From 759452156a311e99cd9293b642f94c48fb455b4b Mon Sep 17 00:00:00 2001 From: mtwesley Date: Sun, 24 Nov 2024 21:12:14 -0500 Subject: [PATCH] disabling workflows for now --- .github/workflows/R-CMD-check.yaml | 214 +++++++++++----------- .github/workflows/greta-install-deps.yaml | 108 +++++------ .github/workflows/pr-commands.yaml | 110 +++++------ .github/workflows/test-coverage.yaml | 128 ++++++------- 4 files changed, 280 insertions(+), 280 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 2bfc291..5b57a0c 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,108 +1,108 @@ -# NOTE: This workflow is overkill for most R packages -# check-standard.yaml is likely a better choice -# usethis::use_github_action("check-standard") will install it. -# -# 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 -on: - push: - branches: - - main - - master - pull_request: - branches: - - main - - master - -name: R-CMD-check - -concurrency: - group: ${{ github.workflow }}-${{ github.head_ref }} - cancel-in-progress: true - -jobs: - R-CMD-check: - runs-on: ${{ matrix.config.os }} - - name: ${{ matrix.config.os }} (${{ matrix.config.r }}) - - strategy: - fail-fast: false - matrix: - config: - - {os: macOS-latest, r: 'release'} - - {os: windows-latest, r: 'release'} - - {os: windows-latest, r: 'oldrel'} - - {os: ubuntu-18.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" } - - {os: ubuntu-18.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"} - - {os: ubuntu-18.04, r: 'oldrel-1', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"} - - {os: ubuntu-18.04, r: 'oldrel-2', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"} - - env: - RSPM: ${{ matrix.config.rspm }} - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - RETICULATE_AUTOCONFIGURE: 'FALSE' - TF_VERSION: '1.14.0' - - steps: - - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@v2 - id: install-r - with: - r-version: ${{ matrix.config.r }} - http-user-agent: ${{ matrix.config.http-user-agent }} - - - uses: r-lib/actions/setup-pandoc@v2 - - - uses: r-lib/actions/setup-r-dependencies@v2 - with: - cache-version: 2 - extra-packages: | - local::. - any::keras - any::rcmdcheck - - - name: Install Miniconda - run: | - reticulate::install_miniconda() - shell: Rscript {0} - - - name: Set options for conda binary for macOS - if: runner.os == 'macOS' - run: | - echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile - - - name: Install TensorFlow - run: | - cat("::group::Create Environment", sep = "\n") - reticulate::conda_create('r-reticulate', packages = c('python==3.7')) - cat("::endgroup::", sep = "\n") - - cat("::group::Install Tensorflow", sep = "\n") - keras::install_keras(tensorflow = Sys.getenv('TF_VERSION'), - extra_packages = c('IPython', 'requests', 'certifi', 'urllib3', 'tensorflow-probability==0.7.0', 'numpy==1.16.4')) - cat("::endgroup::", sep = "\n") - shell: Rscript {0} - - - - name: Python + TF details - run: | - tensorflow::tf_config() - tensorflow::tf_version() - reticulate::py_module_available("tensorflow_probability") - reticulate::py_config() - shell: Rscript {0} - - - name: Session info - run: | - options(width = 100) - pkgs <- installed.packages()[, "Package"] - sessioninfo::session_info(pkgs, include_base = TRUE) - shell: Rscript {0} - - - uses: r-lib/actions/check-r-package@v2 - with: - args: 'c("--no-manual", "--as-cran", "--no-multiarch")' +# # NOTE: This workflow is overkill for most R packages +# # check-standard.yaml is likely a better choice +# # usethis::use_github_action("check-standard") will install it. +# # +# # 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 +# on: +# push: +# branches: +# - main +# - master +# pull_request: +# branches: +# - main +# - master + +# name: R-CMD-check + +# concurrency: +# group: ${{ github.workflow }}-${{ github.head_ref }} +# cancel-in-progress: true + +# jobs: +# R-CMD-check: +# runs-on: ${{ matrix.config.os }} + +# name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + +# strategy: +# fail-fast: false +# matrix: +# config: +# - {os: macOS-latest, r: 'release'} +# - {os: windows-latest, r: 'release'} +# - {os: windows-latest, r: 'oldrel'} +# - {os: ubuntu-18.