Enable updating existing experiment repo

src/experiment_runner/experiment_runner.py

@@ -2,6 +2,8 @@
 from payu.branch import clone, list_branches
 from .base_experiment import BaseExperiment
 from .pbs_job_manager import PBSJobManager
+import subprocess
+import git
 
 
 class ExperimentRunner(BaseExperiment):
@@ -42,19 +44,77 @@ def _create_cloned_directory(self) -> None:
         for clone_dir, branch in zip(all_cloned_directories, self.running_branches):
             if clone_dir.exists():
                 print(f"-- Test dir: {clone_dir} already exists, skipping cloning.")
+                if not self._update_existing_repo(clone_dir, branch):
+                    print(
+                        f"Failed to update existing repo {clone_dir}, leaving as it is."
+                    )
             else:
                 print(f"-- Cloning branch '{branch}' into {clone_dir}...")
-                clone(
-                    repository=self.base_directory,
-                    directory=clone_dir,
-                    branch=branch,
-                    keep_uuid=self.keep_uuid,
-                    model_type=self.model_type,
-                    config_path=self.config_path,
-                    lab_path=self.lab_path,
-                    new_branch_name=self.new_branch_name,
-                    restart_path=self.restart_path,
-                    parent_experiment=self.parent_experiment,
-                    start_point=self.start_point,
-                )
+                self._do_clone(clone_dir, branch)
+
         return all_cloned_directories
+
+    def _do_clone(self, clone_dir: Path, branch: str):
+        clone(
+            repository=self.base_directory,
+            directory=clone_dir,
+            branch=branch,
+            keep_uuid=self.keep_uuid,
+            model_type=self.model_type,
+            config_path=self.config_path,
+            lab_path=self.lab_path,
+            new_branch_name=self.new_branch_name,
+            restart_path=self.restart_path,
+            parent_experiment=self.parent_experiment,
+            start_point=self.start_point,
+        )
+
+    def _update_existing_repo(self, clone_dir: Path, target_ref: str) -> bool:
+        """
+        Updates the repo without removing the dir or untracked files
+        target_ref: branch to checkout
+        """
+
+        try:
+            repo = git.Repo(str(clone_dir))
+            remote = repo.remotes.origin
+            remote.fetch(prune=True)
+
+            # save current HEAD
+            current_commit = repo.head.commit.hexsha
+
+            # ensure branch exists
+            if target_ref in repo.heads:
+                repo.git.checkout(target_ref)
+            else:
+                repo.git.checkout("-b", target_ref, f"origin/{target_ref}")
+
+            # try pulling with rebase
+            try:
+                repo.git.pull("--rebase", "--autostash", "origin", target_ref)
+            except git.exc.GitCommandError as e:
+                repo.git.reset("--keep", f"origin/{target_ref}")
+
+            # save new HEAD after update
+            new_commit = repo.head.commit.hexsha
+
+            rel_path = clone_dir.relative_to(self.test_path)
+
+            if current_commit == new_commit:
+                print(f"-- Repo {rel_path} is already up to date with {target_ref}.")
+            else:
+                print(
+                    f"-- Repo {rel_path} updated from {current_commit[:7]} to {new_commit[:7]} on branch {target_ref}."
+                )
+                changed = repo.git.diff(
+                    "--name-only", current_commit, new_commit
+                ).splitlines()
+                if changed:
+                    print("-- Changed files:")
+                    for file in changed:
+                        print(f"   -- {file}")
+
+            return True
+        except git.exc.GitCommandError as e:
+            print(f"Failed updating existing repo {rel_path}: {e}")
+            return False