From 62dee6901090954a43183f0256ad0c7e3db81331 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Tue, 28 Jan 2025 15:42:08 +0100
Subject: [PATCH 01/58] Add script to change testing depth of some tests

---
 .github/workflows/build-check-install.yaml | 31 ++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 681b227f..4ef68ca0 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -515,6 +515,37 @@ jobs:
           path: "${{ inputs.additional-caches }}"
           key: additional-caches-${{ runner.os }}
 
+      - name: Check only affected modules
+        if: startsWith(${{ github.event.repository.name }}, "teal.modules.") && github.event_name == 'pull_request'
+        run: |
+          # Get the list of files that have changed
+          files=$(git diff --name-only main..)
+
+          # Base directories
+          src_dir="R/"
+          test_dir="tests/testthat/"
+
+          # Loop through each modified file and determine which tests to run
+          for file in $files; do
+
+              # Extract the base name of the file, examples:
+              # tests/testthat/test-shinytest2-foo.R -> foo
+              # R/foo.R -> foo
+              base_name=$(basename "$file" .R | sed s/test-shinytest2-//g)
+
+              # Find matching test files
+              test_files=$(grep -l "$base_name" "$test_dir"test-shinytest2-*.R)
+
+              if [ -z "$test_files" ]; then
+                  echo "No test files found for modified file about $base_name."
+              else
+                  echo "${file} matches ${test_files}"
+                  sed -i 's/skip_if_too_deep(5)/skip_if_too_deep(3)/g' "$test_files"
+              fi
+          done
+          TESTING_DEPTH=3
+        shell: bash
+
       - name: Build R package 🏗
         run: |
           if [ "${{ inputs.additional-env-vars }}" != "" ]

From aff016aa6e81a27b7248255414e8ffea1e341816 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Fri, 31 Jan 2025 11:56:06 +0100
Subject: [PATCH 02/58] Look up for only R or tests files (not vignettes, CI/CD
 or dependencies)

---
 .github/workflows/build-check-install.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 4ef68ca0..52d34167 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -518,8 +518,8 @@ jobs:
       - name: Check only affected modules
         if: startsWith(${{ github.event.repository.name }}, "teal.modules.") && github.event_name == 'pull_request'
         run: |
-          # Get the list of files that have changed
-          files=$(git diff --name-only main..)
+          # Get the list of R files that have changed
+          files=$(git diff --name-only main.. -- tests/* R/*.R)
 
           # Base directories
           src_dir="R/"

From c142c72ba0adc3f0498b547e67f8cca4cc819944 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Fri, 31 Jan 2025 11:59:12 +0100
Subject: [PATCH 03/58] Reorganize code

---
 .github/workflows/build-check-install.yaml | 25 ++++++++++++++--------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 52d34167..d1ec061c 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -532,18 +532,25 @@ jobs:
               # tests/testthat/test-shinytest2-foo.R -> foo
               # R/foo.R -> foo
               base_name=$(basename "$file" .R | sed s/test-shinytest2-//g)
+              # Find matching test files (parenthesis to not match arguments)
+              test_files=$(grep -l "$base_name(" "$test_dir"test-shinytest2-*.R)
 
-              # Find matching test files
-              test_files=$(grep -l "$base_name" "$test_dir"test-shinytest2-*.R)
-
-              if [ -z "$test_files" ]; then
-                  echo "No test files found for modified file about $base_name."
-              else
-                  echo "${file} matches ${test_files}"
+              # Modify in place so that only modified modules are tested.
+              if [[ -n "$test_files" ]]
+              then {
                   sed -i 's/skip_if_too_deep(5)/skip_if_too_deep(3)/g' "$test_files"
-              fi
+                  TESTING_DEPTH=3
+              } else {
+                  # Flag for helpers
+                  helper_modified="yes"
+              } fi
+
+              # R file without corresponding test file: assume it affects all
+              if [[ -n "$helper_modified" ]]
+              then {
+                  TESTING_DEPTH=5
+              } fi
           done
-          TESTING_DEPTH=3
         shell: bash
 
       - name: Build R package 🏗

From 7c1c12b94bc18986522e86f39ffd1665dc9d4d80 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Fri, 31 Jan 2025 12:56:57 +0100
Subject: [PATCH 04/58] Add chekout action to be on the package repository

---
 .github/workflows/build-check-install.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index d1ec061c..9dcee110 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -517,6 +517,7 @@ jobs:
 
       - name: Check only affected modules
         if: startsWith(${{ github.event.repository.name }}, "teal.modules.") && github.event_name == 'pull_request'
+        uses: actions/checkout@v4.1.1
         run: |
           # Get the list of R files that have changed
           files=$(git diff --name-only main.. -- tests/* R/*.R)

From dcaedbfd7dba3aa0158b207b615ce84b03c95421 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Fri, 31 Jan 2025 14:23:56 +0100
Subject: [PATCH 05/58] Add emoji

---
 .github/workflows/build-check-install.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 9dcee110..7fd1192c 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -515,7 +515,7 @@ jobs:
           path: "${{ inputs.additional-caches }}"
           key: additional-caches-${{ runner.os }}
 
-      - name: Check only affected modules
+      - name: Check only affected modules 🎯
         if: startsWith(${{ github.event.repository.name }}, "teal.modules.") && github.event_name == 'pull_request'
         uses: actions/checkout@v4.1.1
         run: |

From efdc03b7fa99d31ef8b1dedd90ff6226037bf7b6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Fri, 31 Jan 2025 14:55:37 +0100
Subject: [PATCH 06/58] Reset to the previous TESTING_DEPTH

---
 .github/workflows/build-check-install.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 7fd1192c..cfe8195d 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -535,6 +535,7 @@ jobs:
               base_name=$(basename "$file" .R | sed s/test-shinytest2-//g)
               # Find matching test files (parenthesis to not match arguments)
               test_files=$(grep -l "$base_name(" "$test_dir"test-shinytest2-*.R)
+              td=$TESTING_DEPTH
 
               # Modify in place so that only modified modules are tested.
               if [[ -n "$test_files" ]]
@@ -546,10 +547,10 @@ jobs:
                   helper_modified="yes"
               } fi
 
-              # R file without corresponding test file: assume it affects all
+              # R file without corresponding test file: reset the testing depth
               if [[ -n "$helper_modified" ]]
               then {
-                  TESTING_DEPTH=5
+                  TESTING_DEPTH=td
               } fi
           done
         shell: bash

From 044ccf654acea43333fcb9a92ebb552162d5e46d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 3 Feb 2025 09:43:27 +0100
Subject: [PATCH 07/58] Uses and run aren't compatible

---
 .github/workflows/build-check-install.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index cfe8195d..7a4c119f 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -515,9 +515,11 @@ jobs:
           path: "${{ inputs.additional-caches }}"
           key: additional-caches-${{ runner.os }}
 
+      - name: Setup git checkout ⚙️
+        uses: actions/checkout@v4.1.1
+
       - name: Check only affected modules 🎯
         if: startsWith(${{ github.event.repository.name }}, "teal.modules.") && github.event_name == 'pull_request'
-        uses: actions/checkout@v4.1.1
         run: |
           # Get the list of R files that have changed
           files=$(git diff --name-only main.. -- tests/* R/*.R)

From 161b1c659b78bbfda5e3c27a460b7dbc8a086d00 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 3 Feb 2025 09:57:06 +0100
Subject: [PATCH 08/58] Checkout to the right directory

---
 .github/workflows/build-check-install.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 7a4c119f..0006b0e8 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -517,6 +517,7 @@ jobs:
 
       - name: Setup git checkout ⚙️
         uses: actions/checkout@v4.1.1
+        working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
       - name: Check only affected modules 🎯
         if: startsWith(${{ github.event.repository.name }}, "teal.modules.") && github.event_name == 'pull_request'

