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fixing gh actions
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dipterix committed Jun 23, 2023
1 parent 67cdbb9 commit a6298b4
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95 changes: 18 additions & 77 deletions .github/workflows/R-CMD-check.yaml
Original file line number Diff line number Diff line change
@@ -1,14 +1,10 @@
# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
branches:
- main
- master
branches: [main, master]
pull_request:
branches:
- main
- master
branches: [main, master]

name: R-CMD-check

Expand All @@ -22,87 +18,32 @@ jobs:
fail-fast: false
matrix:
config:
- {os: macos-latest, r: 'release'}
- {os: windows-latest, r: 'release'}
- {os: macOS-latest, r: 'release'}
- {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
- {os: ubuntu-latest, r: 'release'}
- {os: ubuntu-latest, r: 'oldrel-1'}

env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
HDF5_VERSION: 1.12.0
HDF5_DIR: ${{ github.workspace }}/cache/hdf5
R_KEEP_PKG_SOURCE: yes

steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- name: Cache HDF5
uses: actions/cache@v2
with:
path: ${{ env.HDF5_DIR }}
key: ${{ runner.os }}-hdf5-${{ env.HDF5_VERSION }}

- name: Build HDF5
if: runner.os != 'Windows' && steps.cache-hdf5.outputs.cache-hit != 'true'
run: |
chmod a+x ./inst/hdf5_installer.sh
./inst/hdf5_installer.sh
ls ${{ env.HDF5_DIR }}
- uses: r-lib/actions/setup-pandoc@v2

- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}

- name: Install remotes
run: |
install.packages('remotes')
shell: Rscript {0}

- name: Install system dependencies
if: runner.os == 'Linux'
run: |
while read -r cmd
do
eval sudo $cmd
done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true

- name: Query dependencies
run: |
install.packages('ravemanager', repos = c(beauchamplab = "https://beauchamplab.r-universe.dev", dipterix = "https://dipterix.r-universe.dev", CRAN = "https://cloud.r-project.org"))
Sys.setenv("RAVE_LIB_PATH" = .libPaths()[[1]])
ravemanager::install(finalize = FALSE)
rave::download_sample_data('YAB', replace_if_exists = TRUE)
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}

- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v2
- uses: r-lib/actions/setup-r-dependencies@v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-

- name: Install dependencies
run: |
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("rcmdcheck")
shell: Rscript {0}

- name: Check
env:
_R_CHECK_CRAN_INCOMING_REMOTE_: false
run: |
options(crayon.enabled = TRUE)
rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
shell: Rscript {0}
extra-packages: any::rcmdcheck
needs: check

- name: Upload check results
if: failure()
uses: actions/upload-artifact@main
- uses: r-lib/actions/check-r-package@v2
with:
name: ${{ runner.os }}-r${{ matrix.config.r }}-results
path: check
upload-snapshots: true
79 changes: 31 additions & 48 deletions .github/workflows/pkgdown.yaml
Original file line number Diff line number Diff line change
@@ -1,65 +1,48 @@
# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
branches:
- main
- master
branches: [main, master]
pull_request:
branches: [main, master]
release:
types: [published]
workflow_dispatch:

name: pkgdown

jobs:
pkgdown:
runs-on: macOS-latest
runs-on: ubuntu-latest
# Only restrict concurrency for non-PR jobs
concurrency:
group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
HDF5_VERSION: 1.12.0
HDF5_DIR: ${{ github.workspace }}/cache/hdf5
permissions:
contents: write
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- name: Cache HDF5
uses: actions/cache@v2
with:
path: ${{ env.HDF5_DIR }}
key: ${{ runner.os }}-hdf5-${{ env.HDF5_VERSION }}

- name: Build HDF5
if: steps.cache-hdf5.outputs.cache-hit != 'true'
run: |
chmod a+x ./inst/hdf5_installer.sh
./inst/hdf5_installer.sh
ls ${{ env.HDF5_DIR }}
- uses: r-lib/actions/setup-r@v1
- uses: r-lib/actions/setup-pandoc@v2

- uses: r-lib/actions/setup-pandoc@v1

- name: Query dependencies
run: |
h5cc=file.path(Sys.getenv("HDF5_DIR"), "bin/h5cc")
h5cc=normalizePath(h5cc)
install.packages("hdf5r", configure.args=sprintf("--with-hdf5=%s", h5cc))
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}
- uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true

- name: Cache R packages
uses: actions/cache@v2
- uses: r-lib/actions/setup-r-dependencies@v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
extra-packages: any::pkgdown, local::.
needs: website

- name: Install dependencies
run: |
remotes::install_deps(dependencies = TRUE)
install.packages("pkgdown", type = "binary")
- name: Build site
run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
shell: Rscript {0}

- name: Install package
run: R CMD INSTALL .

- name: Deploy package
run: |
git config --local user.email "[email protected]"
git config --local user.name "GitHub Actions"
Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
- name: Deploy to GitHub pages 🚀
if: github.event_name != 'pull_request'
uses: JamesIves/[email protected]
with:
clean: false
branch: gh-pages
folder: docs
7 changes: 3 additions & 4 deletions DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -19,11 +19,10 @@ Description: R Analysis and Visualization of 'ECOG/iEEG' Data
License: GPL-3
Encoding: UTF-8
Language: en-US
URL: https://rave.wiki
URL: https://rave.wiki,
https://beauchamplab.github.io/rave/
BugReports: https://github.com/beauchamplab/rave/issues
RoxygenNote: 7.2.1
Depends:
R (>= 3.6.0)
RoxygenNote: 7.2.3
Imports:
utils,
stats,
Expand Down
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -6,6 +6,6 @@
For all RAVE info, including installation instructions, visit https://rave.wiki

<!-- badges: start -->
[![R-CMD-check](https://github.com/beauchamplab/rave/workflows/R-CMD-check/badge.svg)](https://github.com/beauchamplab/rave/actions)
[![R-CMD-check](https://github.com/beauchamplab/rave/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/beauchamplab/rave/actions/workflows/R-CMD-check.yaml)
<!-- badges: end -->

5 changes: 4 additions & 1 deletion _pkgdown.yml
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@@ -1 +1,4 @@
url: https://beauchamplab.github.io/rave
url: https://beauchamplab.github.io/rave/
template:
bootstrap: 5

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