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Adding testcase yaml file gotm runs to actions #174

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62cc765
Adding testcase yaml file gotm runs to actions
wathen Jul 3, 2026
2b67ea2
Updating testcase yaml files to run in seperate workflow
wathen Jul 3, 2026
a7bd302
Adding default values of exulim for ersem-15.06 and ersem-Blackford20…
wathen Jul 3, 2026
cf1385c
Updating ersem-Blackford2024 exulim testcase param
wathen Jul 3, 2026
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19 changes: 19 additions & 0 deletions .github/workflows/ersem.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,25 @@ jobs:
python -m pip install pytest
pytest github-actions/gotm-fabm-ersem/test_state_variables.py github-actions/gotm-fabm-ersem/test_gotm.py

test-gotm-testcase-yamls-debian:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Setup python
uses: actions/setup-python@v2
with:
python-version: '3.x'
- name: Installing GOTM-FABM-ERSEM dependences
run: ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-dep-debian.sh
- name: Building and installing GOTM-FABM-ERSEM
run: |
BRANCH=${{ github.head_ref }}
./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh -b $BRANCH -f '-DCMAKE_Fortran_FLAGS="-fcheck=all"'
- name: Running GOTM testcase YAML tests
run: |
python -m pip install pytest
pytest github-actions/gotm-fabm-ersem/test_testcase_yamls.py

build-fabm0d-gotm-ersem-debian:
runs-on: ubuntu-latest
steps:
Expand Down
60 changes: 60 additions & 0 deletions github-actions/gotm-fabm-ersem/gotm-testcase-yaml.sh
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@@ -0,0 +1,60 @@
#!/bin/bash

set -euo pipefail

if [ "$#" -ne 1 ]; then
echo "Usage: $0 <testcase-yaml>" >&2
exit 2
fi

TESTCASE_YAML="$1"
if [ ! -f "${TESTCASE_YAML}" ]; then
echo "Testcase YAML not found: ${TESTCASE_YAML}" >&2
exit 2
fi

SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
REPO_DIR="$(cd "${SCRIPT_DIR}/../.." && pwd)"
SETUPS_DIR="${GOTM_ERSEM_SETUPS_DIR:-${REPO_DIR}/ersem-setups}"
L4_DIR="${SETUPS_DIR}/L4"
GOTM_BIN="${GOTM_BIN:-${HOME}/local/gotm/bin/gotm}"
GOTM_TEST_STOP="${GOTM_TEST_STOP:-2007-02-01 00:00:00}"

if [ ! -x "${GOTM_BIN}" ]; then
echo "GOTM executable not found or not executable: ${GOTM_BIN}" >&2
exit 2
fi

if [ ! -d "${SETUPS_DIR}" ]; then
echo "Cloning config repo"
git clone https://github.com/pmlmodelling/ersem-setups.git "${SETUPS_DIR}"
fi

ORIGINAL_GOTM_YAML="$(mktemp "${L4_DIR}/gotm.yaml.original.XXXXXX")"
TEST_GOTM_YAML="$(mktemp "${L4_DIR}/gotm.yaml.testcase.XXXXXX")"
cp "${L4_DIR}/gotm.yaml" "${ORIGINAL_GOTM_YAML}"

cleanup() {
cp "${ORIGINAL_GOTM_YAML}" "${L4_DIR}/gotm.yaml"
rm -f "${ORIGINAL_GOTM_YAML}" "${TEST_GOTM_YAML}"
}
trap cleanup EXIT

awk -v stop="${GOTM_TEST_STOP}" '
/^time:[[:space:]]*$/ { in_time = 1 }
/^[^[:space:]]/ && !/^time:[[:space:]]*$/ { in_time = 0 }
in_time && /^[[:space:]]+stop:[[:space:]]/ {
sub(/stop:.*/, "stop: " stop)
updated = 1
}
{ print }
END { if (!updated) exit 1 }
' "${L4_DIR}/gotm.yaml" > "${TEST_GOTM_YAML}"

echo "Running GOTM with testcase YAML: ${TESTCASE_YAML}"
echo "Using temporary gotm.yaml stop date: ${GOTM_TEST_STOP}"
cp "${TEST_GOTM_YAML}" "${L4_DIR}/gotm.yaml"
cp "${TESTCASE_YAML}" "${L4_DIR}/fabm.yaml"
cd "${L4_DIR}"

"${GOTM_BIN}" --ignore_unknown_config
42 changes: 42 additions & 0 deletions github-actions/gotm-fabm-ersem/test_testcase_yamls.py
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@@ -0,0 +1,42 @@
"""
Check that GOTM runs with every testcase YAML configuration.
"""

import subprocess
from pathlib import Path

import pytest


REPO_DIR = Path(__file__).resolve().parents[2]
TESTCASE_DIR = REPO_DIR / "testcases"
RUNNER = Path(__file__).with_name("gotm-testcase-yaml.sh")