From 6e0c72a079282699b40597a61961e143dd2857cb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 3 Feb 2025 10:03:54 +0100
Subject: [PATCH 09/58] Use path instead of working-directory

---
 .github/workflows/build-check-install.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 0006b0e8..73457693 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -517,7 +517,8 @@ jobs:
 
       - name: Setup git checkout ⚙️
         uses: actions/checkout@v4.1.1
-        working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+        with:
+          path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
       - name: Check only affected modules 🎯
         if: startsWith(${{ github.event.repository.name }}, "teal.modules.") && github.event_name == 'pull_request'

From 9d31c30ab6a310cfb6d72b3b9b07f15a1f929c65 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 3 Feb 2025 10:13:46 +0100
Subject: [PATCH 10/58] Move the working directory where it should be

---
 .github/workflows/build-check-install.yaml | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 73457693..0a37978b 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -515,14 +515,16 @@ jobs:
           path: "${{ inputs.additional-caches }}"
           key: additional-caches-${{ runner.os }}
 
-      - name: Setup git checkout ⚙️
-        uses: actions/checkout@v4.1.1
-        with:
-          path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
-
       - name: Check only affected modules 🎯
         if: startsWith(${{ github.event.repository.name }}, "teal.modules.") && github.event_name == 'pull_request'
         run: |
+          echo pwd
+
+          # Set working directory where the git repo is
+          cd ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+
+          ls -lh
+
           # Get the list of R files that have changed
           files=$(git diff --name-only main.. -- tests/* R/*.R)
 

From 25ce19d2f9364d42df240eeb8cbc2a8c6574a351 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 3 Feb 2025 10:26:41 +0100
Subject: [PATCH 11/58] Add some more info to help debug what is happening

---
 .github/workflows/build-check-install.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 0a37978b..1bd4bd9f 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -518,12 +518,13 @@ jobs:
       - name: Check only affected modules 🎯
         if: startsWith(${{ github.event.repository.name }}, "teal.modules.") && github.event_name == 'pull_request'
         run: |
-          echo pwd
-
           # Set working directory where the git repo is
           cd ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
+          # Debugging
+          pwd
           ls -lh
+          git branch
 
           # Get the list of R files that have changed
           files=$(git diff --name-only main.. -- tests/* R/*.R)

From b684dfc18bba1c6d7269b801deabf60549461787 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 3 Feb 2025 10:48:36 +0100
Subject: [PATCH 12/58] Get the default branch of the repository to compare
 with.

---
 .github/workflows/build-check-install.yaml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 1bd4bd9f..227ec421 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -515,6 +515,14 @@ jobs:
           path: "${{ inputs.additional-caches }}"
           key: additional-caches-${{ runner.os }}
 
+      - name: Checkout default branch (PR) ⚙️
+        uses: actions/checkout@v4.1.1
+        if: github.event_name == 'pull_request'
+        with:
+          path: ${{ github.event.repository.name }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          fetch-depth: 1
+
       - name: Check only affected modules 🎯
         if: startsWith(${{ github.event.repository.name }}, "teal.modules.") && github.event_name == 'pull_request'
         run: |

From 09dd369c84e53c567f7cbfd1bb8bca2f7b24e85c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 3 Feb 2025 11:06:35 +0100
Subject: [PATCH 13/58] Modify fetch-depth to have also the default branch

---
 .github/workflows/build-check-install.yaml | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 227ec421..d7e71d6d 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -297,7 +297,7 @@ jobs:
           ref: ${{ steps.branch-name.outputs.head_ref_branch }}
           path: ${{ github.event.repository.name }}
           repository: ${{ github.event.pull_request.head.repo.full_name }}
-          fetch-depth: 0
+          fetch-depth: 2
 
       - name: Checkout repo 🛎
         uses: actions/checkout@v4.1.1
@@ -515,14 +515,6 @@ jobs:
           path: "${{ inputs.additional-caches }}"
           key: additional-caches-${{ runner.os }}
 
-      - name: Checkout default branch (PR) ⚙️
-        uses: actions/checkout@v4.1.1
-        if: github.event_name == 'pull_request'
-        with:
-          path: ${{ github.event.repository.name }}
-          repository: ${{ github.event.pull_request.head.repo.full_name }}
-          fetch-depth: 1
-
       - name: Check only affected modules 🎯
         if: startsWith(${{ github.event.repository.name }}, "teal.modules.") && github.event_name == 'pull_request'
         run: |

From aa02b04356650586df1532e20bcc86a30079698f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 3 Feb 2025 11:54:46 +0100
Subject: [PATCH 14/58] Check other folders

---
 .github/workflows/build-check-install.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index d7e71d6d..55b77179 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -524,7 +524,10 @@ jobs:
           # Debugging
           pwd
           ls -lh
+          ls -lh ..
           git branch
+          git -C .. branch
+
 
           # Get the list of R files that have changed
           files=$(git diff --name-only main.. -- tests/* R/*.R)

From 31e58e7e82a5f46733c70ed7fd2edacbaa28fc19 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 3 Feb 2025 12:10:29 +0100
Subject: [PATCH 15/58] Fetch all branches

---
 .github/workflows/build-check-install.yaml | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 55b77179..7fe457e9 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -297,7 +297,7 @@ jobs:
           ref: ${{ steps.branch-name.outputs.head_ref_branch }}
           path: ${{ github.event.repository.name }}
           repository: ${{ github.event.pull_request.head.repo.full_name }}
-          fetch-depth: 2
+          fetch-depth: 0
 
       - name: Checkout repo 🛎
         uses: actions/checkout@v4.1.1
@@ -522,12 +522,9 @@ jobs:
           cd ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
           # Debugging
-          pwd
-          ls -lh
-          ls -lh ..
-          git branch
-          git -C .. branch
 
+          git fetch --all
+          git branch
 
           # Get the list of R files that have changed
           files=$(git diff --name-only main.. -- tests/* R/*.R)

From decb120db9742081b5bc4f5db835c1c756c4c82a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 3 Feb 2025 12:27:56 +0100
Subject: [PATCH 16/58] Directly fetch the main branch from origin

---
 .github/workflows/build-check-install.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 7fe457e9..970598dd 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -523,7 +523,7 @@ jobs:
 
           # Debugging
 
-          git fetch --all
+          git fetch origin main
           git branch
 
           # Get the list of R files that have changed

From 8c0189380ef28b93b1f1803e8d69ef11d147013d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 3 Feb 2025 12:28:58 +0100
Subject: [PATCH 17/58] Print remotes for debugging

---
 .github/workflows/build-check-install.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 970598dd..91a69402 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -523,6 +523,7 @@ jobs:
 
           # Debugging
 
+          git remote -v
           git fetch origin main
           git branch
 

From 8f4afc7a91d980d32f4a71dc82d6c12b384c8a90 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 3 Feb 2025 12:48:10 +0100
Subject: [PATCH 18/58] Change quotes and to pull instead just fetch

---
 .github/workflows/build-check-install.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 91a69402..e1b6211f 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -516,7 +516,7 @@ jobs:
           key: additional-caches-${{ runner.os }}
 
       - name: Check only affected modules 🎯
-        if: startsWith(${{ github.event.repository.name }}, "teal.modules.") && github.event_name == 'pull_request'
+        if: startsWith(${{ github.event.repository.name }}, 'teal.modules.') && github.event_name == 'pull_request'
         run: |
           # Set working directory where the git repo is
           cd ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
@@ -524,7 +524,7 @@ jobs:
           # Debugging
 
           git remote -v
-          git fetch origin main
+          git pull origin main
           git branch
 
           # Get the list of R files that have changed

From bc4f2dba21968811f9cc78c12b335858ba6ae8df Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 3 Feb 2025 14:20:08 +0100
Subject: [PATCH 19/58] Add three dots and the branch name.

