85 | * Fix bug in computing state when nodes lack `num_date` attributes
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86 |
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87 | ## version 2.2.3 - 2020/01/06
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88 | * Improved display of numerical values in the tip clicked modal. [See PR 840](https://github.com/nextstrain/auspice/pull/840)
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89 | * Fix certain cases where the back button resulted in an inconsistent state being displayed. [See PR 841](https://github.com/nextstrain/auspice/pull/841)
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90 |
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91 | ## version 2.2.2 - 2020/01/03
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92 | * Remove unnecessary console log statements.
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93 |
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94 | ## version 2.2.1 - 2020/01/03
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95 | * Improve conversion functions to go between numeric & calendar dates. [See PR 839](https://github.com/nextstrain/auspice/pull/839)
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96 |
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97 | ## version 2.2.0 - 2019/12/16
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98 | * Update datasets fetched via `npm run get-data` to reflect the move to v2 (unified) JSONs.
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99 | * 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](https://github.com/nextstrain/auspice/pull/834) and [augur PR 423](https://github.com/nextstrain/augur/pull/423).
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100 | * Copy contributing docs into a top-level CONTRIBUTING.md file. [See PR 833](https://github.com/nextstrain/auspice/pull/833).
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101 | * Include fonts & other CSS assets in the auspice build to improve the behavior of auspice when offline. [See PR 826](https://github.com/nextstrain/auspice/pull/826).
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102 | * 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](https://github.com/nextstrain/auspice/pull/821).
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103 | * Performance improvement: Stream (v2) datasets between auspice server & auspice client. [See PR 825](https://github.com/nextstrain/auspice/pull/825).
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104 |
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105 | ## version 2.1.0 - 2019/11/15
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106 | * 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.
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107 | [See PR 824](https://github.com/nextstrain/auspice/pull/824).
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108 | * Added GISAID and GISRS logos to the footer for flu datasets.
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109 | [See PR 822](https://github.com/nextstrain/auspice/pull/822).
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110 | * Bugfix: Fix the broken implementation of the "serverAddress" client customisation and update [the relevant documentation](https://nextstrain.github.io/auspice/customise-client/api)
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111 | * Bugfix: Colorings in v2 JSONs were not being correctly ordered. They now maintain the order specified in the JSON.
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112 | The ordering of v1 JSONs is still sorted, as per auspice v1 behavior.
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113 | [See PR 823](https://github.com/nextstrain/auspice/pull/823).
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114 | * Bugifx: The "download author data (TSV)" button no longer appears if no author information is defined in the dataset.
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115 | * Minor auspice docs improvements.
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116 |
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117 | ## version 2.0.3 - 2019/11/06
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118 | 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](https://github.com/nextstrain/auspice/pull/819).
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119 |
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120 | ## version 2.0.2 - 2019/10/30
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121 | Bugfix: The ability to download per-strain metadata as a TSV file is now working again.
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122 | See [issue #816](https://github.com/nextstrain/auspice/issues/816).
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123 |
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124 | ## version 2.0.1 - 2019/10/25
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125 | Improved handling of traits associated with tips:
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126 | * Added documentation around how auspice displays missing or unknown trait values
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127 | * It a trait is defined as a coloring, then use the provided title in the tree info boxes
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128 | * Improve logic as to whether a value is inferred (i.e. display associate confidence) or known. See [this issue](https://github.com/nextstrain/augur/issues/386) for more details.
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129 |
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130 | Fix a bug where two trees couldn't be colored by date.
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131 |
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132 | ## version 2.0.0 - 2019/10/21
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133 |
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134 | Please see the [release notes](https://nextstrain.github.io/auspice/releases/v2) for a full list of features and changes associated with auspice's v2 release.
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135 | Associated with the v2 release are much improved documentation at [nextstrain.github.io/auspice](https://nextstrain.github.io/auspice)
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136 |
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137 | Here is a summary of the main changes:
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138 |
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139 | * Pie charts to represent discrete variables on a map
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140 | * New dataset JSON format:
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141 | * Strings parsed unchanged
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142 | * Both metadata and tree data in a single JSON
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143 | * Gene / Genome definitions are now in GFF format
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144 | * Changes to how node data is stored
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145 | * Multiple maintainers
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146 | * Continous, Categorical, Ordinal, and Boolean Color Scales
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147 | * More information in tree info boxes
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148 | * Display of second trees
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149 | * Display better dates on the tree axis
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150 | * Map "reset zoom" button zooms to include all demes
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151 | * Consistent colouring of missing data in the tree
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152 | * Removal of Twitter & Google Analytics
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153 | * Improvements in the entropy panel
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154 | * Auspice responds to server redirects for datasets
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155 | * Importing (server) code from Auspice
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156 | * New Auspice subcommand: `auspice convert`
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157 | * Ability to show a "build" source URL in the sidebar
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158 | * `auspice view` uses a custom Auspice client if present
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159 |
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160 | ## version 1.39.1 - 2019/10/21
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161 |
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162 | This release marks the final v1 release before auspice v2 is released.
