From 1c35728e1eef796657529e1518bc23b8ee938a5c Mon Sep 17 00:00:00 2001
From: James Bruten <109733895+james-bruten-mo@users.noreply.github.com>
Date: Mon, 19 Jan 2026 15:57:58 +0000
Subject: [PATCH 1/7] incremenental with core working

---
 build/extract/get_git_sources.py | 186 +++++++++++++++++++++++++++++++
 build/local_build.py             |  95 ++++++----------
 2 files changed, 223 insertions(+), 58 deletions(-)
 create mode 100644 build/extract/get_git_sources.py

diff --git a/build/extract/get_git_sources.py b/build/extract/get_git_sources.py
new file mode 100644
index 000000000..bd790dd18
--- /dev/null
+++ b/build/extract/get_git_sources.py
@@ -0,0 +1,186 @@
+# *****************************COPYRIGHT*******************************
+# (C) Crown copyright Met Office. All rights reserved.
+# For further details please refer to the file COPYRIGHT.txt
+# which you should have received as part of this distribution.
+# *****************************COPYRIGHT*******************************
+"""
+Clone sources for a rose-stem run for use with git bdiff module in scripts
+"""
+
+import re
+import subprocess
+from typing import Optional
+from pathlib import Path
+from shutil import rmtree
+import shlex
+
+
+def get_source(
+    source: str,
+    ref: str,
+    dest: Path,
+    repo: str,
+    use_mirrors: bool = False,
+    mirror_loc: Path = "",
+) -> None:
+
+    if ".git" in source:
+        if use_mirrors:
+            mirror_loc = Path(mirror_loc) / "MetOffice" / repo
+            print(f"Cloning/Updating {repo} from {mirror_loc} at ref {ref}")
+            clone_repo_mirror(source, repo, mirror_loc, dest)
+        else:
+            print(f"Cloning/Updating {repo} from {source} at ref {ref}")
+            clone_repo(source, ref, dest)
+    else:
+        print(f"Syncing {repo} at ref {ref}")
+        sync_repo(source, ref, dest)
+
+
+def run_command(
+    command: str, rval: bool = False, check: bool = True
+) -> Optional[subprocess.CompletedProcess]:
+    """
+    Run a subprocess command and return the result object
+    Inputs:
+        - command, str with command to run
+    Outputs:
+        - result object from subprocess.run
+    """
+    command = shlex.split(command)
+    result = subprocess.run(
+        command,
+        capture_output=True,
+        text=True,
+        timeout=300,
+        shell=False,
+        check=False,
+    )
+    if check and result.returncode:
+        print(result.stdout, end="\n\n\n")
+        raise RuntimeError(
+            f"[FAIL] Issue found running command {command}\n\n{result.stderr}"
+        )
+    if rval:
+        return result
+
+
+def clone_repo_mirror(
+    source: str, repo_ref: str, parent: str, mirror_loc: Path, loc: Path
+) -> None:
+    """
+    Clone a repo source using a local git mirror.
+    Assume the mirror is set up as per the Met Office
+    """
+
+    # Remove if this clone already exists
+    if not loc.exists():
+        command = f"git clone {mirror_loc} {loc}"
+        run_command(command)
+
+    # If not provided a ref, return
+    if not repo_ref:
+        run_command(f"git -C {loc} pull")
+        return
+
+    source = source.removeprefix("git@github.com:")
+    user = source.split("/")[0]
+    # Check that the user is different to the Upstream User
+    if user in parent.split("/")[0]:
+        user = None
+
+    # If the ref is a hash then we don't need the fork user as part of the fetch.
+    # Equally, if the user is the Upstream User, it's not needed
+    if not user or re.match(r"^\s*([0-9a-f]{40})\s*$", repo_ref):
+        fetch = repo_ref
+    else:
+        fetch = f"{user}/{repo_ref}"
+    commands = (
+        f"git -C {loc} fetch origin {fetch}",
+        f"git -C {loc} checkout FETCH_HEAD",
+    )
+    for command in commands:
+        run_command(command)
+
+
+def clone_repo(repo_source: str, repo_ref: str, loc: Path) -> None:
+    """
+    Clone the repo and checkout the provided ref
+    Only if a remote source
+    """
+
+    # Remove if this clone already exists
+    if not loc.exists():
+        # Create a clean clone location
+        loc.mkdir(parents=True)
+
+        commands = (
+            f"git -C {loc} init",
+            f"git -C {loc} remote add origin {repo_source}",
+            f"git -C {loc} fetch origin {repo_ref}",
+            f"git -C {loc} checkout FETCH_HEAD",
+            f"git -C {loc} fetch origin main:main",
+        )
+        for command in commands:
+            run_command(command)
+    else:
+        commands = (
+            f"git -C {loc} fetch origin {repo_ref}",
+            f"git -C {loc} checkout FETCH_HEAD",
+        )
+        for command in commands:
+            run_command(command)
+
+
+def sync_repo(repo_source: str, repo_ref: str, loc: Path) -> None:
+    """
+    Rsync a local git clone and checkout the provided ref
+    """
+
+    # Remove if this clone already exists
+    if loc.exists():
+        rmtree(loc)
+
+    # Create a clean clone location
+    loc.mkdir(parents=True)
+
+    exclude_dirs = (
+        "applications/*/working",
+        "applications/*/test",
+        "applications/*/bin",
+        "science/*/working",
+        "science/*/test",
+        "science/*/bin",
+        "interfaces/*/working",
+        "interfaces/*/test",
+        "interfaces/*/bin",
+        "components/*/working",
+        "components/*/test",
+        "components/*/bin",
+        "infrastructure/*/working",
+        "infrastructure/*/test",
+        "infrastructure/*/bin",
+        "mesh_tools/*/working",
+        "mesh_tools/*/test",
+        "mesh_tools/*/bin",
+    )
+
+    # Trailing slash required for rsync
+    command = f"rsync -av {repo_source}/ {loc}"
+    for item in exclude_dirs:
+        command = f"{command} --exclude '{item}'"
+    run_command(command)
+
+    # Fetch the main branch from origin
+    # Ignore errors - these are likely because the main branch already exists
+    # Instead write them as warnings
+    command = f"git -C {loc} fetch origin main:main"
+    result = run_command(command, check=False, rval=True)
+    if result.returncode:
+        print("Warning - fetching main from origin resulted in an error")
+        print("This is likely due to the main branch already existing")
+        print(f"Error message:\n\n{result.stderr}")
+
+    if repo_ref:
+        command = f"git -C {loc} checkout {repo_ref}"
+        run_command(command)
diff --git a/build/local_build.py b/build/local_build.py
index 2c9d445e4..03212b3df 100755
--- a/build/local_build.py
+++ b/build/local_build.py
@@ -17,6 +17,8 @@
 import subprocess
 import argparse
 import yaml
+from pathlib import Path
+from extract.get_git_sources import get_source
 