---
 .github/workflows/build-check-install.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index e1b6211f..e2bf6129 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -528,7 +528,7 @@ jobs:
           git branch
 
           # Get the list of R files that have changed
-          files=$(git diff --name-only main.. -- tests/* R/*.R)
+          files=$(git diff --name-only main...${{ github.head_ref }} -- tests/* R/*.R)
 
           # Base directories
           src_dir="R/"

From eb4b3b39f9aebdff7ba3830ef65af50464ab5757 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 3 Feb 2025 15:00:22 +0100
Subject: [PATCH 20/58] Fetch the branch specifically

---
 .github/workflows/build-check-install.yaml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index e2bf6129..1bda1b21 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -294,7 +294,6 @@ jobs:
         uses: actions/checkout@v4.1.1
         if: github.event_name == 'pull_request'
         with:
-          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
           path: ${{ github.event.repository.name }}
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           fetch-depth: 0
@@ -523,8 +522,8 @@ jobs:
 
           # Debugging
 
-          git remote -v
-          git pull origin main
+          # https://github.com/pylint-dev/pylint/blob/acf7705968da21b0396a6532cd8e8b0f1f8cc806/.github/workflows/changelog.yml#L64
+          git fetch --no-tags origin +refs/heads/${{ github.base_ref }}:refs/remotes/origin/${{ github.base_ref }}
           git branch
 
           # Get the list of R files that have changed

From 38b63dee0b54d8b50dd360b1b40258feb081ed54 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 3 Feb 2025 15:09:16 +0100
Subject: [PATCH 21/58] Use only git-diff to compare between branches?

---
 .github/workflows/build-check-install.yaml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 1bda1b21..84254225 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -522,12 +522,10 @@ jobs:
 
           # Debugging
 
-          # https://github.com/pylint-dev/pylint/blob/acf7705968da21b0396a6532cd8e8b0f1f8cc806/.github/workflows/changelog.yml#L64
-          git fetch --no-tags origin +refs/heads/${{ github.base_ref }}:refs/remotes/origin/${{ github.base_ref }}
-          git branch
 
           # Get the list of R files that have changed
-          files=$(git diff --name-only main...${{ github.head_ref }} -- tests/* R/*.R)
+          # https://github.com/cloudnativeto/envoy/blob/de67446fa8af973761bb4716f5143d73643baf8b/.github/workflows/get_build_targets.sh_bak#L9
+          files=$(git diff --name-only HEAD FETCH_HEAD -- tests/* R/*.R)
 
           # Base directories
           src_dir="R/"

From 76cfbf0197e36400ff964cfc4a12a93ad9619abd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Tue, 4 Feb 2025 15:18:27 +0100
Subject: [PATCH 22/58] Undo changes and finish loop if any helper is modified

---
 .github/workflows/build-check-install.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 84254225..974be44f 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -550,6 +550,8 @@ jobs:
               } else {
                   # Flag for helpers
                   helper_modified="yes"
+                  git restore .
+                  break
               } fi
 
               # R file without corresponding test file: reset the testing depth

From 5a5537dce992cd8321615269049e2d85dfc93f75 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Tue, 4 Feb 2025 15:19:17 +0100
Subject: [PATCH 23/58] Make it more general for other teal.* packages

---
 .github/workflows/build-check-install.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 974be44f..b549ddbd 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -515,7 +515,7 @@ jobs:
           key: additional-caches-${{ runner.os }}
 
       - name: Check only affected modules 🎯
-        if: startsWith(${{ github.event.repository.name }}, 'teal.modules.') && github.event_name == 'pull_request'
+        if: startsWith(${{ github.event.repository.name }}, 'teal.') && github.event_name == 'pull_request'
         run: |
           # Set working directory where the git repo is
           cd ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}

From 9e129a00ee1e0ac305013e1edc861ee856cf445b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 5 Feb 2025 11:00:03 +0100
Subject: [PATCH 24/58] Address comments and provide informative log

---
 .github/workflows/build-check-install.yaml | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index b549ddbd..75487d3f 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -246,6 +246,12 @@ on:
         required: false
         type: boolean
         default: false
+      fast-tests:
+        description: |
+          Should shinytests2 tests only run per modified teal module? If enabled if only there is a module modificated only that shinytest2 file will be tested.
+        required: false
+        type: string
+        default: false
 
 concurrency:
   group: r-cmd-${{ inputs.concurrency-group }}-${{ github.event.pull_request.number || github.ref }}
@@ -515,13 +521,13 @@ jobs:
           key: additional-caches-${{ runner.os }}
 
       - name: Check only affected modules 🎯
-        if: startsWith(${{ github.event.repository.name }}, 'teal.') && github.event_name == 'pull_request'
+        if: ${{ inputs.fast-tests }} != 'true' && startsWith(${{ github.event.repository.name }}, 'teal.') && github.event_name == 'pull_request'
         run: |
           # Set working directory where the git repo is
           cd ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
-          # Debugging
 
+          test_all=git log -1 --pretty=%B | grep -F " [run-all-tests] "
 
           # Get the list of R files that have changed
           # https://github.com/cloudnativeto/envoy/blob/de67446fa8af973761bb4716f5143d73643baf8b/.github/workflows/get_build_targets.sh_bak#L9
@@ -543,19 +549,21 @@ jobs:
               td=$TESTING_DEPTH
 
               # Modify in place so that only modified modules are tested.
-              if [[ -n "$test_files" ]]
+              if [[ -n "$test_files" && ! -n "$test_all"]]
               then {
                   sed -i 's/skip_if_too_deep(5)/skip_if_too_deep(3)/g' "$test_files"
                   TESTING_DEPTH=3
+                  echo "Testing with shinytest2 for $test_files"
               } else {
                   # Flag for helpers
                   helper_modified="yes"
                   git restore .
+                  echo "Run all tests"
                   break
               } fi
 
               # R file without corresponding test file: reset the testing depth
-              if [[ -n "$helper_modified" ]]
+              if [[ -n "$helper_modified" || -n "$test_all"]]
               then {
                   TESTING_DEPTH=td
               } fi

From 05175640c7fe5c517fe8d81053710c06f11f8e2e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 5 Feb 2025 11:43:34 +0100
Subject: [PATCH 25/58] Add missing subprocess

---
 .github/workflows/build-check-install.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 75487d3f..3e40a5a2 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -527,7 +527,7 @@ jobs:
           cd ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
 
-          test_all=git log -1 --pretty=%B | grep -F " [run-all-tests] "
+          test_all=$(git log -1 --pretty=%B | grep -F " [run-all-tests] ")
 
           # Get the list of R files that have changed
           # https://github.com/cloudnativeto/envoy/blob/de67446fa8af973761bb4716f5143d73643baf8b/.github/workflows/get_build_targets.sh_bak#L9

From f4a1bc8a01470b92b6a0d5e4a65afc035ae765ba Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 5 Feb 2025 11:56:56 +0100
Subject: [PATCH 26/58] Fix syntax errors

---
 .github/workflows/build-check-install.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 3e40a5a2..f6c0fc54 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -549,23 +549,23 @@ jobs:
               td=$TESTING_DEPTH
 
               # Modify in place so that only modified modules are tested.
-              if [[ -n "$test_files" && ! -n "$test_all"]]
+              if [[ -n "$test_files" && ! -n "$test_all" ]];
               then {
                   sed -i 's/skip_if_too_deep(5)/skip_if_too_deep(3)/g' "$test_files"
                   TESTING_DEPTH=3
-                  echo "Testing with shinytest2 for $test_files"
+                  echo "Testing with shinytest2 for $test_files";
               } else {
                   # Flag for helpers
                   helper_modified="yes"
                   git restore .
                   echo "Run all tests"
-                  break
+                  break;
               } fi
 