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163 | Auspice v1 may still receive bug-fixes, and will be [npm-tagged](https://docs.npmjs.com/cli/dist-tag) with "version1" so that it may be installed via `npm install --global auspice@version1`.
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164 |
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165 | * Minor dependency version upgrades.
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166 |
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167 | ## version 1.39.0 - 2019/09/12
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168 | * Slight changes to the auspice splash page wording to remove the word "Locally".
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169 | * `getDataset` API calls may now return code 204 ("no content") resulting in the auspice splash page displayed without an error message.
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170 | * Default styling of narrative text much improved.
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171 |
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172 |
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173 | ## version 1.38.2 - 2019/09/06
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174 |
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175 | * Fix footer for INRB Ebola builds.
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176 |
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177 | ## version 1.38.1 - 2019/09/06
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178 |
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179 | * Update footer for INRB Ebola builds.
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180 | cd
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181 | ## version 1.38.0 - 2019/08/29
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182 |
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183 | * Add support for frequency projections. [See PR 777](https://github.com/nextstrain/auspice/pull/777)
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184 | * Local Auspice servers listen on only localhost by default instead of all interfaces. [See PR 781](https://github.com/nextstrain/auspice/pull/781)
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185 | * update dependencies
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186 |
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187 |
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188 | ## version 1.37.5 - 2019/08/09
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189 | * Allo increased zoom levels in map. [See PR 765](https://github.com/nextstrain/auspice/pull/765
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190 |
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191 | ## version 1.37.4 - 2019/08/04
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192 | * Improved layout of unrooted trees when zoomed into a clade. [See PR 754](https://github.com/nextstrain/auspice/pull/754)
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193 | * Remove link to "deprecated" nextflu.org site from flu page footer.
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194 |
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195 | ## version 1.37.3 - 2019/07/29
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196 | * Reinstate github dataset link in sidebar for community builds
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197 |
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198 | ## version 1.37.2 - 2019/07/20
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199 | * 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](https://github.com/nextstrain/auspice/issues/744) and [PR 746](https://github.com/nextstrain/auspice/pull/746).
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200 | * Fix bug where auspice would crash if the JSON contained an "annotation" property but not a "annotation.nuc" key. See [issue #732](https://github.com/nextstrain/auspice/issues/732)
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201 | * The Map panel title is now "Grography" when transmissions are not inferred. See [issue #743](https://github.com/nextstrain/auspice/issues/743)
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202 |
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203 | ## version 1.37.1 - 2019/07/13
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204 | * Fig a bug where "unknown" values of a discrete scales (e.g. "?") could be given a colour. They are now grey.
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205 |
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206 | ## version 1.37.0 - 2019/07/09
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207 | * Fix two bugs relating to narratives and the Map component. [See PR 736](https://github.com/nextstrain/auspice/pull/736)
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208 | * Improve logic behind when to display tip labels on the tree
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209 |
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210 | ## version 1.36.6 - 2019/05/18
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211 | * Improve minor axis tick spacing on tree. [See PR 725](https://github.com/nextstrain/auspice/pull/725)
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212 | * Entropy calculations ignore ambiguous bases [See PR 723](https://github.com/nextstrain/auspice/pull/723)
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213 |
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214 |
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215 | ## version 1.36.5 - 2019/04/17
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216 | * Fix a bug in the initial rendering of the date slider. [See PR 713](https://github.com/nextstrain/auspice/pull/713)
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217 |
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218 | ## version 1.36.4 - 2019/03/16
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219 | * Fix map deme border coloring.
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220 |
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221 | ## version 1.36.3 - 2019/03/11
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222 | * Various map improvements, including transmission ribbons, improved initial map
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223 | bounds and improved deme circle sizing.
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224 | [See PR 712](https://github.com/nextstrain/auspice/pull/712)
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225 | * Check mutation type against tree. (See PR 709)[https://github.com/nextstrain/auspice/pull/709]
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226 |
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227 | ## version 1.36.2 - 2019/03/04
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228 | * Update footer information. Don't display "live" footers for "community" URLs.
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229 |
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230 | ## version 1.36.1 - 2019/02/27
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231 | * Update npm packages identified as security vulnerabilities
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232 | * Fixes a bug (only in v1.36.0) where, for some datasets, interacting with the tree would cause the app to crash. [Issue 708](https://github.com/nextstrain/auspice/issues/708)
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233 | * `auspice build` now exits (with non-zero exit code) if there are errors during webpack bundling
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234 |
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235 | ## version 1.36.0 - 2019/02/25
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236 | * Improve app load times using code splitting. [See PR 701](https://github.com/nextstrain/auspice/pull/701)
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237 |
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238 | ## version 1.35.5 - 2019/02/08
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239 | * Add acknowledgements to mumps page.
