From 12cc7a593434356a83eb37982c28ad513e36257c Mon Sep 17 00:00:00 2001
From: pardallio <pardalmiguel@hotmail.com>
Date: Fri, 29 May 2026 17:03:00 +0000
Subject: [PATCH 1/8] adds bundle merge functionality

---
 bin/ecbundle         |   3 ++
 bin/ecbundle-merge   |  75 ++++++++++++++++++++++++++
 ecbundle/__init__.py |   1 +
 ecbundle/merge.py    | 126 +++++++++++++++++++++++++++++++++++++++++++
 ecbundle/project.py  |   3 ++
 5 files changed, 208 insertions(+)
 create mode 100755 bin/ecbundle-merge
 create mode 100644 ecbundle/merge.py

diff --git a/bin/ecbundle b/bin/ecbundle
index 642e9c2..32558ad 100755
--- a/bin/ecbundle
+++ b/bin/ecbundle
@@ -37,6 +37,9 @@ elif [[ "create" == "$1"* ]]; then
 elif [[ "populate" == "$1"* ]]; then
   shift
   ${SCRIPT_DIR}/ecbundle-populate "$@"
+elif [[ "merge" == "$1"* ]]; then
+  shift
+  ${SCRIPT_DIR}/ecbundle-merge "$@"
 else
   echo "ERROR: Expected 'build' or 'create' or 'populate' as first argument"
   usage
diff --git a/bin/ecbundle-merge b/bin/ecbundle-merge
new file mode 100755
index 0000000..6a2572a
--- /dev/null
+++ b/bin/ecbundle-merge
@@ -0,0 +1,75 @@
+#!/usr/bin/env python3
+
+# (C) Copyright 2020- ECMWF.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+# In applying this licence, ECMWF does not waive the privileges and immunities
+# granted to it by virtue of its status as an intergovernmental organisation nor
+# does it submit to any jurisdiction.
+
+"""
+Script to merge and update bundle files
+"""
+
+import os
+import sys
+from argparse import SUPPRESS, ArgumentParser, RawTextHelpFormatter
+
+sys.path.insert(0, os.path.realpath(os.path.dirname(os.path.realpath(__file__))+'/..'))
+from ecbundle import BundleMerger
+from ecbundle.logging import DEBUG, colors, error, logger, success
+
+
+def main():
+
+    # Parse arguments
+    parser = ArgumentParser(description=__doc__,
+                            formatter_class=RawTextHelpFormatter)
+
+    # --------------------------------------------------------------------------
+    # Parse common subcommands
+    # --------------------------------------------------------------------------
+    parser.add_argument('--no-colour', '--no-color',
+                        help='Disable color output',
+                        action='store_true')
+
+    parser.add_argument('--verbose', '-v',
+                        help='Verbose output',
+                        action='store_true')
+
+    parser.add_argument('--bundle',
+                        help='Configuration of bundle', default="bundle.yml")
+
+    parser.add_argument('--bundle-update',
+                        help='Configuration of bundle update', default="bundle-update.yml")
+
+    parser.add_argument('-o',
+                        help='output file', default="merged-bundle.yml")
+
+    # --------------------------------------------------------------------------
+
+    # Close parser and populate variable args
+    args = parser.parse_args()
+
+    # Explicitly disable coloured logs
+    if args.no_colour:
+        colors.disable()
+
+    # Log everything, including commands executed
+    if args.verbose:
+        logger.setLevel(DEBUG)
+
+
+    errcode = 0
+
+    if BundleMerger(**vars(args)).merge() != 0:
+        errcode = 1 # error
+
+    if errcode == 1:
+        error("\n!!! Errors occured !!!")
+
+    return errcode
+
+if __name__ == '__main__':
+    sys.exit(main())
diff --git a/ecbundle/__init__.py b/ecbundle/__init__.py
index 1e2dde7..998c03f 100644
--- a/ecbundle/__init__.py
+++ b/ecbundle/__init__.py
@@ -12,6 +12,7 @@
 from ecbundle.download import *  # noqa
 from ecbundle.git import *  # noqa
 from ecbundle.logging import *  # noqa
+from ecbundle.merge import *  # noqa
 from ecbundle.option import *  # noqa
 from ecbundle.populate import *  # noqa
 from ecbundle.project import *  # noqa
diff --git a/ecbundle/merge.py b/ecbundle/merge.py
new file mode 100644
index 0000000..4adbacf
--- /dev/null
+++ b/ecbundle/merge.py
@@ -0,0 +1,126 @@
+# (C) Copyright 2020- ECMWF.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+# In applying this licence, ECMWF does not waive the privileges and immunities
+# granted to it by virtue of its status as an intergovernmental organisation nor
+# does it submit to any jurisdiction.
+
+import os
+import copy
+from collections import OrderedDict
+
+from .bundle import Bundle
+from .logging import error, header, success
+from .util import fullpath, mkdir_p, symlink_force
+
+__all__ = ["BundleMerger"]
+
+
+class BundleMerger(object):
+    def __init__(self, **kwargs):
+        self.config = kwargs
+
+    def get(self, key, default=None):
+        return self.config[key] if self.config[key] is not None else default
+    
+    def deep_merge(self, original, updates):
+        """Recursively merge `updates` into `original`.
+
+        Rules:
+        - Dictionaries and  are merged recursively.
+        - lists and scalar values are replaced entirely.
+        - Keys missing from `updates` remain unchanged.
+        """
+        if isinstance(original, dict) and isinstance(updates, dict):
+            merged = copy.deepcopy(original)
+            for key, value in updates.items():
+                if key in merged:
+                    if isinstance(merged[key], dict) and isinstance(value, dict):
+                        merged[key] = self.deep_merge(merged[key], value)
+                    else:
+                        merged[key] = copy.deepcopy(value)
+
+                else:
+                    merged[key] = copy.deepcopy(value)
+
+        else:
+            return copy.deepcopy(updates)
+
+        return merged
+    
+    def bundle(self,update=False):
+        arg="bundle"
+        if update:
+            arg += "_update"
+        bundle_path = fullpath(self.get(arg, None))
+        if bundle_path:
+            if os.path.isfile(bundle_path):
+                return Bundle(bundle_path, env=True)
+            if not os.path.isdir(bundle_path):
+                error(
+                    f"ERROR: --{arg} argument is not a valid bundle file path"
+                )
+                return None
+
+        return None
+
+    def merge(self):
+        bundle = self.bundle()
+        bundle_update = self.bundle(update = True)
+        if not (bundle and bundle_update) :
+            return 1
+
+        success("\nMerging bundle  ")
+        header(f"    {bundle_update.file()} into {bundle.file()}")
+        
+        # merging projects
+        project_dict = {
+            item.config["name"]: {
+                k: v for k, v in item.config.items() if k != "name"
+            }
+            for item in bundle.projects()
+        }
+        
+        updated_project_dict = {
+            item.config["name"]: {
+                k: v for k, v in item.config.items() if k != "name"
+            }
+            for item in bundle_update.projects()
+        }
+        
+        updated_dict = self.deep_merge(project_dict,updated_project_dict)
+
+        bundle.config["projects"] = [{key:value} for key,value in updated_dict.items()]
+
+        # merging options
+        option_dict = {
+            item.config["name"]: {
+                k: v for k, v in item.config.items() if k != "name"
+            }
+            for item in bundle.options()
+        }
+
+        updated_option_dict = {
+            item.config["name"]: {
+                k: v for k, v in item.config.items() if k != "name"
+            }
+            for item in bundle_update.options()
+        }
+        
+        updated_dict = self.deep_merge(option_dict,updated_option_dict)
+
+        bundle.config["options"] = [{key:value} for key,value in updated_dict.items()]
+
+        # merge remaining keys
+
+        for key in bundle_update.config.keys():
+            if key not in ["projects","options"]:
+                bundle.config[key] = bundle_update.get(key)
+
+        with open(self.get("o", None), "w", encoding="utf-8") as f:
+            f.write(bundle.yaml())
+
+        return 0
+
+
diff --git a/ecbundle/project.py b/ecbundle/project.py
index dfe8fe5..a55b28e 100644
--- a/ecbundle/project.py
+++ b/ecbundle/project.py
@@ -74,6 +74,9 @@ def require(self):
         else:
             return None
 