 
 def subprocess_run(command):
@@ -45,7 +47,7 @@ def get_root_path():
     Get the root path of the current working copy
     """
 
-    return os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+    return Path(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
 
 
 def determine_core_source(root_dir):
@@ -56,7 +58,7 @@ def determine_core_source(root_dir):
 
     # Read through the dependencies file and populate revision and source
     # variables for requested repo
-    with open(os.path.join(root_dir, "dependencies.yaml"), "r") as stream:
+    with open(root_dir / "dependencies.yaml", "r") as stream:
         dependencies = yaml.safe_load(stream)
     return dependencies["lfric_core"]
 
@@ -70,9 +72,9 @@ def determine_project_path(project, root_dir):
 
     # Find the project in either science/ interfaces/ or applications/
     for drc in ["science/", "interfaces/", "applications/"]:
-        path = os.path.join(root_dir, drc)
+        path = root_dir / drc
         for item in os.listdir(path):
-            item_path = os.path.join(path, item)
+            item_path = path / item
             if item_path and item == project:
                 return item_path
 
@@ -82,45 +84,6 @@ def determine_project_path(project, root_dir):
     )
 
 
-def clone_dependency(values, temp_dep):
-    """
-    Clone the physics dependencies into a temporary directory
-    """
-
-    source = values["source"]
-    ref = values["ref"]
-
-    commands = (
-        f"git -C {temp_dep} init",
-        f"git -C {temp_dep} remote add origin {source}",
-        f"git -C {temp_dep} fetch origin {ref}",
-        f"git -C {temp_dep} checkout FETCH_HEAD"
-    )
-    for command in commands:
-        subprocess_run(command)
-
-
-def get_lfric_core(core_source, working_dir):
-    """
-    Clone the lfric_core source if the source is a git url
-    rsync this export into the working dir as the lfric_core source - done so
-    incremental builds can still be used.
-    If core_source is a local working copy just rsync from there.
-    """
-
-    if core_source["source"].endswith(".git"):
-        print("Cloning LFRic Core from Github")
-        lfric_core_loc = f"{working_dir}/scratch/core"
-        clone_dependency(core_source["source"], core_source["ref"], lfric_core_loc)
-        print("rsyncing the exported lfric_core source")
-    else:
-        lfric_core_loc = core_source["source"]
-        print("rsyncing the local lfric_core source")
-
-    rsync_command = f"rsync -acvzq {lfric_core_loc}/ {working_dir}/lfric_core"
-    subprocess_run(rsync_command)
-
-
 def build_makefile(
     root_dir,
     project_path,
@@ -140,13 +103,13 @@ def build_makefile(
     if target == "clean":
         working_path = working_dir
     else:
-        working_path = os.path.join(working_dir, f"{target}_{project}")
+        working_path = working_dir / f"{target}_{project}"
 
     print(f"Calling make command for makefile at {project_path}")
     make_command = (
         f"make {target} -C {project_path} -j {ncores} "
         f"WORKING_DIR={working_path} "
-        f"CORE_ROOT_DIR={working_dir}/lfric_core "
+        f"CORE_ROOT_DIR={working_dir / 'scratch' / 'lfric_core'} "
         f"APPS_ROOT_DIR={root_dir} "
     )
     if optlevel:
@@ -171,14 +134,24 @@ def main():
     )
     parser.add_argument(
         "project",
-        help="project to build. Will search in both "
-        "science and projects dirs.",
+        help="project to build. Will search in both " "science and projects dirs.",
     )
     parser.add_argument(
         "-c",
         "--core_source",
         default=None,
-        help="Source for lfric_core. Defaults to looking in " "dependencies file.",
+        help="Source for lfric_core. Defaults to looking in dependencies file.",
+    )
+    parser.add_argument(
+        "-m",
+        "--mirrors",
+        action="store_true",
+        help="If true, attempts to use local git mirrors",
+    )
+    parser.add_argument(
+        "--mirror_loc",
+        default="/data/users/gitassist/git_mirrors",
+        help="Location of github mirrors",
     )
     parser.add_argument(
         "-w",
@@ -237,24 +210,30 @@ def main():
 
