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Merge branch 'main' into pr/710
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strengejacke committed Jun 19, 2022
2 parents b6fdc8d + 4d38d04 commit 823490c
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107 changes: 30 additions & 77 deletions .github/workflows/R-check.yaml
Original file line number Diff line number Diff line change
@@ -1,12 +1,16 @@
# 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
#
# NOTE: This workflow is overkill for most R packages and
# check-standard.yaml is likely a better choice.
# usethis::use_github_action("check-standard") will install it.
on:
push:
branches:
- main
branches: [main, master]
pull_request:
branches:
- main
branches: [main, master]

name: R-check
name: R-CMD-check

jobs:
R-CMD-check:
Expand All @@ -18,90 +22,39 @@ jobs:
fail-fast: false
matrix:
config:
- {os: macOS-latest, r: 'devel'}
- {os: macOS-latest, r: 'release'}
- {os: macOS-latest, r: 'oldrel'}
- {os: macOS-latest, r: 'release'}

- {os: windows-latest, r: 'devel'}
- {os: windows-latest, r: 'release'}
- {os: windows-latest, r: 'oldrel'}
- {os: ubuntu-18.04, r: 'devel'}
- {os: ubuntu-18.04, r: 'release'}
- {os: ubuntu-18.04, r: 'oldrel'}
# - {os: ubuntu-18.04, r: '3.5.0'}
# - {os: ubuntu-18.04, r: '3.4.0'}
- {os: windows-latest, r: 'oldrel-1'}

# Use older ubuntu to maximise backward compatibility
- {os: ubuntu-18.04, r: 'devel', http-user-agent: 'release'}
- {os: ubuntu-18.04, r: 'release'}
- {os: ubuntu-18.04, r: 'oldrel-1'}

env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes
_R_CHECK_CRAN_INCOMING_: false
_R_CHECK_FORCE_SUGGESTS_: false

steps:
- uses: actions/checkout@v2

- uses: r-lib/actions/setup-r@master
- uses: r-lib/actions/setup-pandoc@v2

- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true

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

- name: Query dependencies
run: |
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}

- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v1
- 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 system dependencies
if: runner.os == 'Linux'
env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
run: |
Rscript -e "remotes::install_github('r-hub/sysreqs')"
sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
sudo -s eval "$sysreqs"
- name: Install dependencies
run: |
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("rcmdcheck")
remotes::install_github("crj32/M3C") # package is not on CRAN but bioconductor
shell: Rscript {0}

- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
if (requireNamespace("sessioninfo")) {
sessioninfo::session_info(pkgs, include_base = TRUE)
} else {
utils::sessionInfo(pkgs)
}
shell: Rscript {0}

- name: Check
env:
_R_CHECK_CRAN_INCOMING_: false
_R_CHECK_FORCE_SUGGESTS_: false
# _R_CHECK_DEPENDS_ONLY_: true
run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
shell: Rscript {0}

- name: Show testthat output
if: always()
run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash
extra-packages: any::rcmdcheck, any::XML
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
41 changes: 0 additions & 41 deletions .github/workflows/pkgdown.old_yml

This file was deleted.

65 changes: 32 additions & 33 deletions .github/workflows/pkgdown.yml
Original file line number Diff line number Diff line change
@@ -1,51 +1,50 @@
# 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
branches: [main, master]
pull_request:
branches: [main, master]
release:
types: [published]
workflow_dispatch:

name: pkgdown

jobs:
pkgdown:
runs-on: macOS-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 }}
steps:
- uses: actions/checkout@v2

- uses: r-lib/actions/setup-r@master
- uses: r-lib/actions/setup-pandoc@v2

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

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

- name: Query dependencies
run: |
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}

- name: Cache R packages
uses: actions/cache@v1
- uses: r-lib/actions/setup-r@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-
use-public-rspm: true

- name: Install dependencies
run: |
install.packages("remotes")
# To get links for homepage
remotes::install_cran("devtools")
remotes::install_deps(dependencies = TRUE)
remotes::install_dev("pkgdown")
- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: |
any::pkgdown
local::.
any::BH
any::RcppEigen
needs: website