+    def get_dict(self):
+        return self.config
+
     def optional(self):
         return self.get("optional", False)
 

From 357036ba1424097a6f318c6ee1000c00bea056e9 Mon Sep 17 00:00:00 2001
From: pardallio <pardalmiguel@hotmail.com>
Date: Mon, 1 Jun 2026 13:18:09 +0000
Subject: [PATCH 2/8] linting

---
 ecbundle/merge.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ecbundle/merge.py b/ecbundle/merge.py
index 4adbacf..afba190 100644
--- a/ecbundle/merge.py
+++ b/ecbundle/merge.py
@@ -6,8 +6,8 @@
 # granted to it by virtue of its status as an intergovernmental organisation nor
 # does it submit to any jurisdiction.
 
-import os
 import copy
+import os
 from collections import OrderedDict
 
 from .bundle import Bundle

From cc01e162847ab4925f7048bf2c615df5c0bb1f33 Mon Sep 17 00:00:00 2001
From: pardallio <pardalmiguel@hotmail.com>
Date: Mon, 1 Jun 2026 13:37:48 +0000
Subject: [PATCH 3/8] linting

---
 ecbundle/merge.py | 54 +++++++++++++++++++----------------------------
 1 file changed, 22 insertions(+), 32 deletions(-)

diff --git a/ecbundle/merge.py b/ecbundle/merge.py
index afba190..d23bbad 100644
--- a/ecbundle/merge.py
+++ b/ecbundle/merge.py
@@ -23,7 +23,7 @@ def __init__(self, **kwargs):
 
     def get(self, key, default=None):
         return self.config[key] if self.config[key] is not None else default
-    
+
     def deep_merge(self, original, updates):
         """Recursively merge `updates` into `original`.
 
