From 2bfd17069a9a2d507803a58fe397c058011fb3f1 Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Mon, 18 Dec 2023 17:04:22 -0500
Subject: [PATCH 01/23] Update testing.yml

---
 .github/workflows/testing.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 14e25870..fce4ce66 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -26,7 +26,7 @@ jobs:
           ref: refs/pull/${{ github.event.issue.number }}/head
       - name: Build and run PR
         id: build-and-run
-        uses: SegmentLinking/TrackLooper-actions/standalone@v1
+        uses: SegmentLinkingTests/TrackLooper-actions/standalone@v1
         with:
           pr-number: ${{ github.event.issue.number }}
       - name: Upload plots to archival repo
@@ -96,7 +96,7 @@ jobs:
           echo "cmssw-branch=$cmssw_branch" >> $GITHUB_ENV
       - name: Build and run PR
         id: build-and-run
-        uses: SegmentLinking/TrackLooper-actions/cmssw@v1
+        uses: SegmentLinkingTests/TrackLooper-actions/cmssw@v1
         with:
           pr-number: ${{ github.event.issue.number }}
           cmssw-branch: ${{ env.cmssw-branch }}

From 1c969d42097698332df4c02568ede7c98585eee5 Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Mon, 18 Dec 2023 17:17:19 -0500
Subject: [PATCH 02/23] Update testing.yml

---
 .github/workflows/testing.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index fce4ce66..2b576950 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -17,7 +17,7 @@ jobs:
     if: >
       github.event.issue.pull_request &&
       contains(github.event.comment.body, '/run standalone') &&
-      (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'CONTRIBUTOR')
+      github.event.comment.user.login == 'ariostas'
     runs-on: ubuntu-latest
     steps:
       - name: Checkout PR
@@ -63,7 +63,7 @@ jobs:
     if: >
       github.event.issue.pull_request && 
       contains(github.event.comment.body, '/run cmssw') &&
-      (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'CONTRIBUTOR')
+      github.event.comment.user.login == 'ariostas'
     runs-on: ubuntu-latest
     steps:
       - name: Checkout PR

From 24a8e49364285a3a96ee80e805cfa90b44b0732e Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Wed, 3 Jan 2024 14:41:05 -0500
Subject: [PATCH 03/23] Update testing.yml

---
 .github/workflows/testing.yml | 31 +++++++++++++++++++++++++++----
 1 file changed, 27 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 2b576950..1c22a1f7 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -5,7 +5,7 @@ on:
     types: [created]
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.event.issue.number }}
+  group: ${{ github.workflow }}-${{ github.event.issue.number }}-${{ github.event.comment.user.login }}-${{ contains(github.event.comment.body, '/run standalone') }}-${{ contains(github.event.comment.body, '/run cmssw') }}
   cancel-in-progress: true
 
 permissions:
@@ -19,11 +19,16 @@ jobs:
       contains(github.event.comment.body, '/run standalone') &&
       github.event.comment.user.login == 'ariostas'
     runs-on: ubuntu-latest
+    timeout-minutes: 60
     steps:
       - name: Checkout PR
         uses: actions/checkout@v4
         with:
           ref: refs/pull/${{ github.event.issue.number }}/head
+      - name: Get commit SHA
+        run: |  
+          sha=$(git rev-parse HEAD)
+          echo "COMMIT_SHA=$sha" >> $GITHUB_ENV
       - name: Build and run PR
         id: build-and-run
         uses: SegmentLinkingTests/TrackLooper-actions/standalone@v1
@@ -58,6 +63,13 @@ jobs:
               repo: context.repo.repo,
               body: `There was a problem while building and running in standalone mode. You can find a log of the job [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}).`
             })
+      - uses: LouisBrunner/checks-action@v1.6.1
+        if: always()
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          sha: ${{ env.COMMIT_SHA }}
+          name: Standalone run
+          conclusion: ${{ job.status }}
        
   cmssw:
     if: >
@@ -65,11 +77,16 @@ jobs:
       contains(github.event.comment.body, '/run cmssw') &&
       github.event.comment.user.login == 'ariostas'
     runs-on: ubuntu-latest
+    timeout-minutes: 150
     steps:
       - name: Checkout PR
         uses: actions/checkout@v4
         with:
           ref: refs/pull/${{ github.event.issue.number }}/head
+      - name: Get commit SHA
+        run: |  
+          sha=$(git rev-parse HEAD)
+          echo "COMMIT_SHA=$sha" >> $GITHUB_ENV
       - name: Get CMSSW branch name
         env:
           COMMENT_BODY: ${{ github.event.comment.body }}
@@ -83,9 +100,8 @@ jobs:
               words=($line)
               cmssw_branch="${words[2]}"
               # Validate the extracted branch to avoid code injection
-              if ! [[ $cmssw_branch =~ ^[[:alnum:]_-]+$ ]]; then
-                echo "Branch name is invalid. Ignoring..."
-                cmssw_branch=
+              if [ -z "$cmssw_branch" ]; then
+                cmssw_branch=(git check-ref-format --branch $cmssw_branch || echo "default")
               fi
             fi
           done <<< "$COMMENT_BODY"
@@ -129,3 +145,10 @@ jobs:
               repo: context.repo.repo,
               body: `There was a problem while building and running with CMSSW. You can find a log of the job [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}).`
             })
+      - uses: LouisBrunner/checks-action@v1.6.1
+        if: always()
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          sha: ${{ env.COMMIT_SHA }}
+          name: CMSSW run
+          conclusion: ${{ job.status }}

From 18edd2764fd13acf544ab5d4e754f50baf112fc7 Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Wed, 3 Jan 2024 14:44:30 -0500
Subject: [PATCH 04/23] Update testing.yml

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 1c22a1f7..3daf9981 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -100,7 +100,7 @@ jobs:
               words=($line)
               cmssw_branch="${words[2]}"
               # Validate the extracted branch to avoid code injection
-              if [ -z "$cmssw_branch" ]; then
+              if [ -n "$cmssw_branch" ]; then
                 cmssw_branch=(git check-ref-format --branch $cmssw_branch || echo "default")
               fi
             fi

From 9430724f9b98740ce48f0982a29f238ebf313284 Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Wed, 3 Jan 2024 14:48:35 -0500
Subject: [PATCH 05/23] Update testing.yml