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" } +# - {os: ubuntu-18.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"} +# - {os: ubuntu-18.04, r: 'oldrel-1', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"} +# - {os: ubuntu-18.04, r: 'oldrel-2', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"} + +# env: +# RSPM: ${{ matrix.config.rspm }} +# GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} +# RETICULATE_AUTOCONFIGURE: 'FALSE' +# TF_VERSION: '1.14.0' + +# steps: + +# - uses: actions/checkout@v2 + +# - uses: r-lib/actions/setup-r@v2 +# id: install-r +# with: +# r-version: ${{ matrix.config.r }} +# http-user-agent: ${{ matrix.config.http-user-agent }} + +# - uses: r-lib/actions/setup-pandoc@v2 + +# - uses: r-lib/actions/setup-r-dependencies@v2 +# with: +# cache-version: 2 +# extra-packages: | +# local::. +# any::keras +# any::rcmdcheck + +# - name: Install Miniconda +# run: | +# reticulate::install_miniconda() +# shell: Rscript {0} + +# - name: Set options for conda binary for macOS +# if: runner.os == 'macOS' +# run: | +# echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile + +# - name: Install TensorFlow +# run: | +# cat("::group::Create Environment", sep = "\n") +# reticulate::conda_create('r-reticulate', packages = c('python==3.7')) +# cat("::endgroup::", sep = "\n") + +# cat("::group::Install Tensorflow", sep = "\n") +# keras::install_keras(tensorflow = Sys.getenv('TF_VERSION'), +# extra_packages = c('IPython', 'requests', 'certifi', 'urllib3', 'tensorflow-probability==0.7.0', 'numpy==1.16.4')) +# cat("::endgroup::", sep = "\n") +# shell: Rscript {0} + + +# - name: Python + TF details +# run: | +# tensorflow::tf_config() +# tensorflow::tf_version() +# reticulate::py_module_available("tensorflow_probability") +# reticulate::py_config() +# shell: Rscript {0} + +# - name: Session info +# run: | +# options(width = 100) +# pkgs <- installed.packages()[, "Package"] +# sessioninfo::session_info(pkgs, include_base = TRUE) +# shell: Rscript {0} + +# - uses: r-lib/actions/check-r-package@v2 +# with: +# args: 'c("--no-manual", "--as-cran", "--no-multiarch")' diff --git a/.github/workflows/greta-install-deps.yaml b/.github/workflows/greta-install-deps.yaml index 7f946c2..66bfccb 100644 --- a/.github/workflows/greta-install-deps.yaml +++ b/.github/workflows/greta-install-deps.yaml @@ -1,54 +1,54 @@ -on: - push: - branches: - - main - - master - pull_request: - branches: - - main - - master - -name: greta-install-deps - -jobs: - test-coverage: - runs-on: ubuntu-18.04 - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - steps: - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@v1 - - - uses: r-lib/actions/setup-pandoc@v1 - - - name: Fix Conda permissions on macOS - if: runner.os == 'macOS' - run: sudo chown -R $UID $CONDA - - - name: Remotes install greta - run: | - install.packages('remotes') - remotes::install_github("greta-dev/greta") - shell: Rscript {0} - - - name: Greta install deps - run: | - library(greta) - install_greta_deps(timeout = 50) - shell: Rscript {0} - - - name: Check the installation happened properly? - run: | - greta:::have_greta_conda_env() - greta:::have_conda() - greta:::have_python() - greta:::have_tf() - greta:::have_tfp() - shell: Rscript {0} - - - name: Greta run model - run: | - library(greta) - model(normal(0,1)) - shell: Rscript {0} +# on: +# push: +# branches: +# - main +# - master +# pull_request: +# branches: +# - main +# - master + +# name: greta-install-deps + +# jobs: +# test-coverage: +# runs-on: ubuntu-18.04 +# env: +# GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} +# steps: +# - uses: actions/checkout@v2 + +# - uses: r-lib/actions/setup-r@v1 + +# - uses: r-lib/actions/setup-pandoc@v1 + +# - name: Fix Conda permissions on macOS +# if: runner.os == 'macOS' +# run: sudo chown -R $UID $CONDA + +# - name: Remotes install greta +# run: | +# install.packages('remotes') +# remotes::install_github("greta-dev/greta") +# shell: Rscript {0} + +# - name: Greta install deps +# run: | +# library(greta) +# install_greta_deps(timeout = 50) +# shell: Rscript {0} + +# - name: Check the installation happened properly? +# run: | +# greta:::have_greta_conda_env() +# greta:::have_conda() +# greta:::have_python() +# greta:::have_tf() +# greta:::have_tfp() +# shell: Rscript {0} + +# - name: Greta run model +# run: | +# library(greta) +# model(normal(0,1)) +# shell: Rscript {0} diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml index e5edf9f..360f2f3 100644 --- a/.github/workflows/pr-commands.yaml +++ b/.github/workflows/pr-commands.yaml @@ -1,55 +1,55 @@ -on: - issue_comment: - types: [created] -name: Commands -jobs: - document: - if: startsWith(github.event.comment.body, '/document') - name: document - runs-on: macOS-latest - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - steps: - - uses: actions/checkout@v2 - - uses: r-lib/actions/pr-fetch@v1 - with: - repo-token: ${{ secrets.GITHUB_TOKEN }} - - uses: r-lib/actions/setup-r@v1 - - name: Install dependencies - run: Rscript -e 'install.packages(c("remotes", "roxygen2"))' -e 'remotes::install_deps(dependencies = TRUE)' - - name: Document - run: Rscript -e 'roxygen2::roxygenise()' - - name: commit - run: | - git config --local user.email "actions@github.com" - git config --local user.name "GitHub Actions" - git add man/\* NAMESPACE - git commit -m 'Document' - - uses: r-lib/actions/pr-push@v1 - with: - repo-token: ${{ secrets.GITHUB_TOKEN }} - style: - if: startsWith(github.event.comment.body, '/style') - name: style - runs-on: macOS-latest - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - steps: - - uses: actions/checkout@v2 - - uses: r-lib/actions/pr-fetch@v1 - with: - repo-token: ${{ secrets.GITHUB_TOKEN }} - - uses: r-lib/actions/setup-r@v1 - - name: Install dependencies - run: Rscript -e 'install.packages("styler")' - - name: Style - run: Rscript -e 'styler::style_pkg()' - - name: commit - run: | - git config --local user.email "actions@github.com" - git config --local user.name "GitHub Actions" - git add \*.R - git commit -m 'Style' - - uses: r-lib/actions/pr-push@v1 - with: - repo-token: ${{ secrets.GITHUB_TOKEN }} +# on: +# issue_comment: +# types: [created] +# name: Commands +# jobs: +# document: +# if: startsWith(github.event.comment.body, '/document') +# name: document +# runs-on: macOS-latest +# env: +# GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} +# steps: +# - uses: actions/checkout@v2 +# - uses: r-lib/actions/pr-fetch@v1 +# with: +# repo-token: ${{ secrets.GITHUB_TOKEN }} +# - uses: r-lib/actions/setup-r@v1 +# - name: Install dependencies +# run: Rscript -e 'install.packages(c("remotes", "roxygen2"))' -e 'remotes::install_deps(dependencies = TRUE)' +# - name: Document +# run: Rscript -e 'roxygen2::roxygenise()' +# - name: commit +# run: | +# git config --local user.email "actions@github.com" +# git config --local user.name "GitHub Actions" +# git add man/\* NAMESPACE +# git commit -m 'Document' +# - uses: r-lib/actions/pr-push@v1 +# with: +# repo-token: ${{ secrets.GITHUB_TOKEN }} +# style: +# if: startsWith(github.event.comment.body, '/style') +# name: style +# runs-on: macOS-latest +# env: +# GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} +# steps: +# - uses: actions/checkout@v2 +# - uses: r-lib/actions/pr-fetch@v1 +# with: +# repo-token: ${{ secrets.GITHUB_TOKEN }} +# - uses: r-lib/actions/setup-r@v1 +# - name: Install dependencies +# run: Rscript -e 'install.packages("styler")' +# - name: Style +# run: Rscript -e 