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Take XIOS file frequency configuration from iodef.xml where possible #212

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6c1886f
Add test framework for iodef.xml files
EdHone Dec 8, 2025
1f519e7
New test and tweak for file functionality
EdHone Dec 9, 2025
de2bea2
fix tests and gitignore
EdHone Jan 5, 2026
b76ed1c
Remove original iodef.xml
EdHone Jan 5, 2026
a156a9c
Test tweaks)
EdHone Jan 7, 2026
acb8fcc
Make testing framework thread-safe
EdHone Jan 9, 2026
b8bcb9e
Testing framework fully fixed
EdHone Jan 12, 2026
5f5620a
Sci/tech review comments
EdHone Jan 26, 2026
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2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -71,3 +71,5 @@ infrastructure/**/bin
infrastructure/**/working
infrastructure/**/test
infrastructure/**/documents
science/**/bin
science/**/working
77 changes: 63 additions & 14 deletions components/lfric-xios/build/testframework/xiostest.py
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Expand Up @@ -8,6 +8,7 @@
import subprocess
from pathlib import Path
import sys
import shutil
from typing import List

from testframework import MpiTest
Expand All @@ -20,40 +21,85 @@ class LFRicXiosTest(MpiTest):
Base for LFRic-XIOS integration tests.
"""

def __init__(self, command=sys.argv[1], processes=1):
def __init__(self, command=sys.argv[1], processes=1, iodef_file=None):
if iodef_file is None:
self.iodef_file = "iodef.xml"
else:
self.iodef_file = iodef_file

super().__init__(command, processes)

self.xios_out: List[XiosOutput] = []
self.xios_err: List[XiosOutput] = []

def gen_data(self, source: Path, dest: Path):
# Setup test working directory
self.test_top_level: Path = Path(os.getcwd())
self.resources_dir: Path = self.test_top_level / "resources"
self.test_working_dir: Path = self.test_top_level / "working" / type(self).__name__
if not os.path.exists(self.test_working_dir):
os.makedirs(self.test_working_dir)

# Create symlink to test executable in working directory
if not os.path.exists(Path(self.test_working_dir) / command[0].split("/")[-1]):
os.symlink(Path(command[0]), Path(self.test_working_dir) / command[0].split("/")[-1])

# Change to test working directory
os.chdir(self.test_working_dir)


def gen_data(self, source: str, dest: str):
"""
Create input data files from CDL formatted text.
Create input data files from CDL formatted text. Looks for source file
in resources/data directory and generates dest file in test working directory.
"""
dest_path: Path = Path(self.test_working_dir) / Path(dest)
source_path: Path = Path(self.resources_dir, 'data') / Path(source)
dest_path.unlink(missing_ok=True)

proc = subprocess.Popen(
['ncgen', '-k', 'nc4', '-o', f'{dest}', f'{source}'],
['ncgen', '-k', 'nc4', '-o', f'{dest_path}', f'{source_path }'],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
)
_, err = proc.communicate()
if proc.returncode != 0:
raise Exception("Test data generation failed:\n" + f"{err}")

def gen_config(self, config_source: Path, config_out: Path, new_config: dict):


def gen_config(self, config_source: str, config_out: str, new_config: dict):
"""
Create an LFRic configuration namelist.
Create an LFRic configuration namelist. Looks for source file
in resources/configs directory and generates dest file in test working directory.
"""
config_in = open(config_source, 'r')
config_in = open(Path(self.resources_dir, 'configs', config_source), 'r')
config = config_in.readlines()
for key in new_config.keys():
for i in range(len(config)):
if key in config[i]:
config[i] = f" {key}={new_config[key]}\n"
if type(new_config[key]) == str:
config[i] = f" {key}='{new_config[key]}'\n"
else:
config[i] = f" {key}={new_config[key]}\n"
config_in.close()

f = open(config_out, "w")
f = open(Path(self.test_working_dir, config_out), "w")
for line in config:
f.write(line)
f.close()
f.close()


def performTest(self):
"""
Removes any old log files and runs the executable.
"""

# Handle iodef file
if os.path.exists(self.iodef_file):
os.remove(self.iodef_file)
shutil.copy(self.resources_dir / self.iodef_file, self.test_working_dir / "iodef.xml")

return super().performTest()


def nc_kgo_check(self, output: Path, kgo: Path):
"""
Expand Down Expand Up @@ -92,8 +138,11 @@ def post_execution(self, return_code):
"""

for proc in range(self._processes):
self.xios_out.append(XiosOutput(f"xios_client_{proc}.out"))
self.xios_err.append(XiosOutput(f"xios_client_{proc}.err"))
self.xios_out.append(XiosOutput(self.test_working_dir / f"xios_client_{proc}.out"))
self.xios_err.append(XiosOutput(self.test_working_dir / f"xios_client_{proc}.err"))

