From 0b107622d5d63d5a5c8dcec453bc5bd4c2205218 Mon Sep 17 00:00:00 2001
From: Purnendu Chakraborty <purnendu.chakraborty@nasa.gov>
Date: Wed, 18 Dec 2024 12:19:29 -0600
Subject: [PATCH 1/8] clone.py - (1) streamlined (2) branches are no longer in
 a detached state (3) updated tests (4) new tests

---
 src/mepo/cmdline/parser.py  |  18 ++-
 src/mepo/command/clone.py   | 215 ++++++++++++++++--------------------
 src/mepo/command/reset.py   |   2 +-
 src/mepo/git.py             |  41 +++----
 tests/test_component.py     |   5 +-
 tests/test_mepo_clone.py    |  92 +++++++++++++++
 tests/test_mepo_commands.py |   4 +-
 7 files changed, 224 insertions(+), 153 deletions(-)
 create mode 100644 tests/test_mepo_clone.py

diff --git a/src/mepo/cmdline/parser.py b/src/mepo/cmdline/parser.py
index 48811a46..416528ce 100644
--- a/src/mepo/cmdline/parser.py
+++ b/src/mepo/cmdline/parser.py
@@ -101,7 +101,7 @@ def __clone(self):
             aliases=mepoconfig.get_command_alias("clone"),
         )
         clone.add_argument(
-            "repo_url", metavar="URL", nargs="?", default=None, help="URL to clone"
+            "url", metavar="URL", nargs="?", default=None, help="URL to clone"
         )
         clone.add_argument(
             "directory",
@@ -122,7 +122,7 @@ def __clone(self):
             metavar="registry",
             nargs="?",
             default=None,
-            help="Registry (default: components.yaml)",
+            help="Registry (default: %(default)s)",
         )
         clone.add_argument(
             "--style",
@@ -142,8 +142,18 @@ def __clone(self):
             metavar="partial-type",
             nargs="?",
             default=None,
-            choices=["off", "blobless", "treeless"],
-            help='Style of partial clone, default: None, allowed options: %(choices)s. Off means a "normal" full git clone, blobless means cloning with "--filter=blob:none" and treeless means cloning with "--filter=tree:0". NOTE: We do *not* recommend using "treeless" as it is very aggressive and will cause problems with many git commands.',
+            choices=[None, "blobless", "treeless"],
+            help=(
+                """
+                Style of partial clone, default: %(default)s.
+                Allowed options: %(choices)s.
+                None: normal full git clone,
+                blobless: cloning with "--filter=blob:none",
+                treeless: cloning with "--filter=tree:0".
+                NOTE: We do *not* recommend using "treeless" as it is very
+                aggressive and will cause problems with many git commands.
+                """
+            ),
         )
 
     def __list(self):
diff --git a/src/mepo/command/clone.py b/src/mepo/command/clone.py
index 66718a25..53a69a99 100644
--- a/src/mepo/command/clone.py
+++ b/src/mepo/command/clone.py
@@ -1,145 +1,120 @@
 import os
 import pathlib
-import shutil
-import shlex
 from urllib.parse import urlparse
+from types import SimpleNamespace
 
-from .init import run as mepo_init_run
+from .init import run as mepo_init
 from ..state import MepoState
 from ..state import StateDoesNotExistError
 from ..git import GitRepository
-from ..utilities import shellcmd
 from ..utilities import colors
 from ..utilities import mepoconfig
 
-
 def run(args):
-
-    # This protects against someone using branch without a URL
-    if args.branch and not args.repo_url:
+    """
+    Entry point of clone.
+    Steps -
+    1. Clone fixture - if url is passed
+    2. Read state - if state does not exist, initialize mepo (write state) first
+    3. Clone components
+    4. Checkout all repos to the specified branch
+    """
+    CWD = os.getcwd()
+
+    if args.branch is not None and args.url is None:
         raise RuntimeError("The branch argument can only be used with a URL")
 