               # R file without corresponding test file: reset the testing depth
-              if [[ -n "$helper_modified" || -n "$test_all"]]
+              if [[ -n "$helper_modified" || -n "$test_all" ]];
               then {
-                  TESTING_DEPTH=td
+                  TESTING_DEPTH=td;
               } fi
           done
         shell: bash

From 65e160d697587e5bfbcb157272e847356ebe9a15 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 5 Feb 2025 12:15:32 +0100
Subject: [PATCH 27/58] Further improvements

---
 .github/workflows/build-check-install.yaml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index f6c0fc54..af1a9428 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -534,7 +534,6 @@ jobs:
           files=$(git diff --name-only HEAD FETCH_HEAD -- tests/* R/*.R)
 
           # Base directories
-          src_dir="R/"
           test_dir="tests/testthat/"
 
           # Loop through each modified file and determine which tests to run
@@ -549,7 +548,7 @@ jobs:
               td=$TESTING_DEPTH
 
               # Modify in place so that only modified modules are tested.
-              if [[ -n "$test_files" && ! -n "$test_all" ]];
+              if [ -n "$test_files" ] && [ -z "$test_all" ];
               then {
                   sed -i 's/skip_if_too_deep(5)/skip_if_too_deep(3)/g' "$test_files"
                   TESTING_DEPTH=3
@@ -563,9 +562,9 @@ jobs:
               } fi
 
               # R file without corresponding test file: reset the testing depth
-              if [[ -n "$helper_modified" || -n "$test_all" ]];
+              if [ -n "$helper_modified" ] || [ -n "$test_all" ];
               then {
-                  TESTING_DEPTH=td;
+                  TESTING_DEPTH=$td;
               } fi
           done
         shell: bash

From 642a189c718262f09c2b4d20370ec50ecfa2b897 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 5 Feb 2025 12:35:12 +0100
Subject: [PATCH 28/58] Make it more general and improve logging

---
 .github/workflows/build-check-install.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index af1a9428..7431482a 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -521,13 +521,13 @@ jobs:
           key: additional-caches-${{ runner.os }}
 
       - name: Check only affected modules 🎯
-        if: ${{ inputs.fast-tests }} != 'true' && startsWith(${{ github.event.repository.name }}, 'teal.') && github.event_name == 'pull_request'
+        if: ${{ inputs.fast-tests }} == 'true' && github.event_name == 'pull_request'
         run: |
           # Set working directory where the git repo is
           cd ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
 
-          test_all=$(git log -1 --pretty=%B | grep -F " [run-all-tests] ")
+          test_all=$(git show -s --pretty=%B | grep -F "[run-all-tests]")
 
           # Get the list of R files that have changed
           # https://github.com/cloudnativeto/envoy/blob/de67446fa8af973761bb4716f5143d73643baf8b/.github/workflows/get_build_targets.sh_bak#L9
@@ -564,6 +564,7 @@ jobs:
               # R file without corresponding test file: reset the testing depth
               if [ -n "$helper_modified" ] || [ -n "$test_all" ];
               then {
+                  echo "Skip step or helper modifications detected."
                   TESTING_DEPTH=$td;
               } fi
           done

From 3a583527b06188d9b943b4030902f87455d6eb8a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 5 Feb 2025 13:52:18 +0100
Subject: [PATCH 29/58] Restore only modifications on tests files

---
 .github/workflows/build-check-install.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 7431482a..4e3322bc 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -556,7 +556,7 @@ jobs:
               } else {
                   # Flag for helpers
                   helper_modified="yes"
-                  git restore .
+                  git restore $test_dir
                   echo "Run all tests"
                   break;
               } fi

From 48dcd5231847d08004561a16b789a24a0811639d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 5 Feb 2025 14:12:21 +0100
Subject: [PATCH 30/58] Simplify a bit more

---
 .github/workflows/build-check-install.yaml | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 4e3322bc..e4e05da8 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -526,15 +526,12 @@ jobs:
           # Set working directory where the git repo is
           cd ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
-
-          test_all=$(git show -s --pretty=%B | grep -F "[run-all-tests]")
+          test_all=$(git show -s --pretty=%B | grep -F "[run-all-tests]" )
+          test_dir="tests/testthat/"
 
           # Get the list of R files that have changed
           # https://github.com/cloudnativeto/envoy/blob/de67446fa8af973761bb4716f5143d73643baf8b/.github/workflows/get_build_targets.sh_bak#L9
-          files=$(git diff --name-only HEAD FETCH_HEAD -- tests/* R/*.R)
-
-          # Base directories
-          test_dir="tests/testthat/"
+          files=$(git diff --name-only HEAD FETCH_HEAD -- $test_dir R/*.R)
 
           # Loop through each modified file and determine which tests to run
           for file in $files; do

From ab60d1c3e68760922805ef7d85ae5fcfeb0339d0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 5 Feb 2025 14:49:43 +0100
Subject: [PATCH 31/58] Fix when to run this step!

Add more logging features
---
 .github/workflows/build-check-install.yaml | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index e4e05da8..d3cdd3f4 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -250,7 +250,7 @@ on:
         description: |
           Should shinytests2 tests only run per modified teal module? If enabled if only there is a module modificated only that shinytest2 file will be tested.
         required: false
-        type: string
+        type: boolean
         default: false
 
 concurrency:
@@ -521,18 +521,31 @@ jobs:
           key: additional-caches-${{ runner.os }}
 
       - name: Check only affected modules 🎯
-        if: ${{ inputs.fast-tests }} == 'true' && github.event_name == 'pull_request'
+        if: inputs.fast-tests == 'true' && github.event_name == 'pull_request'
         run: |
           # Set working directory where the git repo is
           cd ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
-          test_all=$(git show -s --pretty=%B | grep -F "[run-all-tests]" )
+          # Exit early if tag is on commit message even if it set to true
+          test_all=$( git log -1 --pretty=%B | grep -F "[run-all-tests]" )
+          if [ -z "$test_all" ]
+          then {
+            echo "Last commit message forces to test everything."
+            exit 0
+          } fi
+
           test_dir="tests/testthat/"
 
           # Get the list of R files that have changed
           # https://github.com/cloudnativeto/envoy/blob/de67446fa8af973761bb4716f5143d73643baf8b/.github/workflows/get_build_targets.sh_bak#L9
           files=$(git diff --name-only HEAD FETCH_HEAD -- $test_dir R/*.R)
 
+          if [ -n "files" ]
+          then {
+            echo "No R files affected: test everything."
+            exit 0
+          } fi
+
           # Loop through each modified file and determine which tests to run
           for file in $files; do
 

From cd1922d6c1b84dfa20bdddc18fadab1171d5249f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 5 Feb 2025 15:28:00 +0100
Subject: [PATCH 32/58] Use logical/boolean instead of text

---
 .github/workflows/build-check-install.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index d3cdd3f4..aec84dfb 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -521,7 +521,7 @@ jobs:
           key: additional-caches-${{ runner.os }}
 
       - name: Check only affected modules 🎯
-        if: inputs.fast-tests == 'true' && github.event_name == 'pull_request'
+        if: inputs.fast-tests == true && github.event_name == 'pull_request'
         run: |
           # Set working directory where the git repo is
           cd ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}

From a27ebdf51d28981c1f62f27e841e70c685272c14 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 5 Feb 2025 15:55:43 +0100
Subject: [PATCH 33/58] Run target always not only on pull_requests

---
 .github/workflows/build-check-install.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index aec84dfb..0c636072 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -521,7 +521,7 @@ jobs:
           key: additional-caches-${{ runner.os }}
 
       - name: Check only affected modules 🎯
-        if: inputs.fast-tests == true && github.event_name == 'pull_request'
+        if: inputs.fast-tests == true
         run: |
           # Set working directory where the git repo is
           cd ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}