     # Set the working dir default of the project directory
     if not args.working_dir:
-        args.working_dir = os.path.join(project_path, "working")
+        args.working_dir = Path(project_path) / "working"
     else:
         # If the working dir doesn't end in working, set that here
         if not args.working_dir.strip("/").endswith("working"):
-            args.working_dir = os.path.join(args.working_dir, "working")
-    # Ensure that working_dir is an absolute path
-    args.working_dir = os.path.abspath(args.working_dir)
-    # Create the working_dir
-    subprocess_run(f"mkdir -p {args.working_dir}")
+            args.working_dir = Path(args.working_dir) / "working"
+    # Ensure that working_dir is an absolute path and make the directory
+    args.working_dir = args.working_dir.resolve()
+    args.working_dir.mkdir(parents=True, exist_ok=True)
 
     # Determine the core source if not provided
     if args.core_source is None:
         core_source = determine_core_source(root_dir)
     else:
-        core_source = {"source": args.core_source}
-
-    # Export and rsync the lfric_core source
-    get_lfric_core(core_source, args.working_dir)
+        core_source = {"source": args.core_source, "ref": ""}
+
+    # Clone/Sync the lfric core source
+    get_source(
+        core_source["source"],
+        core_source["ref"],
+        args.working_dir / "scratch" / "lfric_core",
+        "lfric_core",
+        use_mirrors=args.mirrors,
+        mirror_loc=args.mirror_loc,
+    )
 
     # Build the makefile
     build_makefile(

From cc1d00d689c31b1e640697db939b830e8b815823 Mon Sep 17 00:00:00 2001
From: James Bruten <109733895+james-bruten-mo@users.noreply.github.com>
Date: Tue, 20 Jan 2026 10:17:41 +0000
Subject: [PATCH 2/7] incremental physics builds

---
 applications/lfric_atm/Makefile               |  2 +-
 applications/lfric_coupled/Makefile           |  2 +-
 applications/ngarch/Makefile                  |  2 +-
 build/extract/extract_physics.mk              |  4 +-
 build/extract/extract_science.py              | 63 +++++++++----------
 build/extract/get_git_sources.py              |  2 +-
 build/local_build.py                          | 21 +++----
 interfaces/jules_interface/build/import.mk    |  2 +-
 interfaces/socrates_interface/build/import.mk |  2 +-
 9 files changed, 43 insertions(+), 57 deletions(-)

diff --git a/applications/lfric_atm/Makefile b/applications/lfric_atm/Makefile
index 98f689dee..b7dd2db48 100644
--- a/applications/lfric_atm/Makefile
+++ b/applications/lfric_atm/Makefile
@@ -75,7 +75,7 @@ build: export BIN_DIR     ?= $(PROJECT_DIR)/bin
 build: export CXX_LINK     = YES
 build: export PROGRAMS    := $(basename $(notdir $(shell find source -maxdepth 1 -name '*.[Ff]90' -exec egrep -l "^\s*program" {} \;)))
 build: export PROJECT      = lfric_atm
-build: export SCRATCH_DIR := $(WORKING_DIR)/../physics_scratch
+build: export SCRATCH_DIR := $(WORKING_DIR)/..
 build: export WORKING_DIR := $(WORKING_DIR)
 
 build: export LDFLAGS_GROUPS = OPENMP
diff --git a/applications/lfric_coupled/Makefile b/applications/lfric_coupled/Makefile
index bf65bb5d7..cdd86b357 100644
--- a/applications/lfric_coupled/Makefile
+++ b/applications/lfric_coupled/Makefile
@@ -102,7 +102,7 @@ document-api: api-documentation
 build: export BIN_DIR     ?= $(PROJECT_DIR)/bin
 build: export CXX_LINK     = TRUE
 build: export PROGRAMS    := $(basename $(notdir $(shell find source -maxdepth 1 -name '*.[Ff]90' -print)))
-build: export SCRATCH_DIR := $(WORKING_DIR)/../physics_scratch
+build: export SCRATCH_DIR := $(WORKING_DIR)/..
 build: export PROJECT      = $(PROJECT_NAME)
 build: export WORKING_DIR := $(WORKING_DIR)/$(PROJECT_NAME)
 
diff --git a/applications/ngarch/Makefile b/applications/ngarch/Makefile
index 9fa685560..8b2a32300 100644
--- a/applications/ngarch/Makefile
+++ b/applications/ngarch/Makefile
@@ -100,7 +100,7 @@ document-api: api-documentation
 build: export BIN_DIR     ?= $(PROJECT_DIR)/bin
 build: export CXX_LINK     = TRUE
 build: export PROGRAMS    := $(basename $(notdir $(shell find source -maxdepth 1 -name '*.[Ff]90' -print)))
-build: export SCRATCH_DIR := $(WORKING_DIR)/../physics_scratch
+build: export SCRATCH_DIR := $(WORKING_DIR)/..
 build: export PROJECT      = $(PROJECT_NAME)
 build: export WORKING_DIR := $(WORKING_DIR)
 
diff --git a/build/extract/extract_physics.mk b/build/extract/extract_physics.mk
index a4df2535b..9f8c60e3f 100644
--- a/build/extract/extract_physics.mk
+++ b/build/extract/extract_physics.mk
@@ -21,6 +21,6 @@
 extract:
 	# Retrieve and preprocess the UKCA and CASIM code
 	python $(APPS_ROOT_DIR)/build/extract/extract_science.py -d $(APPS_ROOT_DIR)/dependencies.yaml -w $(SCRATCH_DIR) -e $(APPS_ROOT_DIR)/build/extract/extract.yaml
-	$Qrsync -acvz $(SCRATCH_DIR)/ukca $(WORKING_DIR)/science/
-	$Qrsync -acvz $(SCRATCH_DIR)/casim $(WORKING_DIR)/science/
+	$Qrsync -acvz $(SCRATCH_DIR)/scratch/ukca $(WORKING_DIR)/science/
+	$Qrsync -acvz $(SCRATCH_DIR)/scratch/casim $(WORKING_DIR)/science/
 
diff --git a/build/extract/extract_science.py b/build/extract/extract_science.py
index 042fe6f32..dea295974 100755
--- a/build/extract/extract_science.py
+++ b/build/extract/extract_science.py
@@ -1,11 +1,11 @@
 import argparse
 import subprocess
 import os
-import tempfile
 import yaml
-from shutil import rmtree
 from pathlib import Path
 from typing import Dict, List
+from get_git_sources import get_source
+import shlex
 
 
 def run_command(command):
@@ -14,7 +14,7 @@ def run_command(command):
     Inputs:
         - command, str with command to run
     """
-    command = command.split()
+    command = shlex.split(command)
     result = subprocess.run(
         command,
         capture_output=True,
@@ -40,24 +40,6 @@ def load_yaml(fpath: Path) -> Dict:
     return sources
 
