climate-ref-core 0.5.5__py3-none-any.whl → 0.6.1__py3-none-any.whl

climate_ref_core/dataset_registry.py

@@ -12,6 +12,7 @@ import pathlib
 import shutil
 
 import pooch
+import pooch.hashes
 from loguru import logger
 from rich.progress import track
 
@@ -20,11 +21,59 @@ from climate_ref_core.env import env
 DATASET_URL = env.str("REF_DATASET_URL", default="https://pub-b093171261094c4ea9adffa01f94ee06.r2.dev")
 
 
+def _verify_hash_matches(fname: str | pathlib.Path, known_hash: str) -> bool:
+    """
+    Check if the hash of a file matches a known hash.
+
+    Coverts hashes to lowercase before comparison to avoid system specific
+    mismatches between hashes in the registry and computed hashes.
+
+    This is a tweaked version of the `pooch.hashes.hash_matches` function with a custom error message.
+
+    Parameters
+    ----------
+    fname
+        The path to the file.
+    known_hash
+        The known hash. Optionally, prepend ``alg:`` to the hash to specify the
+        hashing algorithm. Default is SHA256.
+
+    Raises
+    ------
+    ValueError
+        If the hash does not match.
+    FileNotFoundError
+        If the file does not exist.
+
+    Returns
+    -------
+    bool
+        True if the hash matches.
+    """
+    fname = pathlib.Path(fname)
+
+    if not fname.exists():
+        raise FileNotFoundError(f"File {fname!s} does not exist. Cannot verify hash.")
+
+    algorithm = pooch.hashes.hash_algorithm(known_hash)
+    new_hash = pooch.hashes.file_hash(str(fname), alg=algorithm)
+    matches = new_hash.lower() == known_hash.split(":")[-1].lower()
+    if not matches:
+        raise ValueError(
+            f"{algorithm.upper()} hash of downloaded file ({fname!s}) does not match"
+            f" the known hash: expected {known_hash} but got {new_hash}. "
+            f"The file may have been corrupted or the known hash may be outdated. "
+            f"Delete the file and try again."
+        )
+    return matches
+
+
 def fetch_all_files(
     registry: pooch.Pooch,
     name: str,
     output_dir: pathlib.Path | None,
     symlink: bool = False,
+    verify: bool = True,
 ) -> None:
     """
     Fetch all files associated with a pooch registry and write them to an output directory.
@@ -49,12 +98,17 @@ def fetch_all_files(
     symlink
         If True, symlink all files to this directory.
         Otherwise, perform a copy.
+    verify
+        If True, verify the checksums of the local files against the registry.
     """
     if output_dir:
         output_dir.mkdir(parents=True, exist_ok=True)
 
     for key in track(registry.registry.keys(), description=f"Fetching {name} data"):
         fetch_file = registry.fetch(key)
+        expected_hash = registry.registry[key]
+        if not isinstance(expected_hash, str) or not expected_hash:  # pragma: no cover
+            raise ValueError(f"Expected a hash for {key} but got {expected_hash}")
 
         if output_dir is None:
             # Just warm the cache and move onto the next file
@@ -72,6 +126,8 @@ def fetch_all_files(
                 shutil.copy(fetch_file, linked_file)
         else:
             logger.info(f"File {linked_file} already exists. Skipping.")
+        if verify:
+            _verify_hash_matches(linked_file, expected_hash)
 
 
 class DatasetRegistryManager:

climate_ref_core/exceptions.py

@@ -53,3 +53,11 @@ class ExecutionError(RefException):
 
     def __init__(self, message: str) -> None:
         super().__init__(message)
+
+
+class DiagnosticError(RefException):
+    """Error from diagnostic computing"""
+
+    def __init__(self, message: str, result: Any):
+        super().__init__(message)
+        self.result = result

climate_ref_core/executor.py

@@ -9,7 +9,7 @@ from typing import TYPE_CHECKING, Any, Protocol, runtime_checkable
 from loguru import logger
 