From 6e0897f72b04b83b0f97b904ed4694fab44be2c2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 5 Feb 2025 16:28:18 +0100
Subject: [PATCH 34/58] Start from the beginning

---
 .github/workflows/build-check-install.yaml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 0c636072..4eb5265a 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -523,8 +523,7 @@ jobs:
       - name: Check only affected modules 🎯
         if: inputs.fast-tests == true
         run: |
-          # Set working directory where the git repo is
-          cd ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+          ls
 
           # Exit early if tag is on commit message even if it set to true
           test_all=$( git log -1 --pretty=%B | grep -F "[run-all-tests]" )
@@ -540,7 +539,7 @@ jobs:
           # https://github.com/cloudnativeto/envoy/blob/de67446fa8af973761bb4716f5143d73643baf8b/.github/workflows/get_build_targets.sh_bak#L9
           files=$(git diff --name-only HEAD FETCH_HEAD -- $test_dir R/*.R)
 
-          if [ -n "files" ]
+          if [ -n "$files" ]
           then {
             echo "No R files affected: test everything."
             exit 0

From 67c43fc7c4808db09b350f0649cafaf590936bb4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Thu, 6 Feb 2025 09:09:59 +0100
Subject: [PATCH 35/58] Set the working directory to the package

---
 .github/workflows/build-check-install.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 4eb5265a..e64e3c4e 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -523,7 +523,9 @@ jobs:
       - name: Check only affected modules 🎯
         if: inputs.fast-tests == true
         run: |
+          cd ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
           ls
+          pwd
 
           # Exit early if tag is on commit message even if it set to true
           test_all=$( git log -1 --pretty=%B | grep -F "[run-all-tests]" )

From 38d02c24430397f5415577c66d3b07fac8fca20a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Thu, 6 Feb 2025 09:37:14 +0100
Subject: [PATCH 36/58] Check if main commands are available

---
 .github/workflows/build-check-install.yaml | 21 +++++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index e64e3c4e..a58f488e 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -522,10 +522,24 @@ jobs:
 
       - name: Check only affected modules 🎯
         if: inputs.fast-tests == true
+        working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
         run: |
-          cd ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
-          ls
-          pwd
+          # Bash script run
+          if ! command -v git 2>&1 >/dev/null
+          then
+              echo "git could not be found"
+              exit 1
+          fi
+          if ! command -v grep 2>&1 >/dev/null
+          then
+              echo "grep could not be found"
+              exit 1
+          fi
+          if ! command -v sed 2>&1 >/dev/null
+          then
+              echo "sed could not be found"
+              exit 1
+          fi
 
           # Exit early if tag is on commit message even if it set to true
           test_all=$( git log -1 --pretty=%B | grep -F "[run-all-tests]" )
@@ -579,7 +593,6 @@ jobs:
                   TESTING_DEPTH=$td;
               } fi
           done
-        shell: bash
 
       - name: Build R package 🏗
         run: |

From ef84cea968b7868f01a054950a6439d8e76fccc7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Thu, 6 Feb 2025 10:02:44 +0100
Subject: [PATCH 37/58] Change output and see what happens

---
 .github/workflows/build-check-install.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index a58f488e..42d18d59 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -525,20 +525,20 @@ jobs:
         working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
         run: |
           # Bash script run
-          if ! command -v git 2>&1 >/dev/null
+          if ! command -v git > /dev/null 2>&1
           then
               echo "git could not be found"
-              exit 1
+              exit 0
           fi
-          if ! command -v grep 2>&1 >/dev/null
+          if ! command -v grep > /dev/null 2>&1
           then
               echo "grep could not be found"
-              exit 1
+              exit 0
           fi
-          if ! command -v sed 2>&1 >/dev/null
+          if ! command -v sed > /dev/null 2>&1
           then
               echo "sed could not be found"
-              exit 1
+              exit 0
           fi
 
           # Exit early if tag is on commit message even if it set to true

From 825ff79b411105b83c7f76fad4641c66a808ffa7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Thu, 6 Feb 2025 11:13:54 +0100
Subject: [PATCH 38/58] Update description

---
 .github/workflows/build-check-install.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 42d18d59..2e85e7c7 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -248,7 +248,9 @@ on:
         default: false
       fast-tests:
         description: |
-          Should shinytests2 tests only run per modified teal module? If enabled if only there is a module modificated only that shinytest2 file will be tested.
+          Should shinytests2 tests only run per modified teal module?
+          If enabled if only there is a module modificated only that shinytest2 file will be tested.
+          Can be ignored if used [run-all-tests] on the commit message.
         required: false
         type: boolean
         default: false

From 577fc842c58f1b6095591fab527d7b839b2376da Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Thu, 6 Feb 2025 12:02:34 +0100
Subject: [PATCH 39/58] Change bash

---
 .github/workflows/build-check-install.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 2e85e7c7..45d14ef9 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -595,6 +595,7 @@ jobs:
                   TESTING_DEPTH=$td;
               } fi
           done
+        shell: bash
 
       - name: Build R package 🏗
         run: |

From b843d4ef6dae5dc942081f9e3ece59da2ef5e49e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Thu, 6 Feb 2025 14:15:07 +0100
Subject: [PATCH 40/58] Fix issue with grep

---
 .github/workflows/build-check-install.yaml | 20 ++++----------------
 1 file changed, 4 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 45d14ef9..41ae0702 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -527,24 +527,12 @@ jobs:
         working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
         run: |
           # Bash script run
-          if ! command -v git > /dev/null 2>&1
-          then
-              echo "git could not be found"
-              exit 0
-          fi
-          if ! command -v grep > /dev/null 2>&1
-          then
-              echo "grep could not be found"
-              exit 0
-          fi
-          if ! command -v sed > /dev/null 2>&1
-          then
-              echo "sed could not be found"
-              exit 0
-          fi
+          commit_msg=$( git log -1 --pretty=%B )
 
+          echo "Commit msg is ${commit_msg}"
           # Exit early if tag is on commit message even if it set to true
-          test_all=$( git log -1 --pretty=%B | grep -F "[run-all-tests]" )
+          test_all=$( echo "${commit_msg}" | grep -zvF "[run-all-tests]" | tr -d '\0')
+
           if [ -z "$test_all" ]
           then {
             echo "Last commit message forces to test everything."

From dbe3631f626e0251298eca228152cf05ea293bf0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Thu, 6 Feb 2025 15:22:46 +0100
Subject: [PATCH 41/58] Update script to be more informative

---
 .github/workflows/build-check-install.yaml | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 41ae0702..3a4787c1 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -543,9 +543,9 @@ jobs:
 
           # Get the list of R files that have changed
           # https://github.com/cloudnativeto/envoy/blob/de67446fa8af973761bb4716f5143d73643baf8b/.github/workflows/get_build_targets.sh_bak#L9
-          files=$(git diff --name-only HEAD FETCH_HEAD -- $test_dir R/*.R)
+          files=$(git diff --name-only main.. -- $test_dir R/*.R)
 
-          if [ -n "$files" ]
+          if [ -z "$files" ]
           then {
             echo "No R files affected: test everything."
             exit 0
@@ -554,6 +554,8 @@ jobs:
           # Loop through each modified file and determine which tests to run
           for file in $files; do
 
+              echo "Check for $file"
+
               # Extract the base name of the file, examples:
               # tests/testthat/test-shinytest2-foo.R -> foo
               # R/foo.R -> foo
@@ -563,11 +565,12 @@ jobs:
               td=$TESTING_DEPTH
 