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240 | * Preserve URL during 404. [Issue #700](https://github.com/nextstrain/auspice/issues/700)
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241 |
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242 | ## version 1.35.4 - 2019/01/28
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243 | * Restore download modal functionality. [Issue 699](https://github.com/nextstrain/auspice/issues/699)
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244 |
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245 | ## version 1.35.3 - 2019/01/25
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246 | * Show useful help message if port is in use. [See PR 694](https://github.com/nextstrain/auspice/pull/694)
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247 | * Fixed a bug where URL query strings may become corrupted in certain cases. [See PR 695](https://github.com/nextstrain/auspice/pull/695)
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248 | * Restore (deprecated) "npm run {server,dev}" commands. [See PR 692](https://github.com/nextstrain/auspice/pull/692)
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249 | * Fix broken links in documentation. [See PR 690](https://github.com/nextstrain/auspice/pull/690)
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250 | * Update WNV footer text
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251 |
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252 | ## version 1.35.2 - 2019/01/16
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253 | * Auspice is now extensible (at build stage), allowing customisations and serverless builds. [See PR 688](https://github.com/nextstrain/auspice/pull/688)
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254 | * Documentation is now available via github pages -- [nextstrain.github.io/auspice](https://nextstrain.github.io/auspice/)
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255 |
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256 | ## version 1.34.4 - 2019/01/15
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257 | * Update mumps footer
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258 |
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259 | ## version 1.34.3 - 2018/12/18
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260 | * Don't display deme circle if lat/long is absent
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261 |
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262 | ## version 1.34.2 - 2018/12/05
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263 | * Update mumps footer
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264 | * Modify the casing of how labels are displayed [See PR 685](https://github.com/nextstrain/auspice/pull/685)
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265 |
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266 | ## version 1.34.1 - 2018/11/29
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267 | * Small change to make the 'Second Tree' option appear when virus segments are named according to "segment1", "segment2" etcetera. [See PR 684](https://github.com/nextstrain/auspice/pull/684)
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268 |
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269 | ## version 1.34.0 - 2018/11/19
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270 | * Community builds are now sourced from githubusercontent, which is the official source for "raw" files from GitHub. [PR 682](https://github.com/nextstrain/auspice/pull/682)
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271 |
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272 | ## version 1.33.0 - 2018/11/18
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273 | * Gene names can now include `-` and `_`, as well as code improvements to genotype encoding/decoding -- [PR 681](https://github.com/nextstrain/auspice/pull/681)
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274 |
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275 | ## version 1.32.0 - 2018/11/02
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276 | * Allow `hidden` property on tree nodes -- [PR 676](https://github.com/nextstrain/auspice/pull/676)
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277 | * Update packages & package.json metadata -- [PR 677](https://github.com/nextstrain/auspice/pull/677) [PR 678](https://github.com/nextstrain/auspice/pull/678) [PR 679](https://github.com/nextstrain/auspice/pull/679)
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278 | * Restore hot-reloading ability for development (above PRs)
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279 |
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280 | ## version 1.31.0 - 2018/10/29
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281 | * Allow time-only trees or div-only trees -- [PR 670](https://github.com/nextstrain/auspice/pull/670)
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282 | * Minor fixes to handle trees with missing data -- [PR 673](https://github.com/nextstrain/auspice/pull/673)
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283 |
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284 |
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285 | ## version 1.30.3 - 2018/09/19
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286 | * Colours were sometimes inconsistent when two trees were displayed -- [PR 665](https://github.com/nextstrain/auspice/pull/665)
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287 | * Clicking on a tip while two trees were displayed no longer causes a crash -- [PR 666](https://github.com/nextstrain/auspice/pull/666)
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288 |
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289 | ## version 1.30.2 - 2018/09/07
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290 |
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291 | * Publish the package to the npm registry from the release branch automatically. [[#660](https://github.com/nextstrain/auspice/pull/660), [#662](https://github.com/nextstrain/auspice/pull/662)]
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292 | * Fix inability to run `npm` locally introduced by repo's `.npmrc` file. [[#661](https://github.com/nextstrain/auspice/issues/661)]
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293 |
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294 | ## version 1.30.1 - 2018/09/05
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295 |
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296 | ## version 1.30.0 - 2018/09/05
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297 |
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298 | * Auspice is now globally installable and published as a npm package [npmjs.com/package/auspice](https://www.npmjs.com/package/auspice)
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299 | * AA entropy calculation bug fixed - [PR 657](https://github.com/nextstrain/auspice/pull/657)
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300 | * Narrative scroll bars are fixed for Linux & Windows browsers - [PR 653](https://github.com/nextstrain/auspice/pull/653)
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301 | * Tree legend placement improved - [PR 650](https://github.com/nextstrain/auspice/pull/650)
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302 | * `npm run start` is no longer deprecated
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303 |
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304 | ## version 1.29.0 - 2018/08/31
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305 | * The visibility of nodes on the tree now more accurately reflects the selected date range - [PR 644](https://github.com/nextstrain/auspice/pull/644)
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306 | * Info text is easier to read & the date range reflects the genomes in view - [PR 639](https://github.com/nextstrain/auspice/pull/639)
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307 |
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308 | ### Narrative improvements
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309 | * Toggle between narrative & interactive mode is much clearer - [PR 648](https://github.com/nextstrain/auspice/pull/648)
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310 | * URL queries with no clade set zoom to the entire tree - [PR 644](https://github.com/nextstrain/auspice/pull/644)
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311 |
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312 | ## version 1.28.0 - 2018/08/25
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313 | * Narratives -- see [nextstrain.org/docs/visualisation/narratives](https://nextstrain.org/docs/visualisation/narratives) for documentation.