 
-def clone_dependency(values: Dict, temp_dep: Path) -> None:
-    """
-    Clone the physics dependencies into a temporary directory
-    """
-
-    source = values["source"]
-    ref = values["ref"]
-
-    commands = (
-        f"git -C {temp_dep} init",
-        f"git -C {temp_dep} remote add origin {source}",
-        f"git -C {temp_dep} fetch origin {ref}",
-        f"git -C {temp_dep} checkout FETCH_HEAD"
-    )
-    for command in commands:
-        run_command(command)
-
-
 def extract_files(dependency: str, values: Dict, files: List[str], working: Path):
     """
     Clone the dependency to a temporary location
@@ -65,30 +47,41 @@ def extract_files(dependency: str, values: Dict, files: List[str], working: Path
     Then delete the temporary directory
     """
 
-    tempdir = Path(tempfile.mkdtemp())
+    use_mirrors: bool = (os.getenv('LOCAL_BUILD_MIRRORS', 'False') == 'True')
+    mirror_loc: Path = os.getenv("MIRROR_LOC")
+
     if (
         "PHYSICS_ROOT" not in os.environ
         or not Path(os.environ["PHYSICS_ROOT"]).exists()
     ):
-        temp_dep = tempdir / dependency
-        temp_dep.mkdir(parents=True)
-        clone_dependency(values, temp_dep)
+        clone_loc = working / "clones" / dependency
+        get_source(
+            values["source"],
+            values["ref"],
+            clone_loc,
+            dependency,
+            use_mirrors,
+            mirror_loc
+        )
     else:
-        temp_dep = Path(os.environ["PHYSICS_ROOT"]) / dependency
+        clone_loc = Path(os.environ["PHYSICS_ROOT"]) / dependency
 
-    working_dep = working / dependency
+    working_dep = working / "scratch" / dependency
 
     # make the working directory location
-    working_dep.mkdir(parents=True)
+    working_dep.mkdir(parents=True, exist_ok=True)
 
+    # rsync extract files from clone loc to the working directory
+    copy_command = "rsync --include='**/' "
     for extract_file in files:
-        source_file = temp_dep / extract_file
-        dest_file = working_dep / extract_file
-        run_command(f"mkdir -p {dest_file.parents[0]}")
-        copy_command = f"cp -r {source_file} {dest_file}"
-        run_command(copy_command)
-
-    rmtree(tempdir)
+        if not extract_file:
+            continue
+        if Path(clone_loc / extract_file).is_dir():
+            extract_file = extract_file.rstrip("/")
+            extract_file += "/**"
+        copy_command += f"--include='{extract_file}' "
+    copy_command += f"--exclude='*' -avmq {clone_loc}/ {working_dep}"
+    run_command(copy_command)
 
 
 def parse_args() -> argparse.Namespace:
diff --git a/build/extract/get_git_sources.py b/build/extract/get_git_sources.py
index bd790dd18..2c46108fb 100644
--- a/build/extract/get_git_sources.py
+++ b/build/extract/get_git_sources.py
@@ -27,7 +27,7 @@ def get_source(
     if ".git" in source:
         if use_mirrors:
             mirror_loc = Path(mirror_loc) / "MetOffice" / repo
-            print(f"Cloning/Updating {repo} from {mirror_loc} at ref {ref}")
+            print(f"Cloning/Updating {repo} from mirror {mirror_loc} at ref {ref}")
             clone_repo_mirror(source, repo, mirror_loc, dest)
         else:
             print(f"Cloning/Updating {repo} from {source} at ref {ref}")
diff --git a/build/local_build.py b/build/local_build.py
index 03212b3df..c4cfde039 100755
--- a/build/local_build.py
+++ b/build/local_build.py
@@ -93,7 +93,6 @@ def build_makefile(
     target,
     optlevel,
     psyclone,
-    um_fcm_platform,
     verbose,
 ):
     """
@@ -116,8 +115,6 @@ def build_makefile(
         make_command += f"PROFILE={optlevel} "
     if psyclone:
         make_command += f"PSYCLONE_TRANSFORMATION={psyclone} "
-    if um_fcm_platform:
-        make_command += f"UM_FCM_TARGET_PLATFORM={um_fcm_platform} "
     if verbose:
         make_command += "VERBOSE=1 "
 
@@ -186,14 +183,6 @@ def main():
         help="Value passed to PSYCLONE_TRANSFORMATION variable in makefile. "
         "Defaults to the makefile default",
     )
-    parser.add_argument(
-        "-u",
-        "--um_fcm_platform",
-        default=None,
-        help="Value passed to UM_FCM_TARGET_PLATFORM variable in makefile, "
-        "used for build settings for extracted UM physics. Defaults to the "
-        "makefile default.",
-    )
     parser.add_argument(
         "-v",
         "--verbose",
@@ -202,6 +191,11 @@ def main():
     )
     args = parser.parse_args()
 
