102 add fab script

CONTRIBUTORS.md

@@ -1,7 +1,8 @@
 # Contributors
 
-| GitHub user     | Real Name        | Affiliation | Date       |
-| --------------- | ---------------- | ----------- | ---------- |
-| yaswant         | Yaswant Pradhan  | Met Office  | 2026-06-30 |
-| doucla          | Douglas Clark    | UKCEH       | 2026-07-03 |
-| james-bruten-mo | James Bruten     | Met Office  | 2026-07-09 |
+| GitHub user     | Real Name        | Affiliation                      | Date       |
+| --------------- | ---------------- | -------------------------------- | ---------- |
+| yaswant         | Yaswant Pradhan  | Met Office                       | 2026-06-30 |
+| doucla          | Douglas Clark    | UKCEH                            | 2026-07-03 |
+| james-bruten-mo | James Bruten     | Met Office                       | 2026-07-09 |
+| hiker           | Joerg Henrichs   | Bureau of Meteorology, Australia | 2026-08-18 |

fab/fab_jules.py

@@ -0,0 +1,326 @@
+#!/usr/bin/env python3
+##############################################################################
+# (c) Crown copyright Met Office. All rights reserved.
+# For further details please refer to the file COPYRIGHT
+# which you should have received as part of this distribution
+##############################################################################
+
+'''
+This module contains a BAF-based build script for Jules.
+'''
+
+import argparse
+import logging
+from pathlib import Path
+import sys
+from typing import cast, Iterable, Optional, Union
+
+
+from fab.api import (Category, FabBase, fcm_export, Exclude, find_source_files,
+                     git_checkout, Include, root_inc_files)
+
+logger = logging.getLogger(__name__)
+
+
+class JulesBuild(FabBase):
+    '''
+    A class to build Jules using BAF as base class.
+
+    :param str name: name of the build.
+    '''
+
+    def __init__(self, name: str):
+        '''
+        Build Jules using Fab.
+
+        :name: The base name to use for the project directory
+        '''
+        # If the sources need to be checked out or not
+        self._checkout = False
+
+        # The revision number to check out (if requested)
+        self._revision = None
+
+        # The root of the jules repository. Defined in
+        # handle_command_line_options
+        self._root = None
+
+        super().__init__(name)
+
+    def define_command_line_options(
+            self,
+            parser: Optional[argparse.ArgumentParser] = None
+            ) -> argparse.ArgumentParser:
+        '''
+        This adds a revision option to the command line options inherited
+        from the base class.
+
+        :param Optional[argparse.ArgumentParser] parser: a pre-defined
+        argument parser. If not, a new instance will be created.
+        :returns: the argument parser with the jules specific options added.
+        :rtype :py:class:`argparse.ArgumentParser`
+        '''
+
+        parser = super().define_command_line_options(parser)
+        parser = cast(argparse.ArgumentParser, parser)
+        parser.add_argument(
+            "--revision", "-r", type=str, default="vn7.8",
+            help="Sets the Jules revision to checkout (only used if"
+                 "--checkout is used). Defaults to 'vn7.8'.")
+        parser.add_argument(
+            "--checkout", default=False, action="store_true",
+            help="If specified, will checkout jules from git or svn, "
+                 "otherwise this script is excepted to be in a cloned "
+                 "git version.")
+        parser.add_argument(
+            "--rivers", default=False, action="store_true",
+            help="If specified, the stand-alone rivers binary will be "
+                 "compiled.")
+        parser.add_argument(
+            "--ascii-out", default=False, action="store_true",
+            help="If specified, NetCDF will be disabled and output "
+                 "will be in ASCII instead.")
+        return parser
+
+    def handle_command_line_options(self,
+                                    parser: argparse.ArgumentParser) -> None:
+        '''
+        Grab the requested (or default) arguments for checkout and Jules
+        revision to use and store it in an attribute. Do consistency checks
+        to make sure a revision is only specified if also a checkout is
+        requested.
+
+        :param parser: the argument parser.
+
+        :raises ValueError: if a revision is specified, but no checkout
+            is requested.
+        '''
+
+        super().handle_command_line_options(parser)
+        self._checkout = self.args.checkout
+        self._revision = self.args.revision
+        self._ascii_out = self.args.ascii_out
+        self._rivers = self.args.rivers
+        if self._rivers:
+            self.set_root_symbol("river")
+
+        if not self._checkout and "--revision" in sys.argv[1:]:
+            raise ValueError(f"You specified revision '{self._revision}', "
+                             f"but did not request a checkout.")
+
+    def define_project_name(self, name: str) -> str:
+        '''
+        This method adds version number, ascii output (if selected), and
