Code

All features 202403#14

Code

Open

russHyde wants to merge 69 commits intomrc-ide:mainmrc-ide/tfpbrowser:mainfrom jumpingrivers:draft-all-features-202403jumpingrivers/tfpbrowser:draft-all-features-202403Copy head branch name to clipboard

+1,895-927

Commits

Commits on Feb 8, 2024

• Fix typo in title

  timbrock

  committed
  898d5ab

  Copy full SHA for 898d5ab

Commits on Mar 14, 2024

• Merge pull request #67 from jumpingrivers/fix-title

  Show description for d38a270
  russHyde

  authored
  d38a270

  Copy full SHA for d38a270

• chore: bump lint GHA workflow

  russHyde

  committed
  93d8657

  Copy full SHA for 93d8657

• chore: bump R CMD check workflow

  russHyde

  committed
  3f94091

  Copy full SHA for 3f94091

• env: bump renv definition to include Bioc 3.18 (because we couldn't install Bioc 3.17 packages in GHA runs)

  russHyde

  committed
  1db2abe

  Copy full SHA for 1db2abe

• fix renv activate script for renv >=v1

  russHyde

  committed
  3b81763

  Copy full SHA for 3b81763

• refac: use {styler} to fix some indentation lints

  russHyde

  committed
  f19dae2

  Copy full SHA for f19dae2

• refac: fix some undesirable op lints

  russHyde

  committed
  5fca50c

  Copy full SHA for 5fca50c

• chore: bump roxygen2 version

  russHyde

  committed
  d4f2232

  Copy full SHA for d4f2232

• refac: style the code that imports the about.md page

  russHyde

  committed
  61dc14c

  Copy full SHA for 61dc14c

• feat: add 'About' page text based on Kieran's word document

  russHyde

  committed
  f5267d1

  Copy full SHA for f5267d1

Commits on Mar 18, 2024

• Merge pull request #69 from jumpingrivers/about-page

  Show description for 1966165
  timbrock

  authored
  1966165

  Copy full SHA for 1966165

• refac: extract function for cluster-stats UI

  russHyde

  committed
  bd18837

  Copy full SHA for bd18837

• refac: separate content for cluster-stats from details/summary

  russHyde

  committed
  7e0b3fa

  Copy full SHA for 7e0b3fa

• bump to bootstrap v5

  russHyde

  committed
  c174ad9

  Copy full SHA for c174ad9

• add help icon alongside details/summary for cluster-statistics

  russHyde

  committed
  7e75760

  Copy full SHA for 7e75760

• feat: add help text to help icon for 'Cluster Statistics' panel

  russHyde

  committed
  67ed1a0

  Copy full SHA for 67ed1a0

Commits on Mar 19, 2024

• feat: add a help icon inside the cluster-statistics accordion summary

  russHyde

  committed
  6f2542d

  Copy full SHA for 6f2542d

Commits on Mar 21, 2024

• add margin/padding around accordion (using the values for the outdated summary/details)

  russHyde

  committed
  50f872d

  Copy full SHA for 50f872d

• increase help-icon size from 1em to 1.5em

  russHyde

  committed
  e0172f5

  Copy full SHA for e0172f5

• namespace some shiny functions

  russHyde

  committed
  a9dc079

  Copy full SHA for a9dc079

• env: add bsicons to DESCRIPTION

  russHyde

  committed
  36d45fc

  Copy full SHA for 36d45fc

Commits on Apr 16, 2024

• Merge pull request #71 from jumpingrivers/cluster-stats-help

  Show description for a62e560
  russHyde

  authored
  a62e560

  Copy full SHA for a62e560

Commits on Apr 19, 2024

• env: bump the version of {renv}

  russHyde

  committed
  26b1884

  Copy full SHA for 26b1884

• env: add {bsicons} to renv.lock

  russHyde

  committed
  78d5e7a

  Copy full SHA for 78d5e7a

• fix: get_data_dir() should return fully-specified path for data directory

  russHyde

  committed
  c3dc4a2

  Copy full SHA for c3dc4a2

• [TEMP] use renv::use() to specify env for creating browser data

  Show description for 34151f4
  russHyde

  committed
  34151f4

  Copy full SHA for 34151f4

• update version of tfpscanner used in browser-data script

  russHyde

  committed
  4dfdd56

  Copy full SHA for 4dfdd56

• configure / run create_browser_data() in browser-data script

  russHyde

  committed
  b0460c4

  Copy full SHA for b0460c4

• browser-data script outputs a message on how to use the new browser-data in the app

  russHyde

  committed
  a47a47a

  Copy full SHA for a47a47a

• comment-wash the create_browser_data script

  russHyde

  committed
  ce391af

  Copy full SHA for ce391af

• fix: normalisePath -> normalizePath

  russHyde

  committed
  938a71e

  Copy full SHA for 938a71e

• temp

  russHyde

  committed
  7cc51b6

  Copy full SHA for 7cc51b6

• define {svglite} in the env for create_browser_data()

  russHyde

  committed
  621352d

  Copy full SHA for 621352d

• match create-browser env to tfpbrowser env

  russHyde

  committed
  4cc490c

  Copy full SHA for 4cc490c

• dynamically match the create-browser env to the renv.lock, for it's required packages