# Return to top level directory
os.chdir(self.test_top_level)


class XiosOutput:
Expand All @@ -102,7 +151,7 @@ class XiosOutput:
"""

def __init__(self, filename):
self.path: Path = Path(os.getcwd()) / Path(filename)
self.path: Path = Path(filename)

with open(self.path, "rt") as handle:
self.contents = handle.read()
Expand Down
3 changes: 2 additions & 1 deletion components/lfric-xios/integration-test/lfric_xios_context_test.py
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Expand Up @@ -20,7 +20,8 @@ class LfricXiosContextTest(LFRicXiosTest):
"""

def __init__(self):
super().__init__(command=[sys.argv[1], "resources/configs/context.nml"], processes=1)
super().__init__(command=[sys.argv[1], "context.nml"], processes=1)
self.gen_config( "context.nml", "context.nml", {} )

def test(self, returncode: int, out: str, err: str):
"""
Expand Down
86 changes: 86 additions & 0 deletions components/lfric-xios/integration-test/lfric_xios_temporal_iodef_test.f90
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@@ -0,0 +1,86 @@
!-----------------------------------------------------------------------------
! (C) Crown copyright 2025 Met Office. All rights reserved.
! The file LICENCE, distributed with this code, contains details of the terms
! under which the code may be used.
!-----------------------------------------------------------------------------

! Tests the LFRic-XIOS temporal reading functionality using iodef file configuration.
! Correct behaviour is to read only the minimal required time-entries from
! input file at the correct times. The validity of the data written from this
! test is checked against the input data in the python part of the test.
program lfric_xios_temporal_iodef_test

use constants_mod, only: r_def
use event_mod, only: event_action
use event_actor_mod, only: event_actor_type
use field_mod, only: field_type, field_proxy_type
use file_mod, only: FILE_MODE_READ, FILE_MODE_WRITE
use io_context_mod, only: callback_clock_arg
use lfric_xios_action_mod, only: advance
use lfric_xios_context_mod, only: lfric_xios_context_type
use lfric_xios_driver_mod, only: lfric_xios_initialise, lfric_xios_finalise
use lfric_xios_file_mod, only: lfric_xios_file_type, OPERATION_TIMESERIES
use linked_list_mod, only: linked_list_type
use log_mod, only: log_event, log_level_info
use test_db_mod, only: test_db_type

implicit none

type(test_db_type) :: test_db
type(lfric_xios_context_type), target, allocatable :: io_context

procedure(callback_clock_arg), pointer :: before_close
type(linked_list_type), pointer :: file_list
class(event_actor_type), pointer :: context_actor
procedure(event_action), pointer :: context_advance
type(field_type), pointer :: rfield
type(field_proxy_type) :: rproxy

call test_db%initialise()
call lfric_xios_initialise( "test", test_db%comm, .false. )

! =============================== Start test ================================

allocate(io_context)
call io_context%initialise( "test_io_context", 1, 10 )

file_list => io_context%get_filelist()
call file_list%insert_item( lfric_xios_file_type( "lfric_xios_temporal_input", &
xios_id="lfric_xios_temporal_input", &
io_mode=FILE_MODE_READ, &
operation=OPERATION_TIMESERIES, &
fields_in_file=test_db%temporal_fields ) )
call file_list%insert_item( lfric_xios_file_type( "lfric_xios_temporal_output", &
xios_id="lfric_xios_temporal_output", &
io_mode=FILE_MODE_WRITE, &
operation=OPERATION_TIMESERIES, &
freq=1, &
fields_in_file=test_db%temporal_fields ) )

before_close => null()
call io_context%initialise_xios_context( test_db%comm, &
test_db%chi, test_db%panel_id, &
test_db%clock, test_db%calendar, &
before_close )


context_advance => advance
context_actor => io_context
call test_db%clock%add_event( context_advance, context_actor )
call io_context%set_active(.true.)

do while (test_db%clock%tick())
call test_db%temporal_fields%get_field("temporal_field", rfield)
rproxy = rfield%get_proxy()
call log_event("Valid data for this TS:", log_level_info)
print*,rproxy%data(1)
end do

deallocate(io_context)

! ============================== Finish test =================================

call lfric_xios_finalise()
call test_db%finalise()

end program lfric_xios_temporal_iodef_test
113 changes: 113 additions & 0 deletions components/lfric-xios/integration-test/lfric_xios_temporal_iodef_test.py
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@@ -0,0 +1,113 @@
#!/usr/bin/env python3
##############################################################################
# (C) Crown copyright 2025 Met Office. All rights reserved.
# The file LICENCE, distributed with this code, contains details of the terms
# under which the code may be used.
##############################################################################
"""
A set of tests which exercise the temporal reading functionality provided by
the LFRic-XIOS component. For these tests the file is configured mainly via
the iodef.xml file, rather than the fortran API.
The tests cover the reading of a piece of non-cyclic temporal data with data
points ranging from 15:01 to 15:10 in 10 1-minute intervals. The model start
time is changed to change how the model interacts with the data.
"""
from testframework import TestEngine, TestFailed
from xiostest import LFRicXiosTest
from pathlib import Path
import sys

