Add skeleton fab script

CONTRIBUTORS.md

@@ -1,27 +1,28 @@
 # Contributors
 
-| GitHub user      | Real Name              | Affiliation | Date       |
-| ---------------- | ---------------------- | ----------- | ---------- |
-| andrewcoughtrie  | Andrew Coughtrie       | Met Office  | 2025.12.12 |
-| james-bruten-mo  | James Bruten           | Met Office  | 2025-12-09 |
-| jedbakerMO       | Jed Baker              | Met Office  | 2025-12-29 |
-| jennyhickson     | Jenny Hickson          | Met Office  | 2025-12-10 |
-| mo-marqh         | Mark Hedley            | Met Office  | 2025-12-11 |
-| mo-rickywong     | Ricky Wong             | Met Office  | 2025-01-30 |
-| mike-hobson      | Mike Hobson            | Met Office  | 2025-12-17 |
-| MatthewHambley   | Matthew Hambley        | Met Office  | 2025-12-15 |
-| mo-lottieturner  | Lottie Turner          | Met Office  | 2025-12-16 |
-| tommbendall      | Thomas Bendall         | Met Office  | 2026-01-23 |
-| yaswant          | Yaswant Pradhan        | Met Office  | 2025-12-16 |
-| stevemullerworth | Steve Mullerworth      | Met Office  | 2026-01-08 |
-| harry-shepherd   | Harry Shepherd         | Met Office  | 2026-01-08 |
-| EdHone           | Ed Hone                | Met Office  | 2026-01-09 |
-| tom-j-h          | Tom Hill               | Met Office  | 2026-01-19 |
-| mo-alistairp     | Alistair Pirrie        | Met Office  | 2026-01-12 |
-| t00sa            | Sam Clarke-Green       | Met Office  | 2026-01-27 |
-| MetBenjaminWent  | Benjamin Went          | Met Office  | 2026-01-30 |
-| jcsmeto          | James Cunningham-Smith | Met Office  | 2026-02-06 |
-| thomasmelvin     | Thomas Melvin          | Met Office  | 2026-01-15 |
-| ericaneininger   | Erica Neininger        | Met Office  | 2026-03-02 |
-| mo-lucy-gordon   | Lucy Gordon            | Met Office  | 2026-03-18 |
-| shreybh1         | Shrey Bhardwaj         | Met Office  | 2026-03-26 |
+| GitHub user      | Real Name              | Affiliation           | Date       |
+| ---------------- | -----------------      | --------------------- | ---------- |
+| andrewcoughtrie  | Andrew Coughtrie       | Met Office            | 2025.12.12 |
+| james-bruten-mo  | James Bruten           | Met Office            | 2025-12-09 |
+| jedbakerMO       | Jed Baker              | Met Office            | 2025-12-29 |
+| jennyhickson     | Jenny Hickson          | Met Office            | 2025-12-10 |
+| mo-marqh         | Mark Hedley            | Met Office            | 2025-12-11 |
+| mo-rickywong     | Ricky Wong             | Met Office            | 2025-01-30 |
+| mike-hobson      | Mike Hobson            | Met Office            | 2025-12-17 |
+| MatthewHambley   | Matthew Hambley        | Met Office            | 2025-12-15 |
+| mo-lottieturner  | Lottie Turner          | Met Office            | 2025-12-16 |
+| tommbendall      | Thomas Bendall         | Met Office            | 2026-01-23 |
+| yaswant          | Yaswant Pradhan        | Met Office            | 2025-12-16 |
+| stevemullerworth | Steve Mullerworth      | Met Office            | 2026-01-08 |
+| harry-shepherd   | Harry Shepherd         | Met Office            | 2026-01-08 |
+| EdHone           | Ed Hone                | Met Office            | 2026-01-09 |
+| tom-j-h          | Tom Hill               | Met Office            | 2026-01-19 |
+| mo-alistairp     | Alistair Pirrie        | Met Office            | 2026-01-12 |
+| t00sa            | Sam Clarke-Green       | Met Office            | 2026-01-27 |
+| MetBenjaminWent  | Benjamin Went          | Met Office            | 2026-01-30 |
+| jcsmeto          | James Cunningham-Smith | Met Office            | 2026-02-06 |
+| thomasmelvin     | Thomas Melvin          | Met Office            | 2026-01-15 |
+| ericaneininger   | Erica Neininger        | Met Office            | 2026-03-02 |
+| mo-lucy-gordon   | Lucy Gordon            | Met Office            | 2026-03-18 |
+| shreybh1         | Shrey Bhardwaj         | Met Office            | 2026-03-26 |
+| hiker            | Joerg Henrichs         | Bureau of Meteorology | 2026-02-11 |