               # Modify in place so that only modified modules are tested.
-              if [ -n "$test_files" ] && [ -z "$test_all" ];
+              if [ -n "$test_files" ] && [ -n "$test_all" ];
               then {
                   sed -i 's/skip_if_too_deep(5)/skip_if_too_deep(3)/g' "$test_files"
-                  TESTING_DEPTH=3
+                  export TESTING_DEPTH="3"
                   echo "Testing with shinytest2 for $test_files";
+                  echo "Settin testing_depth=$TESTING_DEPTH"
               } else {
                   # Flag for helpers
                   helper_modified="yes"
@@ -577,12 +580,13 @@ jobs:
               } fi
 
               # R file without corresponding test file: reset the testing depth
-              if [ -n "$helper_modified" ] || [ -n "$test_all" ];
+              if [ -n "$helper_modified" ] || [ -z "$test_all" ];
               then {
                   echo "Skip step or helper modifications detected."
-                  TESTING_DEPTH=$td;
+                  export TESTING_DEPTH="$td";
               } fi
           done
+          echo Using "TESTING_DEPTH=${TESTING_DEPTH}"
         shell: bash
 
       - name: Build R package 🏗

From ccc51b313d204a1b3b61cc21a83f4226369fe033 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Fri, 7 Feb 2025 09:26:54 +0100
Subject: [PATCH 42/58] Revert to head and fetch

---
 .github/workflows/build-check-install.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 3a4787c1..13f3b5ca 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -543,7 +543,7 @@ jobs:
 
           # Get the list of R files that have changed
           # https://github.com/cloudnativeto/envoy/blob/de67446fa8af973761bb4716f5143d73643baf8b/.github/workflows/get_build_targets.sh_bak#L9
-          files=$(git diff --name-only main.. -- $test_dir R/*.R)
+          files=$(git diff --name-only HEAD FETCH_HEAD -- $test_dir R/*.R)
 
           if [ -z "$files" ]
           then {

From f39761f04410a9f7c50354dfe5abeb995b26eeb7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Fri, 7 Feb 2025 10:17:28 +0100
Subject: [PATCH 43/58] Fix path to git diff

---
 .github/workflows/build-check-install.yaml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 13f3b5ca..5fe839c8 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -540,10 +540,13 @@ jobs:
           } fi
 
           test_dir="tests/testthat/"
+          git version
+          git branch
+          git status
 
           # Get the list of R files that have changed
           # https://github.com/cloudnativeto/envoy/blob/de67446fa8af973761bb4716f5143d73643baf8b/.github/workflows/get_build_targets.sh_bak#L9
-          files=$(git diff --name-only HEAD FETCH_HEAD -- $test_dir R/*.R)
+          files=$(git diff --name-only HEAD FETCH_HEAD -- "$test_dir"/*.R R/*.R)
 
           if [ -z "$files" ]
           then {

From 45b3b316693dd9b20963a9cec964e517fbf70be7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Fri, 7 Feb 2025 10:55:31 +0100
Subject: [PATCH 44/58] Pull branch before comparing it

---
 .github/workflows/build-check-install.yaml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 5fe839c8..30d76663 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -540,13 +540,15 @@ jobs:
           } fi
 
           test_dir="tests/testthat/"
-          git version
+          git branch
+          git pull main
           git branch
           git status
 
           # Get the list of R files that have changed
           # https://github.com/cloudnativeto/envoy/blob/de67446fa8af973761bb4716f5143d73643baf8b/.github/workflows/get_build_targets.sh_bak#L9
-          files=$(git diff --name-only HEAD FETCH_HEAD -- "$test_dir"/*.R R/*.R)
+          files=$( git diff main.. --name-only -- "$test_dir"/*.R R/*.R )
+          echo "$files"
 
           if [ -z "$files" ]
           then {

From 111855dd478102bff39f8ce6d52cc89c0ed6d9ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Fri, 7 Feb 2025 11:19:24 +0100
Subject: [PATCH 45/58] Pull directly from remote

---
 .github/workflows/build-check-install.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 30d76663..07be0ed7 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -541,7 +541,9 @@ jobs:
 
           test_dir="tests/testthat/"
           git branch
-          git pull main
+          git remote -v
+          remote_repo="https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git"
+          git pull "$remote_repo" main
           git branch
           git status
 

From bfd6310f47818a10241a399ce6b71a4f0306df4f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Fri, 7 Feb 2025 11:39:59 +0100
Subject: [PATCH 46/58] setup merging strategy

---
 .github/workflows/build-check-install.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 07be0ed7..7ad51c68 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -542,6 +542,7 @@ jobs:
           test_dir="tests/testthat/"
           git branch
           git remote -v
+          git config pull.rebase true
           remote_repo="https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git"
           git pull "$remote_repo" main
           git branch

From ca95d1eb090872a370ad48ebf14e8e60fd29c813 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Fri, 7 Feb 2025 12:13:10 +0100
Subject: [PATCH 47/58] Stash before merging

---
 .github/workflows/build-check-install.yaml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 7ad51c68..7e99a7c0 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -540,13 +540,14 @@ jobs:
           } fi
 
           test_dir="tests/testthat/"
-          git branch
-          git remote -v
+          git status
+          git stash
           git config pull.rebase true
           remote_repo="https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git"
           git pull "$remote_repo" main
+          git stash pop
+
           git branch
-          git status
 
           # Get the list of R files that have changed
           # https://github.com/cloudnativeto/envoy/blob/de67446fa8af973761bb4716f5143d73643baf8b/.github/workflows/get_build_targets.sh_bak#L9

From abdbb86102362f183200e441e4e1bfb2de59d7f2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Fri, 7 Feb 2025 14:12:27 +0100
Subject: [PATCH 48/58] Testing external action

---
 .github/workflows/build-check-install.yaml | 26 +++++++++-------------
 1 file changed, 11 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 7e99a7c0..03876736 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -521,10 +521,19 @@ jobs:
         with:
           path: "${{ inputs.additional-caches }}"
           key: additional-caches-${{ runner.os }}
+          steps:
+      - name: Get changed files 📃
+        id: changed-files
+        uses: tj-actions/changed-files@v45
+        files: |
+          tests/testthat/**.R
+          R/**.R
 
       - name: Check only affected modules 🎯
         if: inputs.fast-tests == true
         working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+        env:
+          ALL_CHANGED_FILES: ${{ steps.changed-files.outputs.all_changed_files }}
         run: |
           # Bash script run
           commit_msg=$( git log -1 --pretty=%B )
@@ -540,28 +549,15 @@ jobs:
           } fi
 
           test_dir="tests/testthat/"
-          git status
-          git stash
-          git config pull.rebase true
-          remote_repo="https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git"
-          git pull "$remote_repo" main
-          git stash pop
-
-          git branch
-
-          # Get the list of R files that have changed
-          # https://github.com/cloudnativeto/envoy/blob/de67446fa8af973761bb4716f5143d73643baf8b/.github/workflows/get_build_targets.sh_bak#L9
-          files=$( git diff main.. --name-only -- "$test_dir"/*.R R/*.R )
-          echo "$files"
 
-          if [ -z "$files" ]
+          if [ -z "${ALL_CHANGED_FILES} ]
           then {
             echo "No R files affected: test everything."
             exit 0
           } fi
 
           # Loop through each modified file and determine which tests to run
-          for file in $files; do
+          for file in "${ALL_CHANGED_FILES}"; do
 
               echo "Check for $file"
 

From ed42539f9468fb62d83daf0d5db6d6c661d54749 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Fri, 7 Feb 2025 14:19:08 +0100
Subject: [PATCH 49/58] fix syntax

---
 .github/workflows/build-check-install.yaml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 03876736..59f8f0e1 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -525,9 +525,10 @@ jobs:
       - name: Get changed files 📃
         id: changed-files
         uses: tj-actions/changed-files@v45
-        files: |
-          tests/testthat/**.R
-          R/**.R
+        with:
+          files: |
+            tests/testthat/**.R
+            R/**.R
 
       - name: Check only affected modules 🎯
         if: inputs.fast-tests == true

From 123af45ca3707393b05b3c7facbe59fc0a5f36f2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Fri, 7 Feb 2025 17:01:32 +0100
Subject: [PATCH 50/58] Modify documentation and path

---
 .github/workflows/build-check-install.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 59f8f0e1..17a41638 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -248,8 +248,8 @@ on:
         default: false
       fast-tests:
         description: |
-          Should shinytests2 tests only run per modified teal module?
-          If enabled if only there is a module modificated only that shinytest2 file will be tested.
+          Should shinytests2 tests only run per modified module?
+          If enabled and there is a module modificated only that shinytest2 file will be tested.
           Can be ignored if used [run-all-tests] on the commit message.
         required: false
         type: boolean
@@ -526,6 +526,7 @@ jobs:
         id: changed-files
         uses: tj-actions/changed-files@v45
         with:
+          path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
           files: |
             tests/testthat/**.R
             R/**.R

From a1510055b2a5334e4ee7922caa5562f95e1cca05 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 10 Feb 2025 09:26:34 +0100
Subject: [PATCH 51/58] Fix syntax problems..