@@ -48,9 +48,9 @@ def deep_merge(self, original, updates):
             return copy.deepcopy(updates)
 
         return merged
-    
-    def bundle(self,update=False):
-        arg="bundle"
+
+    def bundle(self, update=False):
+        arg = "bundle"
         if update:
             arg += "_update"
         bundle_path = fullpath(self.get(arg, None))
@@ -58,69 +58,59 @@ def bundle(self,update=False):
             if os.path.isfile(bundle_path):
                 return Bundle(bundle_path, env=True)
             if not os.path.isdir(bundle_path):
-                error(
-                    f"ERROR: --{arg} argument is not a valid bundle file path"
-                )
+                error(f"ERROR: --{arg} argument is not a valid bundle file path")
                 return None
 
         return None
 
     def merge(self):
         bundle = self.bundle()
-        bundle_update = self.bundle(update = True)
-        if not (bundle and bundle_update) :
+        bundle_update = self.bundle(update=True)
+        if not (bundle and bundle_update):
             return 1
 
         success("\nMerging bundle  ")
         header(f"    {bundle_update.file()} into {bundle.file()}")
-        
+
         # merging projects
         project_dict = {
-            item.config["name"]: {
-                k: v for k, v in item.config.items() if k != "name"
-            }
+            item.config["name"]: {k: v for k, v in item.config.items() if k != "name"}
             for item in bundle.projects()
         }
-        
+
         updated_project_dict = {
-            item.config["name"]: {
-                k: v for k, v in item.config.items() if k != "name"
-            }
+            item.config["name"]: {k: v for k, v in item.config.items() if k != "name"}
             for item in bundle_update.projects()
         }
-        
-        updated_dict = self.deep_merge(project_dict,updated_project_dict)
 
-        bundle.config["projects"] = [{key:value} for key,value in updated_dict.items()]
+        updated_dict = self.deep_merge(project_dict, updated_project_dict)
+
+        bundle.config["projects"] = [
+            {key: value} for key, value in updated_dict.items()
+        ]
 
         # merging options
         option_dict = {
-            item.config["name"]: {
-                k: v for k, v in item.config.items() if k != "name"
-            }
+            item.config["name"]: {k: v for k, v in item.config.items() if k != "name"}
             for item in bundle.options()
         }
 
         updated_option_dict = {
-            item.config["name"]: {
-                k: v for k, v in item.config.items() if k != "name"
-            }
+            item.config["name"]: {k: v for k, v in item.config.items() if k != "name"}
             for item in bundle_update.options()
         }
-        
-        updated_dict = self.deep_merge(option_dict,updated_option_dict)
 
-        bundle.config["options"] = [{key:value} for key,value in updated_dict.items()]
+        updated_dict = self.deep_merge(option_dict, updated_option_dict)
+
+        bundle.config["options"] = [{key: value} for key, value in updated_dict.items()]
 
         # merge remaining keys
 
         for key in bundle_update.config.keys():
-            if key not in ["projects","options"]:
+            if key not in ["projects", "options"]:
                 bundle.config[key] = bundle_update.get(key)
 
         with open(self.get("o", None), "w", encoding="utf-8") as f:
             f.write(bundle.yaml())
 
         return 0
-
-

From 796ecb4b4cbe068bc35ac618a9630f918fada07a Mon Sep 17 00:00:00 2001
From: pardallio <pardalmiguel@hotmail.com>
Date: Mon, 1 Jun 2026 13:40:50 +0000
Subject: [PATCH 4/8] linting

---
 ecbundle/merge.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/ecbundle/merge.py b/ecbundle/merge.py
index d23bbad..73c6f65 100644
--- a/ecbundle/merge.py
+++ b/ecbundle/merge.py
@@ -8,11 +8,10 @@
 
 import copy
 import os
-from collections import OrderedDict
 
 from .bundle import Bundle
 from .logging import error, header, success
-from .util import fullpath, mkdir_p, symlink_force
+from .util import fullpath
 
 __all__ = ["BundleMerger"]
 

From 96d13e8d4b3cd9d94e4e9fbfdffdce5e5a6b852b Mon Sep 17 00:00:00 2001
From: pardallio <pardalmiguel@hotmail.com>
Date: Wed, 8 Jul 2026 10:08:29 +0000
Subject: [PATCH 5/8] enhance bundle merging: add support for multiple update
 bundles and improve error handling

---
 bin/ecbundle-merge |  15 +++---
 ecbundle/merge.py  | 117 +++++++++++++++++++++++----------------------
 2 files changed, 69 insertions(+), 63 deletions(-)

diff --git a/bin/ecbundle-merge b/bin/ecbundle-merge
index 6a2572a..86deec0 100755
--- a/bin/ecbundle-merge
+++ b/bin/ecbundle-merge
@@ -37,13 +37,13 @@ def main():
     parser.add_argument('--verbose', '-v',
                         help='Verbose output',
                         action='store_true')
+    
+    parser.add_argument('bundles',
+                        help='Bundle files: the first is the original bundle, '
+                             'any following are update bundles applied in order',
+                        nargs='+')
 