+    # If using mirrors, set environment variable for science extract step
+    if args.mirrors:
+        os.environ["USE_MIRRORS"] = True
+        os.environ["LOCAL_BUILD_MIRRORS"] = args.mirror_loc
+
     # Find the root directory of the working copy
     root_dir = get_root_path()
 
@@ -231,8 +225,8 @@ def main():
         core_source["ref"],
         args.working_dir / "scratch" / "lfric_core",
         "lfric_core",
-        use_mirrors=args.mirrors,
-        mirror_loc=args.mirror_loc,
+        args.mirrors,
+        args.mirror_loc,
     )
 
     # Build the makefile
@@ -245,7 +239,6 @@ def main():
         args.target,
         args.optlevel,
         args.psyclone,
-        args.um_fcm_platform,
         args.verbose,
     )
 
diff --git a/interfaces/jules_interface/build/import.mk b/interfaces/jules_interface/build/import.mk
index bb1c8870b..bfc1bff97 100644
--- a/interfaces/jules_interface/build/import.mk
+++ b/interfaces/jules_interface/build/import.mk
@@ -9,7 +9,7 @@ export PROJECT_SOURCE = $(APPS_ROOT_DIR)/interfaces/jules_interface/source
 import-jules_interface:
     # Get a copy of the source code from the JULES repository
 	python $(APPS_ROOT_DIR)/build/extract/extract_science.py -d $(APPS_ROOT_DIR)/dependencies.yaml -w $(SCRATCH_DIR) -e $(APPS_ROOT_DIR)/interfaces/jules_interface/build/extract.yaml
-	$Qrsync -acvz $(SCRATCH_DIR)/jules $(WORKING_DIR)/
+	$Qrsync -acvz $(SCRATCH_DIR)/scratch/jules $(WORKING_DIR)/
 
     # Extract the interface code
 	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/extract.mk \
diff --git a/interfaces/socrates_interface/build/import.mk b/interfaces/socrates_interface/build/import.mk
index 35e5a09b3..fa488ad74 100644
--- a/interfaces/socrates_interface/build/import.mk
+++ b/interfaces/socrates_interface/build/import.mk
@@ -9,7 +9,7 @@ export PROJECT_SOURCE = $(APPS_ROOT_DIR)/interfaces/socrates_interface/source
 import-socrates_interface:
     # Get a copy of the source code from the SCORATES repository
 	python $(APPS_ROOT_DIR)/build/extract/extract_science.py -d $(APPS_ROOT_DIR)/dependencies.yaml -w $(SCRATCH_DIR) -e $(APPS_ROOT_DIR)/interfaces/socrates_interface/build/extract.yaml
-	$Qrsync -acvz $(SCRATCH_DIR)/socrates $(WORKING_DIR)/
+	$Qrsync -acvz $(SCRATCH_DIR)/scratch/socrates $(WORKING_DIR)/
 
     # Extract the interface code
 	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/extract.mk \

From 132ccf8c799a6ee76344d1ea8ae37804353f5c75 Mon Sep 17 00:00:00 2001
From: James Bruten <109733895+james-bruten-mo@users.noreply.github.com>
Date: Tue, 20 Jan 2026 14:31:11 +0000
Subject: [PATCH 3/7] incremental builds

---
 applications/lfric_atm/build/compile_options.mk |  3 ++-
 build/extract/extract_physics.mk                |  5 +----
 build/extract/extract_science.py                | 12 ++++++------
 interfaces/jules_interface/build/import.mk      |  3 +--
 interfaces/socrates_interface/build/import.mk   |  3 +--
 5 files changed, 11 insertions(+), 15 deletions(-)

diff --git a/applications/lfric_atm/build/compile_options.mk b/applications/lfric_atm/build/compile_options.mk
index 143f09ae6..842a61d60 100644
--- a/applications/lfric_atm/build/compile_options.mk
+++ b/applications/lfric_atm/build/compile_options.mk
@@ -13,7 +13,8 @@ $(info UM physics specific compile options)
 
 include $(PROJECT_DIR)/build/fortran/$(FORTRAN_COMPILER).mk
 
-science/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+casim/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+ukca/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 jules/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 socrates/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 legacy/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
diff --git a/build/extract/extract_physics.mk b/build/extract/extract_physics.mk
index 9f8c60e3f..7e43cd1b0 100644
--- a/build/extract/extract_physics.mk
+++ b/build/extract/extract_physics.mk
@@ -20,7 +20,4 @@
 
 extract:
 	# Retrieve and preprocess the UKCA and CASIM code
-	python $(APPS_ROOT_DIR)/build/extract/extract_science.py -d $(APPS_ROOT_DIR)/dependencies.yaml -w $(SCRATCH_DIR) -e $(APPS_ROOT_DIR)/build/extract/extract.yaml
-	$Qrsync -acvz $(SCRATCH_DIR)/scratch/ukca $(WORKING_DIR)/science/
-	$Qrsync -acvz $(SCRATCH_DIR)/scratch/casim $(WORKING_DIR)/science/
-
+	python $(APPS_ROOT_DIR)/build/extract/extract_science.py -d $(APPS_ROOT_DIR)/dependencies.yaml -w $(WORKING_DIR) -e $(APPS_ROOT_DIR)/build/extract/extract.yaml
diff --git a/build/extract/extract_science.py b/build/extract/extract_science.py
index dea295974..5bde7a834 100755
--- a/build/extract/extract_science.py
+++ b/build/extract/extract_science.py
@@ -54,7 +54,7 @@ def extract_files(dependency: str, values: Dict, files: List[str], working: Path
         "PHYSICS_ROOT" not in os.environ
         or not Path(os.environ["PHYSICS_ROOT"]).exists()
     ):
-        clone_loc = working / "clones" / dependency
+        clone_loc = working / ".." / "scratch" / dependency
         get_source(
             values["source"],
             values["ref"],
@@ -66,10 +66,10 @@ def extract_files(dependency: str, values: Dict, files: List[str], working: Path
     else:
         clone_loc = Path(os.environ["PHYSICS_ROOT"]) / dependency
 