 from climate_ref_core.diagnostics import ExecutionDefinition, ExecutionResult
-from climate_ref_core.exceptions import InvalidExecutorException
+from climate_ref_core.exceptions import DiagnosticError, InvalidExecutorException
 from climate_ref_core.logging import redirect_logs
 
 if TYPE_CHECKING:
@@ -20,6 +20,7 @@ if TYPE_CHECKING:
 def execute_locally(
     definition: ExecutionDefinition,
     log_level: str,
+    raise_error: bool = False,
 ) -> ExecutionResult:
     """
     Run a diagnostic execution
@@ -46,10 +47,15 @@ def execute_locally(
 
         with redirect_logs(definition, log_level):
             return definition.diagnostic.run(definition=definition)
-    except Exception:
+    except Exception as e:
         # If the diagnostic fails, we want to log the error and return a failure result
         logger.exception(f"Error running {definition.execution_slug()!r}")
-        return ExecutionResult.build_from_failure(definition)
+        result = ExecutionResult.build_from_failure(definition)
+
+        if raise_error:
+            raise DiagnosticError(str(e), result) from e
+        else:
+            return result
 
 
 @runtime_checkable

climate_ref_core/logging.py

@@ -2,13 +2,16 @@
 Logging utilities
 
 The REF uses [loguru](https://loguru.readthedocs.io/en/stable/), a simple logging framework.
+The log level and format are configured via the REF configuration file.
 """
 
 import contextlib
 import inspect
 import logging
+import multiprocessing
 import sys
 from collections.abc import Generator
+from pathlib import Path
 from typing import Any
 
 import pooch
@@ -24,6 +27,28 @@ Filename for the execution log.
 This file is written via [climate_ref_core.logging.redirect_logs][].
 """
 
+DEFAULT_LOG_FORMAT = (
+    "<green>{time:YYYY-MM-DD HH:mm:ss.SSS Z}</green> | <level>{level: <8}</level> | "
+    "<cyan>{name}</cyan> - <level>{message}</level>"
+)
+"""
+Default log format used by the REF
+"""
+
+VERBOSE_LOG_FORMAT = (
+    "<green>{time:YYYY-MM-DD HH:mm:ss.SSS Z} e{elapsed}s</green> | "
+    "<level>{level: <8}</level> | "
+    "{process.name}:{process.id} | "
+    "<cyan>{name}</cyan>:<cyan>{function}</cyan>:<cyan>{line}</cyan> - "
+    "<level>{message}</level>"
+)
+"""
+The verbose log format is used for debugging and development.
+
+This is the format that is used when writing the log messages to file for later debugging.
+It contains information about the process and function that the log message was generated in.
+"""
+
 
 class _InterceptHandler(logging.Handler):
     def emit(self, record: logging.LogRecord) -> None:
@@ -43,6 +68,35 @@ class _InterceptHandler(logging.Handler):
         logger.opt(depth=depth, exception=record.exc_info).log(level, record.getMessage())
 
 
+def initialise_logging(level: int | str, format: str, log_directory: str | Path) -> None:  # noqa: A002 # pragma: no cover
+    """
+    Initialise the logging for the REF
+
+    This sets up the default log handler and configures the REF logger.
+    """
+    capture_logging()
+    log_directory = Path(log_directory)
+    process_name = multiprocessing.current_process().name
+
+    # Remove any existing handlers
+    logger.remove()
+
+    # Write out debug logs to a file
+    log_directory.mkdir(parents=True, exist_ok=True)
+    filename = f"climate-ref_{{time:YYYY-MM-DD_HH-mm}}_{process_name}.log"
+    logger.add(
+        sink=log_directory / filename,
+        retention=10,
+        level="DEBUG",
+        format=VERBOSE_LOG_FORMAT,
+        colorize=False,
+    )
+    logger.info("Starting REF logging")
+    logger.info(f"arguments: {sys.argv}")
+
+    add_log_handler(level=level, format=format, colorize=True)
+
+
 def capture_logging() -> None:
     """
     Capture logging from the standard library and redirect it to Loguru
@@ -56,6 +110,7 @@ def capture_logging() -> None:
     logging.basicConfig(handlers=[_InterceptHandler()], level=0, force=True)
 