-    parser.add_argument('--bundle',
-                        help='Configuration of bundle', default="bundle.yml")
-
-    parser.add_argument('--bundle-update',
-                        help='Configuration of bundle update', default="bundle-update.yml")
-
+    
     parser.add_argument('-o',
                         help='output file', default="merged-bundle.yml")
 
@@ -52,6 +52,9 @@ def main():
     # Close parser and populate variable args
     args = parser.parse_args()
 
+    if len(args.bundles) < 2:
+            parser.error('at least one update bundle is required in addition to the original')
+
     # Explicitly disable coloured logs
     if args.no_colour:
         colors.disable()
diff --git a/ecbundle/merge.py b/ecbundle/merge.py
index 73c6f65..938bde0 100644
--- a/ecbundle/merge.py
+++ b/ecbundle/merge.py
@@ -10,7 +10,7 @@
 import os
 
 from .bundle import Bundle
-from .logging import error, header, success
+from .logging import error, header, success,info
 from .util import fullpath
 
 __all__ = ["BundleMerger"]
@@ -21,14 +21,14 @@ def __init__(self, **kwargs):
         self.config = kwargs
 
     def get(self, key, default=None):
-        return self.config[key] if self.config[key] is not None else default
+        return self.config[key] if self.config.get(key) is not None else default
 
     def deep_merge(self, original, updates):
         """Recursively merge `updates` into `original`.
 
         Rules:
-        - Dictionaries and  are merged recursively.
-        - lists and scalar values are replaced entirely.
+        - Dictionaries are merged recursively.
+        - Lists and scalar values are replaced entirely.
         - Keys missing from `updates` remain unchanged.
         """
         if isinstance(original, dict) and isinstance(updates, dict):
@@ -39,77 +39,80 @@ def deep_merge(self, original, updates):
                         merged[key] = self.deep_merge(merged[key], value)
                     else:
                         merged[key] = copy.deepcopy(value)
-
                 else:
                     merged[key] = copy.deepcopy(value)
+            return merged
 
-        else:
-            return copy.deepcopy(updates)
-
-        return merged
+        return copy.deepcopy(updates)
 
-    def bundle(self, update=False):
-        arg = "bundle"
-        if update:
-            arg += "_update"
-        bundle_path = fullpath(self.get(arg, None))
-        if bundle_path:
-            if os.path.isfile(bundle_path):
-                return Bundle(bundle_path, env=True)
-            if not os.path.isdir(bundle_path):
-                error(f"ERROR: --{arg} argument is not a valid bundle file path")
-                return None
+    def _load_bundle(self, path, label):
+        """Load a bundle file from `path`, or return None with an error."""
+        bundle_path = fullpath(path)
+        if bundle_path and os.path.isfile(bundle_path):
+            return Bundle(bundle_path, env=True)
 
+        error(f"ERROR: {label} '{path}' is not a valid bundle file path")
         return None
 
-    def merge(self):
-        bundle = self.bundle()
-        bundle_update = self.bundle(update=True)
-        if not (bundle and bundle_update):
-            return 1
-
-        success("\nMerging bundle  ")
-        header(f"    {bundle_update.file()} into {bundle.file()}")
-
-        # merging projects
-        project_dict = {
+    def _merge_named_list(self, base_bundle, key, base_items, update_items):
+        """Merge a named-item list (projects/options) from update into base."""
+        base_dict = {
             item.config["name"]: {k: v for k, v in item.config.items() if k != "name"}
-            for item in bundle.projects()
+            for item in base_items
         }
-
-        updated_project_dict = {
+        update_dict = {
             item.config["name"]: {k: v for k, v in item.config.items() if k != "name"}
-            for item in bundle_update.projects()
+            for item in update_items
         }
 
-        updated_dict = self.deep_merge(project_dict, updated_project_dict)
+        merged = self.deep_merge(base_dict, update_dict)
+        base_bundle.config[key] = [{name: value} for name, value in merged.items()]
 
-        bundle.config["projects"] = [
-            {key: value} for key, value in updated_dict.items()
-        ]
+    def _apply_update(self, bundle, bundle_update):
+        """Fold a single update bundle into `bundle` in place."""
+        header("\nMerging bundle")
+        info(f"    {bundle_update.file()}")
 
-        # merging options
-        option_dict = {
-            item.config["name"]: {k: v for k, v in item.config.items() if k != "name"}
-            for item in bundle.options()
-        }
+        self._merge_named_list(bundle, "projects",
+                            bundle.projects(), bundle_update.projects())
+        self._merge_named_list(bundle, "options",
+                            bundle.options(), bundle_update.options())
 
-        updated_option_dict = {
-            item.config["name"]: {k: v for k, v in item.config.items() if k != "name"}
-            for item in bundle_update.options()
-        }
+        for key in bundle_update.config.keys():
+            if key not in ("projects", "options"):
+                bundle.config[key] = bundle_update.get(key)
+        success(f"Bundle succesfully merged")
 
-        updated_dict = self.deep_merge(option_dict, updated_option_dict)
+    def merge(self):
+        bundles = self.get("bundles", [])
+        if not bundles or len(bundles) < 2:
+            error("ERROR: need at least one original bundle and one update bundle")
+            return 1
+        
+        header("\nMerging bundles:")
+        for bundle in bundles:
+            info(f" - {bundle}")
 
