Add pytests and CI for simple configuration checks

test/conftest.py

@@ -2,6 +2,8 @@
 import pytest
 from pathlib import Path
 
+import yaml
+
 
 @pytest.fixture(scope="session")
 def output_path(request):
@@ -37,6 +39,22 @@ def checksum_path(request, control_path):
     return Path(path)
 
 
+@pytest.fixture(scope="session")
+def metadata(control_path: Path):
+    metadata_path = control_path / 'metadata.yaml'
+    with open(metadata_path) as f:
+        content = yaml.safe_load(f)
+    return content
+
+
+@pytest.fixture(scope="session")
+def config(control_path: Path):
+    config_path = control_path / 'config.yaml'
+    with open(config_path) as f:
+        config_content = yaml.safe_load(f)
+    return config_content
+
+
 # Set up command line options and default for directory paths
 def pytest_addoption(parser):
     """Attaches optional command line arguments"""
@@ -66,15 +84,6 @@ def pytest_configure(config):
     config.addinivalue_line(
         "markers", "config: mark as configuration tests in quick CI checks"
     )
-    config.addinivalue_line(
-        "markers", "metadata: mark as metadata tests in quick CI checks"
-    )
     config.addinivalue_line(
         "markers", "access_om2: mark as access-om2 specific tests"
     )
-    config.addinivalue_line(
-        "markers", "access_om2_bgc: mark as access-om2-bgc specific tests"
-    )
-    config.addinivalue_line(
-        "markers", "highres: mark tests as high resolution model configuration tests"
-    )

test/requirements.txt

@@ -2,3 +2,4 @@ pytest==8.0.1
 jsonschema==4.21.1
 requests==2.31.0
 PyYAML==6.0.1
+f90nml==1.4.4

test/test_access_om2_config.py

@@ -0,0 +1,116 @@
+from datetime import timedelta
+import re
+
+import pytest
+import f90nml
+
+from util import get_git_branch_name
+
+# Mutually exclusive topic keywords
+TOPIC_KEYWORDS = {
+    'spatial extent': {'global', 'regional'},
+    'forcing product':	{'JRA55', 'ERA5'},
+    'forcing mode': {'repeat-year', 'ryf', 'repeat-decade', 'rdf',
+                        'interannual', 'iaf'},
+    'model': {'access-om2', 'access-om2-025', 'access-om2-01'}
+}
+
+
+class AccessOM2Branch:
+    """Use the naming patterns of the branch name to infer informatiom of
+    the ACCESS-OM2 config"""
+
+    def __init__(self, branch_name):
+        self.branch_name = branch_name
+        self.set_resolution()
+
+        self.is_high_resolution = self.resolution in ['025deg', '01deg']
+        self.is_bgc = 'bgc' in branch_name
+
+    def set_resolution(self):
+        # Resolutions are ordered, so the start of the list are matched first
+        resolutions = ['025deg', '01deg', '1deg']
+        self.resolution = None
+        for res in resolutions:
+            if res in self.branch_name:
+                self.resolution = res
+                return
+        # TODO Should unknown resolutions fail the pytests or be ignored?
+
+
+@pytest.fixture(scope="class")
+def branch(control_path):
+    branch_name = get_git_branch_name(control_path)
+    assert branch_name is not None, (
+        f"Failed getting git branch name of control path: {control_path}"
+    )
+    return AccessOM2Branch(branch_name)
+
+
+@pytest.mark.access_om2
+class TestAccessOM2:
+    """ACCESS-OM2 Specific configuration and metadata tests"""
+
+    def test_mppncombine_fast_collate_exe(self, config, branch):
+        if branch.is_high_resolution:
+            pattern = r'/g/data/vk83/apps/mppnccombine-fast/.*/bin/mppnccombine-fast'
+            if 'collate' in config:
+                assert re.match(pattern, config['collate']['exe']), (
+                    "Expect collate executable set to mppnccombine-fast"
+                    )
+
+    def test_metadata_realm(self, metadata, branch):
+        expected_realms = ['ocean', 'seaIce']
+        expected_config = 'realm:\n - ocean\n - seaIce'
+        if branch.is_bgc:
+            expected_realms.append('ocnBgchem')
+            expected_config += '\n - ocnBgchem'
+
+        assert ('realm' in metadata
+                and metadata['realm'] == expected_realms), (
+                    'Expected metadata realm set to:\n' + expected_config
+                    )
+
+    def test_restart_period(self, branch, control_path):
+        accessom2_nml_path = control_path / 'accessom2.nml'
+        assert accessom2_nml_path.exists()
+
+        accessom2_nml = f90nml.read(accessom2_nml_path)
+        restart_period = accessom2_nml['date_manager_nml']['restart_period']
+
+        # TODO: Use set of expected periods?
+        if branch.resolution == '1deg':
+            expected_period = [5, 0, 0]
+        elif branch.resolution == '025deg':
+            if branch.is_bgc:
+                expected_period = [1, 0, 0]
+            else:
+                expected_period = [2, 0, 0]
+        elif branch.resolution == '01deg':
+            if branch.is_bgc:
+                expected_period = [0, 1, 0]
+            else:
+                expected_period = [0, 3, 0]
+        else:
+            return
+        assert restart_period == expected_period
+
+    def test_metadata_keywords(self, metadata):
+
+        assert 'keywords' in metadata
+        metadata_keywords = set(metadata['keywords'])
+
+        expected_keywords = set()
+        for topic, keywords in TOPIC_KEYWORDS.items():
+            mutually_exclusive = metadata_keywords.intersection(keywords)
+            assert len(mutually_exclusive) <= 1, (
+                f"Topic {topic} has multiple mutually exlusive keywords: " +
+                str(mutually_exclusive)
+                )
+
+            expected_keywords = expected_keywords.union(keywords)
+
+        unrecognised_keywords = metadata_keywords.difference(expected_keywords)
+        assert len(unrecognised_keywords) == 0, (
+            f"Metadata has unrecognised keywords: {unrecognised_keywords}"
+            )

