From 8aa53dbec718956a791dc56062af688a41f0a758 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Thu, 5 Mar 2026 14:19:14 -0500
Subject: [PATCH 1/2] docs(ptm): Fix documentation regarding MSstatsPTM
 groupComparisonPTM

---
 R/main_calculations.R | 3 +--
 man/apply_adj.Rd      | 3 +--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/R/main_calculations.R b/R/main_calculations.R
index b297658..e1fc395 100644
--- a/R/main_calculations.R
+++ b/R/main_calculations.R
@@ -486,8 +486,7 @@ tmt_model = function(data, input, contrast.matrix, busy_indicator = TRUE){
 #' 
 #' @return list of PTM modeling results
 #' @examples
-#' model = MSstatsPTM::groupComparisonPTM(MSstatsPTM::summary.data, 
-#'                                        data.type = "LabelFree")
+#' model = MSstatsPTM::groupComparisonPTM(MSstatsPTM::summary.data)
 #' apply_adj(model$PTM.Model, model$PROTEIN.Model)
 #' 
 apply_adj = function(ptm_model, protein_model){
diff --git a/man/apply_adj.Rd b/man/apply_adj.Rd
index 677b0cf..71191a0 100644
--- a/man/apply_adj.Rd
+++ b/man/apply_adj.Rd
@@ -18,8 +18,7 @@ list of PTM modeling results
 Main PTM function to model MSstatsShiny data.
 }
 \examples{
-model = MSstatsPTM::groupComparisonPTM(MSstatsPTM::summary.data, 
-                                       data.type = "LabelFree")
+model = MSstatsPTM::groupComparisonPTM(MSstatsPTM::summary.data)
 apply_adj(model$PTM.Model, model$PROTEIN.Model)
 
 }

From 9685dd7f03fe4166e664a68218d01168c4cbf374 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Thu, 5 Mar 2026 17:51:24 -0500
Subject: [PATCH 2/2] delete codium pr agent

---
 .github/workflows/codium-pr-agent.yml | 19 -------------------
 1 file changed, 19 deletions(-)
 delete mode 100644 .github/workflows/codium-pr-agent.yml

diff --git a/.github/workflows/codium-pr-agent.yml b/.github/workflows/codium-pr-agent.yml
deleted file mode 100644
index aa55650..0000000
--- a/.github/workflows/codium-pr-agent.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-on:
-  pull_request:
-    types: [opened]
-jobs:
-  pr_agent_job:
-    if: ${{ github.event.sender.type != 'Bot' }}
-    runs-on: ubuntu-latest
-    permissions:
-      pull-requests: write
-      contents: read
-    name: Run pr agent on every pull request
-    steps:
-      - name: PR Agent action step
-        id: pragent
-        uses: Codium-ai/pr-agent@main
-        env:
-          OPENAI_KEY: ${{ secrets.MSSTATS_OPENAI_KEY }}
-          OPENAI_ORG: ${{ secrets.MSSTATS_OPENAI_ORG }}
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
\ No newline at end of file