-    if args.allrepos and not args.branch:
-        raise RuntimeError("The allrepos option must be used with a branch/tag.")
-
-    # We can get the blobless and treeless options from the config or the args
-    if args.partial:
-        # We need to set partial to None if it's off, otherwise we use the
-        # string. This is safe because argparse only allows for 'off',
-        # 'blobless', or 'treeless'
-        partial = None if args.partial == "off" else args.partial
-    elif mepoconfig.has_option("clone", "partial"):
-        allowed = ["blobless", "treeless"]
-        partial = mepoconfig.get("clone", "partial")
-        if partial not in allowed:
-            raise Exception(
-                f"Detected partial clone type [{partial}] from .mepoconfig is not an allowed partial clone type: {allowed}"
-            )
-        else:
-            print(f"Found partial clone type [{partial}] in .mepoconfig")
-    else:
-        partial = None
-
-    # If you pass in a registry, with clone, it could be outside the repo.
-    # So use the full path
-    passed_in_registry = False
-    if args.registry:
-        passed_in_registry = True
-        args.registry = os.path.abspath(args.registry)
-    else:
-        # If we don't pass in a registry, we need to "reset" the arg to the
-        # default name because we pass args to mepo_init
-        args.registry = "components.yaml"
-
-    if args.repo_url:
-        p = urlparse(args.repo_url)
-        last_url_node = p.path.rsplit("/")[-1]
-        url_suffix = pathlib.Path(last_url_node).suffix
-        if args.directory:
-            local_clone(args.repo_url, args.branch, args.directory, partial)
-            os.chdir(args.directory)
-        else:
-            if url_suffix == ".git":
-                git_url_directory = pathlib.Path(last_url_node).stem
-            else:
-                git_url_directory = last_url_node
-
-            local_clone(args.repo_url, args.branch, git_url_directory, partial)
-            os.chdir(git_url_directory)
-
-    # Copy the new file into the repo only if we pass it in
-    if passed_in_registry:
-        try:
-            shutil.copy(args.registry, os.getcwd())
-        except shutil.SameFileError:
-            pass
+    arg_partial = handle_partial(args.partial)
 
-    # This tries to read the state and if not, calls init,
-    # loops back, and reads the state
+    # Step 1 - clone fixture
+    if args.url is not None:
+        fixture_dir = clone_fixture(args.url, args.branch, args.directory, arg_partial)
+        os.chdir(fixture_dir)
+
+    # Step 2 - Read state - if state does not exist, initialize mepo
     while True:
         try:
             allcomps = MepoState.read_state()
         except StateDoesNotExistError:
-            mepo_init_run(args)
+            mepo_init(SimpleNamespace(style=args.style, registry=get_registry(args.registry)))
             continue
         break
 
-    max_namelen = len(max([comp.name for comp in allcomps], key=len))
-    for comp in allcomps:
-        if not comp.fixture:
-            git = GitRepository(comp.remote, comp.local)
-            version = comp.version.name
-            version = version.replace("origin/", "")
-            recurse = comp.recurse_submodules
+    # Step 3 - Clone componets
+    clone_components(allcomps, arg_partial)
+
+    # Step 4 - Checkout all repos to the specified branch
+    # TODO - pchakrab: DO WE REALLY NEED THIS???
+    if args.allrepos:
+        if args.branch is None:
+            raise RuntimeError("`allrepos` option must be used with a branch/tag.")
+        checkout_components(allcomps, args.branch)
+
+    os.chdir(CWD)
+
+
+def handle_partial(partial):
+    """
+    The `partial` argument to clone can be set either via command line or
+    via .mepoconfig. Non-default value set via command line takes precedence.
+    The default value of `partial` is None, and possible choices are None/blobless/treeless
+    """
+    ALLOWED_NON_DEFAULT = ["blobless", "treeless"]
+    if partial is None:  # default value from command line
+        if mepoconfig.has_option("clone", "partial"):
+            partial = mepoconfig.get("clone", "partial")
+            if partial not in ALLOWED_NON_DEFAULT:
+                raise ValueError(f"Invalid partial type [{partial}] in .mepoconfig")
+            print(f"Found partial clone type [{partial}] in .mepoconfig")
+    return partial
 
-            # According to Git, treeless clones do not interact well with
-            # submodules. So we need to see if any comp has the recurse
-            # option set to True. If so, we need to clone that comp "normally"
 
-            _partial = None if partial == "treeless" and recurse else partial
+def clone_fixture(url, branch=None, directory=None, partial=None):
+    if directory is None:
+        p = urlparse(url)
+        last_url_node = p.path.rsplit("/")[-1]
+        directory = pathlib.Path(last_url_node).stem
+    git = GitRepository(url, directory)
+    git.clone(branch, partial)
+    return directory
 
-            # We need the type to handle hashes in components.yaml
-            _type = comp.version.type
-            git.clone(version, recurse, _type, comp.name, _partial)
-            if comp.sparse:
-                git.sparsify(comp.sparse)
-            print_clone_info(comp, max_namelen)
 