- 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
44 changes: 44 additions & 0 deletions .github/workflows/render-readme.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
# 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]
pull_request:
branches: [main, master]

name: render-readme

jobs:
render-readme:
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

steps:
- name: Checkout repo
uses: actions/checkout@v2
with:
fetch-depth: 0

- uses: r-lib/actions/setup-pandoc@v2

- uses: r-lib/actions/setup-r@v2

- uses: r-lib/actions/setup-renv@v2

- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: |
deps::.
any::parameters
- name: Render README
run: Rscript -e 'rmarkdown::render("README.Rmd")'

- name: Commit Results
run: |
git config --local user.name "$GITHUB_ACTOR"
git config --local user.email "[email protected]"
git commit -m 'Re-build README.Rmd' || echo "No changes to commit"
git push origin || echo "No changes to commit"
23 changes: 18 additions & 5 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Type: Package
Package: parameters
Title: Processing of Model Parameters
Version: 0.18.1.1
Version: 0.18.1.4
Authors@R:
c(person(given = "Daniel",
family = "Lüdecke",
Expand Down Expand Up @@ -72,11 +72,11 @@ License: GPL-3
URL: https://easystats.github.io/parameters/
BugReports: https://github.com/easystats/parameters/issues
Depends:
R (>= 3.4)
R (>= 3.5)
Imports:
bayestestR (>= 0.11.5),
bayestestR (>= 0.12.1),
datawizard (>= 0.4.1),
insight (>= 0.17.1),
insight (>= 0.17.1.8),
graphics,
methods,
stats,
Expand Down Expand Up @@ -178,7 +178,6 @@ Suggests:
sandwich,
see (>= 0.6.9),
sjstats,
spelling,
survey,
survival,
testthat,
Expand All @@ -194,3 +193,17 @@ Language: en-US
RoxygenNote: 7.2.0
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)
Remotes:
easystats/insight
RemoteType: github
RemoteHost: api.github.com
RemoteRepo: glmmTMB
RemoteUsername: glmmTMB
RemoteRef: ci_tweaks
RemoteSha: fd8bb78acd8b198147285ce94b1f67043349f570
RemoteSubdir: glmmTMB
GithubRepo: glmmTMB
GithubUsername: glmmTMB
GithubRef: ci_tweaks
GithubSHA1: fd8bb78acd8b198147285ce94b1f67043349f570
GithubSubdir: glmmTMB
5 changes: 5 additions & 0 deletions NAMESPACE
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
# Generated by roxygen2: do not edit by hand

S3method(as.data.frame,VarCorr.lme)
S3method(as.data.frame,glmmTMB)
S3method(as.data.frame,lm)
S3method(as.data.frame,merMod)
Expand Down Expand Up @@ -245,11 +246,13 @@ S3method(model_parameters,clm2)
S3method(model_parameters,clmm)
S3method(model_parameters,clmm2)
S3method(model_parameters,coeftest)
S3method(model_parameters,comparisons)
S3method(model_parameters,cpglmm)
S3method(model_parameters,data.frame)
S3method(model_parameters,dbscan)
S3method(model_parameters,default)
S3method(model_parameters,deltaMethod)
S3method(model_parameters,deltamethod)
S3method(model_parameters,dep.effect)
S3method(model_parameters,draws)
S3method(model_parameters,emmGrid)
Expand Down Expand Up @@ -287,6 +290,7 @@ S3method(model_parameters,lqm)
S3method(model_parameters,lqmm)
S3method(model_parameters,maov)
S3method(model_parameters,marginaleffects)
S3method(model_parameters,marginalmeans)
S3method(model_parameters,margins)
S3method(model_parameters,maxLik)
S3method(model_parameters,maxim)
Expand Down Expand Up @@ -522,6 +526,7 @@ S3method(plot,parameters_sem)
S3method(plot,parameters_simulate)
S3method(plot,parameters_stan)
S3method(predict,cluster_analysis)
S3method(predict,cluster_meta)
S3method(predict,kmeans)
S3method(predict,parameters_clusters)
S3method(predict,parameters_efa)
Expand Down
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