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314 | * Time slicing & non-highlighted branches are now displayed in a cleaner fashion - [PR 638](https://github.com/nextstrain/auspice/pull/638)
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315 | * Selected clades (i.e. the tree has been zoomed) are now part of URL state - [PR 633](https://github.com/nextstrain/auspice/pull/633)
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316 |
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317 | ## version 1.27.1 - 2018/08/24
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318 | * Fixed broken navigation links
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319 | * Entropy zooming bug fixed - [PR 637](https://github.com/nextstrain/auspice/pull/637)
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320 |
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321 | ## version 1.27.0 - 2018/08/20
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322 | * Saved SVGs now include two trees (if displayed) - [PR 630](https://github.com/nextstrain/auspice/pull/630)
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323 |
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324 | ## version 1.26.0 - 2018/08/20
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325 | * Entropy panel zoom changes are now reflected in URL state - [PR 626](https://github.com/nextstrain/auspice/pull/626)
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326 |
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327 | ## version 1.25.2 - 2018/08/17
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328 |
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329 | * Negative dates (BCE) are now handled correctly - [PR 627](https://github.com/nextstrain/auspice/pull/627)
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330 | * Small entropy zooming fixes - [PR 624](https://github.com/nextstrain/auspice/pull/624)
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331 | * Bugfix to prevent the grid being drawn over the branches / tips in some situations - [PR 629](https://github.com/nextstrain/auspice/pull/629)
|
332 | * Transmissions which involve demes without lat/longs now show an error notification - [PR 608](https://github.com/nextstrain/auspice/pull/608)
|
333 |
|
334 | ## version 1.25.1 - 2018/08/10
|
335 | * Small fixes to entropy zooming behaviour
|
336 | * Gaps are not counted in the entropy calculations & are not displayed in the info panel pop up
|
337 |
|
338 | ## version 1.25.0 - 2018/08/09
|
339 | * New Entropy panel zooming functionality - [PR 609](https://github.com/nextstrain/auspice/pull/609)
|
340 |
|
341 | ## version 1.24.1 - 2018/08/08
|
342 | * Upgrade dependencies
|
343 | * Bugfix when changing between staging datasets - [issue 618](https://github.com/nextstrain/auspice/issues/618)
|
344 |
|
345 | ## version 1.24.0 - 2018/08/05
|
346 | * Tree grid improvements - [PR 610](https://github.com/nextstrain/auspice/pull/610)
|
347 | * Allow negative (i.e. BCE) dates
|
348 | * Display y-dates and horizontal lines in the clock layout view
|
349 | * Improved spacing between grid points
|
350 | * SVG elements in the DOM are now in named groups which improves debugging and prevents incorrect-layering bugs. [PR 612](https://github.com/nextstrain/auspice/pull/612)
|
351 | * Fixed a bug where the available datasets (dropdowns in sidebar) contained invalid values [PR 614](https://github.com/nextstrain/auspice/pull/614)
|
352 | * Community sourced datasets (nextstrain.org/community/...) display a link to the github repo in the sidebar [PR 615](https://github.com/nextstrain/auspice/pull/615)
|
353 | * Since v1.22.3 changing datasets preserved the URL queries (e.g. `?l=radial`).
|
354 | A number of bugs relating to this have been fixed, where these queries were no longer valid for the new dataset.
|
355 | This also fixed potential issues related to loading datasets where the URL queries were invalid.
|
356 | [PR 613](https://github.com/nextstrain/auspice/pull/613)
|
357 |
|
358 |
|
359 | ## version 1.23.2 - 2018/07/30
|
360 | * Increase the padding when displaying two panels side by side to avoid bugs on different browsers / OSs. [issue 574](https://github.com/nextstrain/auspice/issues/574)
|
361 |
|
362 | ## version 1.23.1 - 2018/07/30
|
363 | * Improved the alignment of branch labels for the second tree
|
364 |
|
365 | ## version 1.23.0 - 2018/07/28
|
366 |
|
367 | * The server no longer needs to be transpiled
|
368 | * The interaction between data sources (local / staging / live) has been changed.
|
369 | * The first part of the URL now defines the source, e.g. /flu is live, /local/flu is local, /staging/flu...
|
370 | * Accordingly, `npm run server.js localData` no longer has the effect it used to!