'styler::style_pkg()' +# - name: commit +# run: | +# git config --local user.email "actions@github.com" +# git config --local user.name "GitHub Actions" +# git add \*.R +# git commit -m 'Style' +# - uses: r-lib/actions/pr-push@v1 +# with: +# repo-token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 9644845..abb28f3 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -1,76 +1,76 @@ -on: - push: - branches: - - main - - master - pull_request: - branches: - - main - - master +# on: +# push: +# branches: +# - main +# - master +# pull_request: +# branches: +# - main +# - master -name: test-coverage +# name: test-coverage -jobs: - test-coverage: - runs-on: macOS-latest - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - steps: - - uses: actions/checkout@v2 +# jobs: +# test-coverage: +# runs-on: macOS-latest +# env: +# GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} +# steps: +# - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-r@v1 +# - uses: r-lib/actions/setup-r@v1 - - uses: r-lib/actions/setup-pandoc@v1 +# - uses: r-lib/actions/setup-pandoc@v1 - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} +# - name: Query dependencies +# run: | +# install.packages('remotes') +# saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) +# writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") +# shell: Rscript {0} - - name: Restore R package cache - uses: actions/cache@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: Restore R package cache +# uses: actions/cache@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: | - install.packages(c("remotes")) - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("covr") - shell: Rscript {0} +# - name: Install dependencies +# run: | +# install.packages(c("remotes")) +# remotes::install_deps(dependencies = TRUE) +# remotes::install_cran("covr") +# shell: Rscript {0} - ### - - name: Install Miniconda - run: | - install.packages(c("remotes", "keras")) - reticulate::install_miniconda() - shell: Rscript {0} +# ### +# - name: Install Miniconda +# run: | +# install.packages(c("remotes", "keras")) +# reticulate::install_miniconda() +# shell: Rscript {0} - - name: Set options for conda binary for macOS - if: runner.os == 'macOS' - run: | - echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile +# - name: Set options for conda binary for macOS +# if: runner.os == 'macOS' +# run: | +# echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile -# Perhaps here is where we can install / change the environment that we are -# installing into? Can we call our own greta install functions here? - - name: Install TensorFlow - run: | - reticulate::conda_create(envname = "greta-env",python_version = "3.7") - reticulate::conda_install(envname = "greta-env", packages = c("numpy==1.16.4", "tensorflow-probability==0.7.0", "tensorflow==1.14.0")) - shell: Rscript {0} +# # Perhaps here is where we can install / change the environment that we are +# # installing into? Can we call our own greta install functions here? +# - name: Install TensorFlow +# run: | +# reticulate::conda_create(envname = "greta-env",python_version = "3.7") +# reticulate::conda_install(envname = "greta-env", packages = c("numpy==1.16.4", "tensorflow-probability==0.7.0", "tensorflow==1.14.0")) +# shell: Rscript {0} - - name: Python + TF details - run: | - Rscript -e 'tensorflow::tf_config()' - Rscript -e 'tensorflow::tf_version()' - Rscript -e 'reticulate::py_module_available("tensorflow_probability")' - Rscript -e 'reticulate::py_config()' - ### +# - name: Python + TF details +# run: | +# Rscript -e 'tensorflow::tf_config()' +# Rscript -e 'tensorflow::tf_version()' +# Rscript -e 'reticulate::py_module_available("tensorflow_probability")' +# Rscript -e 'reticulate::py_config()' +# ### - - name: Test coverage - run: covr::codecov() - shell: Rscript {0} +# - name: Test coverage +# run: covr::codecov() +# shell: Rscript {0}