+        MPI and OpenMP information to the project name, so these different
+        binaries can be distinguished.
+
+        :returns: the project directory name to use.
+        '''
+        if self._rivers:
+            name = name + "-rivers"
+        if self._revision:
+            name = name + f"-{self._revision}"
+        if self.args.ascii_out:
+            name = name + "-ascii"
+        if self.args.mpi:
+            name = name + "-mpi"
+        if self.args.openmp:
+            name = name + "-openmp"
+        return super().define_project_name(name)
+
+    def grab_files_step(self) -> None:
+        '''
+        Extracts all the required Jules source files from the repositories.
+
+        :raises RuntimeError: if no checkout is required, but expected Jules
+            directory (rose-meta/jules-shared) does not exist, indicating
+            an invalid directory structure.
+        '''
+        # If no checkout was requested, make sure we have the expected
+        # repository structure.
+        if not self._checkout:
+            # Get the root directory of this Jules:
+            self._root = Path(__file__).resolve().parents[1]
+            jules_shared = self._root / "rose-meta" / "jules-shared"
+            if not jules_shared.exists():
+                raise RuntimeError(f"The expected directory '{jules_shared}' "
+                                   f"does not exist.")
+            return
+
+        # Try to grab sources from GitHub, fallback to FCM if that fails
+
+        try:
+            git_checkout(
+                self.config,
+                src="git@github.com:MetOffice/jules",
+                revision=self._revision,
+                dst_label="jules.git",
+            )
+            self._root = (self.config.project_workspace
+                          / "source" / "jules.git")
+        except Exception as e:
+            logging.warning(f"git_checkout failed: {e}, "
+                            f"falling back to fcm_export")
+            # We export the whole svn repository, to be consistent with
+            # using either a local checkout or git checkout
+            fcm_export(
+                self.config,
+                src="fcm:jules.xm_tr",
+                revision=self._revision,
+                dst_label="jules.svn",
+            )
+            self._root = self.config.project_workspace / "source" / "jules.svn"
+
+    def find_source_files_step(
+            self,
+            path_filters: Optional[Iterable[Union[Exclude, Include]]] = None):
+        '''
+        Finds all the Jules sources files to analyse.
+
+        :param path_filters: optional list of path filters to be passed to
+            Fab find_source_files, default is None.
+        '''
+        if path_filters:
+            local_filters = path_filters.copy()
+        else:
+            local_filters = []
+        local_filters.extend([
+            Exclude("src/control/um/"),
+            Exclude("src/initialisation/um/"),
+            Exclude("src/params/shared/cable_maths_constants_mod.F90"),
+            ]
+        )
+        if self._rivers:
+            # The order is important, the last include/exclude statement
+            # takes precedence. So exclude standalone must come before
+            # including init_initial_mod
+            local_filters.extend([
+                Exclude("src/control/standalone/jules.F90"),
+                Exclude("src/initialisation/standalone/"),
+                Include("src/initialisation/standalone/init_initial_mod.F90"),
+                Include("src/initialisation/standalone/initial_conditions/"
+                        "jules_initial_mod.F90"),
+                Include("src/initialisation/standalone/init_output_mod.F90"),
+                Include("src/initialisation/standalone/init_rivers.F90"),
+                Include("src/initialisation/standalone/init_time_mod.F90"),
+                Include("src/initialisation/standalone/init_drive_mod.F90"),
+                Include("src/initialisation/standalone/"
+                        "init_model_environment_mod.F90"),
+                Include("src/initialisation/standalone/grid/"
+                        "fill_model_grid_arrays_mod.F90"),
+                Include("src/initialisation/standalone/grid/"
+                        "init_input_grid_mod.F90"),
+                Include("src/initialisation/standalone/grid/"
+                        "init_river_out_grid_mod.F90"),
+                Include("src/initialisation/standalone/grid/"
+                        "init_latlon_mod.F90"),
+                Include("src/initialisation/standalone/grid/"
+                        "init_land_frac_mod.F90"),
+                Include("src/initialisation/standalone/grid/"
+                        "init_model_grid_mod.F90"),
+                Include("src/initialisation/standalone/rivers-standalone/"
+                        "ancillaries"),
+                Include("src/initialisation/standalone/ancillaries/"
+                        "init_rivers_props_mod.F90"),
+                Include("src/initialisation/standalone/ancillaries/"
+                        "ancil_namelist_mod.F90"),
+                Include("src/initialisation/standalone/ancillaries/"