|
371 | * Github committed JSONs are now accessible via /community/orgName/repoName (slightly experimental and subject to change)
|
372 | * JSONs are now delivered to the client using compression (when available)
|
373 | * Frequency JSONs are only fetched when the frequency panel is specified (in the meta JSON)
|
374 | * The server combines the tree & meta JSONs into a single "unified" JSON, in preparation for a move to v2.0 JSONs.
|
375 | * Manifest files / parsing have been moved from the server
|
376 | * Various improvements to the narratives (still experimental and the API is subject to change)
|
377 | * Second trees are specified by `/na:ha/` rather than `/na/...?tt=ha`. The old syntax is still supported for backwards compatibility.
|
378 |
|
379 |
|
380 | ## version 1.22.3 - 2018/07/19
|
381 | * Trigger Docker Hub automated build to rebuild via Travis CI when master branch is pushed and tests are successful
|
382 | * Simplify counting of traits across tree
|
383 | * Improve README
|
384 | * Remove Electron
|
385 | * Restored the ability to run the non-dev server with local data [PR 589](https://github.com/nextstrain/auspice/pull/589)
|
386 |
|
387 | ## version 1.22.2 - 2018/07/10
|
388 | * Bugfix in tip attribute counting algorithm
|
389 |
|
390 | ## version 1.22.1 - 2018/07/09
|
391 | * Legend items no longer include duplicates, and include month for dates within the past 10 years - thanks @emmahodcroft[PR 592](https://github.com/nextstrain/auspice/pull/592)
|
392 | * Bugfix related to colorBy values only specified on internal nodes [issue 593](https://github.com/nextstrain/auspice/issues/593)
|
393 |
|
394 | ## version 1.22.0 - 2018/07/03
|
395 | * Auspice can now run with an incomplete metadata file, or even without a metadata file at all! [PR 586](https://github.com/nextstrain/auspice/pull/586)
|
396 | * Download modal reinstated [PR 587](https://github.com/nextstrain/auspice/pull/587)
|
397 | * Improved styling
|
398 | * All panes now saved to a single SVG
|
399 | * Map panning SVG-save bugs (mostly) fixed
|
400 | * TSV used instead of CSV
|
401 | * Fix WNV colorBy link in footer -- [issue 590](https://github.com/nextstrain/auspice/issues/590)
|
402 |
|
403 | ## version 1.21.3 - 2018/06/27
|
404 | * Show tree titles (e.g. `NA`) when two trees are displayed
|
405 | * 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.
|
406 | * Other minor bugfixes & package upgrades
|
407 |
|
408 | ## version 1.21.2 - 2018/06/07
|
409 | * Disable Untangling
|
410 |
|
411 | ## version 1.21.1 - 2018/06/04
|
412 | * Narratives are now sourced from [the static github repo](https://github.com/nextstrain/static/tree/master/narratives)
|
413 |
|
414 | ## version 1.21.0 - 2018/06/01
|
415 | * Untangling via a simple algorithm upon 2nd tree load
|
416 | * Segment names displayed above trees (if 2 trees)
|
417 | * Fix hover-info-box date bug -- [issue 572](https://github.com/nextstrain/auspice/pull/572)
|
418 |
|
419 | ## version 1.20.3 - 2018/05/30
|
420 | * Narratives now accessed via `/narratives/...` URLs
|
421 | * App now works without needing a manifest file (but the datasets dropdown needs it)
|
422 | * Initial load simplified
|
423 | * Sidebar doesn't appear until the data is ready to be displayed
|
424 |
|
425 |
|
426 | ## version 1.20.2 - 2018/05/21
|
427 | * Changes to the frequencies threshold
|
428 |
|
429 | ## version 1.20.1 - 2018/05/21
|
430 | * Changes to the frequencies threshold
|
431 | * Narratives restored
|
432 |
|
433 | ## version 1.20.0 - 2018/05/15
|
434 | **Auspice is now served via the nextstrain.org server together with the static (gatsbyjs) site**
|
435 | * Changes to the server code organisation
|
436 | * Static content removed
|
437 | * New splash page listing the (should only be accessed from local instances or 404s, live site splash is via the static site)
|
438 | * Improved page navigation API
|
439 | * Travis CI 🎉
|
440 | * Auspice version is displayed in the footer
|
441 | * Release script modified (Travis CI listens to `release` and pushes a successful build to S3 which is fetched by the live server)
|
442 |
|
443 |
|
444 | ## version 1.19.1 - 2018/05/09
|
445 | * Fixed a bug where proteins starting with a number (e.g. 2K) were assumed to be nucleotide genotypes.
|
446 |
|
447 | ## version 1.19.0 - 2018/05/09
|
448 | * Improved sidebar styling on both mobile & desktop
|
449 | * Reset layout button doesn't re-instantiate the PhyloTree object, rather it resets the branch thicknesses & sets the whole tree to be in view
|
450 | * Padding improvements - tip labels are now visible, and small clades render better.