---
 .github/workflows/testing.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 3daf9981..0538b1af 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -95,13 +95,13 @@ jobs:
           cmssw_branch=
           while IFS= read -r line; do
             echo "$line"
-            if [[ $line == *"/run cmssw"* ]]; then
+            if [[ $line == "/run cmssw"* ]]; then
               # Check if there is a branch after "/run cmssw"
               words=($line)
               cmssw_branch="${words[2]}"
               # Validate the extracted branch to avoid code injection
               if [ -n "$cmssw_branch" ]; then
-                cmssw_branch=(git check-ref-format --branch $cmssw_branch || echo "default")
+                cmssw_branch=$(git check-ref-format --branch $cmssw_branch || echo "default")
               fi
             fi
           done <<< "$COMMENT_BODY"

From 459ff51fc8a605701a8b1355d800d0b8531e7d5f Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Wed, 3 Jan 2024 15:00:29 -0500
Subject: [PATCH 06/23] Update testing.yml

---
 .github/workflows/testing.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 0538b1af..ac6c12aa 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -11,6 +11,7 @@ concurrency:
 permissions:
   contents: read
   pull-requests: write
+  checks: write
 
 jobs:
   standalone:

From a0f17caf5eef5a8bd4be899ef41903a951f9d11d Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Wed, 3 Jan 2024 16:11:42 -0500
Subject: [PATCH 07/23] Create checks_test.yml

---
 .github/workflows/checks_test.yml | 73 +++++++++++++++++++++++++++++++
 1 file changed, 73 insertions(+)
 create mode 100644 .github/workflows/checks_test.yml

diff --git a/.github/workflows/checks_test.yml b/.github/workflows/checks_test.yml
new file mode 100644
index 00000000..76304a26
--- /dev/null
+++ b/.github/workflows/checks_test.yml
@@ -0,0 +1,73 @@
+name: Testing
+
+on:
+  issue_comment:
+    types: [created]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.issue.number }}-${{ github.event.comment.user.login }}-${{ contains(github.event.comment.body, '/run standalone') }}-${{ contains(github.event.comment.body, '/run cmssw') }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+  pull-requests: write
+  checks: write
+
+jobs:
+  standalone:
+    if: >
+      github.event.issue.pull_request &&
+      contains(github.event.comment.body, '/run standalone') &&
+      github.event.comment.user.login == 'ariostas'
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    steps:
+      - name: Checkout PR
+        uses: actions/checkout@v4
+        with:
+          ref: refs/pull/${{ github.event.issue.number }}/head
+      - name: Get commit SHA
+        run: |  
+          sha=$(git rev-parse HEAD)
+          echo "COMMIT_SHA=$sha" >> $GITHUB_ENV
+      - name: Build and run PR
+        id: build-and-run
+        uses: SegmentLinkingTests/TrackLooper-actions/standalone@v1
+        with:
+          pr-number: ${{ github.event.issue.number }}
+      - name: Upload plots to archival repo
+        uses: s0/git-publish-subdir-action@develop
+        env:
+          REPO: git@github.com:${{ steps.build-and-run.outputs.archive-repo }}.git
+          BRANCH: ${{ steps.build-and-run.outputs.archive-branch }}
+          FOLDER: ${{ steps.build-and-run.outputs.archive-dir }}
+          SSH_PRIVATE_KEY: ${{ secrets.DEPLOY_PRIVATE_KEY }}
+          TARGET_DIR: ${{ steps.build-and-run.outputs.archive-dir }}
+      - name: Comment on PR
+        uses: actions/github-script@v6
+        with:
+          script: |
+            github.rest.issues.createComment({
+              issue_number: context.issue.number,
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              body: `${{ steps.build-and-run.outputs.comment }}`
+            })
+      - name: Comment on PR if job failed.
+        if: failure()
+        uses: actions/github-script@v6
+        with:
+          script: |
+            github.rest.issues.createComment({
+              issue_number: context.issue.number,
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              body: `There was a problem while building and running in standalone mode. You can find a log of the job [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}).`
+            })
+      - uses: LouisBrunner/checks-action@v1.6.1
+        if: always()
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          sha: ${{ env.COMMIT_SHA }}
+          name: Standalone run
+          conclusion: ${{ job.status }}

From 4b66503cee34593e16a075afc494fea00fe6ae2b Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Wed, 3 Jan 2024 16:14:02 -0500
Subject: [PATCH 08/23] Update checks_test.yml

---
 .github/workflows/checks_test.yml | 38 ++-----------------------------
 1 file changed, 2 insertions(+), 36 deletions(-)

diff --git a/.github/workflows/checks_test.yml b/.github/workflows/checks_test.yml
index 76304a26..12dc980f 100644
--- a/.github/workflows/checks_test.yml
+++ b/.github/workflows/checks_test.yml
@@ -1,4 +1,4 @@
-name: Testing
+name: Checks test
 
 on:
   issue_comment:
@@ -17,7 +17,7 @@ jobs:
   standalone:
     if: >
       github.event.issue.pull_request &&
-      contains(github.event.comment.body, '/run standalone') &&
+      contains(github.event.comment.body, '/run check') &&
       github.event.comment.user.login == 'ariostas'
     runs-on: ubuntu-latest
     timeout-minutes: 60
@@ -30,40 +30,6 @@ jobs:
         run: |  
           sha=$(git rev-parse HEAD)
           echo "COMMIT_SHA=$sha" >> $GITHUB_ENV
-      - name: Build and run PR
-        id: build-and-run
-        uses: SegmentLinkingTests/TrackLooper-actions/standalone@v1
-        with:
-          pr-number: ${{ github.event.issue.number }}
-      - name: Upload plots to archival repo
-        uses: s0/git-publish-subdir-action@develop
-        env:
-          REPO: git@github.com:${{ steps.build-and-run.outputs.archive-repo }}.git
-          BRANCH: ${{ steps.build-and-run.outputs.archive-branch }}
-          FOLDER: ${{ steps.build-and-run.outputs.archive-dir }}
-          SSH_PRIVATE_KEY: ${{ secrets.DEPLOY_PRIVATE_KEY }}
-          TARGET_DIR: ${{ steps.build-and-run.outputs.archive-dir }}
-      - name: Comment on PR
-        uses: actions/github-script@v6
-        with:
-          script: |
-            github.rest.issues.createComment({
-              issue_number: context.issue.number,
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              body: `${{ steps.build-and-run.outputs.comment }}`
-            })
-      - name: Comment on PR if job failed.
-        if: failure()
-        uses: actions/github-script@v6
-        with:
-          script: |
-            github.rest.issues.createComment({
-              issue_number: context.issue.number,
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              body: `There was a problem while building and running in standalone mode. You can find a log of the job [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}).`
-            })
       - uses: LouisBrunner/checks-action@v1.6.1
         if: always()
         with:

From 1d39a2a9db107242c33ae639a30ae76f5ceff4b3 Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Wed, 3 Jan 2024 16:15:35 -0500
Subject: [PATCH 09/23] Update checks_test.yml