applications/skeleton/fab_skeleton.py

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+#!/usr/bin/env python3
+
+##############################################################################
+# (c) Crown copyright Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+# Author: J. Henrichs, Bureau of Meteorology
+# Author: J. Lyu, Bureau of Meteorology
+
+"""
+A FAB build script for applications/skeleton. It relies on
+the LFRicBase class contained in the infrastructure directory.
+"""
+
+import logging
+from pathlib import Path
+import sys
+
+from fab.steps.grab.folder import grab_folder
+
+# We need to import the base class:
+sys.path.insert(0, str(Path(__file__).parents[2] / "lfric_build"))
+
+from lfric_base import LFRicBase  # noqa: E402
+
+
+class FabSkeleton(LFRicBase):
+    """
+    A Fab-based build script for skeleton. It relies on the LFRicBase class
+    to implement the actual functionality, and only provides the required
+    source files.
+
+    :param name: The name of the application.
+    """
+
+    def __init__(self, name: str = "skeleton") -> None:
+        super().__init__(name=name)
+        # Store the root of this apps for later
+        this_file = Path(__file__).resolve()
+        self._this_root = this_file.parent
+
+    def grab_files_step(self) -> None:
+        """
+        Grabs the required source files and optimisation scripts.
+        """
+        super().grab_files_step()
+        dirs = ['applications/skeleton/source/']
+
+        # pylint: disable=redefined-builtin
+        for dir in dirs:
+            grab_folder(self.config, src=self.lfric_core_root / dir,
+                        dst_label='')
+
+        # Copy the optimisation scripts into a separate directory
+        grab_folder(self.config, src=self._this_root / "optimisation",
+                    dst_label='optimisation')
+
+    def get_rose_meta(self) -> Path:
+        """
+        :returns: the rose-meta.conf path.
+        """
+        return (self._this_root / 'rose-meta' / 'lfric-skeleton' / 'HEAD' /
+                'rose-meta.conf')
+
+
+# -----------------------------------------------------------------------------
+if __name__ == '__main__':
+
+    logger = logging.getLogger('fab')
+    logger.setLevel(logging.DEBUG)
+    fab_skeleton = FabSkeleton()
+    fab_skeleton.build()

lfric_build/README.md

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+# LFRic Core Fab Build Scripts
+
+Make sure you have Fab version 2.0.1 or later installed (in addition to all
+LFRic core requirements of course).
+
+## Setting up Site- and Platform-specific Settings
+Site- and platform-specific settings are contained in 
+```$LFRIC_CORE/infrastructure/build/site_specific/${SITE}-${PLATFORM}```
+The default settings are in ```site_specific/default``` (and at this
+stage each other site-specific setup inherits the values set in the default,
+and then adds or modifies settings). The Fab build system provides various
+callbacks to the ```config.py``` file in the corresponding directory (details
+are in the [Fab documentation](https://metoffice.github.io/fab/fab_base/config.html).
+
+If there is no existing site-specific setup, it is recommended to copy an existing
+configuration file (e.g. from ```nci_gadi/config.py```). This act as a template
+to indicate where you can specify linker information, select a default compiler
+suite etc.
+
+The default setup contains compiler flags for Cray, GNU, Intel-classic (ifort),
+Intel-LLVM (ifx), and NVIDIA. For modularity's sake (and to keep the file length
+shorter), the default configuration will get the settings from the corresponding
+```setup_...py``` script. There is no need for a site to replicate this structure,
+existing ```config.py``` scripts show how this can be done.
+
+
+## Building the Skeleton Apps
+
+In order to build the skeleton apps, change into the directory
+```$LFRIC_CORE/applications/skeleton```,
+and use the following command:
+
+```
+./fab_skeleton.py --nprocs 4 --suite gnu
+```
+Select an appropriate number of processes to run in parallel, and a compiler
+suite, e.g. one of ```gnu```, ```cray```, ```intel-classic```, ```intel-llvm```
+or ```nvidia```. Once the process is finished, you should have a binary in the
+directory ```./fab-workspace/skeleton-full-debug-COMPILER``` (where
+```COMPILER``` is the compiler used, e.g. ```mpif90-gfortran```).
+
+Likely, you will have to setup corresponding compiler and linker options, e.g.
+include paths, library paths and libraries to link. The directory ```site_specific```
+contains site-specific setup files, and one called ```default``` (which is
+used in the above example if no site is selected). If your site does not exist,
+create a corresponding directory for your site and platform in the format
+```site_platform``` by using an existing site as template. See also the
+[Fab documentation](https://metoffice.github.io/fab/fab_base/config.html)
+for details about specifying compiler and linker options).
+You can then use the command line options ```--site``` and ```--platform```
+to pick your setup, e.g.:
+
+```
+./fab_skeleton.py --nprocs 4 --site nci --platform gadi --suite intel-llvm
+```
+
+This would use the file ```site_specific/nci_gadi/config.py```, and all additional
+compiler and linker options defined there.
+
+Using ```./fab_skeleton.py -h``` will show a help message with all supported command line
+options (and their default value). If a default value is listed using an environment
+variables (```(default: $SITE or 'default')```), the corresponding environment variable
+is used if no command line option has been specified.
+
+A different compilation profile can be specified using ```--profile``` option. Note
+that the available compilation profiles can vary from site to site (see
+[Fab documentation](https://metoffice.github.io/fab/fab_base/config.html) for details).
+
+If Fab has issues finding a compiler, you can use the Fab debug command line option
+```--available-compilers```, which will list all compilers and linkers Fab has
+identified as being available.