YAML_PATTERNS = ("*.yaml", "*.yml")
TESTCASE_YAMLS = sorted(
{path for pattern in YAML_PATTERNS for path in TESTCASE_DIR.rglob(pattern)}
)


def yaml_id(path):
return path.relative_to(TESTCASE_DIR).as_posix()


@pytest.mark.parametrize("testcase_yaml", TESTCASE_YAMLS, ids=yaml_id)
def test_gotm_runs_with_testcase_yaml(testcase_yaml):
"""
Run GOTM with an ERSEM testcase YAML copied to the L4 setup.
"""
result = subprocess.run(
["bash", str(RUNNER), str(testcase_yaml)],
cwd=REPO_DIR,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
text=True,
)

assert result.returncode == 0, (
f"GOTM failed for {testcase_yaml.relative_to(REPO_DIR)}\n"
f"stdout:\n{result.stdout}\n"
f"stderr:\n{result.stderr}"
)
4 changes: 4 additions & 0 deletions testcases/ersem-15.06/fabm-ersem-15.06-L4-ben-docdyn-iop-denit.yaml
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Expand Up @@ -286,6 +286,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.04 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.2 # respired fraction of primary production (-)
qnlc: 0.0042 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.0001 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down Expand Up @@ -352,6 +353,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.04 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.2 # respired fraction of primary production (-)
qnlc: 0.005 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.000225 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down Expand Up @@ -415,6 +417,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.045 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.2 # respired fraction of primary production (-)
qnlc: 0.006 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.00035 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down Expand Up @@ -475,6 +478,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.035 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.2 # respired fraction of primary production (-)
qnlc: 0.0042 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.0001 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down
4 changes: 4 additions & 0 deletions testcases/ersem-15.06/fabm-ersem-15.06-L4-ben-docdyn-iop-n2o.yaml
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Expand Up @@ -279,6 +279,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.04 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.2 # respired fraction of primary production (-)
qnlc: 0.0042 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.0001 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down Expand Up @@ -345,6 +346,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.04 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.2 # respired fraction of primary production (-)
qnlc: 0.005 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.000225 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down Expand Up @@ -408,6 +410,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.045 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.2 # respired fraction of primary production (-)
qnlc: 0.006 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.00035 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down Expand Up @@ -468,6 +471,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.035 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.2 # respired fraction of primary production (-)
qnlc: 0.0042 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.0001 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down
4 changes: 4 additions & 0 deletions testcases/ersem-15.06/fabm-ersem-15.06-L4-ben-docdyn-iop.yaml
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Expand Up @@ -269,6 +269,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.04 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.2 # respired fraction of primary production (-)
qnlc: 0.0042 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.0001 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down Expand Up @@ -335,6 +336,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.04 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.2 # respired fraction of primary production (-)
qnlc: 0.005 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.000225 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down Expand Up @@ -398,6 +400,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.045 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.2 # respired fraction of primary production (-)
qnlc: 0.006 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.00035 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down Expand Up @@ -458,6 +461,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.035 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.2 # respired fraction of primary production (-)
qnlc: 0.0042 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.0001 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down
4 changes: 4 additions & 0 deletions testcases/ersem-15.06/fabm-ersem-15.06-L4-noben-docdyn-iop.yaml
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Expand Up @@ -273,6 +273,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.04 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.2 # respired fraction of primary production (-)
qnlc: 0.0042 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.0001 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down Expand Up @@ -339,6 +340,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.04 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.2 # respired fraction of primary production (-)
qnlc: 0.005 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.000225 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down Expand Up @@ -402,6 +404,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.045 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.2 # respired fraction of primary production (-)
qnlc: 0.006 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.00035 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down Expand Up @@ -462,6 +465,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.035 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.2 # respired fraction of primary production (-)
qnlc: 0.0042 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.0001 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down
4 changes: 4 additions & 0 deletions testcases/ersem-Blackford2024/fabm-ersem-Blackford2004-L4-ben-stdbac-stdlight.yaml
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Expand Up @@ -256,6 +256,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.05 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.05 # excreted fraction of primary production (-)
exulim: 0.95 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.1 # respired fraction of primary production (-)
qnlc: 0.00687 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.000428 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down Expand Up @@ -321,6 +322,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.05 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.25 # respired fraction of primary production (-)
qnlc: 0.00687 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.000428 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down Expand Up @@ -383,6 +385,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.05 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.2 # excreted fraction of primary production (-)
exulim: 0.8 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.25 # respired fraction of primary production (-)
qnlc: 0.00687 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.000428 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down Expand Up @@ -442,6 +445,7 @@ instances:
q10: 2.0 # Q_10 temperature coefficient (-)
srs: 0.05 # specific rest respiration at reference temperature (1/d)
pu_ea: 0.05 # excreted fraction of primary production (-)
exulim: 0.95 # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
pu_ra: 0.25 # respired fraction of primary production (-)
qnlc: 0.00687 # minimum nitrogen to carbon ratio (mmol N/mg C)
qplc: 0.000428 # minimum phosphorus to carbon ratio (mmol P/mg C)
Expand Down
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