---
 .github/workflows/checks_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/checks_test.yml b/.github/workflows/checks_test.yml
index 12dc980f..64b1e6d2 100644
--- a/.github/workflows/checks_test.yml
+++ b/.github/workflows/checks_test.yml
@@ -35,5 +35,5 @@ jobs:
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           sha: ${{ env.COMMIT_SHA }}
-          name: Standalone run
+          name: Test check
           conclusion: ${{ job.status }}

From 0620e9ea2f0749b009ebeaeac057185c7b069259 Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Wed, 3 Jan 2024 16:17:10 -0500
Subject: [PATCH 10/23] Update checks_test.yml

---
 .github/workflows/checks_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/checks_test.yml b/.github/workflows/checks_test.yml
index 64b1e6d2..8f216a43 100644
--- a/.github/workflows/checks_test.yml
+++ b/.github/workflows/checks_test.yml
@@ -35,5 +35,5 @@ jobs:
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           sha: ${{ env.COMMIT_SHA }}
-          name: Test check
+          name: Checks / Test check
           conclusion: ${{ job.status }}

From 92201d82b5dd706d9e7aa363ce6893463c80597d Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Wed, 3 Jan 2024 16:19:41 -0500
Subject: [PATCH 11/23] Update checks_test.yml

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

diff --git a/.github/workflows/checks_test.yml b/.github/workflows/checks_test.yml
index 8f216a43..df59e695 100644
--- a/.github/workflows/checks_test.yml
+++ b/.github/workflows/checks_test.yml
@@ -35,5 +35,6 @@ jobs:
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           sha: ${{ env.COMMIT_SHA }}
-          name: Checks / Test check
+          name: Checks / Test check 2
           conclusion: ${{ job.status }}
+          details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}

From bc9be3672fcfce4dc632f7c07badb3fedf5d0788 Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Wed, 3 Jan 2024 17:19:20 -0500
Subject: [PATCH 12/23] Update checks_test.yml

---
 .github/workflows/checks_test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/checks_test.yml b/.github/workflows/checks_test.yml
index df59e695..b39e91eb 100644
--- a/.github/workflows/checks_test.yml
+++ b/.github/workflows/checks_test.yml
@@ -3,6 +3,7 @@ name: Checks test
 on:
   issue_comment:
     types: [created]
+  pull_request:
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.issue.number }}-${{ github.event.comment.user.login }}-${{ contains(github.event.comment.body, '/run standalone') }}-${{ contains(github.event.comment.body, '/run cmssw') }}

From 52e11c1676daaf6427917b6c41a9b260ebfb20a5 Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Thu, 4 Jan 2024 09:37:29 -0500
Subject: [PATCH 13/23] Updated checks

---
 .github/workflows/{testing.yml => checks.yml} | 65 +++++++++++++++++--
 .github/workflows/checks_test.yml             | 41 ------------
 .github/workflows/static-checks.yml           | 49 --------------
 3 files changed, 61 insertions(+), 94 deletions(-)
 rename .github/workflows/{testing.yml => checks.yml} (65%)
 delete mode 100644 .github/workflows/checks_test.yml
 delete mode 100644 .github/workflows/static-checks.yml

diff --git a/.github/workflows/testing.yml b/.github/workflows/checks.yml
similarity index 65%
rename from .github/workflows/testing.yml
rename to .github/workflows/checks.yml
index ac6c12aa..a926e46e 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/checks.yml
@@ -1,11 +1,13 @@
-name: Testing
+name: Checks
 
 on:
   issue_comment:
     types: [created]
+  pull_request:
+    branches: master
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.event.issue.number }}-${{ github.event.comment.user.login }}-${{ contains(github.event.comment.body, '/run standalone') }}-${{ contains(github.event.comment.body, '/run cmssw') }}
+  group: ${{ github.workflow }}-${{ github.event.issue.number }}-${{ github.event.comment.user.login }}-${{ contains(github.event.comment.body, '/run standalone') }}-${{ contains(github.event.comment.body, '/run cmssw') }}-${{ github.sha }}
   cancel-in-progress: true
 
 permissions:
@@ -30,6 +32,14 @@ jobs:
         run: |  
           sha=$(git rev-parse HEAD)
           echo "COMMIT_SHA=$sha" >> $GITHUB_ENV
+      - uses: LouisBrunner/checks-action@v1.6.1
+        if: always()
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          sha: ${{ env.COMMIT_SHA }}
+          name: standalone
+          status: in_progress
+          details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
       - name: Build and run PR
         id: build-and-run
         uses: SegmentLinkingTests/TrackLooper-actions/standalone@v1
@@ -69,8 +79,9 @@ jobs:
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           sha: ${{ env.COMMIT_SHA }}
-          name: Standalone run
+          name: standalone
           conclusion: ${{ job.status }}
+          details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
        