-        bundle.config["options"] = [{key: value} for key, value in updated_dict.items()]
+        original_path, *update_paths = bundles
 
-        # merge remaining keys
 
-        for key in bundle_update.config.keys():
-            if key not in ["projects", "options"]:
-                bundle.config[key] = bundle_update.get(key)
+        bundle = self._load_bundle(original_path, "original bundle")
+        if bundle is None:
+            return 1
+
+        for path in update_paths:
+            bundle_update = self._load_bundle(path, "update bundle")
+            if bundle_update is None:
+                return 1
+            self._apply_update(bundle, bundle_update)
 
-        with open(self.get("o", None), "w", encoding="utf-8") as f:
-            f.write(bundle.yaml())
 
-        return 0
+        output_path = self.get("output", "merged-bundle.yml")
+        
+        header("\nWriting merge result into:")
+        info(f" - {output_path}")
+
+        with open(output_path, "w", encoding="utf-8") as f:
+            f.write(bundle.yaml())
+        success(f"Bundles succesfully merged\n")
+        return 0
\ No newline at end of file

From 328625d3a457f2eaf9f9ba25aa10ab6d408a0ee6 Mon Sep 17 00:00:00 2001
From: pardallio <pardalmiguel@hotmail.com>
Date: Wed, 8 Jul 2026 10:08:51 +0000
Subject: [PATCH 6/8] add test cases and configuration files for bundle merging
 functionality

---
 tests/bundle_merge/bundle-merge-base.yml      |  22 ++
 .../bundle-merge-update-options.yml           |   9 +
 .../bundle-merge-update-options2.yml          |   9 +
 .../bundle-merge-update-toplevel.yml          |   2 +
 tests/bundle_merge/bundle-merge-update.yml    |   4 +
 tests/bundle_merge/bundle-merge-update2.yml   |   6 +
 tests/bundle_merge/test_merge.py              | 250 ++++++++++++++++++
 7 files changed, 302 insertions(+)
 create mode 100644 tests/bundle_merge/bundle-merge-base.yml
 create mode 100644 tests/bundle_merge/bundle-merge-update-options.yml
 create mode 100644 tests/bundle_merge/bundle-merge-update-options2.yml
 create mode 100644 tests/bundle_merge/bundle-merge-update-toplevel.yml
 create mode 100644 tests/bundle_merge/bundle-merge-update.yml
 create mode 100644 tests/bundle_merge/bundle-merge-update2.yml
 create mode 100644 tests/bundle_merge/test_merge.py