|
451 | * Tip names now shown for up to 100 taxa
|
452 | * Branch thickness restored -- [issue 544](https://github.com/nextstrain/auspice/pull/544)
|
453 | * Tree panning has been removed (we no longer use `react-svg-pan-zoom`)
|
454 |
|
455 | ## version 1.18.10 - 2018/05/07
|
456 |
|
457 | * Separate Nucleotide mutations from gaps / Ns in info-box - thanks @emmahodcroft [PR 552](https://github.com/nextstrain/auspice/pull/552)
|
458 | * Frequencies y-axis is no longer rounded to the nearest 0.05
|
459 |
|
460 | ## version 1.18.9 - 2018/05/03
|
461 | * update flu footer
|
462 | * start using travis CI
|
463 |
|
464 | ## version 1.18.8 - 2018/05/02
|
465 | * temporary fix for map transmissionIndices errors (bug still exists, [issue 547](https://github.com/nextstrain/auspice/issues/547))
|
466 |
|
467 | ## version 1.18.7 - 2018/05/02
|
468 | * Fix frequencies panel x-axis bug
|
469 | * Linting
|
470 | * Minor style changes
|
471 |
|
472 | ## version 1.18.6 - 2018/04/30
|
473 | * update WNV footer
|
474 |
|
475 | ## version 1.18.5 - 2018/04/27
|
476 | * update WNV footer
|
477 |
|
478 | ## version 1.18.4 - 2018/04/26
|
479 | * Use exponential notation for the clock rate
|
480 |
|
481 | ## version 1.18.3 - 2018/04/23
|
482 | * Updated the footer for LASV & WNV
|
483 |
|
484 | ## version 1.18.2 - 2018/04/16
|
485 | * LBI color scale domain is [0, 0.7] [Issue 541](https://github.com/nextstrain/auspice/issues/541)
|
486 | * Fix bug with antigenic advance & frequencies [Issue 540](https://github.com/nextstrain/auspice/issues/540)
|
487 | * Hovering over a tree legend value of zero now correctly highlights matching tips
|
488 | * Undefined color traits are now grey on a discrete scale
|
489 | * Removed all references to `node.attr.strain` (tree JSON) and `seq_author_map` (meta JSON)
|
490 |
|
491 | ## version 1.18.1 - 2018/04/15
|
492 | * Make date slider spacing consistent between animation and drag
|
493 |
|
494 | ## version 1.18.0 - 2018/04/14
|
495 | * Tanglegrams enabled! (bugfixes & reinstate controls dropdown)
|
496 | * Status pages: nextstrain.org/status & nextstrain.org/status/staging
|
497 | * Narrative files are sourced from nextstrain.org repository
|
498 |
|
499 | ## version 1.17.4 - 2018/04/10
|
500 | * Updated LASV footer
|
501 |
|
502 | ## version 1.17.3 - 2018/04/04
|
503 |
|
504 | * Allowed arbitrary user manifests to be served
|
505 | * Changed how the tanglegram updates, so that it is now triggered straight after the trees update.
|
506 | * Updated the files downloaded from `get_data.sh`
|
507 | * Add lassa (LASV) footer acknowledgments.
|
508 |
|
509 | ## version 1.17.2 - 2018/04/02
|
510 | * Job ad on splash page.
|
511 |
|
512 | ## version 1.17.1 - 2018/03/28
|
513 | * Fix tree SVG bug [Issue 535](https://github.com/nextstrain/auspice/issues/535)
|
514 |
|
515 | ## version 1.17.0 - 2018/03/26
|
516 |
|
517 | #### Narrative
|
518 | * Now exposed via a "hidden" URL query. E.g. `flu/h3n2/3y?n=1`
|
519 | * Frequencies added to narrative
|
520 | * block in focus is part of the URL query, and can be reloaded via the URL
|
521 |
|
522 | #### Second Tree / Tanglegram
|
523 | * Second tree can be loaded via a URL (e.g. `?tt=na`). Sidebar dropdown currently disabled.
|
524 | * In this mode, trees are forced to be rectangular, and the map & frequencies are not displayed.
|
525 | * Tanglegram exists, but no untangling (yet)
|
526 | * Bugs still exist (which is why the sidebar has been disabled)
|
527 |
|
528 | #### Internals
|
529 | * All JSONs (incl. frequencies, narrative) are loaded within a single Promise & dispatch
|
530 | * `phylotree.change()` only ever called once, and always in componentDidUpdate (fixes bugs where it fired in both CWRP and CDU)
|
531 | * old & deprecated code removed
|
532 |
|
533 |
|
534 | ## version 1.16.5 - 2018/03/26
|
535 | * Authors filter is now an explicit setting in the JSONs [PR 532](https://github.com/nextstrain/auspice/pull/532)
|
536 |
|
537 |
|
538 | ## version 1.16.4 - 2018/03/22
|
539 | * Flu footer updated
|
540 | * Fix bug in genotype colouring [PR 531](https://github.com/nextstrain/auspice/pull/531)
|
541 | * Adjust vaccine cross styling & remove dashed line [PR 529](https://github.com/nextstrain/auspice/pull/529)
|
542 |
|
543 |
|
544 | ## version 1.16.3 - 2018/03/21
|
545 | * Flu footer updated
|
546 |
|
547 |
|
548 | ## version 1.16.2 - 2018/03/21
|
549 | * Add redirect of www.nextstrain.org to nextstrain.org via express middleware [PR 528](https://github.com/nextstrain/auspice/pull/528)
|
550 |
|
551 |
|
552 | ## version 1.16.1 - 2018/03/16
|
553 | * Fix bug in the color scales where clades were coloured white after switching trees.