lfric_build/configurator.py

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+##############################################################################
+# (c) Crown copyright Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+# Author J. Henrichs, Bureau of Meteorology
+# Author J. Lyu, Bureau of Meteorology
+
+"""
+This file defines the configurator script sequence for LFRic.
+"""
+
+import logging
+from pathlib import Path
+from typing import cast, Optional
+
+from fab.api import BuildConfig, find_source_files, Category
+from fab.tools.shell import Shell
+
+from rose_picker import RosePicker
+
+logger = logging.getLogger('fab')
+
+
+def configurator(config: BuildConfig,
+                 lfric_core_source: Path,
+                 rose_meta_conf: Path,
+                 include_paths: Optional[list[Path]] = None,
+                 config_dir: Optional[Path] = None) -> None:
+    """
+    This method implements the LFRic configurator tool.
+
+    :param config: the Fab build config instance
+    :param lfric_core_source: the path to the LFRic core directory
+    :param rose_meta_conf: the path to the rose-meta configuration file
+    :param include_paths: additional include paths (each path will be added,
+        as well as the path with /'rose-meta')
+    :param config_dir: the directory for the generated configuration files
+    """
+
+    tools = lfric_core_source / 'infrastructure' / 'build' / 'tools'
+    config_dir = config_dir or config.build_output / 'configuration'
+    config_dir.mkdir(parents=True, exist_ok=True)
+
+    # rose picker
+    # -----------
+    # creates rose-meta.json and config_namelists.txt in
+    # gungho/build
+    logger.info('rose_picker')
+
+    include_dirs = [lfric_core_source / 'rose-meta']
+    if include_paths:
+        for path in include_paths:
+            include_dirs.append(path / 'rose-meta')
+
+    rose_picker = RosePicker()
+    rose_picker.execute(rose_meta_conf, config_dir,
+                        include_paths=include_dirs)
+    rose_meta = config_dir / 'rose-meta.json'
+
+    shell = config.tool_box.get_tool(Category.SHELL)
+    shell = cast(Shell, shell)
+
+    # build_config_loaders
+    # --------------------
+    # builds a bunch of f90s from the json
+    logger.info('GenerateNamelistLoader')
+    shell.exec(f"{tools / 'GenerateNamelistLoader'} -verbose {rose_meta} "
+               f"-directory {config_dir}")
+
+    # create configuration_mod.f90 in source root
+    # -------------------------------------------
+    logger.info('GenerateConfigLoader')
+    with open(config_dir / 'config_namelists.txt', encoding="utf8") as f_in:
+        names = [name.strip() for name in f_in.readlines()]
+
+    shell.exec(f"{tools / 'GenerateConfigLoader'} "
+               f"{' '.join(names)} "
+               f"-o {config_dir}")
+
+    logger.info('GenerateExtendedNamelistType')
+    shell.exec(f"{tools / 'GenerateExtendedNamelistType'} {rose_meta} "
+               f"-directory {config_dir}")
+
+    duplicates: list[str] = []
+    with open(config_dir / 'duplicate_namelists.txt', encoding="utf8") as f_in:
+        for name in f_in.readlines():
+            duplicates.extend(["-duplicate", name.strip()])
+
+    logger.info('GenerateConfigType')
+    shell.exec(f"{tools / 'GenerateConfigType'} "
+               f"{' '.join(names)} "
+               f"{' '.join(duplicates)} "
+               f"-o {config_dir}")
+
+    # create feign_config_mod.f90 in source root
+    # ------------------------------------------
+    logger.info('GenerateFeigns')
+    feign_config_mod_fpath = config_dir / 'feign_config_mod.f90'
+    shell.exec(f"{tools / 'GenerateFeigns'} {rose_meta} "
+               f"-output {feign_config_mod_fpath}")
+
+    find_source_files(config, source_root=config_dir)