-    if args.allrepos:
-        for comp in allcomps:
-            if not comp.fixture:
-                git = GitRepository(comp.remote, comp.local)
-                print(
-                    "Checking out %s in %s"
-                    % (
-                        colors.YELLOW + args.branch + colors.RESET,
-                        colors.RESET + comp.name + colors.RESET,
-                    )
-                )
-                git.checkout(args.branch, detach=True)
-
-
-def print_clone_info(comp, name_width):
-    ver_name_type = "({}) {}".format(comp.version.type, comp.version.name)
-    print("{:<{width}} | {:<s}".format(comp.name, ver_name_type, width=name_width))
-
-
-def local_clone(url, branch=None, directory=None, partial=None):
-    cmd1 = "git clone "
-
-    if partial == "blobless":
-        cmd1 += "--filter=blob:none "
-    elif partial == "treeless":
-        cmd1 += "--filter=tree:0 "
-    else:
-        partial = None
-
-    if branch:
-        cmd1 += "--branch {} ".format(branch)
-    cmd1 += "--quiet {}".format(url)
-    if directory:
-        cmd1 += ' "{}"'.format(directory)
-    shellcmd.run(shlex.split(cmd1))
-    if branch:
-        cmd2 = f"git -C {directory} checkout --detach {branch}"
-        shellcmd.run(shlex.split(cmd2))
+def get_registry(arg_registry):
+    registry = "components.yaml"
+    if arg_registry is not None:
+        shutil.copy(arg_registry, os.getcwd())
+        registry = os.path.basename(arg_registry)
+    return registry
+
+
+def clone_components(allcomps, partial):
+    max_namelen = max([len(comp.name) for comp in allcomps])
+    for comp in allcomps:
+        if comp.fixture:
+            continue # not cloning fixture
+        recurse_submodules = comp.recurse_submodules
+        # According to Git, treeless clones do not interact well with
+        # submodules. So if any comp has the recurse option set to True,
+        # we do a non-partial clone
+        partial = None if partial == "treeless" and recurse_submodules else partial
+        version = comp.version.name; version = version.replace("origin/", "")
+        git = GitRepository(comp.remote, comp.local)
+        git.clone(version, recurse_submodules, partial)
+        if comp.sparse:
+            git.sparsify(comp.sparse)
+        print_clone_info(comp.name, comp.version, max_namelen)
+
+
+def checkout_components(allcomps, branch):
+    for comp in allcomps:
+        if comp.fixture:
+            continue # fixture is already on the right branch
+        branch_y = colors.YELLOW + args.branch + colors.RESET
+        print(f"Checking out {branch_y} in {comp.name}")
+        git = GitRepository(comp.remote, comp.local)
+        git.checkout(args.branch)
+
+
+def print_clone_info(comp_name, comp_version, name_width):
+    ver_name_type = f"({comp_version.type}) {comp_version.name}"
+    print(f"{comp_name:<{name_width}} | {ver_name_type:<s}")
diff --git a/src/mepo/command/reset.py b/src/mepo/command/reset.py
index 87cfce6d..cd7e545e 100644
--- a/src/mepo/command/reset.py
+++ b/src/mepo/command/reset.py
@@ -75,7 +75,7 @@ def run(args):
             "Namespace",
             (object,),
             {
-                "repo_url": None,
+                "url": None,
                 "directory": None,
                 "branch": None,
                 "registry": None,
diff --git a/src/mepo/git.py b/src/mepo/git.py
index 5975ab17..efff96f2 100644
--- a/src/mepo/git.py
+++ b/src/mepo/git.py
@@ -44,32 +44,23 @@ def get_local_path(self):
     def get_remote_url(self):
         return self.__remote
 