diff --git a/tests/bundle_merge/bundle-merge-base.yml b/tests/bundle_merge/bundle-merge-base.yml
new file mode 100644
index 0000000..2b406af
--- /dev/null
+++ b/tests/bundle_merge/bundle-merge-base.yml
@@ -0,0 +1,22 @@
+name    : merge-test-full
+cmake   : CMAKE_BUILD_TYPE=Release
+
+options :
+
+    - without-mpi :
+        help    : Disable MPI
+        cmake   : ENABLE_MPI=OFF
+
+    - with-gpu :
+        help    : Enable GPU support
+        cmake   : ENABLE_GPU=ON
+
+projects :
+
+    - project1 :
+        git     : https://github.com/example/project1
+        version : main
+
+    - project2 :
+        git     : https://github.com/example/project2
+        version : main
\ No newline at end of file
diff --git a/tests/bundle_merge/bundle-merge-update-options.yml b/tests/bundle_merge/bundle-merge-update-options.yml
new file mode 100644
index 0000000..80b822b
--- /dev/null
+++ b/tests/bundle_merge/bundle-merge-update-options.yml
@@ -0,0 +1,9 @@
+options :
+
+    - without-mpi :
+        help    : MPI disabled (updated)
+        cmake   : ENABLE_MPI=OFF
+
+    - with-openmp :
+        help    : Enable OpenMP
+        cmake   : ENABLE_OMP=ON
\ No newline at end of file
diff --git a/tests/bundle_merge/bundle-merge-update-options2.yml b/tests/bundle_merge/bundle-merge-update-options2.yml
new file mode 100644
index 0000000..5305f8c
--- /dev/null
+++ b/tests/bundle_merge/bundle-merge-update-options2.yml
@@ -0,0 +1,9 @@
+options :
+
+    - with-openmp :
+        help    : OpenMP (final)
+        cmake   : ENABLE_OMP=ON
+
+    - with-gpu :
+        help    : GPU (final)
+        cmake   : ENABLE_GPU=ON
\ No newline at end of file
diff --git a/tests/bundle_merge/bundle-merge-update-toplevel.yml b/tests/bundle_merge/bundle-merge-update-toplevel.yml
new file mode 100644
index 0000000..ac49adc
--- /dev/null
+++ b/tests/bundle_merge/bundle-merge-update-toplevel.yml
@@ -0,0 +1,2 @@
+name    : merge-test-renamed
+cmake   : CMAKE_BUILD_TYPE=Debug
\ No newline at end of file
diff --git a/tests/bundle_merge/bundle-merge-update.yml b/tests/bundle_merge/bundle-merge-update.yml
new file mode 100644
index 0000000..94f80ab
--- /dev/null
+++ b/tests/bundle_merge/bundle-merge-update.yml
@@ -0,0 +1,4 @@
+projects :  
+  
+    - project1 :  
+        version : updated-branch
\ No newline at end of file
diff --git a/tests/bundle_merge/bundle-merge-update2.yml b/tests/bundle_merge/bundle-merge-update2.yml
new file mode 100644
index 0000000..58c73b3
--- /dev/null
+++ b/tests/bundle_merge/bundle-merge-update2.yml
@@ -0,0 +1,6 @@
+projects :  
+  
+    - project1 :  
+        version : final-branch
+
+      
\ No newline at end of file
diff --git a/tests/bundle_merge/test_merge.py b/tests/bundle_merge/test_merge.py
new file mode 100644
index 0000000..a3703d6
--- /dev/null
+++ b/tests/bundle_merge/test_merge.py
@@ -0,0 +1,250 @@
+# (C) Copyright 2020- ECMWF.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+# In applying this licence, ECMWF does not waive the privileges and immunities
+# granted to it by virtue of its status as an intergovernmental organisation nor
+# does it submit to any jurisdiction.
+
+
+import shutil
+from pathlib import Path
+
+import pytest
+
+from ecbundle import BundleMerger
+
+
+@pytest.fixture
+def here():
+    return Path(__file__).parent.resolve()
+
+
+@pytest.fixture
+def out_dir(here):
+    d = here / "merge-output"
+    if d.exists():
+        shutil.rmtree(d)
+    d.mkdir()
+    yield d
+    if d.exists():
+        shutil.rmtree(d)
+
+
+def _args(bundles, output):
+    return {
+        "no_colour": True,
+        "verbose": False,
+        "bundles": [str(b) for b in bundles],
+        "output": str(output),
+    }
+
+
+def test_merge_single_update(here, out_dir):
+    """Original bundle merged with a single update file."""
+    base = here / "bundle-merge-base.yml"
+    upd = here / "bundle-merge-update.yml"
+    output = out_dir / "merged.yml"
+
+    rc = BundleMerger(**_args([base, upd], output)).merge()
+
+    assert rc == 0
+    assert output.exists()
+    content = output.read_text()
+    assert "project1" in content
+    assert "updated-branch" in content
+
+
+def test_merge_multiple_updates_applied_in_order(here, out_dir):
+    """With two updates, the later one wins on conflicting fields."""
+    base = here / "bundle-merge-base.yml"
+    upd1 = here / "bundle-merge-update.yml"
+    upd2 = here / "bundle-merge-update2.yml"
+    output = out_dir / "merged.yml"
+
+    rc = BundleMerger(**_args([base, upd1, upd2], output)).merge()
+
+    assert rc == 0
+    assert output.exists()
+    content = output.read_text()
+    assert "final-branch" in content
+    assert "updated-branch" not in content
+
+
+def test_merge_preserves_untouched_project(here, out_dir):
+    """A project not mentioned in the update should be preserved unchanged."""
+    base = here / "bundle-merge-base.yml"
+    upd = here / "bundle-merge-update.yml"
+    output = out_dir / "merged.yml"
+
+    rc = BundleMerger(**_args([base, upd], output)).merge()
+
+    assert rc == 0
+    content = output.read_text()
+    # project2 is only in the base, must survive the merge
+    assert "project2" in content
+
+
+def test_merge_missing_original_fails(here, out_dir):
+    """A non-existent original bundle should cause merge to return non-zero."""
+    base = here / "does-not-exist.yml"
+    upd = here / "bundle-merge-update.yml"
+    output = out_dir / "merged.yml"
+
+    rc = BundleMerger(**_args([base, upd], output)).merge()
+
+    assert rc != 0
+
+