  russHyde

  committed
  80b1c2a

  Copy full SHA for 80b1c2a

Commits on May 23, 2024

• refac: put user-modified section at start of script

  russHyde

  committed
  b3c0884

  Copy full SHA for b3c0884

• ensure repos are defined before the script runs

  russHyde

  committed
  7af7313

  Copy full SHA for 7af7313

• ensure renv doesn't use fig-prep script when defining the app environment

  russHyde

  committed
  e91e7c8

  Copy full SHA for e91e7c8

Commits on Jun 13, 2024

• {renv} needn't check the www/data directory

  russHyde

  committed
  c2cae29

  Copy full SHA for c2cae29

• use bioconductor 3.16 for R 4.2.x

  russHyde

  committed
  f2ead90

  Copy full SHA for f2ead90

• env: get ggtree from github, since BioC 3.16 version is incompatible with new {ggplot2}

  russHyde

  committed
  4a90218

  Copy full SHA for 4a90218

• env: define renv.lock using BioC 3.16 dependencies (for R 4.2.x)

  russHyde

  committed
  f342320

  Copy full SHA for f342320

• env(helper-script): hard-code the ggtree dev version used by the script

  russHyde

  committed
  475fa4d

  Copy full SHA for 475fa4d

Commits on Aug 8, 2024

• env: add {markdown} to dependencies - needed when importing .rds files from tfpscanner (but not used directly by tfpbrowser)

  russHyde

  committed
  984a523

  Copy full SHA for 984a523

Commits on Aug 15, 2024

• doc: installing/cloning tfpbrowser code

  russHyde

  committed
  66bb233

  Copy full SHA for 66bb233

• doc: activating the app's package environment

  russHyde

  committed
  8598fd8

  Copy full SHA for 8598fd8

Commits on Sep 3, 2024

• doc: creating and configuring a data directory for tfpbrowser

  russHyde

  committed
  f89f93a

  Copy full SHA for f89f93a

Commits on Sep 10, 2024

• env: fix conflict between DESCRIPTION and renv re ggtree version

  russHyde

  committed
  eaeb8f8

  Copy full SHA for eaeb8f8

• env: infrastructure for building vignettes

  russHyde

  committed
  c2c3a64

  Copy full SHA for c2c3a64

• doc: vignette explaining deployment workflow

  russHyde

  committed
  83eb109

  Copy full SHA for 83eb109

• add app.R so that the app can be deployed to shinyapps.io

  russHyde

  committed
  0e4a785

  Copy full SHA for 0e4a785

• env: use bioconductor 3.16

  russHyde

  committed
  c8f9f9e

  Copy full SHA for c8f9f9e

• doc: alternative deployment method using RStudio 'Publish' button

  russHyde

  committed
  5d617b8

  Copy full SHA for 5d617b8

• doc: store data for deployment outside of inst/ in deployment workflow (since inst already contains inappropriately formatted data)

  russHyde

  committed
  daa1d64

  Copy full SHA for daa1d64

Commits on Sep 12, 2024

• git: ignore dir for built vignettes & their index

  russHyde

  committed
  50435c3

  Copy full SHA for 50435c3

• doc: readme points to deploy vignette for deployment info

  russHyde

  committed
  3ee4517

  Copy full SHA for 3ee4517

• fix lint in vignette

  russHyde

  committed
  1c4e2d7

  Copy full SHA for 1c4e2d7

• fix path in vignette

  russHyde

  committed
  a3f1026

  Copy full SHA for a3f1026

Commits on Oct 15, 2024

• env(create_browser_data): explicitly install rmarkdown

  russHyde

  committed
  b0710b7

  Copy full SHA for b0710b7

• env(create_browser_data): ensure packages are installed without lockfiles, to writeable locations

  russHyde

  committed
  c0a9cba

  Copy full SHA for c0a9cba

• doc: how to get MPI/Rmpi installed on a Windows machine (for use in create_browser_data)

  russHyde

  committed
  65dac85

  Copy full SHA for 65dac85

• refac: move creation of interactive ggiraph graphics into a function

  russHyde

  committed
  7a08565

  Copy full SHA for 7a08565

• refac: reduce some duplicated code for setting girafe options

  russHyde

  committed
  9a66a6f

  Copy full SHA for 9a66a6f

• feat: scatterplots are less tall than dendrograms

  russHyde

  committed
  3bd7e61

  Copy full SHA for 3bd7e61

Commits on Oct 18, 2024

• env: roll-back {promises} so we can install it on Kieran's computer

  russHyde

  committed
  c5d41db

  Copy full SHA for c5d41db

• ensure library for create_browser_data goes into a tempdir

  russHyde

  committed
  4581cc4

  Copy full SHA for 4581cc4

Commits on Oct 25, 2024

• create-browser-data: use tfpscanner version that has correct default for heatmap_offset

  russHyde

  committed
  bc3f17a

  Copy full SHA for bc3f17a

Commits on Nov 8, 2024

• fix: use server-side selectize for mut/seq selection; allows thousands of choices

  russHyde

  committed
  f64a32a

  Copy full SHA for f64a32a