###############################################################################
class LfricXiosFullNonCyclicIodefTest(LFRicXiosTest): # pylint: disable=too-few-public-methods
"""
Tests the LFRic-XIOS temporal reading functionality for a full set of non-cyclic data
"""

def __init__(self):
super().__init__(command=[sys.argv[1], "non_cyclic_full.nml"], processes=1, iodef_file="iodef_temporal.xml")
self.gen_data('temporal_data.cdl', 'lfric_xios_temporal_input.nc')
self.gen_config( "non_cyclic_base.nml", "non_cyclic_full.nml", {} )

def test(self, returncode: int, out: str, err: str):
"""
Test the output of the context test
"""

if returncode != 0:
print(out)
raise TestFailed(f"Unexpected failure of test executable: {returncode}\n" +
f"stderr:\n" +
f"{err}")
if not self.nc_data_match(Path(self.test_working_dir, 'lfric_xios_temporal_input.nc'),
Path(self.test_working_dir, 'lfric_xios_temporal_output.nc'),
'temporal_field'):
raise TestFailed("Output data does not match input data for same time values")

return "Reading full set of non-cylic data okay..."


class LfricXiosFullNonCyclicIodefHighFreqTest(LFRicXiosTest): # pylint: disable=too-few-public-methods
"""
Tests the LFRic-XIOS temporal reading functionality for a full set of
non-cyclic data at higher model frequency
"""

def __init__(self):
super().__init__(command=[sys.argv[1], "non_cyclic_full.nml"], processes=1, iodef_file="iodef_temporal.xml")
self.gen_data('temporal_data.cdl', 'lfric_xios_temporal_input.nc')
self.gen_config( "non_cyclic_base.nml", "non_cyclic_full.nml", {"dt": 10.0,
"timestep_end": '60'} )

def test(self, returncode: int, out: str, err: str):
"""
Test the output of the context test
"""

if returncode != 0:
print(out)
raise TestFailed(f"Unexpected failure of test executable: {returncode}\n" +
f"stderr:\n" +
f"{err}")
if not self.nc_data_match(Path(self.test_working_dir, 'lfric_xios_temporal_input.nc'),
Path(self.test_working_dir, 'lfric_xios_temporal_output.nc'),
'temporal_field'):
raise TestFailed("Output data does not match input data for same time values")

return "Reading full set of non-cylic data okay..."


class LfricXiosFullNonCyclicIodefNoFreqTest(LFRicXiosTest): # pylint: disable=too-few-public-methods
"""
Tests the error handling for the case where there is no frequency set in either
the iodef or the fortran configuration.
"""

def __init__(self):
super().__init__(command=[sys.argv[1], "non_cyclic_full.nml"], processes=1)
self.gen_data('temporal_data.cdl', 'lfric_xios_temporal_input.nc')
self.gen_config( "non_cyclic_base.nml", "non_cyclic_full.nml", {} )

def test(self, returncode: int, out: str, err: str):
"""
Test the output of the context test
"""

expected_xios_errs = ['In file "type_impl.hpp", function "void xios::CType<T>::_checkEmpty() const [with T = xios::CDuration]", line 210 -> Data is not initialized',
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@svadams svadams Jan 26, 2026

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Not entirely comfortable with hard coding XIOS error messages like this, as will this error message be unique to unset frequency (?) However, I understand that XIOS does not throw succinct and meaningful error messages ! On balance it’s better to have this test than not!

'In file "type_impl.hpp", function "void xios::CType<xios::CDuration>::_checkEmpty() const [T = xios::CDuration]", line 210 -> Data is not initialized']

if returncode == 134:
if self.xios_err[0].contents.strip() in expected_xios_errs:
return "Expected failure of test executable due to missing frequency setting."
else:
raise TestFailed("Test executable failed, but with unexpected error message.")
elif returncode == 0:
raise TestFailed("Test executable succeeded unexpectedly despite missing frequency setting.")
else:
raise TestFailed("Test executable failed with unexpected return code.")


##############################################################################
if __name__ == "__main__":
TestEngine.run(LfricXiosFullNonCyclicIodefTest())
TestEngine.run(LfricXiosFullNonCyclicIodefHighFreqTest())
TestEngine.run(LfricXiosFullNonCyclicIodefNoFreqTest())
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