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v7.2 release candidate#1159

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dondi merged 97 commits intomasterdondi/GRNsight:masterfrom betadondi/GRNsight:betaCopy head branch name to clipboardDec 4, 2024

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Commits on Apr 23, 2024

• Issue #1080. Can display warning the first time that Enable Node Coloring is clicked and viewing a PPI. Want to change so that Warnings List is already collapsed and can view warning message immedi…

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Commits on Oct 2, 2024

• Set new version number for post-7.1.1 work.

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Commits on Oct 9, 2024

• now display node coloring warning each time there is a PPI network and nodeColoringEnabled.

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• Merge branch 'master' into beta

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• New version because of Zenodo bump.

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Commits on Oct 10, 2024

• Remove testing schema that I forgot to delete

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• #1106 Allowing query all the genes even if it's not in grn network table

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Commits on Oct 16, 2024

• #1080. Can toggle between enabling and disabling node coloring for PPIs, but need to make sure node coloring sidebar not disabled when first load PPI and that don't get long list of console warning…

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• #1080. Now node coloring sidebar not disabled when load PPI as first network

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• #1080. removing unecessary comments and console.logs, changed warning for PPIs to be in warnings list

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• Merge pull request #1123 from dondi/maika-1106

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• Merge pull request #1124 from dondi/maika-1106-2

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• Merge pull request #1125 from dondi/cecilia-1080

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• Version bump.

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• #1118 github action

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Commits on Oct 17, 2024

• #1102 Adding tests and errors message for uploading mixed type relationship SIF file

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• #1055 Make the node coloring menu for top bar and side bar to be consistent, and fix lint errors

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Commits on Oct 23, 2024

• #1080 now sidebar options display again when node coloring enabled

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• added ppiNodeColorWarningDisplayed to grnState, so now only display warning when user first displays node coloring with PPI

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• Merge pull request #1127 from dondi/maika-1102

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• Merge pull request #1128 from dondi/maika-1055

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• Version bump.

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• #1080. Now nodes display white instead of gray color thanks to fix from Maika

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• merged beta into cecilia-1080

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• Issue #1080. added === 0 so use triple equals sign

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Commits on Oct 24, 2024

• adding console.log and removing comments to understand errors in console

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• #1130. removed call to tic() in restrictGraphToViewport since graph refreshes whenever restrictGraphToViewport is clicked already. This removes error with path containing NaNs from displaying in th…

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• #1130. added BOUNDARY_MARGIN to constants, but now receiving error about attribute not having .length. will probably have to go back to #1080 and reserve issue there

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• Merge branch 'cecilia-1130' into cecilia-1080

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• #1068 Allow node coloring for PPI by matching the gene name

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Commits on Oct 25, 2024

• #1059 Cloning the svgElement to prevent changes to the current display graph

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• #1098 Fixing issue where file selector appears twice after importing wrong file

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• no longer receiving issue about length when load Barreto, need to make usr eot update logic for when check node adaptive or though

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• #1080. removing console.logs

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Commits on Oct 27, 2024

• #1080. fixing lint errors and can enable and disable nav and sidebar correctly for node coloring. investigating why when load a database, it says it's NETWORK_PPI_MODE and even though node coloring…

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• #1080. display warning when PPI mode enabled, but for some reason PPI warning displays when load a database too

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• Issue #1080. was accidentally assigning grnState.mode to NETWORK_PPI_MODE, and removed that code so that now databases load in correct mode

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Commits on Oct 30, 2024

• #1080. Can now enable and disable node coloring with PPIs where navbar and side menu display the same status of node coloring and when node coloring disabled, the navbar and sidebar options for nod…

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• Sync package-lock.json with package.json

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• Merge pull request #1129 from dondi/cecilia-1080

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• Merge pull request #1132 from dondi/maika-1059

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• system dependencies needed by the 'canvas' package

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• #1078 style fix

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• #1098 reverse back the changes to when upload class is changed, trigger uploadHandler

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• #1197 Modify alpha value on optimization_parameters from 0.002 to 0.02

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Commits on Oct 31, 2024

• fixing syntax error

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Commits on Nov 4, 2024

• Merge pull request #1136 from dondi/maika-1107

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• #1068 improve the code quality

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• Merge branch 'beta' into maika-1068

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• #1108 When export, making network and network_weights sheets to be identical

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• Merge pull request #1133 from dondi/maika-1098

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• Merge pull request #1134 from dondi/maika-1068

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• Merge pull request #1137 from dondi/maika-1108

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• Version bump.

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Commits on Nov 5, 2024

• #1053 Fixing p.length is unavailable error

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• #1093 svg image appear with white background

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• Fixing the exportToPDF so the image doesn't too scale on width or height

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• Clean code for #59

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Commits on Nov 6, 2024

• #59 change the background color from black to white for PNG export

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• reducing node version workflow

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• Modify the location of the image in pdf

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• #1053 improve code quality

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• #1093 rename variable, and switching to Object.assign for copying style to reexisting nodes

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• Update node.js.yml

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• Update node.js.yml

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• Experimental: change “on” event for running workflow.

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• Try eliminating branch specificity.

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Commits on Nov 13, 2024

• removing the 'xenial-security' repository and installing dependencies directly.

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• downgrading node version to 18.x for compatibility with canvas package

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• Merge pull request #1138 from dondi/maika-1053

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• Merge pull request #1141 from dondi/maika-59

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• Fixing wrong capitlization in naming

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• Merge pull request #1140 from dondi/maika-1093

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• Version bump.

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• Issue #1142. Now warnings list should display correctly. Added line that must have accidentally deleted in previous PR

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Commits on Nov 16, 2024

• Merge pull request #1135 from dondi/issue-1118-github-actions

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• Merge pull request #1143 from dondi/cecilia-1142

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• 7.1.8…when GRNsight got its CI groove back.

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Commits on Nov 20, 2024

• Add npm lint step to GitHub Actions workflow

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• #1144 Adding code to set node-coloring enable only when having expression spreadsheet

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Commits on Nov 27, 2024

• #1144 fix previous commit code that didn't work, changing from workbook.expression -> grnState.workbook.expression

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• Clean code

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• #1030 Remove lint changes and only change the variable name

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• Merge pull request #1154 from dondi/maika-1030

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• Version bump for new environment variable names.

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Commits on Nov 29, 2024

• correcting trailing spaces and missing semicolon according to npm lint

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• updated package json with the canvg package 3.0.10 and added canvas 2.11.2 as a direct dependency rather than transparent. Updated node-versions for testing

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• adding Node.js CI badge to README.md

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Commits on Nov 30, 2024

• Rewrite hasExpressionData function to use -some- call

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Commits on Dec 4, 2024

• Merge pull request #1149 from dondi/#1147-include-npm-lin

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• Merge pull request #1155 from dondi/#1145-gain-compatibility-with-Node-20.x

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• Merge pull request #1156 from dondi/#1146-syncing-github-actions-to-badge

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• Version bump—this one only has CI changes.

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• Remove one hasExpressionData function

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• Merge pull request #1153 from dondi/maika-1144

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• #1144 Remove unused import.

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• Version bump to include #1144 fix.

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