Repository navigation

feat: NACHO 3.0.0 - #139

Merged

mcanouil merged 86 commits into

mainfrom

feat/nacho-3

Oct 18, 2026

Merged

feat: NACHO 3.0.0#139
mcanouil merged 86 commits into
mainfrom
feat/nacho-3

Commits on Sep 27, 2026
- ci: install HTML Tidy before R CMD check (#73)
  mcanouil
  authored
  aeeb22e
- test: add offline GSE270837 and GSE178516 fixtures (#74)
  mcanouil
  authored
  7b12607
Commits on Sep 28, 2026
Commits on Sep 29, 2026
- ci: refresh apt lists before installing tidy (#83)
  mcanouil
  authored
  843e050
- fix: keep inner pipe fields in RCC probe names (#84)
  mcanouil
  authored
  698d7e5
- fix: point NACHO 2 objects to upgrade_nacho() (#85)
  mcanouil
  authored
  2478440
- refactor: tidy internals and data-raw installs (#87)
  mcanouil
  authored
  2e47189
- test: tighten PlexSet and validator assertions (#88)
  mcanouil
  authored
  1fe9456
- fix: accept open thresholds and warn once (#86)
  mcanouil
  authored
  7fa4eaa
Commits on Sep 30, 2026
- docs: add breaking changes and tidy internal docs (#89)
  mcanouil
  authored
  69c58d8
- Merge remote-tracking branch 'origin/main' into feat/nacho-3
  mcanouil
  committed
  dba60d9
Commits on Oct 1, 2026
Commits on Oct 2, 2026
Commits on Oct 3, 2026
- fix: guard Phase 2 helpers against very small data (#104)
  mcanouil
  authored
  8eb3fb7
- test: tighten Phase 2 assertions (#105)
  mcanouil
  authored
  1eb3612
- refactor: tidy Phase 2 internals (#106)
  mcanouil
  authored
  4986af2
Commits on Oct 4, 2026
- feat: add the NACHO brand, fonts and plot theme (#107)
  mcanouil
  authored
  8b69fa7
- feat: render the report with Quarto (#108)
  mcanouil
  authored
  527e3a1
- test: skip GEO download tests when NCBI fails (#110)
  mcanouil
  authored
  57fdd80
Commits on Oct 5, 2026
Commits on Oct 6, 2026
- feat: add interactive plots, linked sample selection and an export page (#115)
  mcanouil
  authored
  7285baf
- test: drive the app in a browser and audit its accessibility (#116)
  mcanouil
  authored
  271ad82
Commits on Oct 8, 2026
Commits on Oct 9, 2026
Commits on Oct 10, 2026
Commits on Oct 11, 2026
Commits on Oct 12, 2026
- fix: keep generated images in their own colours in dark mode (#141)
  mcanouil
  authored
  7a298c2
Commits on Oct 13, 2026
- docs: redesign the website home page (#142)
  mcanouil
  authored
  b2cae97
- chore: add docs directory to .gitignore
  mcanouil
  committed
  f6d120a
- fix: warn when positive controls are unusable
  mcanouil
  committed
  70a82ca
- fix: warn when sample sheet columns are replaced
  mcanouil
  committed
  e6bc6c1
- refactor: compute only PC batch R² for the plot
  mcanouil
  committed
  1d69219
- fix: tighten PCL and positive control warnings
  mcanouil
  committed
  0ebdcbd
- test: add GSE346526 fixture from nSolver 4.0.1.8
  mcanouil
  committed
  db69901
- feat: explain Ligation_NEG failures in whole blood
  mcanouil
  committed
  bf4a419
- fix: keep app uploads inside the upload folder
  mcanouil
  committed
  eb6c993
- fix: refuse an id column with a computed name
  mcanouil
  committed
  598d440
- ci: run R-hub on the release bump branch
  mcanouil
  committed
  57c22e5
Commits on Oct 14, 2026
- fix: refuse housekeeping genes that are not probes
  mcanouil
  committed
  ffe7df8
- style: format with air
  mcanouil
  committed
  c757189
- test: compare upload paths after normalising them
  mcanouil
  committed
  58d44d5
- feat: read and write thresholds as YAML (#143)
  mcanouil
  authored
  46ce71f
- feat: add a guided tour to the app (#144)
  mcanouil
  authored
  328e174
Commits on Oct 15, 2026
- feat: import RCC files in the background (#145)
  mcanouil
  authored
  9b96030
- feat: preview the upload before import (#146)
  mcanouil
  authored
  4e6e5e9
- feat: export an R script that reproduces the app (#149)
  mcanouil
  authored
  88b3c48
- feat: one sortable table on the Samples page (#148)
  mcanouil
  authored
  b6f11ec
- docs: polish the NACHO 3 changelog [skip ci]
  mcanouil
  committed
  2467458
- docs: list only changes since 2.0.8 in the changelog [skip ci]
  mcanouil
  committed
  6f2bccb
- fix: mark the selected sample with a rose ring
  mcanouil
  committed
  44ea673
- docs: refresh the app screenshots and animation
  mcanouil
  committed
  f6e2981
- fix: refuse an id column named like a quality-control column
  mcanouil
  committed
  62ff2fd
- docs: load the miRNA example with the SPRINT limits
  mcanouil
  committed
  082bdf4
Commits on Oct 18, 2026
- feat: open one sidebar section for each page
  mcanouil
  committed
  561c7dd
- docs: show the whole sidebar in the app screenshots
  mcanouil
  committed
  93d8c03
- refactor: let the thresholds module open its panel
  mcanouil
  committed
  03c15ab
- docs: reopen only Imaging for the vignette picture
  mcanouil
  committed
  7a8a8ea
- test: spell out the panel each page opens
  mcanouil
  committed
  b5cdaf0
- test: check each page panel exists in the sidebar
  mcanouil
  committed
  5d0fdfe

Commits

Commits on Sep 27, 2026

Commits on Sep 28, 2026

Commits on Sep 29, 2026

Commits on Sep 30, 2026

Commits on Oct 1, 2026

Commits on Oct 2, 2026

Commits on Oct 3, 2026

Commits on Oct 4, 2026

Commits on Oct 5, 2026

Commits on Oct 6, 2026

Commits on Oct 8, 2026

Commits on Oct 9, 2026

Commits on Oct 10, 2026

Commits on Oct 11, 2026

Commits on Oct 12, 2026

Commits on Oct 13, 2026

Commits on Oct 14, 2026

Commits on Oct 15, 2026

Commits on Oct 18, 2026