From 089ecc1541d21d947f284c8a26de0058571d62f0 Mon Sep 17 00:00:00 2001
From: jiajic <72078254+jiajic@users.noreply.github.com>
Date: Wed, 6 Sep 2023 12:19:59 -0400
Subject: [PATCH 1/3] Update dev_workflow.yml

---
 .github/workflows/dev_workflow.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/dev_workflow.yml b/.github/workflows/dev_workflow.yml
index 62d9e35e..30e5dcbb 100644
--- a/.github/workflows/dev_workflow.yml
+++ b/.github/workflows/dev_workflow.yml
@@ -107,6 +107,7 @@ jobs:
           )
         shell: Rscript {0}
 
+      # add code cov
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
         env:
@@ -139,7 +140,7 @@ jobs:
         run: lintr::lint_package()
         shell: Rscript {0}
         env:
-          LINTR_ERROR_ON_LINT: true
+          LINTR_ERROR_ON_LINT: false
 
 
 

From 73ae625480788060342fb6f5cff0bf894eff63ca Mon Sep 17 00:00:00 2001
From: jiajic <72078254+jiajic@users.noreply.github.com>
Date: Wed, 6 Sep 2023 12:22:01 -0400
Subject: [PATCH 2/3] Update test-GiottoInstructions.R

---
 tests/testthat/test-GiottoInstructions.R | 31 +++++++++++++-----------
 1 file changed, 17 insertions(+), 14 deletions(-)

diff --git a/tests/testthat/test-GiottoInstructions.R b/tests/testthat/test-GiottoInstructions.R
index ed3ab976..d276f952 100644
--- a/tests/testthat/test-GiottoInstructions.R
+++ b/tests/testthat/test-GiottoInstructions.R
@@ -8,19 +8,22 @@ options('giotto.use_conda' = FALSE)
 # silence deprecated internals
 rlang::local_options(lifecycle_verbosity = "quiet")
 
-instrs = createGiottoInstructions(
-  show_plot = TRUE,
-  return_plot = NULL,
-  save_plot = FALSE,
-  save_dir = NULL,
-  plot_format = "png",
-  dpi = 300,
-  units = NULL,
-  height = NULL,
-  width = NULL,
-  is_docker = FALSE,
-  plot_count = 0,
-  fiji_path = NULL)
+suppressWarnings({
+  instrs = createGiottoInstructions(
+    show_plot = TRUE,
+    return_plot = NULL,
+    save_plot = FALSE,
+    save_dir = NULL,
+    plot_format = "png",
+    dpi = 300,
+    units = NULL,
+    height = NULL,
+    width = NULL,
+    is_docker = FALSE,
+    plot_count = 0,
+    fiji_path = NULL)
+})
+
 
 expression_matrix = matrix(1:100, nrow = 10)
 colnames(expression_matrix) = paste0("cell",1:10)
@@ -37,7 +40,7 @@ test_that("Instructions are created", {
 
 # readGiottoInstructions
 test_that("readGiottoInstructions reads a few giotto object params correctly", {
-  
+
   expect_type(readGiottoInstructions(gobject, param = "show_plot"), "logical")
   expect_type(readGiottoInstructions(gobject, param = "plot_format"), "character")
   expect_type(readGiottoInstructions(gobject, param = "dpi"), "double")

From 515d6153ac5daf328179c4942b9334ef036e0d45 Mon Sep 17 00:00:00 2001
From: jiajic <72078254+jiajic@users.noreply.github.com>
Date: Wed, 6 Sep 2023 12:36:50 -0400
Subject: [PATCH 3/3] update workflows and PAT

---
 .github/workflows/dev_workflow.yml  |  2 +-
 .github/workflows/prod_workflow.yml | 52 ++++++++++++++---------------
 2 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/.github/workflows/dev_workflow.yml b/.github/workflows/dev_workflow.yml
index 30e5dcbb..1096948b 100644
--- a/.github/workflows/dev_workflow.yml
+++ b/.github/workflows/dev_workflow.yml
@@ -19,7 +19,7 @@ jobs:
   R-CMD-check:
     name: R CMD Check
     env:
-      GITHUB_PAT: ${{ secrets.WORKFLOW_PAT }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     runs-on: ubuntu-latest
 
     steps:
diff --git a/.github/workflows/prod_workflow.yml b/.github/workflows/prod_workflow.yml
index 7056e97b..52810d79 100644
--- a/.github/workflows/prod_workflow.yml
+++ b/.github/workflows/prod_workflow.yml
@@ -21,7 +21,7 @@ permissions:
 jobs:
   R-CMD-check:
     env:
-      GITHUB_PAT: ${{ secrets.WORKFLOW_PAT }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -159,31 +159,31 @@ jobs:
   #         LINTR_ERROR_ON_LINT: true
 
 
-  render-rmarkdown:
-    name: Update README.Rmd
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout repo
-        uses: actions/checkout@v3
-        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
-
-      - name: Install rmarkdown
-        run: Rscript -e 'install.packages("rmarkdown")'
-
-      - name: Render README
-        run: Rscript -e 'rmarkdown::render("README.Rmd")'
-
-      - name: Commit results
-        run: |
-          git commit README.md -m 'Re-build README.Rmd' || echo "No changes to commit"
-          git push origin || echo "No changes to commit"
+  # render-rmarkdown:
+  #   name: Update README.Rmd
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Checkout repo
+  #       uses: actions/checkout@v3
+  #       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
+  #
+  #     - name: Install rmarkdown
+  #       run: Rscript -e 'install.packages("rmarkdown")'
+  #
+  #     - name: Render README
+  #       run: Rscript -e 'rmarkdown::render("README.Rmd")'
+  #
+  #     - name: Commit results
+  #       run: |
+  #         git commit README.md -m 'Re-build README.Rmd' || echo "No changes to commit"
+  #         git push origin || echo "No changes to commit"