-    def clone(self, version, recurse, type, comp_name, partial=None):
-        cmd1 = "git clone "
-
-        if partial == "blobless":
-            cmd1 += "--filter=blob:none "
-        elif partial == "treeless":
-            cmd1 += "--filter=tree:0 "
-
-        if recurse:
-            cmd1 += "--recurse-submodules "
-
-        cmd1 += "--quiet {} {}".format(self.__remote, self.__local_path_abs)
-        try:
-            shellcmd.run(shlex.split(cmd1))
-        except sp.CalledProcessError:
-            raise RepoAlreadyClonedError(f"Error! Repo [{comp_name}] already cloned")
-
-        cmd2 = "git -C {} checkout {}".format(self.__local_path_abs, version)
-        shellcmd.run(shlex.split(cmd2))
-        cmd3 = "git -C {} checkout --detach".format(self.__local_path_abs)
-        shellcmd.run(shlex.split(cmd3))
+    def clone(self, version=None, recurse=None, partial=None):
+        """
+        Execute `git clone` command
+        version is tag or branch
+        """
+        PARTIAL = {"blobless": " --filter=blob:none", "treeless": " --filter=tree:0"}
+
+        cmd = "git clone "
+        if partial is not None:
+            cmd += PARTIAL[partial]
+        if recurse is not None:
+            cmd += "--recurse-submodules "
+        cmd += " --quiet {} {}".format(self.__remote, self.__local_path_abs)
+        shellcmd.run(shlex.split(cmd))
 
-        # NOTE: The above looks odd because of a quirk of git. You can't do
-        #       git checkout --detach branch unless the branch is local. But
-        #       since this is at clone time, all branches are remote. Thus,
-        #       we have to do a git checkout branch and then detach.
+        if version is not None:
+            self.checkout(version)
 
     def checkout(self, version, detach=False):
         cmd = self.__git + " checkout "
diff --git a/tests/test_component.py b/tests/test_component.py
index bb5d7e60..282531ec 100644
--- a/tests/test_component.py
+++ b/tests/test_component.py
@@ -65,4 +65,7 @@ def test_MepoComponent():
         if name == "fvdycore":
             fvdycore = MepoComponent().registry_to_component(name, comp, None)
     assert fvdycore == get_fvdycore_component()
-    assert fvdycore.serialize() == get_fvdycore_serialized()
+    fvdycore_serialized = fvdycore.serialize()
+    remote = fvdycore_serialized["remote"]
+    fvdycore_serialized["remote"] = remote.replace("git@github.com:", "https://github.com/")
+    assert fvdycore_serialized == get_fvdycore_serialized()
diff --git a/tests/test_mepo_clone.py b/tests/test_mepo_clone.py
new file mode 100644
index 00000000..0e5b172e
--- /dev/null
+++ b/tests/test_mepo_clone.py
@@ -0,0 +1,92 @@
+import os
+import io
+import shutil
+import contextlib
+from types import SimpleNamespace
+
+try:
+    from contextlib import chdir as contextlib_chdir
+except ImportError:
+    from mepo.utilities.chdir import chdir as contextlib_chdir
+
+import mepo.command.clone as mepo_clone
+import mepo.command.status as mepo_status
+
+
+FIXTURE_URL = "https://github.com/GEOS-ESM/GEOSfvdycore.git"
+
+
+def get_mepo_status():
+    args = SimpleNamespace(
+        ignore_permissions=False,
+        nocolor=True,
+        hashes=False,
+        serial=True,
+    )
+    with contextlib.redirect_stdout(io.StringIO()) as output:
+        mepo_status.run(args)
+    return output.getvalue()
+
+
+def test_mepo_clone_url():
+    DIRECTORY = "GEOSfvdycore"
+    if os.path.isdir(DIRECTORY):
+        shutil.rmtree(DIRECTORY)
+    args = SimpleNamespace(
+        style="prefix",
+        registry=None,
+        url=FIXTURE_URL,
+        branch=None,
+        directory=None,
+        partial="blobless",
+        allrepos=False,
+    )
+    mepo_clone.run(args)
+    saved_output = """Checking status...
+GEOSfvdycore           | (b) main
+env                    | (t) v4.29.0 (DH)
+cmake                  | (t) v3.51.0 (DH)
+ecbuild                | (t) geos/v1.3.0 (DH)
+GMAO_Shared            | (t) v1.9.8 (DH)
+GEOS_Util              | (t) v2.1.2 (DH)
+MAPL                   | (t) v2.48.0 (DH)
+FMS                    | (t) geos/2019.01.02+noaff.10 (DH)
+FVdycoreCubed_GridComp | (t) v2.12.0 (DH)
+fvdycore               | (t) geos/v2.9.0 (DH)
+"""
+    with contextlib_chdir(DIRECTORY):
+        status_output = get_mepo_status()
+    assert status_output == saved_output
+    shutil.rmtree(DIRECTORY)
+
+
+def test_mepo_clone_url_branch_directory():
+    DIRECTORY = "clone_url_branch_directory"
+    if os.path.isdir(DIRECTORY):
+        shutil.rmtree(DIRECTORY)
+    args = SimpleNamespace(
+        style="postfix",
+        registry=None,
+        url=FIXTURE_URL,
+        branch="release/MAPL-v3",
+        directory=DIRECTORY,
+        partial="blobless",
+        allrepos=False,
+    )
+    mepo_clone.run(args)
+    saved_output = """Checking status...
+GEOSfvdycore           | (b) release/MAPL-v3
+env                    | (t) v4.29.0 (DH)
+cmake                  | (t) v3.51.0 (DH)
+ecbuild                | (t) geos/v1.3.0 (DH)
+GMAO_Shared            | (t) v1.9.8 (DH)
+GEOS_Util              | (b) release/MAPL-v3
+MAPL                   | (b) release/MAPL-v3
+FMS                    | (t) geos/2019.01.02+noaff.10 (DH)
+FVdycoreCubed_GridComp | (b) release/MAPL-v3
+fvdycore               | (b) geos/release/MAPL-v3
+"""
+    with contextlib_chdir(DIRECTORY):
+        status_output = get_mepo_status()
+    assert status_output == saved_output
+    shutil.rmtree(DIRECTORY)
diff --git a/tests/test_mepo_commands.py b/tests/test_mepo_commands.py
index a4adf0af..5627b279 100644
--- a/tests/test_mepo_commands.py
+++ b/tests/test_mepo_commands.py
@@ -66,8 +66,8 @@ def __mepo_clone(cls):
         args = SimpleNamespace(
             style="prefix",
             registry=None,
-            repo_url=None,
-            allrepos=None,
+            url=None,
+            allrepos=False,
             branch=None,
             directory=None,
             partial="blobless",