     # Disable some overly verbose logs
+    logger.disable("alembic.runtime.migration")
     logger.disable("matplotlib.colorbar")
     logger.disable("matplotlib.ticker")
     logger.disable("matplotlib.font_manager")
@@ -154,4 +209,4 @@ def redirect_logs(definition: ExecutionDefinition, log_level: str) -> Generator[
             add_log_handler(**logger.default_handler_kwargs)  # type: ignore[attr-defined]
 
 
-__all__ = ["EXECUTION_LOG_FILENAME", "add_log_handler", "capture_logging", "logger", "redirect_logs"]
+__all__ = ["EXECUTION_LOG_FILENAME", "capture_logging", "initialise_logging", "redirect_logs"]

climate_ref_core/pycmec/controlled_vocabulary.py

@@ -28,8 +28,8 @@ class DimensionValue:
 
     name: str
     long_name: str
-    description: str | None
-    units: str
+    description: str | None = None
+    units: str | None = None
 
 
 @frozen

climate_ref_core/pycmec/cv_cmip7_aft.yaml

@@ -53,7 +53,15 @@ dimensions:
     - name: global
       long_name: Global
       description: "Global aggregate"
-      units: dimensionless
+    - name: NHEX
+      long_name: Northern Hemisphere Extra-tropics
+      description: "Northern Hemisphere Extra-tropics (30N-90N)"
+    - name: SHEX
+      long_name: Southern Hemisphere Extra-tropics
+      description: "Southern Hemisphere Extra-tropics (30S-90S)"
+    - name: Tropics
+      long_name: Tropics
+      description: "Tropics (30N-30S)"
 - name: season
   long_name: Season
   description: "Parts of the year from which the metric values are calculated"
@@ -63,23 +71,57 @@ dimensions:
     - name: ann
       long_name: Annual
       description: ""
-      units: dimensionless
     - name: djf
       long_name: Dec,Jan,Feb
       description: "December, January, February"
-      units: dimensionless
     - name: mam
       long_name: Mar,Apr,May
       description: "March, April, May"
-      units: dimensionless
     - name: jja
       long_name: Jun,Jul,Aug
       description: "June, July, August"
-      units: dimensionless
     - name: son
       long_name: Sep,Oct,Nov
       description: "September, October, November"
-      units: dimensionless
+- name: mode
+  long_name: Mode of variability
+  description: "Different modes of variability that can be calculated"
+  required: false
+  allow_extra_values: false
+  values:
+    - name: NAM
+      long_name: Northern Annular Mode
+      description: Northern Annular Mode
+    - name: NAO
+      long_name: North Atlantic Oscillation
+      description: North Atlantic Oscillation
+    - name: PNA
+      long_name: Pacific–North America pattern
+      description: Pacific–North America pattern
+    - name: SAM
+      long_name: Southern Annular Mode
+      description: Southern Annular Mode
+    - name: PDO
+      long_name: Pacific decadal oscillation
+      description: Pacific decadal oscillation
+    - name: NPO
+      long_name: North Pacific Oscillation
+      description: North Pacific Oscillation
+    - name: NPGO
+      long_name: North Pacific Gyre Oscillation
+      description: North Pacific Gyre Oscillation
+- name: method
+  long_name: EOF Method
+  description: "Method for calculating the EOFs in PMP's mode of variability diagnostic"
+  required: false
+  allow_extra_values: false
+  values:
+    - name: cbf
+      long_name: Common Basis Function
+      description: "A projection of the leading EOFs of the reference dataset onto the model data"
+    - name: eof1
+      long_name: EOF1
+      description: "The leading EOF of the reference dataset"
 - name: statistic
   long_name: Statistic
   description: ""

climate_ref_core/pycmec/metric.py

@@ -20,7 +20,7 @@ from copy import deepcopy
 from enum import Enum
 from typing import Any, cast
 