test/test_config.py

@@ -16,22 +16,6 @@
 DEFAULT_SCHEMA_VERSION = "1-0-0"
 
 
-@pytest.fixture(scope="class")
-def metadata(control_path: Path):
-    metadata_path = control_path / 'metadata.yaml'
-    with open(metadata_path) as f:
-        content = yaml.safe_load(f)
-    return content
-
-
-@pytest.fixture(scope="class")
-def config(control_path: Path):
-    config_path = control_path / 'config.yaml'
-    with open(config_path) as f:
-        config_content = yaml.safe_load(f)
-    return config_content
-
-
 @pytest.fixture(scope="class")
 def exe_manifest_fullpaths(control_path: Path):
     manifest_path = control_path / 'manifests' / 'exe.yaml'
@@ -160,60 +144,29 @@ def test_no_scripts_in_top_level_directory(self, control_path):
             "'tools' sub-directory"
         )
 
+    def test_validate_metadata(self, metadata):
+        # Schema URL
+        schema_version = metadata.get("schema_version", DEFAULT_SCHEMA_VERSION)
+        url = f"{BASE_SCHEMA_URL}/{schema_version}.json"
 
-@pytest.mark.highres
-def test_mppncombine_fast_collate_exe(config):
-    pattern = r'/g/data/vk83/apps/mppnccombine-fast/.*/bin/mppnccombine-fast'
-    if 'collate' in config:
-        assert re.match(pattern, config['collate']['exe']), (
-            "Expect collate executable set to mppnccombine-fast"
-            )
-
-
-@pytest.mark.metadata
-def test_validate_metadata(metadata):
-    # Schema URL
-    schema_version = metadata.get("schema_version", DEFAULT_SCHEMA_VERSION)
-    url = f"{BASE_SCHEMA_URL}/{schema_version}.json"
-
-    # Get schema from Github
-    response = requests.get(url)
-    assert response.status_code == 200
-    schema = response.json()
+        # Get schema from Github
+        response = requests.get(url)
+        assert response.status_code == 200
+        schema = response.json()
 
-    # In schema version (1-0-0), required fields are name, experiment_uuid,
-    # description and long_description. As name & experiment_uuid are
-    # generated for running experiments, the required fields are removed
-    # from the schema validation for now
-    schema.pop('required')
+        # In schema version (1-0-0), required fields are name, experiment_uuid,
+        # description and long_description. As name & experiment_uuid are
+        # generated for running experiments, the required fields are removed
+        # from the schema validation for now
+        schema.pop('required')
 
-    # Experiment_uuid
-    jsonschema.validate(instance=metadata, schema=schema)
+        # Validate field names and types
+        jsonschema.validate(instance=metadata, schema=schema)
 
-
-@pytest.mark.metadata
-@pytest.mark.parametrize(
-    "field",
-    ["description", "notes", "keywords", "nominal resolution", "version",
-     "reference", "license", "url", "model", "realm"]
-)
-def test_metadata_contains_fields(field, metadata):
-    assert field in metadata, f"{field} field shoud be defined in metadata"
-
-
-@pytest.mark.access_om2_bgc
-def test_metadata_realm(metadata):
-    assert ('realm' in metadata
-            and metadata['realm'] == ['ocean', 'seaIce', 'ocnBgchem']), (
-            'Expected access-om2-bgc metadata realm set to:\n' +
-            'realm:\n - ocean\n - seaIce\n - ocnBgchem'
-            )
-
-
-@pytest.mark.access_om2
-def test_metadata_access_om2_realm(metadata):
-    assert ('realm' in metadata
-            and metadata['realm'] == ['ocean', 'seaIce']), (
-            'Expected access-om2 metadata realm set to:\n' +
-            'realm:\n - ocean\n - seaIce\n'
-            )
+    @pytest.mark.parametrize(
+        "field",
+        ["description", "notes", "keywords", "nominal resolution", "version",
+        "reference", "license", "url", "model", "realm"]
+    )
+    def test_metadata_contains_fields(self, field, metadata):
+        assert field in metadata, f"{field} field shoud be defined in metadata"

test/util.py

@@ -18,3 +18,16 @@ def wait_for_qsub(run_id):
 
         if 'Job has finished' in qsub_out:
             break
+
+
+def get_git_branch_name(path):
+    """Get the git branch name of the given git directory"""
+    try:
+        cmd = 'git rev-parse --abbrev-ref HEAD'
+        result = sp.check_output(cmd, shell=True,
+                                         cwd=path).strip()
+        # Decode byte string to string
+        branch_name = result.decode('utf-8')
+        return branch_name
+    except sp.CalledProcessError:
+        return None