From b2acf28fc7aac244236ffab755925497280feb21 Mon Sep 17 00:00:00 2001
From: Purnendu Chakraborty <purnendu.chakraborty@nasa.gov>
Date: Wed, 18 Dec 2024 17:21:01 -0600
Subject: [PATCH 2/8] Black formatting changes

---
 src/mepo/command/clone.py | 11 +++++++----
 tests/test_component.py   |  4 +++-
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/src/mepo/command/clone.py b/src/mepo/command/clone.py
index 53a69a99..c52d317b 100644
--- a/src/mepo/command/clone.py
+++ b/src/mepo/command/clone.py
@@ -10,6 +10,7 @@
 from ..utilities import colors
 from ..utilities import mepoconfig
 
+
 def run(args):
     """
     Entry point of clone.
@@ -36,7 +37,8 @@ def run(args):
         try:
             allcomps = MepoState.read_state()
         except StateDoesNotExistError:
-            mepo_init(SimpleNamespace(style=args.style, registry=get_registry(args.registry)))
+            registry = get_registry(args.registry)
+            mepo_init(SimpleNamespace(style=args.style, registry=registry))
             continue
         break
 
@@ -91,13 +93,14 @@ def clone_components(allcomps, partial):
     max_namelen = max([len(comp.name) for comp in allcomps])
     for comp in allcomps:
         if comp.fixture:
-            continue # not cloning fixture
+            continue  # not cloning fixture
         recurse_submodules = comp.recurse_submodules
         # According to Git, treeless clones do not interact well with
         # submodules. So if any comp has the recurse option set to True,
         # we do a non-partial clone
         partial = None if partial == "treeless" and recurse_submodules else partial
-        version = comp.version.name; version = version.replace("origin/", "")
+        version = comp.version.name
+        version = version.replace("origin/", "")
         git = GitRepository(comp.remote, comp.local)
         git.clone(version, recurse_submodules, partial)
         if comp.sparse:
@@ -108,7 +111,7 @@ def clone_components(allcomps, partial):
 def checkout_components(allcomps, branch):
     for comp in allcomps:
         if comp.fixture:
-            continue # fixture is already on the right branch
+            continue  # fixture is already on the right branch
         branch_y = colors.YELLOW + args.branch + colors.RESET
         print(f"Checking out {branch_y} in {comp.name}")
         git = GitRepository(comp.remote, comp.local)
diff --git a/tests/test_component.py b/tests/test_component.py
index 282531ec..28f74f25 100644
--- a/tests/test_component.py
+++ b/tests/test_component.py
@@ -67,5 +67,7 @@ def test_MepoComponent():
     assert fvdycore == get_fvdycore_component()
     fvdycore_serialized = fvdycore.serialize()
     remote = fvdycore_serialized["remote"]
-    fvdycore_serialized["remote"] = remote.replace("git@github.com:", "https://github.com/")
+    fvdycore_serialized["remote"] = remote.replace(
+        "git@github.com:", "https://github.com/"
+    )
     assert fvdycore_serialized == get_fvdycore_serialized()

