Add check for staged git changes before running checkout in `payu che…

…ckout`

- Add metadata config for model name (if it is different from model driver name)

payu/git_utils.py

@@ -134,6 +134,14 @@ def checkout_branch(self,
                         new_branch: bool = False,
                         start_point: Optional[str] = None) -> None:
         """Checkout branch and create branch if specified"""
+        # First check for staged changes
+        if self.repo.is_dirty(index=True, working_tree=False):
+            raise PayuBranchError(
+                "There are staged git changes. Please stash or commit them "
+                "before running the checkout command again.\n"
+                "To see what files are staged, run: git status"
+            )
+
         # Existing branches
         local_branches = self.local_branches_dict().keys()
         remote_branches = self.remote_branches_dict()

payu/metadata.py

@@ -14,7 +14,7 @@
 import warnings
 from datetime import datetime
 from pathlib import Path
-from typing import Optional, List, Union
+from typing import Optional, Union
 
 from ruamel.yaml import YAML
 from ruamel.yaml.comments import CommentedMap
@@ -67,17 +67,17 @@ def __init__(self,
                  config_path: Optional[Path] = None,
                  branch: Optional[str] = None,
                  control_path: Optional[Path] = None) -> None:
-        self.lab_archive_path = laboratory_archive_path
         self.config = read_config(config_path)
+        self.metadata_config = self.config.get('metadata', {})
 
         if control_path is None:
             control_path = Path(self.config.get("control_path"))
         self.control_path = control_path
         self.filepath = self.control_path / METADATA_FILENAME
+        self.lab_archive_path = laboratory_archive_path
 
-        # Check for metadata flag - Default True
-        metadata_config = self.config.get('metadata', {})
-        self.enabled = metadata_config.get('enable', True)
+        # Config flag to disable creating metadata files and UUIDs
+        self.enabled = self.metadata_config.get('enable', True)
 
         if self.enabled:
             self.repo = GitRepository(self.control_path, catch_error=True)
@@ -121,9 +121,8 @@ def setup(self,
         if not self.enabled:
             # Set experiment name only - either configured or includes branch
             self.set_experiment_name(ignore_uuid=True)
-            return
 
-        if self.uuid is not None and (keep_uuid or not is_new_experiment):
+        elif self.uuid is not None and (keep_uuid or not is_new_experiment):
             self.set_experiment_name(keep_uuid=keep_uuid,
                                      is_new_experiment=is_new_experiment)
         else:
@@ -135,7 +134,7 @@ def setup(self,
 
         self.archive_path = self.lab_archive_path / self.experiment_name
 
-    def new_experiment_name(self, ignore_uuid: bool = False) -> Path:
+    def new_experiment_name(self, ignore_uuid: bool = False) -> str:
         """Generate a new experiment name"""
         if self.branch is None:
             self.branch = self.repo.get_branch_name()
@@ -291,11 +290,9 @@ def update_file(self,
 
     def get_model_name(self) -> str:
         """Get model name from config file"""
-        model_name = self.config.get('model')
-        if model_name == 'access':
-            # TODO: Is access used for anything other than ACCESS-ESM1-5?
-            # If so, won't set anything here.
-            model_name = 'ACCESS-ESM1-5'
+        # Use model name unless specific model is specified in metadata config
+        default_model_name = self.config.get('model')
+        model_name = self.metadata_config.get('model', default_model_name)
         return model_name.upper()
 
     def get_parent_experiment(self, prior_restart_path: Path) -> None:
@@ -326,9 +323,8 @@ def commit_file(self) -> None:
 
     def copy_to_archive(self) -> None:
         """Copy metadata file to archive"""
-        archive_path = self.lab_archive_path / self.experiment_name
-        mkdir_p(archive_path)
-        shutil.copy(self.filepath, archive_path / METADATA_FILENAME)
+        mkdir_p(self.archive_path)
+        shutil.copy(self.filepath, self.archive_path / METADATA_FILENAME)
         # Note: The existence of an archive is used for determining
         # experiment names and whether to generate a new UUID
 

test/test_git_utils.py

@@ -141,7 +141,7 @@ def test_git_checkout_new_branch_existing():
     repo = create_new_repo(repo_path)
     existing_branch = repo.active_branch
 
-    # Test create branch with existing branch
+    # Test checkout branch with existing branch
     repo = GitRepository(repo_path)
     with pytest.raises(PayuBranchError):
         repo.checkout_branch(str(existing_branch),
@@ -153,12 +153,30 @@ def test_git_checkout_non_existent_branch():
     repo_path = tmpdir / 'remoteRepo'
     create_new_repo(repo_path)
 
-    # Test create branch with  non-existent branch
+    # Test checkout branch with non-existent branch
     repo = GitRepository(repo_path)
     with pytest.raises(PayuBranchError):
         repo.checkout_branch("Gibberish")
 
 
+def test_git_checkout_staged_changes():
+    # Setup
+    repo_path = tmpdir / 'remoteRepo'
+    create_new_repo(repo_path)
+
+    repo = GitRepository(repo_path)
+    file_path = repo_path / 'newTestFile.txt'
+    file_path.touch()
+
+    # Test checkout branch works with untracked files
+    repo.checkout_branch(new_branch=True, branch_name="NewBranch")
+
+    # Test checkout raises error with staged changes
+    repo.repo.index.add([file_path])
+    with pytest.raises(PayuBranchError):
+        repo.checkout_branch(new_branch=True, branch_name="NewBranch2")
+
+
 def test_git_checkout_existing_branch():
     # Setup
     remote_repo_path = tmpdir / 'remoteRepo'