---
 .github/workflows/build-check-install.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 17a41638..aa5d7c56 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -552,14 +552,14 @@ jobs:
 
           test_dir="tests/testthat/"
 
-          if [ -z "${ALL_CHANGED_FILES} ]
+          if [ -z "${ALL_CHANGED_FILES}" ]
           then {
             echo "No R files affected: test everything."
             exit 0
           } fi
 
           # Loop through each modified file and determine which tests to run
-          for file in "${ALL_CHANGED_FILES}"; do
+          for file in $ALL_CHANGED_FILES; do
 
               echo "Check for $file"
 

From 0ee07f3685f9266df044f6a1d74190c727a2171a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 10 Feb 2025 10:26:32 +0100
Subject: [PATCH 52/58] Fix conditionals & export TESTING_DEPTH for GHA

---
 .github/workflows/build-check-install.yaml | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index aa5d7c56..c524a9a7 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -540,7 +540,7 @@ jobs:
           # Bash script run
           commit_msg=$( git log -1 --pretty=%B )
 
-          echo "Commit msg is ${commit_msg}"
+          echo "Commit msg is: ${commit_msg}"
           # Exit early if tag is on commit message even if it set to true
           test_all=$( echo "${commit_msg}" | grep -zvF "[run-all-tests]" | tr -d '\0')
 
@@ -552,7 +552,7 @@ jobs:
 
           test_dir="tests/testthat/"
 
-          if [ -z "${ALL_CHANGED_FILES}" ]
+          if [ -z "$ALL_CHANGED_FILES" ]
           then {
             echo "No R files affected: test everything."
             exit 0
@@ -572,12 +572,11 @@ jobs:
               td=$TESTING_DEPTH
 
               # Modify in place so that only modified modules are tested.
-              if [ -n "$test_files" ] && [ -n "$test_all" ];
+              if [ -n "$test_files" ];
               then {
                   sed -i 's/skip_if_too_deep(5)/skip_if_too_deep(3)/g' "$test_files"
-                  export TESTING_DEPTH="3"
+                  TESTING_DEPTH="3"
                   echo "Testing with shinytest2 for $test_files";
-                  echo "Settin testing_depth=$TESTING_DEPTH"
               } else {
                   # Flag for helpers
                   helper_modified="yes"
@@ -590,9 +589,12 @@ jobs:
               if [ -n "$helper_modified" ] || [ -z "$test_all" ];
               then {
                   echo "Skip step or helper modifications detected."
-                  export TESTING_DEPTH="$td";
+                  TESTING_DEPTH="$td";
               } fi
           done
+
+          # https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions#setting-an-environment-variable
+          echo "TESTING_DEPTH=${TESTING_DEPTH}" >> "$GITHUB_ENV"
           echo Using "TESTING_DEPTH=${TESTING_DEPTH}"
         shell: bash
 

From cae30561c3232585c17d796e8e2299b2e501d60c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 10 Feb 2025 10:55:03 +0100
Subject: [PATCH 53/58] Compare against main

---
 .github/workflows/build-check-install.yaml | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index c524a9a7..1383ca0f 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -527,9 +527,10 @@ jobs:
         uses: tj-actions/changed-files@v45
         with:
           path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+          base_sha: "main"
           files: |
-            tests/testthat/**.R
-            R/**.R
+            tests/testthat/*.R
+            R/*.R
 
       - name: Check only affected modules 🎯
         if: inputs.fast-tests == true
@@ -558,6 +559,15 @@ jobs:
             exit 0
           } fi
 
+          # Set default TESTING_DEPTH
+          td=$TESTING_DEPTH
+          if [ -z "$td" ]
+          then {
+            echo "No TESTING_DEPTH default"
+            td=5
+          } fi
+
+          echo "$ALL_CHANGED_FILES"
           # Loop through each modified file and determine which tests to run
           for file in $ALL_CHANGED_FILES; do
 
@@ -569,7 +579,6 @@ jobs:
               base_name=$(basename "$file" .R | sed s/test-shinytest2-//g)
               # Find matching test files (parenthesis to not match arguments)
               test_files=$(grep -l "$base_name(" "$test_dir"test-shinytest2-*.R)
-              td=$TESTING_DEPTH
 
               # Modify in place so that only modified modules are tested.
               if [ -n "$test_files" ];
@@ -594,8 +603,8 @@ jobs:
           done
 
           # https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions#setting-an-environment-variable
-          echo "TESTING_DEPTH=${TESTING_DEPTH}" >> "$GITHUB_ENV"
           echo Using "TESTING_DEPTH=${TESTING_DEPTH}"
+          echo "TESTING_DEPTH=${TESTING_DEPTH}" >> "$GITHUB_ENV"
         shell: bash
 
       - name: Build R package 🏗

From 626121fe5a8ffafeecab156fa9e48bc883bdf0b0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 10 Feb 2025 14:46:23 +0100
Subject: [PATCH 54/58] Generalize the wording of the step

---
 .github/workflows/build-check-install.yaml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 1383ca0f..837ff876 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -246,9 +246,9 @@ on:
         required: false
         type: boolean
         default: false
-      fast-tests:
+      selected-shinytests:
         description: |
-          Should shinytests2 tests only run per modified module?
+          Should shinytests2 tests only run per modified corresponding R file in R/ folder?
           If enabled and there is a module modificated only that shinytest2 file will be tested.
           Can be ignored if used [run-all-tests] on the commit message.
         required: false
@@ -524,6 +524,7 @@ jobs:
           steps:
       - name: Get changed files 📃
         id: changed-files
+        if: inputs.selected-shinytests == true
         uses: tj-actions/changed-files@v45
         with:
           path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
@@ -533,7 +534,7 @@ jobs:
             R/*.R
 
       - name: Check only affected modules 🎯
-        if: inputs.fast-tests == true
+        if: inputs.selected-shinytests == true
         working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
         env:
           ALL_CHANGED_FILES: ${{ steps.changed-files.outputs.all_changed_files }}

From c6fa899f3903943b6019c70d23f01e6d85d69755 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Mon, 10 Feb 2025 14:55:30 +0100
Subject: [PATCH 55/58] Improve wording to describe how it is done and the
 function being rewritten

---
 .github/workflows/build-check-install.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 837ff876..74fcc6bd 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -250,7 +250,8 @@ on:
         description: |
           Should shinytests2 tests only run per modified corresponding R file in R/ folder?
           If enabled and there is a module modificated only that shinytest2 file will be tested.
-          Can be ignored if used [run-all-tests] on the commit message.
+          Might not apply to most packages! Because it replaces skip_if_too_deep(5) to skip_if_too_deep(3).
+          Will be ignored if the commit message contains [run-all-tests].
         required: false
         type: boolean
         default: false