-    working_dep = working / "scratch" / dependency
 
     # make the working directory location
-    working_dep.mkdir(parents=True, exist_ok=True)
+    working_dir = working / dependency
+    working_dir.mkdir(parents=True, exist_ok=True)
 
     # rsync extract files from clone loc to the working directory
     copy_command = "rsync --include='**/' "
@@ -80,7 +80,7 @@ def extract_files(dependency: str, values: Dict, files: List[str], working: Path
             extract_file = extract_file.rstrip("/")
             extract_file += "/**"
         copy_command += f"--include='{extract_file}' "
-    copy_command += f"--exclude='*' -avmq {clone_loc}/ {working_dep}"
+    copy_command += f"--exclude='*' -avmq {clone_loc}/ {working_dir}"
     run_command(copy_command)
 
 
@@ -94,10 +94,10 @@ def parse_args() -> argparse.Namespace:
         "-d",
         "--dependencies",
         default="./dependencies.yaml",
-        help="The dependencies file for the apps working copy.",
+        help="The dependencies file for the apps working copy",
     )
     parser.add_argument(
-        "-w", "--working", default=".", help="Location to perform extract steps in."
+        "-w", "--working", default=".", help="Build location"
     )
     parser.add_argument(
         "-e",
diff --git a/interfaces/jules_interface/build/import.mk b/interfaces/jules_interface/build/import.mk
index bfc1bff97..73b35d289 100644
--- a/interfaces/jules_interface/build/import.mk
+++ b/interfaces/jules_interface/build/import.mk
@@ -8,8 +8,7 @@ export PROJECT_SOURCE = $(APPS_ROOT_DIR)/interfaces/jules_interface/source
 .PHONY: import-jules_interface
 import-jules_interface:
     # Get a copy of the source code from the JULES repository
-	python $(APPS_ROOT_DIR)/build/extract/extract_science.py -d $(APPS_ROOT_DIR)/dependencies.yaml -w $(SCRATCH_DIR) -e $(APPS_ROOT_DIR)/interfaces/jules_interface/build/extract.yaml
-	$Qrsync -acvz $(SCRATCH_DIR)/scratch/jules $(WORKING_DIR)/
+	python $(APPS_ROOT_DIR)/build/extract/extract_science.py -d $(APPS_ROOT_DIR)/dependencies.yaml -w $(WORKING_DIR) -e $(APPS_ROOT_DIR)/interfaces/jules_interface/build/extract.yaml
 
     # Extract the interface code
 	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/extract.mk \
diff --git a/interfaces/socrates_interface/build/import.mk b/interfaces/socrates_interface/build/import.mk
index fa488ad74..a12f78739 100644
--- a/interfaces/socrates_interface/build/import.mk
+++ b/interfaces/socrates_interface/build/import.mk
@@ -8,8 +8,7 @@ export PROJECT_SOURCE = $(APPS_ROOT_DIR)/interfaces/socrates_interface/source
 .PHONY: import-socrates_interface
 import-socrates_interface:
     # Get a copy of the source code from the SCORATES repository
-	python $(APPS_ROOT_DIR)/build/extract/extract_science.py -d $(APPS_ROOT_DIR)/dependencies.yaml -w $(SCRATCH_DIR) -e $(APPS_ROOT_DIR)/interfaces/socrates_interface/build/extract.yaml
-	$Qrsync -acvz $(SCRATCH_DIR)/scratch/socrates $(WORKING_DIR)/
+	python $(APPS_ROOT_DIR)/build/extract/extract_science.py -d $(APPS_ROOT_DIR)/dependencies.yaml -w $(WORKING_DIR) -e $(APPS_ROOT_DIR)/interfaces/socrates_interface/build/extract.yaml
 
     # Extract the interface code
 	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/extract.mk \

From 82f3795839762d771f25e5a6509201cb7e6f7a41 Mon Sep 17 00:00:00 2001
From: James Bruten <109733895+james-bruten-mo@users.noreply.github.com>
Date: Tue, 20 Jan 2026 15:02:44 +0000
Subject: [PATCH 4/7] minor changes

---
 applications/jules/build/compile_options.mk         | 3 ++-
 applications/lfric_coupled/build/compile_options.mk | 3 ++-
 applications/ngarch/build/compile_options.mk        | 3 ++-
 build/extract/get_git_sources.py                    | 2 +-
 build/local_build.py                                | 2 +-
 5 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/applications/jules/build/compile_options.mk b/applications/jules/build/compile_options.mk
index bf4bad539..3ab2dcbf3 100644
--- a/applications/jules/build/compile_options.mk
+++ b/applications/jules/build/compile_options.mk
@@ -13,7 +13,8 @@ $(info UM physics specific compile options)
 
 include $(PROJECT_DIR)/build/fortran/$(FORTRAN_COMPILER).mk
 
-science/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+casim/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+ukca/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 jules/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 socrates/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 legacy/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
diff --git a/applications/lfric_coupled/build/compile_options.mk b/applications/lfric_coupled/build/compile_options.mk
index 10ad895f2..9623d56e1 100644
--- a/applications/lfric_coupled/build/compile_options.mk
+++ b/applications/lfric_coupled/build/compile_options.mk
@@ -9,7 +9,8 @@ $(info UM physics specific compile options for $(FORTRAN_COMPILER) compiler)
 