   cmssw:
     if: >
@@ -88,6 +99,14 @@ jobs:
         run: |  
           sha=$(git rev-parse HEAD)
           echo "COMMIT_SHA=$sha" >> $GITHUB_ENV
+      - uses: LouisBrunner/checks-action@v1.6.1
+        if: always()
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          sha: ${{ env.COMMIT_SHA }}
+          name: cmssw
+          status: in_progress
+          details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
       - name: Get CMSSW branch name
         env:
           COMMENT_BODY: ${{ github.event.comment.body }}
@@ -151,5 +170,43 @@ jobs:
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           sha: ${{ env.COMMIT_SHA }}
-          name: CMSSW run
+          name: cmssw
           conclusion: ${{ job.status }}
+          details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
+
+  linter:
+    if: ${{ github.event_name }} == 'pull_request'
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+      - name: Checkout PR
+        uses: actions/checkout@v4
+      - name: Mount cvmfs
+        uses: cvmfs-contrib/github-action-cvmfs@v3
+      - name: Gather paths of needed headers
+        shell: bash
+        run: |
+          source setup.sh
+          INCLUDE_FLAGS="-I$TRACKLOOPERDIR -I$BOOST_ROOT/include -I$ALPAKA_ROOT/include -I$CUDA_HOME/include -I$ROOT_ROOT/include -I$CMSSW_BASE/src"
+          INCLUDE_FLAGS="$INCLUDE_FLAGS -I/cvmfs/cms.cern.ch/el8_amd64_gcc11/external/gcc/11.4.1-30ebdc301ebd200f2ae0e3d880258e65/include/c++/11.4.1"
+          INCLUDE_FLAGS="$INCLUDE_FLAGS -I/cvmfs/cms.cern.ch/el8_amd64_gcc11/external/gcc/11.4.1-30ebdc301ebd200f2ae0e3d880258e65/include/c++/11.4.1/x86_64-redhat-linux-gnu/"
+          INCLUDE_FLAGS="$INCLUDE_FLAGS -I/cvmfs/cms.cern.ch/el8_amd64_gcc11/external/gcc/11.4.1-30ebdc301ebd200f2ae0e3d880258e65/lib/gcc/x86_64-redhat-linux-gnu/11.4.1/include"
+          echo "include-flags=$INCLUDE_FLAGS" >> $GITHUB_ENV
+          # Note: Ideally we would use compiledb to generate a compile_commands.json file, but I couldn't get it to work properly with clang-tidy.
+          # This alternative of simply passing some extra arguments to clang-tidy seems to work fine (at least for now).
+      - name: Run linter
+        uses: cpp-linter/cpp-linter-action@v2
+        id: linter
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          style: file
+          thread-comments: true
+          # only use checks in .clang-tidy file
+          tidy-checks: ''
+          lines-changed-only: true
+          ignore: .github|bin|code|data|efficiency
+          extra-args: '-ferror-limit=0 -std=c++17 -DALPAKA_ACC_CPU_B_SEQ_T_SEQ_ENABLED ${{ env.include-flags }}'
+      - name: Fail job if there were checks that failed
+        if: steps.linter.outputs.checks-failed > 0
+        run: exit 1
diff --git a/.github/workflows/checks_test.yml b/.github/workflows/checks_test.yml
deleted file mode 100644
index b39e91eb..00000000
--- a/.github/workflows/checks_test.yml
+++ /dev/null
@@ -1,41 +0,0 @@
-name: Checks test
-
-on:
-  issue_comment:
-    types: [created]
-  pull_request:
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.issue.number }}-${{ github.event.comment.user.login }}-${{ contains(github.event.comment.body, '/run standalone') }}-${{ contains(github.event.comment.body, '/run cmssw') }}
-  cancel-in-progress: true
-
-permissions:
-  contents: read
-  pull-requests: write
-  checks: write
-
-jobs:
-  standalone:
-    if: >
-      github.event.issue.pull_request &&
-      contains(github.event.comment.body, '/run check') &&
-      github.event.comment.user.login == 'ariostas'
-    runs-on: ubuntu-latest
-    timeout-minutes: 60
-    steps:
-      - name: Checkout PR
-        uses: actions/checkout@v4
-        with:
-          ref: refs/pull/${{ github.event.issue.number }}/head
-      - name: Get commit SHA
-        run: |  
-          sha=$(git rev-parse HEAD)
-          echo "COMMIT_SHA=$sha" >> $GITHUB_ENV
-      - uses: LouisBrunner/checks-action@v1.6.1
-        if: always()
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          sha: ${{ env.COMMIT_SHA }}
-          name: Checks / Test check 2
-          conclusion: ${{ job.status }}
-          details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
diff --git a/.github/workflows/static-checks.yml b/.github/workflows/static-checks.yml
deleted file mode 100644
index e30ec8d7..00000000
--- a/.github/workflows/static-checks.yml
+++ /dev/null
@@ -1,49 +0,0 @@
-name: Static checks
-
-on:
-  pull_request:
-    branches: master
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.issue.number }}
-  cancel-in-progress: true
-
-permissions:
-  contents: read
-  pull-requests: write
-
-jobs:
-  linter:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout PR
-        uses: actions/checkout@v4
-      - name: Mount cvmfs
-        uses: cvmfs-contrib/github-action-cvmfs@v3
-      - name: Gather paths of needed headers
-        shell: bash
-        run: |
-          source setup.sh
-          INCLUDE_FLAGS="-I$TRACKLOOPERDIR -I$BOOST_ROOT/include -I$ALPAKA_ROOT/include -I$CUDA_HOME/include -I$ROOT_ROOT/include -I$CMSSW_BASE/src"
-          INCLUDE_FLAGS="$INCLUDE_FLAGS -I/cvmfs/cms.cern.ch/el8_amd64_gcc11/external/gcc/11.4.1-30ebdc301ebd200f2ae0e3d880258e65/include/c++/11.4.1"
-          INCLUDE_FLAGS="$INCLUDE_FLAGS -I/cvmfs/cms.cern.ch/el8_amd64_gcc11/external/gcc/11.4.1-30ebdc301ebd200f2ae0e3d880258e65/include/c++/11.4.1/x86_64-redhat-linux-gnu/"
-          INCLUDE_FLAGS="$INCLUDE_FLAGS -I/cvmfs/cms.cern.ch/el8_amd64_gcc11/external/gcc/11.4.1-30ebdc301ebd200f2ae0e3d880258e65/lib/gcc/x86_64-redhat-linux-gnu/11.4.1/include"
-          echo "include-flags=$INCLUDE_FLAGS" >> $GITHUB_ENV
-          # Note: Ideally we would use compiledb to generate a compile_commands.json file, but I couldn't get it to work properly with clang-tidy.
-          # This alternative of simply passing some extra arguments to clang-tidy seems to work fine (at least for now).
-      - name: Run linter
-        uses: cpp-linter/cpp-linter-action@v2
-        id: linter
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          style: file
-          thread-comments: true
-          # only use checks in .clang-tidy file
-          tidy-checks: ''
-          lines-changed-only: true
-          ignore: .github|bin|code|data|efficiency
-          extra-args: '-ferror-limit=0 -std=c++17 -DALPAKA_ACC_CPU_B_SEQ_T_SEQ_ENABLED ${{ env.include-flags }}'
-      - name: Fail job if there were checks that failed
-        if: steps.linter.outputs.checks-failed > 0
-        run: exit 1

From 63c413550490e78cf08cbc7b78607d7eafbc2865 Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Thu, 4 Jan 2024 10:52:20 -0500
Subject: [PATCH 14/23] Added app