+def test_merge_missing_update_fails(here, out_dir):
+    """A non-existent update bundle should cause merge to return non-zero."""
+    base = here / "bundle-merge-base.yml"
+    upd = here / "does-not-exist-update.yml"
+    output = out_dir / "merged.yml"
+
+    rc = BundleMerger(**_args([base, upd], output)).merge()
+
+    assert rc != 0
+
+
+def test_merge_requires_at_least_one_update(here, out_dir):
+    """Passing only the original bundle should be rejected by merge()."""
+    base = here / "bundle-merge-base.yml"
+    output = out_dir / "merged.yml"
+
+    rc = BundleMerger(**_args([base], output)).merge()
+
+    assert rc != 0
+
+
+# ---------------------------------------------------------------------------
+# Options section
+# ---------------------------------------------------------------------------
+
+def test_merge_updates_existing_option(here, out_dir):
+    """An option present in both base and update should take the update's values."""
+    base = here / "bundle-merge-base.yml"
+    upd = here / "bundle-merge-update-options.yml"
+    output = out_dir / "merged.yml"
+
+    rc = BundleMerger(**_args([base, upd], output)).merge()
+
+    assert rc == 0
+    content = output.read_text()
+    assert "without-mpi" in content
+    assert "MPI disabled (updated)" in content
+    # Original help text must be gone
+    assert "Disable MPI" not in content
+
+
+def test_merge_adds_new_option(here, out_dir):
+    """An option only in the update should be added to the merged bundle."""
+    base = here / "bundle-merge-base.yml"
+    upd = here / "bundle-merge-update-options.yml"
+    output = out_dir / "merged.yml"
+
+    rc = BundleMerger(**_args([base, upd], output)).merge()
+
+    assert rc == 0
+    content = output.read_text()
+    assert "with-openmp" in content
+    assert "ENABLE_OMP=ON" in content
+
+
+def test_merge_preserves_untouched_option(here, out_dir):
+    """An option not mentioned in the update should remain in the merged bundle."""
+    base = here / "bundle-merge-base.yml"
+    upd = here / "bundle-merge-update-options.yml"
+    output = out_dir / "merged.yml"
+
+    rc = BundleMerger(**_args([base, upd], output)).merge()
+
+    assert rc == 0
+    content = output.read_text()
+    # with-gpu is only in the base, must survive
+    assert "with-gpu" in content
+    assert "ENABLE_GPU=ON" in content
+
+
+def test_merge_multiple_option_updates_apply_in_order(here, out_dir):
+    """With two option updates, later values override earlier ones."""
+    base = here / "bundle-merge-base.yml"
+    upd1 = here / "bundle-merge-update-options.yml"
+    upd2 = here / "bundle-merge-update-options2.yml"
+    output = out_dir / "merged.yml"
+
+    rc = BundleMerger(**_args([base, upd1, upd2], output)).merge()
+
+    assert rc == 0
+    content = output.read_text()
+    # Values from the second update must win
+    assert "OpenMP (final)" in content
+    assert "GPU (final)" in content
+    # Values overridden by the second update must not remain
+    assert "Enable OpenMP" not in content
+    assert "Enable GPU support" not in content
+
+
+# ---------------------------------------------------------------------------
+# Top-level scalar keys
+# ---------------------------------------------------------------------------
+
+def test_merge_overrides_toplevel_scalars(here, out_dir):
+    """Top-level scalar keys like `name` and `cmake` must be overridden by the update."""
+    base = here / "bundle-merge-base.yml"
+    upd = here / "bundle-merge-update-toplevel.yml"
+    output = out_dir / "merged.yml"
+
+    rc = BundleMerger(**_args([base, upd], output)).merge()
+
+    assert rc == 0
+    content = output.read_text()
+    assert "merge-test-renamed" in content
+    assert "CMAKE_BUILD_TYPE=Debug" in content
+    # Original scalar values must be gone
+    assert "merge-test-full" not in content
+    assert "CMAKE_BUILD_TYPE=Release" not in content
+
+
+def test_merge_toplevel_update_preserves_projects_and_options(here, out_dir):
+    """An update that only touches top-level keys must leave projects/options intact."""
+    base = here / "bundle-merge-base.yml"
+    upd = here / "bundle-merge-update-toplevel.yml"
+    output = out_dir / "merged.yml"
+
+    rc = BundleMerger(**_args([base, upd], output)).merge()
+
+    assert rc == 0
+    content = output.read_text()
+    assert "project1" in content
+    assert "project2" in content
+    assert "without-mpi" in content
+    assert "with-gpu" in content
+
+
+def test_merge_mixed_updates_across_sections(here, out_dir):
+    """Chained updates touching different sections should all be reflected."""
+    base = here / "bundle-merge-base.yml"
+    upd_projects = here / "bundle-merge-update.yml"          # touches projects
+    upd_options = here / "bundle-merge-update-options.yml"   # touches options
+    upd_toplevel = here / "bundle-merge-update-toplevel.yml" # touches scalars
+    output = out_dir / "merged.yml"
+
+    rc = BundleMerger(
+        **_args([base, upd_projects, upd_options, upd_toplevel], output)
+    ).merge()
+
+    assert rc == 0
+    content = output.read_text()
+
+    # Projects update
+    assert "updated-branch" in content
+    # Options update
+    assert "with-openmp" in content
+    assert "MPI disabled (updated)" in content
+    # Top-level update
+    assert "merge-test-renamed" in content
+    assert "CMAKE_BUILD_TYPE=Debug" in content
+    # Untouched items still present
+    assert "project2" in content
+    assert "with-gpu" in content
\ No newline at end of file