-from loguru import logger
+import numpy as np
 from pydantic import (
     BaseModel,
     ConfigDict,
@@ -190,7 +190,6 @@ class MetricResults(RootModel[Any]):
             expected_keys = set(metdims[dim_name].keys())
             if not (dict_keys.issubset(expected_keys)):
                 msg = f"Unknown dimension values: {dict_keys - expected_keys} for {dim_name}"
-                logger.error(msg)
                 if not ALLOW_EXTRA_KEYS:  # pragma: no cover
                     raise ValueError(f"{msg}\nExpected keys: {expected_keys}")
                 else:
@@ -228,7 +227,7 @@ class StrNumDict(RootModel[Any]):
     """A class contains string key and numeric value"""
 
     model_config = ConfigDict(strict=True)
-    root: dict[str, float | int]
+    root: dict[str, float | int | None]
 
 
 def remove_dimensions(raw_metric_bundle: dict[str, Any], dimensions: str | list[str]) -> dict[str, Any]:
@@ -542,6 +541,13 @@ def _walk_results(
             yield ScalarMetricValue(
                 dimensions=metadata, value=value, attributes=results.get(MetricCV.ATTRIBUTES.value)
             )
+        elif value is None:
+            # Replace any None values with NaN
+            # This translates null values in JSON to Python NaN's
+            # Missing values are different from NaN values
+            yield ScalarMetricValue(
+                dimensions=metadata, value=np.nan, attributes=results.get(MetricCV.ATTRIBUTES.value)
+            )
         else:
             yield from _walk_results(dimensions[1:], value, {**metadata})
 

{climate_ref_core-0.5.5.dist-info → climate_ref_core-0.6.1.dist-info}/METADATA

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: climate-ref-core
-Version: 0.5.5
+Version: 0.6.1
 Summary: Core library for the CMIP Rapid Evaluation Framework
 Author-email: Jared Lewis <jared.lewis@climate-resource.com>, Mika Pflueger <mika.pflueger@climate-resource.com>, Bouwe Andela <b.andela@esciencecenter.nl>, Jiwoo Lee <lee1043@llnl.gov>, Min Xu <xum1@ornl.gov>, Nathan Collier <collierno@ornl.gov>, Dora Hegedus <dora.hegedus@stfc.ac.uk>
-License: Apache-2.0
+License-Expression: Apache-2.0
 License-File: LICENCE
 License-File: NOTICE
 Classifier: Development Status :: 3 - Alpha
@@ -29,6 +29,7 @@ Requires-Dist: pydantic>=2.10.6
 Requires-Dist: requests
 Requires-Dist: rich
 Requires-Dist: ruamel-yaml>=0.18
+Requires-Dist: setuptools>=75.8.0
 Requires-Dist: typing-extensions
 Description-Content-Type: text/markdown
 

