Add support for cloning configuration using a commit hash

docs/source/usage.rst

@@ -115,16 +115,21 @@ For example::
 Where ``${REPOSITORY}`` is the git URL or path of the repository to clone from, 
 for example, https://github.com/payu-org/mom-example.git.
 
-To clone and checkout an existing git branch, use the ``--branch`` flag and 
+To clone and checkout an existing git branch, use the ``-B/--branch`` flag and
 specify the branch name::
 
       payu clone --branch ${EXISTING_BRANCH} ${REPOSITORY} my_expt
 
-To create and checkout a new git branch use ``--new-branch`` and specify a 
-new branch name:
+To create and checkout a new git branch use ``-b/--new-branch`` and specify a
+new branch name::
 
       payu clone --new-branch ${NEW_BRANCH} ${REPOSITORY} my_expt
 
+To create a new git branch starting from a tag or commit, use ``-s/--start-point``
+flag::
+
+      payu clone -b ${NEW_BRANCH} -s {COMMIT_HASH|TAG} ${REPOSITORY} my_expt
+
 To see more configuration options for ``payu clone``, 
 run:: 
 

payu/branch.py

@@ -212,6 +212,7 @@ def switch_symlink(lab_dir_path: Path, control_path: Path,
 def clone(repository: str,
           directory: Path,
           branch: Optional[str] = None,
+          start_point: Optional[str] = None,
           new_branch_name: Optional[str] = None,
           keep_uuid: bool = False,
           model_type: Optional[str] = None,
@@ -227,11 +228,11 @@ def clone(repository: str,
         directory: Path
             The control directory where the repository will be cloned
         branch: Optional[str]
-            Name of branch to clone and checkout
+            Name of branch to checkout during the git clone
+        start_point: Optional[str]
+            Branch-name/commit/tag to start new branch from
         new_branch_name: Optional[str]
-            Name of new branch to create and checkout.
-            If branch is also defined, the new branch will start from the
-            latest commit of the branch.
+            Name of new branch to create and checkout
         keep_uuid: bool, default False
             Keep UUID unchanged, if it exists
         config_path: Optional[Path]
@@ -248,6 +249,10 @@ def clone(repository: str,
             Parent experiment UUID to add to generated metadata
 
     Returns: None
+
+    Note: branch, if defined, can be set to avoid initially checking out the
+    default branch during git clone - this is useful for repositories where
+    the default branch is not a payu configuration.
     """
     # Resolve directory to an absolute path
     control_path = directory.resolve()
@@ -278,7 +283,8 @@ def clone(repository: str,
                             control_path=control_path,
                             model_type=model_type,
                             lab_path=lab_path,
-                            parent_experiment=parent_experiment)
+                            parent_experiment=parent_experiment,
+                            start_point=start_point)
         else:
             # Checkout branch
             if branch is None:

payu/subcommands/args.py

@@ -191,6 +191,17 @@
     }
 }
 
+# Clone branch
+clone_start_point = {
+    'flags': ('--start-point', '-s'),
+    'parameters': {
+        'action':   'store',
+        'dest': 'start_point',
+        'default':  None,
+        'help': 'New branch will start from this commit or tag'
+    }
+}
+
 # Clone create branch
 new_branch_name = {
     'flags': ('--new-branch', '-b'),

payu/subcommands/clone_cmd.py

@@ -18,7 +18,7 @@
              args.keep_uuid, args.clone_branch,
              args.repository, args.local_directory,
              args.new_branch_name, args.restart_path,
-             args.parent_experiment]
+             args.parent_experiment, args.clone_start_point]
 
 
 def transform_strings_to_path(path_str=None):
@@ -27,7 +27,7 @@ def transform_strings_to_path(path_str=None):
 
 def runcmd(model_type, config_path, lab_path, keep_uuid,
            branch, repository, local_directory, new_branch_name, restart_path,
-           parent_experiment):
+           parent_experiment, start_point):
     """Execute the command."""
     config_path = transform_strings_to_path(config_path)
     restart_path = transform_strings_to_path(restart_path)
@@ -43,7 +43,8 @@ def runcmd(model_type, config_path, lab_path, keep_uuid,
           lab_path=lab_path,
           new_branch_name=new_branch_name,
           restart_path=restart_path,
-          parent_experiment=parent_experiment)
+          parent_experiment=parent_experiment,
+          start_point=start_point)
 
 
 runscript = runcmd

test/test_branch.py

@@ -536,6 +536,53 @@ def test_clone(mock_uuid):
     assert [head.name for head in cloned_repo2.heads] == ["Branch1", "Branch2"]
 
 
+@pytest.mark.parametrize(
+    "start_point_type", ["commit", "tag"]
+)
+def test_clone_startpoint(start_point_type):
+    # Create a repo to clone
+    source_repo_path = tmpdir / "sourceRepo"
+    source_repo_path.mkdir()
+    source_repo = setup_control_repository(path=source_repo_path)
+
+    # Create branch1
+    branch1 = source_repo.create_head("Branch1")
+    branch1_commit = branch1.object.hexsha
+    if start_point_type == "tag":
+        source_repo.create_tag('v1.0', ref=branch1.commit)
+        start_point = 'v1.0'
+    elif start_point_type == "commit":
+        start_point = branch1_commit
+
+    # Add another commit on main branch so the commit is different to branch1
+    (source_repo_path / "mock_file.txt").touch()
+    source_repo.index.add("mock_file.txt")
+    source_repo.index.commit("Another commit with a mock file")
+
+    source_repo_commit = source_repo.active_branch.object.hexsha
+    assert source_repo_commit != branch1_commit
+
+    # Run Clone
+    cloned_repo_path = tmpdir / "clonedRepo"
+    with cd(tmpdir):
+        clone(
+            repository=str(source_repo_path),
+            directory=cloned_repo_path,
+            lab_path=labdir,
+            new_branch_name="Branch3",
+            start_point=start_point
+        )
+
+    cloned_repo = git.Repo(cloned_repo_path)
+
+    # Check branched starting from start point
+    second_latest_commit = list(cloned_repo.iter_commits(max_count=2))[1]
+    assert second_latest_commit.hexsha == branch1_commit
+
+    # Latest commit is different (new commit from metadata)
+    assert source_repo_commit != cloned_repo.active_branch.object.hexsha
+
+
 def add_and_commit_metadata(repo, metadata):
     """Helper function to create/update metadata file and commit"""
     metadata_path = ctrldir / "metadata.yaml"