From bc17130b162463e7f71ea7b59534b240377401b5 Mon Sep 17 00:00:00 2001
From: Joe Zuntz <joezuntz@googlemail.com>
Date: Thu, 8 Oct 2026 10:49:51 +0100
Subject: [PATCH 1/2] Have the dry-run pipeline print which stages would skip

---
 ceci/pipeline/dry_run.py | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/ceci/pipeline/dry_run.py b/ceci/pipeline/dry_run.py
index 473bf73..656e19f 100644
--- a/ceci/pipeline/dry_run.py
+++ b/ceci/pipeline/dry_run.py
@@ -13,7 +13,10 @@ class DryRunPipeline(Pipeline):
     """
 
     def initiate_run(self, overall_inputs):
-        return []
+        return {
+            "commands": [],
+            "completed_stages": [],
+        }
 
     def should_skip_stage(self, stage):
         return False
@@ -30,13 +33,20 @@ def enqueue_job(self, stage, pipeline_files):
         if sys.stdout.isatty():
             cmd = cmd.replace(stage.instance_name, embolden(stage.instance_name), 1)
 
-        self.run_info.append(cmd)
+        # make a list of complete stages and print at the end
+        if super().should_skip_stage(stage):
+            self.run_info["completed_stages"].append(stage.instance_name)
+
+        self.run_info["commands"].append(cmd)
         return outputs
 
     def run_jobs(self):
-        for cmd in self.run_info:
+        for cmd in self.run_info["commands"]:
             print(cmd)
             print("\n")
+        print("\n")
+        for name in self.run_info["completed_stages"]:
+            print(f"# {name} is complete and could be skipped")
         return 0
 
     def find_all_outputs(self):

From 65fd87f915d2799e05ed63d8d4b01a5e1c5bea01 Mon Sep 17 00:00:00 2001
From: joezuntz <joezuntz@googlemail.com>
Date: Thu, 8 Oct 2026 10:57:26 +0100
Subject: [PATCH 2/2] Update stage skipping condition for dry run

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 ceci/pipeline/dry_run.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ceci/pipeline/dry_run.py b/ceci/pipeline/dry_run.py
index 656e19f..8390189 100644
--- a/ceci/pipeline/dry_run.py
+++ b/ceci/pipeline/dry_run.py
@@ -34,7 +34,7 @@ def enqueue_job(self, stage, pipeline_files):
             cmd = cmd.replace(stage.instance_name, embolden(stage.instance_name), 1)
 
         # make a list of complete stages and print at the end
-        if super().should_skip_stage(stage):
+        if self.run_config["resume"] in (True, "resume") and super().should_skip_stage(stage):
             self.run_info["completed_stages"].append(stage.instance_name)
 
         self.run_info["commands"].append(cmd)