Merge pull request #60 from esm-tools/test/pi-mesh

PI Mesh Test Fixtures

conftest.py

@@ -14,6 +14,8 @@
     "tests.fixtures.config_files",
     "tests.fixtures.CV_Dir",
     "tests.fixtures.CMIP_Tables_Dir",
+    "tests.fixtures.example_data.fesom_2p6_pimesh",
+    "tests.fixtures.example_data.pi_uxarray",
 ]
 
 

setup.py

@@ -44,6 +44,7 @@ def read(filename):
         "flexparser < 0.4",  # NOTE(PG): See https://tinyurl.com/ypf99xnh
         "flox",
         "imohash",
+        "netcdf4",
         "numbagg",
         "pendulum",
         "pint-xarray",

src/pymorize/caching.py

@@ -23,7 +23,7 @@ def generate_cache_key(task, inputs):
 def manual_checkpoint(data, rule):
     """Manually insert a checkpoint in the flow"""
     logger.info("Manually inserting checkpoint")
-    return Completed(message="Checkpoint reached", return_value=data)
+    return Completed(message="Checkpoint reached", data=data)
 
 
 def inspect_cache(cache_dir="~/.prefect/storage"):

src/pymorize/cmorizer.py

@@ -224,7 +224,8 @@ def validate(self):
         # :PS: @PG the following functions are not defined yet
         # self._check_rules_for_table()
         # self._check_rules_for_output_dir()
-        self._check_is_subperiod()
+        # FIXME(PS): Turn off this check, see GH #59 (https://tinyurl.com/3z7d8uuy)
+        # self._check_is_subperiod()
 
     def _check_is_subperiod(self):
         logger.info("checking frequency in netcdf file and in table...")

src/pymorize/generic.py

@@ -246,4 +246,7 @@ def multiyear_monthly_mean(data, rule_spec, *args, **kwargs):
 
 
 def trigger_compute(data, rule_spec, *args, **kwargs):
-    return data.compute()
+    if hasattr(data, "compute"):
+        return data.compute()
+    # Data doesn't have a compute method, do nothing
+    return data

src/pymorize/pipeline.py

@@ -7,7 +7,7 @@
 import randomname
 from prefect import flow
 from prefect.cache_policies import INPUTS, TASK_SOURCE
-from prefect.tasks import Task, task_input_hash
+from prefect.tasks import Task
 from prefect_dask import DaskTaskRunner
 
 from .caching import generate_cache_key
@@ -21,13 +21,18 @@ def __init__(
         *args,
         name=None,
         workflow_backend="prefect",
+        cache_policy=None,
         dask_cluster=None,
         cache_expiration=None,
     ):
         self._steps = args
         self.name = name or randomname.get_name()
         self._workflow_backend = workflow_backend
         self._cluster = dask_cluster
+        self._prefect_cache_kwargs = {}
+        if cache_policy is None:
+            self._cache_policy = TASK_SOURCE + INPUTS
+            self._prefect_cache_kwargs["cache_policy"] = self._cache_policy
 
         if cache_expiration is None:
             self._cache_expiration = timedelta(days=1)
@@ -36,6 +41,7 @@ def __init__(
                 self._cache_expiration = cache_expiration
             else:
                 raise TypeError("Cache expiration must be a timedelta!")
+        self._prefect_cache_kwargs["cache_expiration"] = self._cache_expiration
 
         if self._workflow_backend == "prefect":
             self._prefectize_steps()
@@ -51,7 +57,7 @@ def __str__(self):
         return "\n".join(r_val)
 
     def assign_cluster(self, cluster):
-        logger.debug("Assinging cluster to this pipeline")
+        logger.debug("Assigning cluster to this pipeline")
         self._cluster = cluster
 
     def _prefectize_steps(self):
@@ -64,9 +70,8 @@ def _prefectize_steps(self):
             prefect_tasks.append(
                 Task(
                     fn=step,
+                    **self._prefect_cache_kwargs,
                     # cache_key_fn=generate_cache_key,
-                    cache_expiration=self._cache_expiration,
-                    cache_policy=TASK_SOURCE + INPUTS,
                 )
             )
 

tests/configs/test_config_fesom_2p6_pimesh.yaml

@@ -0,0 +1,23 @@
+pymorize:
+  warn_on_no_rule: False
+  parallel: False
+general:
+  name: "fesom_2p6_pimesh"
+  description: "This is a test configuration using esm-tools generated test data on PI Mesh"
+  maintainer: "pgierz"
+  email: "[email protected]"
+  cmor_version: "CMIP6"
+  mip: "CMIP"
+  frequency: "mon"
+  CMIP_Tables_Dir: "./cmip6-cmor-tables/Tables"
+rules:
+  - name: "temp"
+    experiment_id: "piControl"
+    output_directory: "./output"
+    source_id: "FESOM"
+    variant_label: "r1i1p1f1"
+    inputs:
+      - path: "REPLACE_ME/outdata/fesom"
+        pattern: "temp.fesom..*.nc"
+    cmor_variable: "thetao"
+    model_variable: "temp"

tests/configs/test_config_pi_uxarray.yaml

@@ -0,0 +1,23 @@
+pymorize:
+  warn_on_no_rule: False
+  parallel: False
+general:
+  name: "pi_uxarray"
+  description: "This is a test configuration using the UXArray test data on PI Mesh"
+  maintainer: "pgierz"
+  email: "[email protected]"
+  cmor_version: "CMIP6"
+  mip: "CMIP"
+  frequency: "mon"
+  CMIP_Tables_Dir: "./cmip6-cmor-tables/Tables"
+rules:
+  - name: "temp"
+    experiment_id: "piControl"
+    output_directory: "./output"
+    source_id: "FESOM"
+    variant_label: "r1i1p1f1"
+    inputs:
+      - path: "REPLACE_ME"
+        pattern: "temp.fesom..*.nc"
+    cmor_variable: "thetao"
+    model_variable: "temp"