|
554 |
|
555 |
|
556 | ## version 1.16.0 - 2018/03/16
|
557 | ### Browser support
|
558 | * Now works on Internet Explorer 11 (tested on windows 7)
|
559 | * Grid layout issue fixed for Firefox on linux/windows
|
560 | * Embedding Nextstrain in an iFrame works - see `/scripts/gisaid_iframe.html`
|
561 |
|
562 |
|
563 | ## version 1.15.1 - 2018/03/14
|
564 | * Fix Firefox branch / tip hover bug [Issue 525](https://github.com/nextstrain/auspice/issues/525)
|
565 |
|
566 |
|
567 | ## version 1.15.0 - 2018/03/12
|
568 | * Multiple genotypes (for the same amino acid) by typing in multiple comma separated AA/nuc positions.
|
569 | [PR 523](https://github.com/nextstrain/auspice/pull/523).
|
570 |
|
571 |
|
572 | ## version 1.14.4 - 2018/03/05
|
573 | * Restore staging server toggle [issue 514](https://github.com/nextstrain/auspice/issues/514)
|
574 |
|
575 |
|
576 | ## version 1.14.3 - 2018/03/01
|
577 | * Bug fix where tip colours reverted to their initial colours after a layout change. [issue 519](https://github.com/nextstrain/auspice/issues/519)
|
578 |
|
579 | ## version 1.14.2 - 2018/02/28
|
580 | * [PR 518](https://github.com/nextstrain/auspice/pull/518)
|
581 | * Frequency y-axis is now dynamic
|
582 | * Frequency text box is more readable
|
583 | * Frequency normalisation has been removed
|
584 |
|
585 | ## version 1.14.1 - 2018/02/27
|
586 | * Style tip stroke separately from branch stroke (`node.stroke` replaced with `node.branchStroke` & `node.tipStroke`)
|
587 |
|
588 | ## version 1.14.0 - 2018/02/27
|
589 |
|
590 | ### Features
|
591 | * Strain search (using [awesomplete](https://leaverou.github.io/awesomplete/)).
|
592 | This highlights the path to a single tip and increases the tip radius.
|
593 | Strain is stored in the URL query (`s=...`) and can be restored via URL.
|
594 | Selected strain also appears in the info panel (top of screen).
|
595 | * Amino acid branch labels (for every tree) as well as clade labels if specified by the `clade_annotation` attribute.
|
596 | AA labels are shown where the descendent visible tips account for more than 5% of the total visible tips (same as nextflu).
|
597 | Clade labels are always displayed.
|
598 | * Default geneotype gene is now HA1 if available (previously nucleotide).
|
599 | * ColorBy ordering (sidebar dropdown) is now ordered (via an array in `globals.js`)
|
600 |
|
601 | ### Internals
|
602 | * The JSON processing on initial load has been shifted from the reducers to a single action - fewer dispatches, fewer potential bugs, faster code.
|
603 | * Frequencies are initialised in a single action (previously 2).
|
604 | * tip-frequencies are now downloaded via `get_data.sh`
|
605 | * Frequency actions are not dispatched unless the frequency panel is loaded.
|
606 |
|
607 | ## version 1.13.2 - 2018/02/26
|
608 | * Improve consistency of panel controls
|
609 | * Show `unassigned` in tree legend (if applicable)
|
610 |
|
611 | ## version 1.13.1 - 2018/02/26
|
612 | * Tree button "reset layout" now at top right
|
613 |
|
614 | ## version 1.13.0 - 2018/02/26
|
615 |
|
616 | ### Features
|
617 | * Frequencies are now displayed via a stream graph panel - see [PR 497](https://github.com/nextstrain/auspice/pull/497).
|
618 | These require the fetching of a separate `tip-frequencies` JSON, and must be specified in the `panels` array of the meta.JSON.
|
619 | * "Panels To Display" toggles in the sidebar allow customisation of the display, and this is reflected in the URL.
|
620 | * The `+` `-` buttons in the tree have been replaced by a "reset tree" button.
|
621 | This resets the bounds to the entire tree & completely re-renders the tree (filters are maintained).
|
622 | Pan behaviour is unchanged.
|
623 |
|
624 | ### Internals
|
625 | * React-PhyloTree interface is completely rewritten to use `phylotree.change()` - see [PR 501](https://github.com/nextstrain/auspice/pull/501) for the API.
|
626 | The new interface is both easier to understand and quicker.
|
627 | * `changePageQuery` (used for changing narrative blocks) is now a single action
|
628 | * Ongoing narrative work (still disabled).