{climate_ref_core-0.5.5.dist-info → climate_ref_core-0.6.1.dist-info}/RECORD

@@ -1,24 +1,24 @@
 climate_ref_core/__init__.py,sha256=MtmPThF2F9_2UODEN6rt1x30LDxrHIZ0wyRN_wsHx5I,127
 climate_ref_core/constraints.py,sha256=QOqMh5jDBxdWTnQw2HNBizJQDF6Uu97rfJp9WudQWHc,11819
-climate_ref_core/dataset_registry.py,sha256=cSzSKcz2juXNQAHO1SEl6e576ZWUuNbLTzrANyDnX3o,5247
+climate_ref_core/dataset_registry.py,sha256=mkes7Pgz_zaS_t_BidiDzSd8dmqAvjx2MlgoFMAhn20,7192
 climate_ref_core/datasets.py,sha256=TK50WQwTfbase26s8wPEGEN1BwcedrOd8nk6IlEf3Ww,6124
 climate_ref_core/diagnostics.py,sha256=5KCtHuhToSpATqjW4HBi56PsOxT5WX4VkqoZPUvYR60,18769
 climate_ref_core/env.py,sha256=Ph2dejVxTELfP3bL0xES086WLGvV5H6KvsOwCkL6m-k,753
-climate_ref_core/exceptions.py,sha256=psdipWURLyMq5hmloGxt-8kyqEe0IsENfraok7KTi8I,1437
-climate_ref_core/executor.py,sha256=NIXIU2rwMnTOR-ztlPlCD-poZO4vxzKQPWYk8veTVkk,5195
-climate_ref_core/logging.py,sha256=EBe5WAk1dtosr8MLkG-i7iDNZTI9ufxI4xsvbq3Gdt8,5260
+climate_ref_core/exceptions.py,sha256=aC_wohLCjOUarZM2VvpGdJzPvYdT31h_MRVbqVk-MIk,1633
+climate_ref_core/executor.py,sha256=QiVOca-d9JxKIktQIinQQYZGr3ecV5mL3nvUwCdMiJQ,5372
+climate_ref_core/logging.py,sha256=cg6CK2DHGjyLaoRJm75p-Ja82hnVhBBQ4riOKk3l9XY,7063
 climate_ref_core/providers.py,sha256=by_ZtoLQgg9A60CbFor2-i5EixtZTZ0z8jQqOGRfvA8,12461
 climate_ref_core/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 climate_ref_core/metric_values/__init__.py,sha256=aHfwRrqzLOmmaBKf1-4q97DnHb8KwmW0Dhwd79ZQiNQ,634
 climate_ref_core/metric_values/typing.py,sha256=2DpzmjqQ7tqOPAyjthZ_O14c0-MhiYt-A_n9p6-bOao,1903
 climate_ref_core/pycmec/README.md,sha256=PzkovlPpsXqFopsYzz5GRvCAipNRGO1Wo-0gc17qr2Y,36
 climate_ref_core/pycmec/__init__.py,sha256=hXvKGEJQWyAp1i-ndr3D4zuYxkRhcR2LfXgFXlhYOk4,28
-climate_ref_core/pycmec/controlled_vocabulary.py,sha256=xio_4jl6mM_WMrwyxo70d0G5dUeIal4IW7eV-EMW4mU,5093
-climate_ref_core/pycmec/cv_cmip7_aft.yaml,sha256=nf7T1S8WJ8ja31DG3E5mxKq3aluF_mwICf38mlFtRDM,2849
-climate_ref_core/pycmec/metric.py,sha256=XXM5DMk0BhpKcPvvCHCcgA6jKoVGMqXcwiG1UerYYps,18181
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+climate_ref_core/pycmec/metric.py,sha256=zymXoutnjbdcxvG_fMJugFLLcBrfSPG0XoV-2tA0ujA,18499
 climate_ref_core/pycmec/output.py,sha256=4-RQ439sfgNLeQZVDPB1pewF_kTwX7nCK0Z4U6bvbd0,5709
-climate_ref_core-0.5.5.dist-info/METADATA,sha256=Hevjf3ZdlpIGHKhFFJDOtDX7BtEOUys35nM42Jru2E4,2889
-climate_ref_core-0.5.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-climate_ref_core-0.5.5.dist-info/licenses/LICENCE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-climate_ref_core-0.5.5.dist-info/licenses/NOTICE,sha256=4qTlax9aX2-mswYJuVrLqJ9jK1IkN5kSBqfVvYLF3Ws,128
-climate_ref_core-0.5.5.dist-info/RECORD,,
+climate_ref_core-0.6.1.dist-info/METADATA,sha256=fVjjH-4zZEbuoFw47Sqo1TRFAWwwiz6BZetTD88xQLE,2934
+climate_ref_core-0.6.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+climate_ref_core-0.6.1.dist-info/licenses/LICENCE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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+climate_ref_core-0.6.1.dist-info/RECORD,,