From 6c83c90b3f5ed0e86562423d8d5f555c6ce4a4c5 Mon Sep 17 00:00:00 2001
From: pardallio <pardalmiguel@hotmail.com>
Date: Wed, 8 Jul 2026 10:13:16 +0000
Subject: [PATCH 7/8] linting

---
 ecbundle/merge.py                | 20 ++++++++++----------
 tests/bundle_merge/test_merge.py | 10 ++++++----
 2 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/ecbundle/merge.py b/ecbundle/merge.py
index 938bde0..050a733 100644
--- a/ecbundle/merge.py
+++ b/ecbundle/merge.py
@@ -10,7 +10,7 @@
 import os
 
 from .bundle import Bundle
-from .logging import error, header, success,info
+from .logging import error, header, info, success
 from .util import fullpath
 
 __all__ = ["BundleMerger"]
@@ -73,10 +73,12 @@ def _apply_update(self, bundle, bundle_update):
         header("\nMerging bundle")
         info(f"    {bundle_update.file()}")
 
-        self._merge_named_list(bundle, "projects",
-                            bundle.projects(), bundle_update.projects())
-        self._merge_named_list(bundle, "options",
-                            bundle.options(), bundle_update.options())
+        self._merge_named_list(
+            bundle, "projects", bundle.projects(), bundle_update.projects()
+        )
+        self._merge_named_list(
+            bundle, "options", bundle.options(), bundle_update.options()
+        )
 
         for key in bundle_update.config.keys():
             if key not in ("projects", "options"):
@@ -88,14 +90,13 @@ def merge(self):
         if not bundles or len(bundles) < 2:
             error("ERROR: need at least one original bundle and one update bundle")
             return 1
-        
+
         header("\nMerging bundles:")
         for bundle in bundles:
             info(f" - {bundle}")
 
         original_path, *update_paths = bundles
 
-
         bundle = self._load_bundle(original_path, "original bundle")
         if bundle is None:
             return 1
@@ -106,13 +107,12 @@ def merge(self):
                 return 1
             self._apply_update(bundle, bundle_update)
 
-
         output_path = self.get("output", "merged-bundle.yml")
-        
+
         header("\nWriting merge result into:")
         info(f" - {output_path}")
 
         with open(output_path, "w", encoding="utf-8") as f:
             f.write(bundle.yaml())
         success(f"Bundles succesfully merged\n")
-        return 0
\ No newline at end of file
+        return 0
diff --git a/tests/bundle_merge/test_merge.py b/tests/bundle_merge/test_merge.py
index a3703d6..3596077 100644
--- a/tests/bundle_merge/test_merge.py
+++ b/tests/bundle_merge/test_merge.py
@@ -121,6 +121,7 @@ def test_merge_requires_at_least_one_update(here, out_dir):
 # Options section
 # ---------------------------------------------------------------------------
 
+
 def test_merge_updates_existing_option(here, out_dir):
     """An option present in both base and update should take the update's values."""
     base = here / "bundle-merge-base.yml"
@@ -189,6 +190,7 @@ def test_merge_multiple_option_updates_apply_in_order(here, out_dir):
 # Top-level scalar keys
 # ---------------------------------------------------------------------------
 
+
 def test_merge_overrides_toplevel_scalars(here, out_dir):
     """Top-level scalar keys like `name` and `cmake` must be overridden by the update."""
     base = here / "bundle-merge-base.yml"
@@ -225,9 +227,9 @@ def test_merge_toplevel_update_preserves_projects_and_options(here, out_dir):
 def test_merge_mixed_updates_across_sections(here, out_dir):
     """Chained updates touching different sections should all be reflected."""
     base = here / "bundle-merge-base.yml"
-    upd_projects = here / "bundle-merge-update.yml"          # touches projects
-    upd_options = here / "bundle-merge-update-options.yml"   # touches options
-    upd_toplevel = here / "bundle-merge-update-toplevel.yml" # touches scalars
+    upd_projects = here / "bundle-merge-update.yml"  # touches projects
+    upd_options = here / "bundle-merge-update-options.yml"  # touches options
+    upd_toplevel = here / "bundle-merge-update-toplevel.yml"  # touches scalars
     output = out_dir / "merged.yml"
 
     rc = BundleMerger(
@@ -247,4 +249,4 @@ def test_merge_mixed_updates_across_sections(here, out_dir):
     assert "CMAKE_BUILD_TYPE=Debug" in content
     # Untouched items still present
     assert "project2" in content
-    assert "with-gpu" in content
\ No newline at end of file
+    assert "with-gpu" in content

From 9d3c4a25bd5d49792d1b1e950988713bc2e03ba0 Mon Sep 17 00:00:00 2001
From: pardallio <pardalmiguel@hotmail.com>
Date: Fri, 10 Jul 2026 09:02:23 +0000
Subject: [PATCH 8/8] more linting

---
 ecbundle/merge.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ecbundle/merge.py b/ecbundle/merge.py
index 050a733..8369926 100644
--- a/ecbundle/merge.py
+++ b/ecbundle/merge.py
@@ -83,7 +83,7 @@ def _apply_update(self, bundle, bundle_update):
         for key in bundle_update.config.keys():
             if key not in ("projects", "options"):
                 bundle.config[key] = bundle_update.get(key)
-        success(f"Bundle succesfully merged")
+        success("Bundle succesfully merged")
 
     def merge(self):
         bundles = self.get("bundles", [])
@@ -114,5 +114,5 @@ def merge(self):
 
         with open(output_path, "w", encoding="utf-8") as f:
             f.write(bundle.yaml())
-        success(f"Bundles succesfully merged\n")
+        success("Bundles succesfully merged\n")
         return 0