|
629 | * React sidebar has been removed (no UI changes).
|
630 |
|
631 | ## version 1.12.0 - 2018/02/14
|
632 |
|
633 | ### Features
|
634 | * Vaccine strains are shown at their use date (in temporal trees), with dotted lines connecting them to their tips (representing collection date) ([PR 498](https://github.com/nextstrain/auspice/pull/498))
|
635 |
|
636 | ### Internals
|
637 | * `updateGeometryFade` uses counters to know when transitions are finished rather than `setTimeout`
|
638 |
|
639 | ## version 1.11.0 - 2018/02/05
|
640 |
|
641 | ### Features
|
642 | * Vaccine strains are now displayed if they are specified in `metaJSON.vaccine_choices` ([PR 490](https://github.com/nextstrain/auspice/pull/490))
|
643 |
|
644 | ### Internals
|
645 | * Tree components and PhyloTree have been reorganized (in `src/components/tree`) and the syntax improved ([PR 493](https://github.com/nextstrain/auspice/pull/493))
|
646 | * Upgraded to React 16, as well as upgrading redux & react-svg-pan-zoom ([PR 494](https://github.com/nextstrain/auspice/pull/494))
|
647 |
|
648 | ## version 1.10.0 - 2018/02/05
|
649 |
|
650 | ### Features
|
651 | * Local Branching Index (LBI) coloring can be calculated in Auspice (code identical to nextflu) if specified in `color_options` (meta JSON) ([PR 491](https://github.com/nextstrain/auspice/pull/491))
|
652 |
|
653 | ### Internals
|
654 | * `get_data.sh` script updated to no longer download sequences & entropy JSONs
|
655 | * action logging middleware available for debugging / development
|
656 |
|
657 | ## version 1.9.0 - 2018/01/30
|
658 |
|
659 | ### Animation
|
660 | * Animations can now loop! This is selected via a toggle in the sidebar.
|
661 | * 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.
|
662 | * The code for the animation (i.e. the setInterval code) has been moved out of `Map` and into a separate `AnimationController` component.
|
663 | * Animation is stopped & started by examining redux state, rather than with imperative controls.
|
664 |
|
665 | ### misc
|
666 | * The narrative machinery has been moved forward, but this functionality is still disabled and not present in production code.
|
667 | * The (rather expensive) `calendarToNumeric` calculations have become part of `state.controls` so that components no longer have to calculate them from the string form.
|
668 |
|
669 | ## version 1.8.0 - 2018/01/18
|
670 |
|
671 | #### entropy calculated via tree
|
672 | * The entropy panel data is now computed within Auspice by examining mutations throughout the tree, and is throttled to improve speed under load.
|
673 | * Both entropy and number of mutations are available via a toggle similar to AA/NT
|
674 | * This results in `entropy.JSON` no longer being fetched.
|
675 | * The entropy data is stored in redux state rather than the react component
|
676 | * The D3 code has been reorganised
|
677 | * Note that the entropy values are slightly different to those exported by Augur in some situations - see https://github.com/nextstrain/auspice/pull/478#issuecomment-358496901
|
678 |
|
679 | #### genotype calculated via tree
|
680 | * This results in `sequences.JSON` no longer being fetched.
|
681 | * Augur was updated to export `annotations` which are needed for entropy gene display.
|
682 |
|
683 | #### middleware / react router
|
684 | * All changes to the URL are now performed via middleware rather than side-effects within the action definition.
|
685 | * React router has been removed
|
686 | * Browser back/forward is detected via `window.addEventListener('popstate', this.onURLChanged)` which also fires on initial page load.
|
687 | * Pages are selected via the `<PageSelect>` component.
|
688 |
|
689 | #### other
|
690 | * The number of proteins displayed while hovering over a branch has been limited to 7 (issue #484)
|
691 | * The presence of author data is checked before display (issue #488)
|
692 | * This changelog has been created and a step in the `releaseNewVersion` script added to prepend the version number upon release.
|
693 |
|
694 |
|
695 |
|
696 | ## version 1.7.2 - 2018/1/4
|
697 |
|
698 | #### Narrative / situational report
|
699 | * Functionality has been added, but is currently disabled via a flag in `globals.js`.
|
700 | * This is currently rendered in a right-hand sidebar. This feature is not yet complete.
|
701 |
|
702 | #### URL queries
|
703 |
|
704 | * The following state has been added to the URL query:
|
705 | * filters, e.g. `f_authors=Tong_et_al,Capobianchi_et_al&f_division=kerouane`
|
706 | * genotype URLs (these were previously set as the URL but not parsed)
|
707 | * panel layout (grid/full)
|
708 | * A number of bugs regarding URL query state parsing (esp with genotype colorBys) have been fixed.
|
709 |
|
710 | ## version 1.7.1 - 2017/10/31
|
711 |
|
712 | * Added mumps acknowledgment
|
713 |
|
714 | ## version 1.7.0 - 2017/10/17
|
715 | ## version - 2018/01/18
|