---
 .github/workflows/static-checks.yml           | 49 +++++++++++++++
 .github/workflows/{checks.yml => testing.yml} | 61 ++++++-------------
 2 files changed, 66 insertions(+), 44 deletions(-)
 create mode 100644 .github/workflows/static-checks.yml
 rename .github/workflows/{checks.yml => testing.yml} (74%)

diff --git a/.github/workflows/static-checks.yml b/.github/workflows/static-checks.yml
new file mode 100644
index 00000000..85d87bf9
--- /dev/null
+++ b/.github/workflows/static-checks.yml
@@ -0,0 +1,49 @@
+name: Static checks
+
+on:
+  pull_request:
+    branches: master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.issue.number }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+  pull-requests: write
+
+jobs:
+  linter:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout PR
+        uses: actions/checkout@v4
+      - name: Mount cvmfs
+        uses: cvmfs-contrib/github-action-cvmfs@v3
+      - name: Gather paths of needed headers
+        shell: bash
+        run: |
+          source setup.sh
+          INCLUDE_FLAGS="-I$TRACKLOOPERDIR -I$BOOST_ROOT/include -I$ALPAKA_ROOT/include -I$CUDA_HOME/include -I$ROOT_ROOT/include -I$CMSSW_BASE/src"
+          INCLUDE_FLAGS="$INCLUDE_FLAGS -I/cvmfs/cms.cern.ch/el8_amd64_gcc11/external/gcc/11.4.1-30ebdc301ebd200f2ae0e3d880258e65/include/c++/11.4.1"
+          INCLUDE_FLAGS="$INCLUDE_FLAGS -I/cvmfs/cms.cern.ch/el8_amd64_gcc11/external/gcc/11.4.1-30ebdc301ebd200f2ae0e3d880258e65/include/c++/11.4.1/x86_64-redhat-linux-gnu/"
+          INCLUDE_FLAGS="$INCLUDE_FLAGS -I/cvmfs/cms.cern.ch/el8_amd64_gcc11/external/gcc/11.4.1-30ebdc301ebd200f2ae0e3d880258e65/lib/gcc/x86_64-redhat-linux-gnu/11.4.1/include"
+          echo "include-flags=$INCLUDE_FLAGS" >> $GITHUB_ENV
+          # Note: Ideally we would use compiledb to generate a compile_commands.json file, but I couldn't get it to work properly with clang-tidy.
+          # This alternative of simply passing some extra arguments to clang-tidy seems to work fine (at least for now).
+      - name: Run linter
+        uses: cpp-linter/cpp-linter-action@v2
+        id: linter
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          style: file
+          thread-comments: true
+          # only use checks in .clang-tidy file
+          tidy-checks: ''
+          lines-changed-only: true
+          ignore: .github|bin|code|data|efficiency
+          extra-args: '-ferror-limit=0 -std=c++17 -DALPAKA_ACC_CPU_B_SEQ_T_SEQ_ENABLED ${{ env.include-flags }}'
+      - name: Fail job if there were checks that failed
+        if: steps.linter.outputs.checks-failed > 0
+        run: exit 1
\ No newline at end of file
diff --git a/.github/workflows/checks.yml b/.github/workflows/testing.yml
similarity index 74%
rename from .github/workflows/checks.yml
rename to .github/workflows/testing.yml
index a926e46e..a529aeac 100644
--- a/.github/workflows/checks.yml
+++ b/.github/workflows/testing.yml
@@ -3,11 +3,9 @@ name: Checks
 on:
   issue_comment:
     types: [created]
-  pull_request:
-    branches: master
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.event.issue.number }}-${{ github.event.comment.user.login }}-${{ contains(github.event.comment.body, '/run standalone') }}-${{ contains(github.event.comment.body, '/run cmssw') }}-${{ github.sha }}
+  group: ${{ github.workflow }}-${{ github.event.issue.number }}-${{ github.event.comment.user.login }}-${{ contains(github.event.comment.body, '/run standalone') }}-${{ contains(github.event.comment.body, '/run cmssw') }}
   cancel-in-progress: true
 
 permissions:
@@ -32,10 +30,16 @@ jobs:
         run: |  
           sha=$(git rev-parse HEAD)
           echo "COMMIT_SHA=$sha" >> $GITHUB_ENV
+      - name: Create App Token
+        uses: actions/create-github-app-token@v1
+        id: app-token
+        with: 
+          app-id: 778431
+          private-key: ${{ secrets.APP_PRIVATE_KEY }}
       - uses: LouisBrunner/checks-action@v1.6.1
         if: always()
         with:
-          token: ${{ secrets.GITHUB_TOKEN }}
+          token: ${{ steps.app-token.outputs.token }}
           sha: ${{ env.COMMIT_SHA }}
           name: standalone
           status: in_progress
@@ -77,7 +81,7 @@ jobs:
       - uses: LouisBrunner/checks-action@v1.6.1
         if: always()
         with:
-          token: ${{ secrets.GITHUB_TOKEN }}
+          token: ${{ steps.app-token.outputs.token }}
           sha: ${{ env.COMMIT_SHA }}
           name: standalone
           conclusion: ${{ job.status }}
@@ -99,10 +103,16 @@ jobs:
         run: |  
           sha=$(git rev-parse HEAD)
           echo "COMMIT_SHA=$sha" >> $GITHUB_ENV
+      - name: Create App Token
+        uses: actions/create-github-app-token@v1
+        id: app-token
+        with: 
+          app-id: 778431
+          private-key: ${{ secrets.APP_PRIVATE_KEY }}
       - uses: LouisBrunner/checks-action@v1.6.1
         if: always()
         with:
-          token: ${{ secrets.GITHUB_TOKEN }}
+          token: ${{ steps.app-token.outputs.token }}
           sha: ${{ env.COMMIT_SHA }}
           name: cmssw
           status: in_progress
@@ -168,45 +178,8 @@ jobs:
       - uses: LouisBrunner/checks-action@v1.6.1
         if: always()
         with:
-          token: ${{ secrets.GITHUB_TOKEN }}
+          token: ${{ steps.app-token.outputs.token }}
           sha: ${{ env.COMMIT_SHA }}
           name: cmssw
           conclusion: ${{ job.status }}
           details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
-
-  linter:
-    if: ${{ github.event_name }} == 'pull_request'
-    runs-on: ubuntu-latest
-    timeout-minutes: 15
-    steps:
-      - name: Checkout PR
-        uses: actions/checkout@v4
-      - name: Mount cvmfs
-        uses: cvmfs-contrib/github-action-cvmfs@v3
-      - name: Gather paths of needed headers
-        shell: bash
-        run: |
-          source setup.sh
-          INCLUDE_FLAGS="-I$TRACKLOOPERDIR -I$BOOST_ROOT/include -I$ALPAKA_ROOT/include -I$CUDA_HOME/include -I$ROOT_ROOT/include -I$CMSSW_BASE/src"
-          INCLUDE_FLAGS="$INCLUDE_FLAGS -I/cvmfs/cms.cern.ch/el8_amd64_gcc11/external/gcc/11.4.1-30ebdc301ebd200f2ae0e3d880258e65/include/c++/11.4.1"
-          INCLUDE_FLAGS="$INCLUDE_FLAGS -I/cvmfs/cms.cern.ch/el8_amd64_gcc11/external/gcc/11.4.1-30ebdc301ebd200f2ae0e3d880258e65/include/c++/11.4.1/x86_64-redhat-linux-gnu/"
-          INCLUDE_FLAGS="$INCLUDE_FLAGS -I/cvmfs/cms.cern.ch/el8_amd64_gcc11/external/gcc/11.4.1-30ebdc301ebd200f2ae0e3d880258e65/lib/gcc/x86_64-redhat-linux-gnu/11.4.1/include"
-          echo "include-flags=$INCLUDE_FLAGS" >> $GITHUB_ENV
-          # Note: Ideally we would use compiledb to generate a compile_commands.json file, but I couldn't get it to work properly with clang-tidy.
-          # This alternative of simply passing some extra arguments to clang-tidy seems to work fine (at least for now).
-      - name: Run linter
-        uses: cpp-linter/cpp-linter-action@v2
-        id: linter
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          style: file
-          thread-comments: true
-          # only use checks in .clang-tidy file
-          tidy-checks: ''
-          lines-changed-only: true
-          ignore: .github|bin|code|data|efficiency
-          extra-args: '-ferror-limit=0 -std=c++17 -DALPAKA_ACC_CPU_B_SEQ_T_SEQ_ENABLED ${{ env.include-flags }}'
-      - name: Fail job if there were checks that failed
-        if: steps.linter.outputs.checks-failed > 0
-        run: exit 1