 include $(PROJECT_DIR)/build/fortran/$(FORTRAN_COMPILER).mk
 
-science/%.o science/%.mod: private FFLAGS_EXTRA += $(FFLAGS_UM_PHYSICS)
+casim/%.o science/%.mod: private FFLAGS_EXTRA += $(FFLAGS_UM_PHYSICS)
+ukca/%.o science/%.mod: private FFLAGS_EXTRA += $(FFLAGS_UM_PHYSICS)
 jules/%.o jules/%.mod: private FFLAGS_EXTRA += $(FFLAGS_UM_PHYSICS)
 socrates/%.o socrates/%.mod: private FFLAGS_EXTRA += $(FFLAGS_UM_PHYSICS)
 legacy/%.o legacy/%.mod: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
diff --git a/applications/ngarch/build/compile_options.mk b/applications/ngarch/build/compile_options.mk
index 810698d65..4ef9b69bd 100644
--- a/applications/ngarch/build/compile_options.mk
+++ b/applications/ngarch/build/compile_options.mk
@@ -13,7 +13,8 @@ $(info UM physics specific compile options)
 
 include $(PROJECT_DIR)/build/fortran/$(FORTRAN_COMPILER).mk
 
-science/%.o science/%.mod: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+casim/%.o science/%.mod: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+ukca/%.o science/%.mod: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 jules/%.o jules/%.mod: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 socrates/%.o socrates/%.mod: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 legacy/%.o legacy/%.mod: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
diff --git a/build/extract/get_git_sources.py b/build/extract/get_git_sources.py
index 2c46108fb..ef890f895 100644
--- a/build/extract/get_git_sources.py
+++ b/build/extract/get_git_sources.py
@@ -28,7 +28,7 @@ def get_source(
         if use_mirrors:
             mirror_loc = Path(mirror_loc) / "MetOffice" / repo
             print(f"Cloning/Updating {repo} from mirror {mirror_loc} at ref {ref}")
-            clone_repo_mirror(source, repo, mirror_loc, dest)
+            clone_repo_mirror(source, ref, repo, mirror_loc, dest)
         else:
             print(f"Cloning/Updating {repo} from {source} at ref {ref}")
             clone_repo(source, ref, dest)
diff --git a/build/local_build.py b/build/local_build.py
index c4cfde039..864052cc5 100755
--- a/build/local_build.py
+++ b/build/local_build.py
@@ -193,7 +193,7 @@ def main():
 
     # If using mirrors, set environment variable for science extract step
     if args.mirrors:
-        os.environ["USE_MIRRORS"] = True
+        os.environ["USE_MIRRORS"] = "True"
         os.environ["LOCAL_BUILD_MIRRORS"] = args.mirror_loc
 
     # Find the root directory of the working copy

From 35903fb308c44f129e1d48122535c70354c008bd Mon Sep 17 00:00:00 2001
From: James Bruten <109733895+james-bruten-mo@users.noreply.github.com>
Date: Tue, 20 Jan 2026 15:25:13 +0000
Subject: [PATCH 5/7] catch missing env var

---
 build/extract/extract_science.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/build/extract/extract_science.py b/build/extract/extract_science.py
index 5bde7a834..43f7a7581 100755
--- a/build/extract/extract_science.py
+++ b/build/extract/extract_science.py
@@ -48,7 +48,12 @@ def extract_files(dependency: str, values: Dict, files: List[str], working: Path
     """
 
     use_mirrors: bool = (os.getenv('LOCAL_BUILD_MIRRORS', 'False') == 'True')
-    mirror_loc: Path = os.getenv("MIRROR_LOC")
+    mirror_loc: Path = os.getenv("MIRROR_LOC", "")
+    if not mirror_loc and use_mirrors:
+        raise KeyError(
+            "Use Mirrors is set true, but the MIRROR_LOC environment variable hasn't"
+            "been set"
+        )
 
     if (
         "PHYSICS_ROOT" not in os.environ

From b6137e1f72a5673a8606808ee9e23654265a4ea2 Mon Sep 17 00:00:00 2001
From: James Bruten <109733895+james-bruten-mo@users.noreply.github.com>
Date: Wed, 21 Jan 2026 14:15:56 +0000
Subject: [PATCH 6/7] update local build docs

---
 .../source/developer_guide/local_builds.rst      | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/documentation/source/developer_guide/local_builds.rst b/documentation/source/developer_guide/local_builds.rst
index 9e5bd9310..c57f67e62 100644
--- a/documentation/source/developer_guide/local_builds.rst
+++ b/documentation/source/developer_guide/local_builds.rst
@@ -67,3 +67,19 @@ This table lists the command line arguments available:
 |                      |                             | will request verbose output |
 |                      |                             | from the makefile.          |
 +----------------------+-----------------------------+-----------------------------+
+| ``-m --mirrors``     | False                       | If True, this will attempt  |
+| ``store_true``       |                             | to extract using local      |
+|                      |                             | github mirrors              |
++----------------------+-----------------------------+-----------------------------+
+| ``--mirror-loc``     | MetOffice Mirror Location   | The path to the github      |
+|                      |                             | mirror location             |
++----------------------+-----------------------------+-----------------------------+
+
+Incremental Builds
+------------------
+
+The local build script will attempt to build incrementally if a previous attempt
+at the build exists. This should happen automatically if the working directory
+is the same. If there are large changes then it may be sensible to start the
+build afresh by cleaning the build ``-t clean`` (or deleting the working
+directory).