From a0e0207898b50f62ce6ff6f6145045436520256a Mon Sep 17 00:00:00 2001
From: Purnendu Chakraborty <purnendu.chakraborty@nasa.gov>
Date: Thu, 19 Dec 2024 08:13:23 -0600
Subject: [PATCH 3/8] Updated test_mepo_clone.py to use
 https://github.com/pchakraborty/GEOSfvdycore-mepo-testing.git instead

---
 .pre-commit-config.yaml  |  2 +-
 tests/test_mepo_clone.py | 44 +++++++++++++++++++---------------------
 2 files changed, 22 insertions(+), 24 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 983fce47..9edf3f08 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -8,4 +8,4 @@ repos:
         # supported by your project here, or alternatively use
         # pre-commit's default_language_version, see
         # https://pre-commit.com/#top_level-default_language_version
-        language_version: python3.11
+        language_version: python3.9
diff --git a/tests/test_mepo_clone.py b/tests/test_mepo_clone.py
index 0e5b172e..6c62a20a 100644
--- a/tests/test_mepo_clone.py
+++ b/tests/test_mepo_clone.py
@@ -13,7 +13,8 @@
 import mepo.command.status as mepo_status
 
 
-FIXTURE_URL = "https://github.com/GEOS-ESM/GEOSfvdycore.git"
+FIXTURE_NAME = "GEOSfvdycore-mepo-testing"
+FIXTURE_URL = f"https://github.com/pchakraborty/{FIXTURE_NAME}.git"
 
 
 def get_mepo_status():
@@ -29,9 +30,8 @@ def get_mepo_status():
 
 
 def test_mepo_clone_url():
-    DIRECTORY = "GEOSfvdycore"
-    if os.path.isdir(DIRECTORY):
-        shutil.rmtree(DIRECTORY)
+    if os.path.isdir(FIXTURE_NAME):
+        shutil.rmtree(FIXTURE_NAME)
     args = SimpleNamespace(
         style="prefix",
         registry=None,
@@ -44,20 +44,19 @@ def test_mepo_clone_url():
     mepo_clone.run(args)
     saved_output = """Checking status...
 GEOSfvdycore           | (b) main
-env                    | (t) v4.29.0 (DH)
-cmake                  | (t) v3.51.0 (DH)
-ecbuild                | (t) geos/v1.3.0 (DH)
-GMAO_Shared            | (t) v1.9.8 (DH)
-GEOS_Util              | (t) v2.1.2 (DH)
-MAPL                   | (t) v2.48.0 (DH)
+env                    | (t) v4.29.1 (DH)
+cmake                  | (t) v3.55.0 (DH)
+ecbuild                | (t) geos/v1.4.0 (DH)
+GMAO_Shared            | (t) v1.9.9 (DH)
+GEOS_Util              | (t) v2.1.3 (DH)
 FMS                    | (t) geos/2019.01.02+noaff.10 (DH)
 FVdycoreCubed_GridComp | (t) v2.12.0 (DH)
-fvdycore               | (t) geos/v2.9.0 (DH)
+fvdycore               | (t) geos/v2.9.1 (DH)
 """
-    with contextlib_chdir(DIRECTORY):
+    with contextlib_chdir(FIXTURE_NAME):
         status_output = get_mepo_status()
     assert status_output == saved_output
-    shutil.rmtree(DIRECTORY)
+    shutil.rmtree(FIXTURE_NAME)
 
