From b8828fc4f4dfd6f9abe7a5cc1e8a4269de357e02 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 26 Sep 2024 13:55:32 +0200
Subject: [PATCH 1/4] for tools check only changes in the REPO

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

diff --git a/.github/workflows/autoupdate.yml b/.github/workflows/autoupdate.yml
index 9be465a..18d4b45 100644
--- a/.github/workflows/autoupdate.yml
+++ b/.github/workflows/autoupdate.yml
@@ -109,7 +109,7 @@ jobs:
                 ;;
               *)
                 TITLE=$(python3 "${{ github.workspace }}/autoupdate/pr_text.py" --repo "$REPO" --log "${{ github.workspace }}/autoupdate.log" --shed "$REPO/.shed.yml" --out "${{ github.workspace }}/body.txt")
-                FILE_TO_CHECK=
+                FILE_TO_CHECK=${REPO}
                 ;;
             esac
             # Check if there is a branch/PR that already exists

From 3085c45fd793ed293fb8faafbb39a5d6a3ab39b0 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 26 Sep 2024 14:08:23 +0200
Subject: [PATCH 2/4] fix cases where the PR is closed and branch deleted

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

diff --git a/.github/workflows/autoupdate.yml b/.github/workflows/autoupdate.yml
index 18d4b45..046635e 100644
--- a/.github/workflows/autoupdate.yml
+++ b/.github/workflows/autoupdate.yml
@@ -162,7 +162,7 @@ jobs:
                 fi
               fi
               echo "There are changes"
-              if [ "$PR_EXISTS" -eq 1 ]; then
+              if [ "$DIFF_BRANCH" = "origin/$REPO" ] ; then
                 # Check if the last commit of the existing branch was manual
                 LAST_AUTHOR=$(git log -1 --pretty=format:'%an' $DIFF_BRANCH)
                 if [ "$LAST_AUTHOR" != "planemo-autoupdate" ]; then

From a5ad00c5bd9dc048f92deef3f9f3a87658086f13 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 26 Sep 2024 15:48:24 +0200
Subject: [PATCH 3/4] deal with autoupdate fails because of malformed xml.

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

diff --git a/.github/workflows/autoupdate.yml b/.github/workflows/autoupdate.yml
index 046635e..6c38676 100644
--- a/.github/workflows/autoupdate.yml
+++ b/.github/workflows/autoupdate.yml
@@ -93,6 +93,10 @@ jobs:
             cd "$REPO"
             # This may fail
             planemo autoupdate . --skiplist "${{ github.workspace }}/autoupdate/${{ matrix.upstream_repo_owner }}_${{ matrix.upstream_repo_name }}_skip_list" 2>&1 1> "${{ github.workspace }}/autoupdate.log" | tee "${{ github.workspace }}/autoupdate.err" || errors="${errors}\nCannot autoupdate $REPO, last line of stderr is\n$(tail -n 1 "${{ github.workspace }}/autoupdate.err")"
+            # Waiting for https://github.com/galaxyproject/planemo/issues/1478 to be solved
+            if [[ "$(tail -n 1 "${{ github.workspace }}/autoupdate.log")" = "Could not update"* ]]; then
+              errors="${errors}\n$(tail -n 1 "${{ github.workspace }}/autoupdate.log")\n$(tail -n 1 "${{ github.workspace }}/autoupdate.err")"
+            fi
             rm -f tool_test_output.* tools.yml
             cd -
             # Check if it changed something

From 7e11d1196def50da8e4b2138dec428086e1c728d Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 26 Sep 2024 22:58:38 +0200
Subject: [PATCH 4/4] keep exit code of 1 even with tee

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

diff --git a/.github/workflows/autoupdate.yml b/.github/workflows/autoupdate.yml
index 6c38676..1cb07b6 100644
--- a/.github/workflows/autoupdate.yml
+++ b/.github/workflows/autoupdate.yml
@@ -92,7 +92,11 @@ jobs:
             echo "Running autoupdate command..."
             cd "$REPO"
             # This may fail
+            # To get an exit code of 1 even with tee:
+            set -o pipefail
             planemo autoupdate . --skiplist "${{ github.workspace }}/autoupdate/${{ matrix.upstream_repo_owner }}_${{ matrix.upstream_repo_name }}_skip_list" 2>&1 1> "${{ github.workspace }}/autoupdate.log" | tee "${{ github.workspace }}/autoupdate.err" || errors="${errors}\nCannot autoupdate $REPO, last line of stderr is\n$(tail -n 1 "${{ github.workspace }}/autoupdate.err")"
+            # Restore
+            set +o pipefail
             # Waiting for https://github.com/galaxyproject/planemo/issues/1478 to be solved
             if [[ "$(tail -n 1 "${{ github.workspace }}/autoupdate.log")" = "Could not update"* ]]; then
               errors="${errors}\n$(tail -n 1 "${{ github.workspace }}/autoupdate.log")\n$(tail -n 1 "${{ github.workspace }}/autoupdate.err")"