From 7500ed610246266dd7df186cb2ad2a65666719e4 Mon Sep 17 00:00:00 2001
From: James Bruten <109733895+james-bruten-mo@users.noreply.github.com>
Date: Wed, 21 Jan 2026 17:06:13 +0000
Subject: [PATCH 7/7] review comments

---
 build/extract/extract_science.py |  8 +-------
 build/extract/get_git_sources.py | 33 ++++++++++++++++++++++++--------
 build/local_build.py             | 10 +++++-----
 3 files changed, 31 insertions(+), 20 deletions(-)

diff --git a/build/extract/extract_science.py b/build/extract/extract_science.py
index 43f7a7581..3ab52c9c3 100755
--- a/build/extract/extract_science.py
+++ b/build/extract/extract_science.py
@@ -47,13 +47,7 @@ def extract_files(dependency: str, values: Dict, files: List[str], working: Path
     Then delete the temporary directory
     """
 
-    use_mirrors: bool = (os.getenv('LOCAL_BUILD_MIRRORS', 'False') == 'True')
     mirror_loc: Path = os.getenv("MIRROR_LOC", "")
-    if not mirror_loc and use_mirrors:
-        raise KeyError(
-            "Use Mirrors is set true, but the MIRROR_LOC environment variable hasn't"
-            "been set"
-        )
 
     if (
         "PHYSICS_ROOT" not in os.environ
@@ -65,7 +59,7 @@ def extract_files(dependency: str, values: Dict, files: List[str], working: Path
             values["ref"],
             clone_loc,
             dependency,
-            use_mirrors,
+            bool(mirror_loc),
             mirror_loc
         )
     else:
diff --git a/build/extract/get_git_sources.py b/build/extract/get_git_sources.py
index ef890f895..2b5c1455b 100644
--- a/build/extract/get_git_sources.py
+++ b/build/extract/get_git_sources.py
@@ -4,7 +4,7 @@
 # which you should have received as part of this distribution.
 # *****************************COPYRIGHT*******************************
 """
-Clone sources for a rose-stem run for use with git bdiff module in scripts
+Helper functions for cloning git sources in command line builds
 """
 
 import re
@@ -66,25 +66,40 @@ def run_command(
 
 
 def clone_repo_mirror(
-    source: str, repo_ref: str, parent: str, mirror_loc: Path, loc: Path
+    repo_source: str, repo_ref: str, parent: str, mirror_loc: Path, loc: Path
 ) -> None:
     """
     Clone a repo source using a local git mirror.
     Assume the mirror is set up as per the Met Office
+    - repo_source: ssh url of the source repository
+    - repo_ref: git ref for the source. An empty string will get the default branch
+    - parent: Owner of the github repository being cloned (required to construct the
+              mirror path)
+    - mirror_loc: path to the local git mirrors
+    - loc: path to clone the repository to
     """
 
-    # Remove if this clone already exists
-    if not loc.exists():
+    # If the repository exists and isn't a git repo, exit now as we don't want to
+    # overwrite it
+    if loc.exists():
+        if not Path(loc / ".git").exists():
+            raise RuntimeError(
+                f"The destination for the clone of {repo_source} already exists but "
+                "isn't a git directory. Exiting so as to not overwrite it."
+            )
+
+    # Clone if the repo doesn't exist
+    else:
         command = f"git clone {mirror_loc} {loc}"
         run_command(command)
 
-    # If not provided a ref, return
+    # If not provided a ref, pull the latest repository and return
     if not repo_ref:
         run_command(f"git -C {loc} pull")
         return
 
-    source = source.removeprefix("git@github.com:")
-    user = source.split("/")[0]
+    repo_source = repo_source.removeprefix("git@github.com:")
+    user = repo_source.split("/")[0]
     # Check that the user is different to the Upstream User
     if user in parent.split("/")[0]:
         user = None
@@ -107,9 +122,11 @@ def clone_repo(repo_source: str, repo_ref: str, loc: Path) -> None:
     """
     Clone the repo and checkout the provided ref
     Only if a remote source
+    - repo_source: ssh url of the source repository
+    - repo_ref: git ref for the source. An empty string will get the default branch
+    - loc: path to clone the repository to
     """
 
-    # Remove if this clone already exists
     if not loc.exists():
         # Create a clean clone location
         loc.mkdir(parents=True)
diff --git a/build/local_build.py b/build/local_build.py
index 864052cc5..7c63d825a 100755
--- a/build/local_build.py
+++ b/build/local_build.py
@@ -47,7 +47,7 @@ def get_root_path():
     Get the root path of the current working copy
     """
 
-    return Path(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+    return Path(__file__).absolute().parent.parent
 
 
 def determine_core_source(root_dir):
@@ -154,7 +154,8 @@ def main():
         "-w",
         "--working_dir",
         default=None,
-        help="Working directory where builds occur. Default to the project "
+        type=Path,
+        help="Working directory where builds occur. Defaults to the project "
         "directory in the working copy.",
     )
     parser.add_argument(
@@ -193,8 +194,7 @@ def main():
 
     # If using mirrors, set environment variable for science extract step
     if args.mirrors:
-        os.environ["USE_MIRRORS"] = "True"
-        os.environ["LOCAL_BUILD_MIRRORS"] = args.mirror_loc
+        os.environ["USE_MIRRORS"] = args.mirror_loc
 
     # Find the root directory of the working copy
     root_dir = get_root_path()
@@ -207,7 +207,7 @@ def main():
         args.working_dir = Path(project_path) / "working"
     else:
         # If the working dir doesn't end in working, set that here
-        if not args.working_dir.strip("/").endswith("working"):
+        if not args.working_dir.name == "working":
             args.working_dir = Path(args.working_dir) / "working"
     # Ensure that working_dir is an absolute path and make the directory
     args.working_dir = args.working_dir.resolve()