tests/fixtures/config_files.py

@@ -6,3 +6,13 @@
 @pytest.fixture
 def test_config():
     return TEST_ROOT / "configs" / "test_config.yaml"
+
+
+@pytest.fixture
+def pi_uxarray_config():
+    return TEST_ROOT / "configs" / "test_config_pi_uxarray.yaml"
+
+
+@pytest.fixture
+def fesom_2p6_pimesh_esm_tools_config():
+    return TEST_ROOT / "configs" / "test_config_fesom_2p6_pimesh.yaml"

tests/fixtures/example_data/fesom_2p6_pimesh.py

@@ -0,0 +1,43 @@
+"""Example data for the FESOM model."""
+
+import tarfile
+from pathlib import Path
+
+import pytest
+import requests
+
+URL = "https://nextcloud.awi.de/s/7gtFn38ZGifMAfw/download/fesom_2p6_pimesh.tar.gz"
+"""str : URL to download the example data from."""
+
+
+@pytest.fixture(scope="session")
+def fesom_2p6_esm_tools_download_data(tmp_path_factory):
+    cache_dir = tmp_path_factory.getbasetemp() / "cached_data"
+    cache_dir.mkdir(exist_ok=True)
+    data_path = cache_dir / "fesom_2p6_pimesh.tar.gz"
+
+    if not data_path.exists():
+        response = requests.get(URL)
+        response.raise_for_status()
+        with open(data_path, "wb") as f:
+            f.write(response.content)
+        print(f"Data downloaded: {data_path}.")
+    else:
+        print(f"Using cached data: {data_path}.")
+
+    return data_path
+
+
+@pytest.fixture(scope="session")
+def fesom_2p6_pimesh_esm_tools_data(fesom_2p6_esm_tools_download_data):
+    data_dir = Path(fesom_2p6_esm_tools_download_data).parent / "fesom_2p6_pimesh"
+
+    # Extract only if the directory doesn't already exist
+    if not data_dir.exists():
+        with tarfile.open(fesom_2p6_esm_tools_download_data, "r:gz") as tar:
+            tar.extractall(data_dir.parent)
+        print(f"Data extracted to: {data_dir}.")
+    else:
+        print(f"Using cached extraction: {data_dir}.")
+
+    return data_dir

tests/fixtures/example_data/pi_uxarray.py

@@ -0,0 +1,38 @@
+"""Example data for the FESOM model."""
+
+import tarfile
+from pathlib import Path
+
+import pytest
+import requests
+
+URL = "https://nextcloud.awi.de/s/swqyFgbL2jjgjRo/download/pi_uxarray.tar"
+"""str : URL to download the example data from."""
+
+
+@pytest.fixture(scope="session")
+def pi_uxarray_download_data(tmp_path_factory):
+    cache_dir = tmp_path_factory.getbasetemp() / "cached_data"
+    cache_dir.mkdir(exist_ok=True)
+    data_path = cache_dir / "pi_uxarray.tar"
+
+    if not data_path.exists():
+        response = requests.get(URL)
+        response.raise_for_status()
+        with open(data_path, "wb") as f:
+            f.write(response.content)
+        print(f"Data downloaded: {data_path}.")
+    else:
+        print(f"Using cached data: {data_path}.")
+
+    return data_path
+
+
+@pytest.fixture(scope="session")
+def pi_uxarray_data(pi_uxarray_download_data):
+
+    data_dir = Path(pi_uxarray_download_data).parent
+    with tarfile.open(pi_uxarray_download_data, "r") as tar:
+        tar.extractall(data_dir)
+
+    return data_dir / "pi_uxarray"

tests/integration/test_fesom_2p6_pimesh_esm_tools.py

@@ -0,0 +1,18 @@
+# import pytest
+import yaml
+
+from pymorize.cmorizer import CMORizer
+from pymorize.logging import logger
+
+
+def test_process(fesom_2p6_pimesh_esm_tools_config, fesom_2p6_pimesh_esm_tools_data):
+    logger.info(f"Processing {fesom_2p6_pimesh_esm_tools_config}")
+    with open(fesom_2p6_pimesh_esm_tools_config, "r") as f:
+        cfg = yaml.safe_load(f)
+    for rule in cfg["rules"]:
+        for input in rule["inputs"]:
+            input["path"] = input["path"].replace(
+                "REPLACE_ME", str(fesom_2p6_pimesh_esm_tools_data)
+            )
+    cmorizer = CMORizer.from_dict(cfg)
+    cmorizer.process()

tests/integration/test_uxarray_pi.py

@@ -0,0 +1,16 @@
+# import pytest
+import yaml
+
+from pymorize.cmorizer import CMORizer
+from pymorize.logging import logger
+
+
+def test_process(pi_uxarray_config, pi_uxarray_data):
+    logger.info(f"Processing {pi_uxarray_config}")
+    with open(pi_uxarray_config, "r") as f:
+        cfg = yaml.safe_load(f)
+    for rule in cfg["rules"]:
+        for input in rule["inputs"]:
+            input["path"] = input["path"].replace("REPLACE_ME", str(pi_uxarray_data))
+    cmorizer = CMORizer.from_dict(cfg)
+    cmorizer.process()