From 40646fdcfe2c6736dbfa24afe568b53cd5f3259f Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Thu, 4 Jan 2024 14:15:37 -0500
Subject: [PATCH 15/23] Update static checks

---
 .github/workflows/static-checks.yml | 22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/static-checks.yml b/.github/workflows/static-checks.yml
index 85d87bf9..0d95e340 100644
--- a/.github/workflows/static-checks.yml
+++ b/.github/workflows/static-checks.yml
@@ -15,22 +15,32 @@ permissions:
 jobs:
   linter:
     runs-on: ubuntu-latest
+    timeout-minutes: 20
     steps:
       - name: Checkout PR
         uses: actions/checkout@v4
       - name: Mount cvmfs
         uses: cvmfs-contrib/github-action-cvmfs@v3
-      - name: Gather paths of needed headers
-        shell: bash
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Generate compilation database
+        working-directory: ./SDL
         run: |
-          source setup.sh
+          pip install compiledb compdb
+          make BACKEND=cpu -Bnwk > build_log.txt
+          compiledb < build_log.txt
+          # This extra step is needed to generate compilation commands for headers
+          compdb list > compile_commands_new.json
+          mv compile_commands_new.json > compile_commands.json
+          # Now we gather some include paths since the compiler is not fully configured to find all the headers.
+          source setup.sh 1> /dev/null 2> /dev/null
           INCLUDE_FLAGS="-I$TRACKLOOPERDIR -I$BOOST_ROOT/include -I$ALPAKA_ROOT/include -I$CUDA_HOME/include -I$ROOT_ROOT/include -I$CMSSW_BASE/src"
           INCLUDE_FLAGS="$INCLUDE_FLAGS -I/cvmfs/cms.cern.ch/el8_amd64_gcc11/external/gcc/11.4.1-30ebdc301ebd200f2ae0e3d880258e65/include/c++/11.4.1"
           INCLUDE_FLAGS="$INCLUDE_FLAGS -I/cvmfs/cms.cern.ch/el8_amd64_gcc11/external/gcc/11.4.1-30ebdc301ebd200f2ae0e3d880258e65/include/c++/11.4.1/x86_64-redhat-linux-gnu/"
           INCLUDE_FLAGS="$INCLUDE_FLAGS -I/cvmfs/cms.cern.ch/el8_amd64_gcc11/external/gcc/11.4.1-30ebdc301ebd200f2ae0e3d880258e65/lib/gcc/x86_64-redhat-linux-gnu/11.4.1/include"
           echo "include-flags=$INCLUDE_FLAGS" >> $GITHUB_ENV
-          # Note: Ideally we would use compiledb to generate a compile_commands.json file, but I couldn't get it to work properly with clang-tidy.
-          # This alternative of simply passing some extra arguments to clang-tidy seems to work fine (at least for now).
       - name: Run linter
         uses: cpp-linter/cpp-linter-action@v2
         id: linter
@@ -43,7 +53,7 @@ jobs:
           tidy-checks: ''
           lines-changed-only: true
           ignore: .github|bin|code|data|efficiency
-          extra-args: '-ferror-limit=0 -std=c++17 -DALPAKA_ACC_CPU_B_SEQ_T_SEQ_ENABLED ${{ env.include-flags }}'
+          extra-args: '-ferror-limit=0 ${{ env.include-flags }}'
       - name: Fail job if there were checks that failed
         if: steps.linter.outputs.checks-failed > 0
         run: exit 1
\ No newline at end of file

From 9262fd7787374b910c773e8a65f0c519b0ed5040 Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Thu, 4 Jan 2024 16:30:30 -0500
Subject: [PATCH 16/23] Update testing.yml

---
 .github/workflows/testing.yml | 27 ++++++++++++++++++++++-----
 1 file changed, 22 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index a529aeac..682440d8 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -5,13 +5,12 @@ on:
     types: [created]
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.event.issue.number }}-${{ github.event.comment.user.login }}-${{ contains(github.event.comment.body, '/run standalone') }}-${{ contains(github.event.comment.body, '/run cmssw') }}
+  group: ${{ github.workflow }}-${{ github.event.issue.number }}-${{ contains(github.event.comment.body, '/run standalone') }}-${{ contains(github.event.comment.body, '/run cmssw') }}
   cancel-in-progress: true
 
 permissions:
   contents: read
   pull-requests: write
-  checks: write
 
 jobs:
   standalone:
@@ -78,14 +77,23 @@ jobs:
               repo: context.repo.repo,
               body: `There was a problem while building and running in standalone mode. You can find a log of the job [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}).`
             })
+      - name: Create App Token
+        if: always()
+        uses: actions/create-github-app-token@v1
+        id: app-token-end
+        with: 
+          app-id: 778431
+          private-key: ${{ secrets.APP_PRIVATE_KEY }}
       - uses: LouisBrunner/checks-action@v1.6.1
         if: always()
         with:
-          token: ${{ steps.app-token.outputs.token }}
+          token: ${{ steps.app-token-end.outputs.token }}
           sha: ${{ env.COMMIT_SHA }}
           name: standalone
           conclusion: ${{ job.status }}
           details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
+          output: |
+            {"summary": "Status: ${{ job.status }}", "text_description": "More details can be found in the job logs [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
        
   cmssw:
     if: >
@@ -93,7 +101,7 @@ jobs:
       contains(github.event.comment.body, '/run cmssw') &&
       github.event.comment.user.login == 'ariostas'
     runs-on: ubuntu-latest
-    timeout-minutes: 150
+    timeout-minutes: 180
     steps:
       - name: Checkout PR
         uses: actions/checkout@v4
@@ -175,11 +183,20 @@ jobs:
               repo: context.repo.repo,
               body: `There was a problem while building and running with CMSSW. You can find a log of the job [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}).`
             })
+      - name: Create App Token
+        if: always()
+        uses: actions/create-github-app-token@v1
+        id: app-token-end
+        with: 
+          app-id: 778431
+          private-key: ${{ secrets.APP_PRIVATE_KEY }}
       - uses: LouisBrunner/checks-action@v1.6.1
         if: always()
         with:
-          token: ${{ steps.app-token.outputs.token }}
+          token: ${{ steps.app-token-end.outputs.token }}
           sha: ${{ env.COMMIT_SHA }}
           name: cmssw
           conclusion: ${{ job.status }}
           details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
+          output: |
+            {"summary": "Status: ${{ job.status }}", "text_description": "More details can be found in the job logs [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}