 
 def test_mepo_clone_url_branch_directory():
@@ -68,23 +67,22 @@ def test_mepo_clone_url_branch_directory():
         style="postfix",
         registry=None,
         url=FIXTURE_URL,
-        branch="release/MAPL-v3",
+        branch="fvdycore-develop",
         directory=DIRECTORY,
         partial="blobless",
         allrepos=False,
     )
     mepo_clone.run(args)
     saved_output = """Checking status...
-GEOSfvdycore           | (b) release/MAPL-v3
-env                    | (t) v4.29.0 (DH)
-cmake                  | (t) v3.51.0 (DH)
-ecbuild                | (t) geos/v1.3.0 (DH)
-GMAO_Shared            | (t) v1.9.8 (DH)
-GEOS_Util              | (b) release/MAPL-v3
-MAPL                   | (b) release/MAPL-v3
+GEOSfvdycore           | (b) fvdycore-develop
+env                    | (t) v4.29.1 (DH)
+cmake                  | (t) v3.55.0 (DH)
+ecbuild                | (t) geos/v1.4.0 (DH)
+GMAO_Shared            | (t) v1.9.9 (DH)
+GEOS_Util              | (t) v2.1.3 (DH)
 FMS                    | (t) geos/2019.01.02+noaff.10 (DH)
-FVdycoreCubed_GridComp | (b) release/MAPL-v3
-fvdycore               | (b) geos/release/MAPL-v3
+FVdycoreCubed_GridComp | (b) develop
+fvdycore               | (b) geos/develop
 """
     with contextlib_chdir(DIRECTORY):
         status_output = get_mepo_status()

From 2a8b76e641db8bd6afb35401d1df1cf01d974228 Mon Sep 17 00:00:00 2001
From: Purnendu Chakraborty <purnendu.chakraborty@nasa.gov>
Date: Thu, 19 Dec 2024 08:23:55 -0600
Subject: [PATCH 4/8] Updated CHANGELOG

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4c76e8b9..c3bd6853 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,10 +13,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Hidden option `--location` for mepo that returns the path to the mepo directory
 - Added ability to print number of stashes in `mepo status`
+- Added new tests for `mepo clone`
 
 ### Changed
 
 - Removed legacy `bin` directory
+- Checked out branches are no longer in 'detached head' state
 
 ## [2.1.0] - 2024-10-02
 

From bb13a773a1e5991afa5ebd8e532af751c573a1d5 Mon Sep 17 00:00:00 2001
From: Purnendu Chakraborty <purnendu.chakraborty@nasa.gov>
Date: Thu, 19 Dec 2024 18:26:36 -0600
Subject: [PATCH 5/8] Some more refactoring

---
 src/mepo/command/clone.py | 54 +++++++++++++++++----------------------
 1 file changed, 23 insertions(+), 31 deletions(-)

diff --git a/src/mepo/command/clone.py b/src/mepo/command/clone.py
index c52d317b..5579b372 100644
--- a/src/mepo/command/clone.py
+++ b/src/mepo/command/clone.py
@@ -15,42 +15,22 @@ def run(args):
     """
     Entry point of clone.
     Steps -
-    1. Clone fixture - if url is passed
+    1. Clone fixture - if url is provided
     2. Read state - if state does not exist, initialize mepo (write state) first
     3. Clone components
     4. Checkout all repos to the specified branch
     """
     CWD = os.getcwd()
 
-    if args.branch is not None and args.url is None:
-        raise RuntimeError("The branch argument can only be used with a URL")
-
     arg_partial = handle_partial(args.partial)
 
-    # Step 1 - clone fixture
     if args.url is not None:
         fixture_dir = clone_fixture(args.url, args.branch, args.directory, arg_partial)
         os.chdir(fixture_dir)
-
-    # Step 2 - Read state - if state does not exist, initialize mepo
-    while True:
-        try:
-            allcomps = MepoState.read_state()
-        except StateDoesNotExistError:
-            registry = get_registry(args.registry)
-            mepo_init(SimpleNamespace(style=args.style, registry=registry))
-            continue
-        break
-
-    # Step 3 - Clone componets
+    allcomps = read_state(args.style, args.registry)
     clone_components(allcomps, arg_partial)
-
-    # Step 4 - Checkout all repos to the specified branch
-    # TODO - pchakrab: DO WE REALLY NEED THIS???
     if args.allrepos:
-        if args.branch is None:
-            raise RuntimeError("`allrepos` option must be used with a branch/tag.")
-        checkout_components(allcomps, args.branch)
+        checkout_all_repos(allcomps, args.branch)
 
     os.chdir(CWD)
 
@@ -81,6 +61,18 @@ def clone_fixture(url, branch=None, directory=None, partial=None):
     return directory
 
 
+def read_state(arg_style, arg_registry):
+    while True:
+        try:
+            allcomps = MepoState.read_state()
+        except StateDoesNotExistError:
+            registry = get_registry(arg_registry)
+            mepo_init(SimpleNamespace(style=arg_style, registry=registry))
+            continue
+        break
+    return allcomps
+
+
 def get_registry(arg_registry):
     registry = "components.yaml"
     if arg_registry is not None:
@@ -108,16 +100,16 @@ def clone_components(allcomps, partial):
         print_clone_info(comp.name, comp.version, max_namelen)
 
