Skip to content

Commit

Permalink
Merge pull request #766 from AlexsLemonade/jashapiro/765-action-new-d…
Browse files Browse the repository at this point in the history
…ocker

Update actions to use new Docker images and spellcheck
jashapiro authored May 20, 2024

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature.
2 parents 5942664 + e09db98 commit 03f0d55
Showing 4 changed files with 46 additions and 33 deletions.
7 changes: 3 additions & 4 deletions .github/workflows/make-live.yml
Original file line number Diff line number Diff line change
@@ -8,14 +8,14 @@ on:
rendering:
description: Should rendering be completed? TRUE or FALSE
required: true
default: 'TRUE'
default: "TRUE"

jobs:
make-live:
# The type of runner that the job will run on
runs-on: ubuntu-latest
container:
image: ccdl/training_dev:latest
image: ccdl/training_rstudio:edge

steps:
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
@@ -59,7 +59,7 @@ jobs:
signoff: false
branch: auto_render_live
delete-branch: true
title: 'GHA: Automated live (rendered) versions of the notebooks'
title: "GHA: Automated live (rendered) versions of the notebooks"
body: |
### Description:
This PR auto-generated from github actions running make-live.R with:
@@ -73,7 +73,6 @@ jobs:
automated
reviewers: $GITHUB_ACTOR


# Write PR info
- name: Check outputs
run: |
2 changes: 1 addition & 1 deletion .github/workflows/render-rmds.yml
Original file line number Diff line number Diff line change
@@ -17,7 +17,7 @@ jobs:
test-render:
runs-on: ubuntu-latest
container:
image: ccdl/training_dev:latest
image: ccdl/training_rstudio:edge

steps:
- name: Checkout code
53 changes: 27 additions & 26 deletions .github/workflows/spell-check.yml
Original file line number Diff line number Diff line change
@@ -1,42 +1,43 @@

name: Spell check R Markdown and Markdown files

# Controls when the action will run.
# Pull requests to master only.
on:
pull_request:
branches:
- master

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
concurrency:
# only one run per branch at a time
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true

jobs:
# This workflow contains a single job called "spell check"
spell-check:
spellcheck:
runs-on: ubuntu-latest
container:
image: rocker/tidyverse:4.2.3
name: Spell check files
permissions:
contents: read
issues: write

# Steps represent a sequence of tasks that will be executed as part of the job
steps:
- uses: actions/checkout@v3

- name: Install packages
run: Rscript --vanilla -e "install.packages(c('spelling'), repos = c(CRAN = '$CRAN'))"
- name: Checkout
uses: actions/checkout@v4

- name: Run spell check
id: spell_check_run
run: |
results=$(Rscript --vanilla "scripts/spell-check.R")
echo "sp_chk_results=$results" >> $GITHUB_OUTPUT
cat spell_check_errors.tsv
- name: Spell check action
uses: alexslemonade/spellcheck@v0
id: spell
with:
dictionary: components/dictionary.txt

- name: Archive spelling errors
uses: actions/upload-artifact@v3
- name: Upload spell check errors
uses: actions/upload-artifact@v4
id: artifact-upload-step
with:
name: spell-check-results
name: spell_check_errors
path: spell_check_errors.tsv

# If there are too many spelling errors, this will stop the workflow
- name: Check spell check results - fail if too many errors
if: ${{ steps.spell_check_run.outputs.sp_chk_results > 0 }}
run: exit 1
- name: Fail if there are spelling errors
if: steps.spell.outputs.error_count > 0
run: |
echo "There were ${{ steps.spell.outputs.error_count }} errors"
column -t spell_check_errors.tsv
exit 1
17 changes: 15 additions & 2 deletions components/dictionary.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
ʹ
⚠️
Adelie
ADT
ADTs
@@ -80,9 +81,9 @@ Danio
Darmanis
DataFrames
dataset
de
deconvolution
deconvolved
de
dendritic
DESeq
DESeq2
@@ -92,6 +93,7 @@ DGE
digoxin
DIPG
directionality
discoverable
dispersions
displaystyle
DocToc
@@ -109,6 +111,7 @@ embryonal
emptyDrops
ENA
endothelium
enforceability
Enricher
Ensdb
Ensembl
@@ -145,6 +148,7 @@ GBM
GC
GeneCard
GeneCards
generis
geo
GG
ggplot
@@ -185,10 +189,12 @@ HPCA
https
HVGs
ICb
ies
IgG
IgSF
Illumina
imap
immunities
immunohistochemical
immunophenotypic
immunostaining
@@ -218,6 +224,9 @@ Lafzi
LFC
LGLs
Liberzon
licensor
licensor's
licensors
linkedTxome
lncRNAs
loadings
@@ -243,6 +252,7 @@ medulloblastoma
MEK
Menyhárt
mer
merchantability
mesenchymal
mesoderm
metacell
@@ -353,6 +363,7 @@ RAS
rds
Reactome
README
redistributions
redux
relevel
renv
@@ -415,7 +426,8 @@ summarization
SummarizedExperiment
symlinked
symlinks
Τ
synched
T
Tabula
Tamayo
TBD
@@ -465,6 +477,7 @@ VST
Wattenberg
Wickham
Wickham's
WIPO
WNT
xenograft
Yu

0 comments on commit 03f0d55

Please sign in to comment.