From 28c656c354c11ef2acd9a41f0f8801775c086f80 Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Thu, 4 Jan 2024 16:56:44 -0500
Subject: [PATCH 17/23] Update testing.yml

---
 .github/workflows/testing.yml | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 682440d8..6b0a1a6c 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -40,9 +40,11 @@ jobs:
         with:
           token: ${{ steps.app-token.outputs.token }}
           sha: ${{ env.COMMIT_SHA }}
-          name: standalone
+          name: Run Standalone PU200
           status: in_progress
           details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
+          output: |
+            {"title": "Status: ${{ job.status }}", "summary": "The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
       - name: Build and run PR
         id: build-and-run
         uses: SegmentLinkingTests/TrackLooper-actions/standalone@v1
@@ -75,7 +77,7 @@ jobs:
               issue_number: context.issue.number,
               owner: context.repo.owner,
               repo: context.repo.repo,
-              body: `There was a problem while building and running in standalone mode. You can find a log of the job [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}).`
+              body: `There was a problem while building and running in standalone mode. The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}).`
             })
       - name: Create App Token
         if: always()
@@ -89,11 +91,11 @@ jobs:
         with:
           token: ${{ steps.app-token-end.outputs.token }}
           sha: ${{ env.COMMIT_SHA }}
-          name: standalone
+          name: Run Standalone PU200
           conclusion: ${{ job.status }}
           details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
           output: |
-            {"summary": "Status: ${{ job.status }}", "text_description": "More details can be found in the job logs [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
+            {"title": "Status: ${{ job.status }}", "summary": "The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
        
   cmssw:
     if: >
@@ -122,9 +124,11 @@ jobs:
         with:
           token: ${{ steps.app-token.outputs.token }}
           sha: ${{ env.COMMIT_SHA }}
-          name: cmssw
+          name: Run CMSSW 21034.1
           status: in_progress
           details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
+          output: |
+            {"title": "Status: ${{ job.status }}", "summary": "The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
       - name: Get CMSSW branch name
         env:
           COMMENT_BODY: ${{ github.event.comment.body }}
@@ -181,7 +185,7 @@ jobs:
               issue_number: context.issue.number,
               owner: context.repo.owner,
               repo: context.repo.repo,
-              body: `There was a problem while building and running with CMSSW. You can find a log of the job [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}).`
+              body: `There was a problem while building and running with CMSSW. The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}).`
             })
       - name: Create App Token
         if: always()
@@ -195,8 +199,8 @@ jobs:
         with:
           token: ${{ steps.app-token-end.outputs.token }}
           sha: ${{ env.COMMIT_SHA }}
-          name: cmssw
+          name: Run CMSSW 21034.1
           conclusion: ${{ job.status }}
           details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
           output: |
-            {"summary": "Status: ${{ job.status }}", "text_description": "More details can be found in the job logs [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
+            {"title": "Status: ${{ job.status }}", "summary": "The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}

From 51ca6ea45db1f756cbc5e52cb836b5aab54015d5 Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Thu, 4 Jan 2024 16:59:39 -0500
Subject: [PATCH 18/23] Update testing.yml

---
 .github/workflows/testing.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 6b0a1a6c..6113eac7 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -44,7 +44,7 @@ jobs:
           status: in_progress
           details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
           output: |
-            {"title": "Status: ${{ job.status }}", "summary": "The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
+            {"title": "This check is in progress...", "summary": "The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
       - name: Build and run PR
         id: build-and-run
         uses: SegmentLinkingTests/TrackLooper-actions/standalone@v1
@@ -128,7 +128,7 @@ jobs:
           status: in_progress
           details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
           output: |
-            {"title": "Status: ${{ job.status }}", "summary": "The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
+            {"title": "This check is in progress...", "summary": "The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
       - name: Get CMSSW branch name
         env:
           COMMENT_BODY: ${{ github.event.comment.body }}

From e26e897bfee6167dc5cfa2c716482d8f4e0a5885 Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Thu, 4 Jan 2024 17:03:28 -0500
Subject: [PATCH 19/23] Update testing.yml

---
 .github/workflows/testing.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 6113eac7..d5baba28 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -44,7 +44,7 @@ jobs:
           status: in_progress
           details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
           output: |
-            {"title": "This check is in progress...", "summary": "The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
+            {"title": "This check has started...", "summary": "The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
       - name: Build and run PR
         id: build-and-run
         uses: SegmentLinkingTests/TrackLooper-actions/standalone@v1
@@ -128,7 +128,7 @@ jobs:
           status: in_progress
           details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
           output: |
-            {"title": "This check is in progress...", "summary": "The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
+            {"title": "This check has started...", "summary": "The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
       - name: Get CMSSW branch name
         env:
           COMMENT_BODY: ${{ github.event.comment.body }}

From 88cfeb154e5e7a14bee80fa222a48d2b5a89e2fe Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Fri, 5 Jan 2024 09:37:41 -0500
Subject: [PATCH 20/23] Update testing.yml

---
 .github/workflows/testing.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index d5baba28..76fe462a 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -19,7 +19,6 @@ jobs:
       contains(github.event.comment.body, '/run standalone') &&
       github.event.comment.user.login == 'ariostas'
     runs-on: ubuntu-latest
-    timeout-minutes: 60
     steps:
       - name: Checkout PR
         uses: actions/checkout@v4
@@ -46,6 +45,7 @@ jobs:
           output: |
             {"title": "This check has started...", "summary": "The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
       - name: Build and run PR
+        timeout-minutes: 60
         id: build-and-run
         uses: SegmentLinkingTests/TrackLooper-actions/standalone@v1
         with:
@@ -103,7 +103,6 @@ jobs:
       contains(github.event.comment.body, '/run cmssw') &&
       github.event.comment.user.login == 'ariostas'
     runs-on: ubuntu-latest
-    timeout-minutes: 180
     steps:
       - name: Checkout PR
         uses: actions/checkout@v4
@@ -153,6 +152,7 @@ jobs:
           echo "Using CMSSW branch: $cmssw_branch"
           echo "cmssw-branch=$cmssw_branch" >> $GITHUB_ENV
       - name: Build and run PR
+        timeout-minutes: 180
         id: build-and-run
         uses: SegmentLinkingTests/TrackLooper-actions/cmssw@v1
         with:

From eed94cda63d30759e74823edaeaf937df6b274b9 Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Fri, 5 Jan 2024 09:50:46 -0500
Subject: [PATCH 21/23] Update testing.yml

---
 .github/workflows/testing.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 76fe462a..00dd638b 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -32,7 +32,7 @@ jobs:
         uses: actions/create-github-app-token@v1
         id: app-token
         with: 
-          app-id: 778431
+          app-id: ${{ secrets.APP_ID }}
           private-key: ${{ secrets.APP_PRIVATE_KEY }}
       - uses: LouisBrunner/checks-action@v1.6.1
         if: always()
@@ -84,7 +84,7 @@ jobs:
         uses: actions/create-github-app-token@v1
         id: app-token-end
         with: 
-          app-id: 778431
+          app-id: ${{ secrets.APP_ID }}
           private-key: ${{ secrets.APP_PRIVATE_KEY }}
       - uses: LouisBrunner/checks-action@v1.6.1
         if: always()
@@ -116,7 +116,7 @@ jobs:
         uses: actions/create-github-app-token@v1
         id: app-token
         with: 
-          app-id: 778431
+          app-id: ${{ secrets.APP_ID }}
           private-key: ${{ secrets.APP_PRIVATE_KEY }}
       - uses: LouisBrunner/checks-action@v1.6.1
         if: always()
@@ -192,7 +192,7 @@ jobs:
         uses: actions/create-github-app-token@v1
         id: app-token-end
         with: 
-          app-id: 778431
+          app-id: ${{ secrets.APP_ID }}
           private-key: ${{ secrets.APP_PRIVATE_KEY }}
       - uses: LouisBrunner/checks-action@v1.6.1
         if: always()

From 97c000f629fd1f9fc12258f5c006bce726e19856 Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Tue, 9 Jan 2024 13:50:36 -0500
Subject: [PATCH 22/23] Match main repo

---
 .github/workflows/testing.yml | 36 +++++++++++++++++++----------------
 1 file changed, 20 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 00dd638b..ad78bdbe 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -1,4 +1,4 @@
-name: Checks
+name: Testing
 
 on:
   issue_comment:
@@ -20,22 +20,23 @@ jobs:
       github.event.comment.user.login == 'ariostas'
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout PR
+      - name: Check out PR
         uses: actions/checkout@v4
         with:
           ref: refs/pull/${{ github.event.issue.number }}/head
       - name: Get commit SHA
-        run: |  
+        run: |
           sha=$(git rev-parse HEAD)
           echo "COMMIT_SHA=$sha" >> $GITHUB_ENV
       - name: Create App Token
         uses: actions/create-github-app-token@v1
         id: app-token
-        with: 
+        with:
           app-id: ${{ secrets.APP_ID }}
           private-key: ${{ secrets.APP_PRIVATE_KEY }}
-      - uses: LouisBrunner/checks-action@v1.6.1
-        if: always()
+          skip-token-revoke: true
+      - name: Create in progress check
+        uses: LouisBrunner/checks-action@v1.6.1
         with:
           token: ${{ steps.app-token.outputs.token }}
           sha: ${{ env.COMMIT_SHA }}
@@ -83,10 +84,11 @@ jobs:
         if: always()
         uses: actions/create-github-app-token@v1
         id: app-token-end
-        with: 
+        with:
           app-id: ${{ secrets.APP_ID }}
           private-key: ${{ secrets.APP_PRIVATE_KEY }}
-      - uses: LouisBrunner/checks-action@v1.6.1
+      - name: Create completed check
+        uses: LouisBrunner/checks-action@v1.6.1
         if: always()
         with:
           token: ${{ steps.app-token-end.outputs.token }}
@@ -109,17 +111,18 @@ jobs:
         with:
           ref: refs/pull/${{ github.event.issue.number }}/head
       - name: Get commit SHA
-        run: |  
+        run: |
           sha=$(git rev-parse HEAD)
           echo "COMMIT_SHA=$sha" >> $GITHUB_ENV
       - name: Create App Token
         uses: actions/create-github-app-token@v1
         id: app-token
-        with: 
+        with:
           app-id: ${{ secrets.APP_ID }}
           private-key: ${{ secrets.APP_PRIVATE_KEY }}
-      - uses: LouisBrunner/checks-action@v1.6.1
-        if: always()
+          skip-token-revoke: true
+      - name: Create in progress check
+        uses: LouisBrunner/checks-action@v1.6.1
         with:
           token: ${{ steps.app-token.outputs.token }}
           sha: ${{ env.COMMIT_SHA }}
@@ -152,7 +155,7 @@ jobs:
           echo "Using CMSSW branch: $cmssw_branch"
           echo "cmssw-branch=$cmssw_branch" >> $GITHUB_ENV
       - name: Build and run PR
-        timeout-minutes: 180
+        timeout-minutes: 200
         id: build-and-run
         uses: SegmentLinkingTests/TrackLooper-actions/cmssw@v1
         with:
@@ -191,10 +194,11 @@ jobs:
         if: always()
         uses: actions/create-github-app-token@v1
         id: app-token-end
-        with: 
+        with:
           app-id: ${{ secrets.APP_ID }}
           private-key: ${{ secrets.APP_PRIVATE_KEY }}
-      - uses: LouisBrunner/checks-action@v1.6.1
+      - name: Create completed check
+        uses: LouisBrunner/checks-action@v1.6.1
         if: always()
         with:
           token: ${{ steps.app-token-end.outputs.token }}
@@ -203,4 +207,4 @@ jobs:
           conclusion: ${{ job.status }}
           details_url: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
           output: |
-            {"title": "Status: ${{ job.status }}", "summary": "The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
+            {"title": "Status: ${{ job.status }}", "summary": "The logs can be found [here](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})."}
\ No newline at end of file

From 483164768c4db95c026c759db97885a21051318f Mon Sep 17 00:00:00 2001
From: Andres Rios Tascon <ariostas@gmail.com>
Date: Tue, 9 Jan 2024 21:29:56 -0500
Subject: [PATCH 23/23] Update README.md

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 7da68668..b81da510 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,6 @@
 # TrackLooper
 
+# test
 
 ## Quick Start