 
-def checkout_components(allcomps, branch):
+def print_clone_info(comp_name, comp_version, name_width):
+    ver_name_type = f"({comp_version.type}) {comp_version.name}"
+    print(f"{comp_name:<{name_width}} | {ver_name_type:<s}")
+
+
+def checkout_all_repos(allcomps, branch):
+    if branch is None:
+        raise RuntimeError("`allrepos` option must be used with a branch/tag.")
     for comp in allcomps:
-        if comp.fixture:
-            continue  # fixture is already on the right branch
         branch_y = colors.YELLOW + args.branch + colors.RESET
         print(f"Checking out {branch_y} in {comp.name}")
         git = GitRepository(comp.remote, comp.local)
         git.checkout(args.branch)
-
-
-def print_clone_info(comp_name, comp_version, name_width):
-    ver_name_type = f"({comp_version.type}) {comp_version.name}"
-    print(f"{comp_name:<{name_width}} | {ver_name_type:<s}")

From bced46a67ceb4bf804d663e0a0b7bdacb1fd410e Mon Sep 17 00:00:00 2001
From: Purnendu Chakraborty <purnendu.chakraborty@nasa.gov>
Date: Fri, 20 Dec 2024 07:24:09 -0600
Subject: [PATCH 6/8] clone.py - updated comments

---
 src/mepo/command/clone.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/mepo/command/clone.py b/src/mepo/command/clone.py
index 5579b372..afb08b25 100644
--- a/src/mepo/command/clone.py
+++ b/src/mepo/command/clone.py
@@ -14,9 +14,19 @@
 def run(args):
     """
     Entry point of clone.
+
+    Multiple ways to run clone
+    1. After fixture has been cloned (via git clone)
+       a. mepo init
+          mepo clone
+       b. mepo clone (initializes mepo)
+    2. Clone fixture as well
+       a. mepo clone <url> [<directory>]
+       b. mepo clone -b <branch> <url> [<directory>]
+
     Steps -
     1. Clone fixture - if url is provided
-    2. Read state - if state does not exist, initialize mepo (write state) first
+    2. Read state - initialize mepo (write state) first, if needed
     3. Clone components
     4. Checkout all repos to the specified branch
     """

From 8e8849376f7c48067bcb11dcd90c48c04817afe6 Mon Sep 17 00:00:00 2001
From: Purnendu Chakraborty <purnendu.chakraborty@nasa.gov>
Date: Fri, 20 Dec 2024 08:48:35 -0600
Subject: [PATCH 7/8] Added deprecation warning for 'mepo init'

---
 src/mepo/cmdline/parser.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/mepo/cmdline/parser.py b/src/mepo/cmdline/parser.py
index 416528ce..3966c119 100644
--- a/src/mepo/cmdline/parser.py
+++ b/src/mepo/cmdline/parser.py
@@ -1,4 +1,5 @@
 import argparse
+import warnings
 
 from .branch_parser import MepoBranchArgParser
 from .stash_parser import MepoStashArgParser
@@ -74,6 +75,7 @@ def parse(self):
         return self.parser.parse_args()
 
     def __init(self):
+        warnings.warn("init will be removed in version 3, use clone instead")
         init = self.subparsers.add_parser(
             "init",
             description="Initialize mepo based on `config-file`",

From 5b092f51420e9c98d8f6b296185abb1ff0508036 Mon Sep 17 00:00:00 2001
From: Purnendu Chakraborty <purnendu.chakraborty@nasa.gov>
Date: Mon, 23 Dec 2024 07:04:10 -0600
Subject: [PATCH 8/8] init removal is a deprecation warning

---
 src/mepo/cmdline/parser.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/mepo/cmdline/parser.py b/src/mepo/cmdline/parser.py
index 3966c119..4f70a4c8 100644
--- a/src/mepo/cmdline/parser.py
+++ b/src/mepo/cmdline/parser.py
@@ -75,7 +75,9 @@ def parse(self):
         return self.parser.parse_args()
 
     def __init(self):
-        warnings.warn("init will be removed in version 3, use clone instead")
+        warnings.warn(
+            "init will be removed in version 3, use clone instead", DeprecationWarning
+        )
         init = self.subparsers.add_parser(
             "init",
             description="Initialize mepo based on `config-file`",