From b6e7d636125a9b8cbe67007f77eb3386c016aeb3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Tue, 11 Feb 2025 10:11:49 +0100
Subject: [PATCH 56/58] Set default before early exiting

---
 .github/workflows/build-check-install.yaml | 52 +++++++++++-----------
 1 file changed, 26 insertions(+), 26 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 74fcc6bd..8982afa5 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -543,6 +543,15 @@ jobs:
           # Bash script run
           commit_msg=$( git log -1 --pretty=%B )
 
+          # Set default TESTING_DEPTH
+          td=$TESTING_DEPTH
+          if [ -z "$td" ]
+          then {
+            echo "No TESTING_DEPTH default"
+            echo "TESTING_DEPTH=5" >> "$GITHUB_ENV"
+            td=5
+          } fi
+
           echo "Commit msg is: ${commit_msg}"
           # Exit early if tag is on commit message even if it set to true
           test_all=$( echo "${commit_msg}" | grep -zvF "[run-all-tests]" | tr -d '\0')
@@ -550,6 +559,8 @@ jobs:
           if [ -z "$test_all" ]
           then {
             echo "Last commit message forces to test everything."
+            echo Using "TESTING_DEPTH=$td"
+            echo "TESTING_DEPTH=$td" >> "$GITHUB_ENV"
             exit 0
           } fi
 
@@ -558,18 +569,11 @@ jobs:
           if [ -z "$ALL_CHANGED_FILES" ]
           then {
             echo "No R files affected: test everything."
+            echo Using "TESTING_DEPTH=$td"
+            echo "TESTING_DEPTH=$td" >> "$GITHUB_ENV"
             exit 0
           } fi
 
-          # Set default TESTING_DEPTH
-          td=$TESTING_DEPTH
-          if [ -z "$td" ]
-          then {
-            echo "No TESTING_DEPTH default"
-            td=5
-          } fi
-
-          echo "$ALL_CHANGED_FILES"
           # Loop through each modified file and determine which tests to run
           for file in $ALL_CHANGED_FILES; do
 
@@ -580,31 +584,27 @@ jobs:
               # R/foo.R -> foo
               base_name=$(basename "$file" .R | sed s/test-shinytest2-//g)
               # Find matching test files (parenthesis to not match arguments)
-              test_files=$(grep -l "$base_name(" "$test_dir"test-shinytest2-*.R)
-
+              test_files=$(grep -l "$base_name(" "$test_dir"test-shinytest2-*.R || echo "")
               # Modify in place so that only modified modules are tested.
-              if [ -n "$test_files" ];
+              if [ -z "$test_files" ];
               then {
-                  sed -i 's/skip_if_too_deep(5)/skip_if_too_deep(3)/g' "$test_files"
-                  TESTING_DEPTH="3"
-                  echo "Testing with shinytest2 for $test_files";
-              } else {
-                  # Flag for helpers
-                  helper_modified="yes"
                   git restore $test_dir
                   echo "Run all tests"
-                  break;
-              } fi
-
-              # R file without corresponding test file: reset the testing depth
-              if [ -n "$helper_modified" ] || [ -z "$test_all" ];
-              then {
-                  echo "Skip step or helper modifications detected."
+                  echo "Helper modifications detected."
                   TESTING_DEPTH="$td";
+                  break;
+              } else {
+                if [ -n "$test_files" ];
+                  then {
+                      sed -i 's/skip_if_too_deep(5)/skip_if_too_deep(3)/g' "$test_files"
+                      TESTING_DEPTH="3"
+                      echo "Testing with shinytest2 for $test_files";
+                  } else {
+                      echo "Something unexpected happened"
+                  } fi
               } fi
           done
 
-          # https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions#setting-an-environment-variable
           echo Using "TESTING_DEPTH=${TESTING_DEPTH}"
           echo "TESTING_DEPTH=${TESTING_DEPTH}" >> "$GITHUB_ENV"
         shell: bash

From 544b78cab18cd27630d1b523c5c569911e94ff70 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Tue, 11 Feb 2025 12:38:22 +0100
Subject: [PATCH 57/58] Some debugging

---
 .github/workflows/build-check-install.yaml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 8982afa5..db7f8c79 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -597,16 +597,17 @@ jobs:
                 if [ -n "$test_files" ];
                   then {
                       sed -i 's/skip_if_too_deep(5)/skip_if_too_deep(3)/g' "$test_files"
-                      TESTING_DEPTH="3"
-                      echo "Testing with shinytest2 for $test_files";
+                      echo "TESTING_DEPTH=3" >> "$GITHUB_ENV"
+                      echo "Testing with shinytest2 only for $test_files";
                   } else {
                       echo "Something unexpected happened"
                   } fi
               } fi
           done
 
-          echo Using "TESTING_DEPTH=${TESTING_DEPTH}"
+          echo "Using TESTING_DEPTH=${TESTING_DEPTH}"
           echo "TESTING_DEPTH=${TESTING_DEPTH}" >> "$GITHUB_ENV"
+          git status
         shell: bash
 
       - name: Build R package 🏗

From e391bb2ba6d0b1318773ff2f4dbb6c0eeaabcece Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Tue, 11 Feb 2025 15:35:26 +0100
Subject: [PATCH 58/58] Save default

---
 .github/workflows/build-check-install.yaml | 25 +++++++++-------------
 1 file changed, 10 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index ece7017e..e863cce2 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -548,7 +548,8 @@ jobs:
           td=$TESTING_DEPTH
           if [ -z "$td" ]
           then {
-            echo "No TESTING_DEPTH default"
+            echo "No TESTING_DEPTH default."
+            echo "Setting TESTING_DEPTH=5"
             echo "TESTING_DEPTH=5" >> "$GITHUB_ENV"
             td=5
           } fi
@@ -560,7 +561,7 @@ jobs:
           if [ -z "$test_all" ]
           then {
             echo "Last commit message forces to test everything."
-            echo Using "TESTING_DEPTH=$td"
+            echo "Using TESTING_DEPTH=$td"
             echo "TESTING_DEPTH=$td" >> "$GITHUB_ENV"
             exit 0
           } fi
@@ -578,7 +579,7 @@ jobs:
           # Loop through each modified file and determine which tests to run
           for file in $ALL_CHANGED_FILES; do
 
-              echo "Check for $file"
+              echo "Check for $file."
 
               # Extract the base name of the file, examples:
               # tests/testthat/test-shinytest2-foo.R -> foo
@@ -590,25 +591,19 @@ jobs:
               if [ -z "$test_files" ];
               then {
                   git restore $test_dir
-                  echo "Run all tests"
-                  echo "Helper modifications detected."
+                  echo "Run all tests: Helpers modifications detected."
                   TESTING_DEPTH="$td";
                   break;
               } else {
-                if [ -n "$test_files" ];
-                  then {
-                      sed -i 's/skip_if_too_deep(5)/skip_if_too_deep(3)/g' "$test_files"
-                      echo "TESTING_DEPTH=3" >> "$GITHUB_ENV"
-                      echo "Testing with shinytest2 only for $test_files";
-                  } else {
-                      echo "Something unexpected happened"
-                  } fi
+                  sed -i 's/skip_if_too_deep(5)/skip_if_too_deep(3)/g' "$test_files"
+                  TESTING_DEPTH=3
+                  echo "TESTING_DEPTH=3" >> "$GITHUB_ENV"
+                  echo "Testing with shinytest2 only for $test_files";
               } fi
           done
 
-          echo "Using TESTING_DEPTH=${TESTING_DEPTH}"
+          echo "At the end, using TESTING_DEPTH=${TESTING_DEPTH}"
           echo "TESTING_DEPTH=${TESTING_DEPTH}" >> "$GITHUB_ENV"
-          git status
         shell: bash
 
       - name: Build R package 🏗