+                        "init_ancillaries_coupling_mod.F90"),
+                Include("src/initialisation/standalone/ancillaries/"
+                        "init_rivers_process_data_mod.F90"),
+                Include("src/initialisation/standalone/ancillaries/"
+                        "jules_overbank_props_mod.F90"),
+                Include("src/initialisation/standalone/ancillaries/"
+                        "jules_rivers_props_mod.F90"),
+                Exclude("src/initialisation/shared/"
+                        "check_compatible_options_mod.F90"),
+                Exclude("src/control/lfric/check_unavailable_options_mod.F90"),
+                Exclude("src/io/dump/read_dump_mod.F90"),
+                Exclude("src/io/dump/write_dump_mod.F90"),
+                ])
+        else:
+            local_filters.extend([
+                Exclude("src/control/rivers-standalone/"),
+                Exclude("src/io/rivers-standalone"),
+                Exclude("src/initialisation/rivers-standalone/"),
+                Exclude("src/control/lfric/check_unavailable_options_mod.F90"),
+                ])
+
+        find_source_files(self.config,
+                          source_root=self._root / "src",
+                          path_filters=local_filters)
+
+        # Add the utility files as required
+        # ---------------------------------
+        utils = self._root / "utils"
+        # For now assume dr hook is always disabled, so use dummy
+        find_source_files(self.config,
+                          source_root=utils / "drhook_dummy")
+        if not self.config.mpi:
+            find_source_files(self.config,
+                              source_root=utils / "mpi_dummy")
+        if self._ascii_out:
+            find_source_files(self.config,
+                              source_root=utils / "netcdf_dummy")
+
+        # move inc files to the root for easy tool use
+        root_inc_files(self.config)
+
+    def define_preprocessor_flags_step(self) -> None:
+        '''
+        Defines the preprocessor flags.
+        '''
+        super().define_preprocessor_flags_step()
+
+        # Define compiler-specific preprocessing flag
+        tb = self.config.tool_box
+        fortran = tb.get_tool(Category.FORTRAN_COMPILER)
+        pre_fortran = tb.get_tool(Category.FORTRAN_PREPROCESSOR)
+        if fortran.suite == "gnu":
+            pre_fortran.add_flags("-DGNU_FORTRAN")
+        elif fortran.suite in ["intel-classic", "intel-llvm"]:
+            pre_fortran.add_flags("-DINTEL_FORTRAN")
+        elif fortran.suite in ["cray"]:
+            pre_fortran.add_flags("-DCRAY_FORTRAN")
+
+        flags = ["-I$output"]
+        if not self.config.mpi:
+            flags.append("-DMPI_DUMMY")
+        if self._ascii_out:
+            flags.append("-DNCDF_DUMMY")
+
+        self.add_preprocessor_flags(flags)
+
+    def get_linker_flags(self) -> list[str]:
+        '''
+        Base class for setting linker flags.
+        :returns: list of flags for the linker.
+        '''
+        libs = []
+        if not self._ascii_out:
+            libs.extend(["netcdf"])
+        return libs
+
+
+if __name__ == "__main__":
+    logger = logging.getLogger(__name__)
+    logger.setLevel(logging.DEBUG)
+
+    class NoFabFilter(logging.Filter):
+        '''A dummy class that disables all Fab noise.
+        '''
+        def filter(self, record):
+            return not record.name.startswith("fab")
+
+    # root_logger = logging.getLogger()
+    # root_logger.setLevel(logging.DEBUG)
+    last_resort_handler = logging.lastResort
+    last_resort_handler.setLevel(logging.DEBUG)
+
+    fab_logger = logging.getLogger("fab")
+    fab_logger.setLevel(logging.DEBUG)
+    fab_handlers = fab_logger.handlers
+    # fab_handlers[0].addFilter(NoFabFilter())
+
+    jb = JulesBuild("jules")
+    jb.build()

fab/nf_config.py

@@ -0,0 +1,37 @@
+##############################################################################
+# (c) Crown copyright Met Office. All rights reserved.
+# For further details please refer to the file COPYRIGHT
+# which you should have received as part of this distribution
+##############################################################################
+
+"""This file contains the class to interface with NetCDF's nf-config script.
+"""
+
+from typing import List
+
+from fab.tools.category import Category
+from fab.tools.tool import Tool
+
+
+class NfConfig(Tool):
+    '''This class interfaces with NetCDF's nf-config tool. It is not added
+    to the ToolRepository, it is intended for site-specific configurations
+    to make it easier to query for NetCDF settings.
+    '''
+
+    def __init__(self):
+        super().__init__("nf-config", "nf-config", Category.MISC)
+
+    def get_compiler_flags(self) -> List[str]:
+        """
+        :returns: the compilation flags to use for NetCDF.
+        """
+        flags = self.run(additional_parameters=["--fflags"])
+        return flags.split()
+
+    def get_linker_flags(self) -> List[str]:
+        """
+        :returns: the linker flags to use for NetCDF.
+        """
+        flags = self.run(additional_parameters=["--flibs"])
+        return flags.split()