climate-ref 0.6.5__tar.gz → 0.7.0__tar.gz

{climate_ref-0.6.5 → climate_ref-0.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: climate-ref
-Version: 0.6.5
+Version: 0.7.0
 Summary: Application which runs 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-Expression: Apache-2.0
@@ -70,7 +70,7 @@ pip install climate-ref
 If you want to use the diagnostic providers for the Assessment Fast Track, you can install them with:
 
 ```bash
-pip install climate-ref[aft-providers]
+pip install "climate-ref[aft-providers]"
 ```
 
 ## Quick Start

{climate_ref-0.6.5 → climate_ref-0.7.0}/README.md

@@ -21,7 +21,7 @@ pip install climate-ref
 If you want to use the diagnostic providers for the Assessment Fast Track, you can install them with:
 
 ```bash
-pip install climate-ref[aft-providers]
+pip install "climate-ref[aft-providers]"
 ```
 
 ## Quick Start

{climate_ref-0.6.5 → climate_ref-0.7.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "climate-ref"
-version = "0.6.5"
+version = "0.7.0"
 description = "Application which runs the CMIP Rapid Evaluation Framework"
 readme = "README.md"
 authors = [

{climate_ref-0.6.5 → climate_ref-0.7.0}/src/climate_ref/cli/__init__.py

@@ -3,11 +3,12 @@
 import importlib
 from enum import Enum
 from pathlib import Path
-from typing import Annotated, Optional
+from typing import Annotated
 
 import typer
 from attrs import define
 from loguru import logger
+from rich.console import Console
 
 from climate_ref import __version__
 from climate_ref.cli import config, datasets, executions, providers, solve
@@ -37,6 +38,7 @@ class CLIContext:
 
     config: Config
     database: Database
+    console: Console
 
 
 def _version_callback(value: bool) -> None:
@@ -46,6 +48,13 @@ def _version_callback(value: bool) -> None:
         raise typer.Exit()
 
 
+def _create_console() -> Console:
+    # Hook for testing to disable color output
+
+    # Rich respects the NO_COLOR environment variabl
+    return Console()
+
+
 def _load_config(configuration_directory: Path | None = None) -> Config:
     """
     Load the configuration from the specified directory
@@ -129,7 +138,7 @@ def main(  # noqa: PLR0913
         typer.Option(case_sensitive=False, help="Set the level of logging information to display"),
     ] = LogLevel.Info,
     version: Annotated[
-        Optional[bool],
+        bool | None,
         typer.Option(
             "--version", callback=_version_callback, is_eager=True, help="Print the version and exit"
         ),
@@ -155,7 +164,7 @@ def main(  # noqa: PLR0913
 
     logger.debug(f"Configuration loaded from: {config._config_file!s}")
 
-    ctx.obj = CLIContext(config=config, database=Database.from_config(config))
+    ctx.obj = CLIContext(config=config, database=Database.from_config(config), console=_create_console())
 
 
 if __name__ == "__main__":

{climate_ref-0.6.5 → climate_ref-0.7.0}/src/climate_ref/cli/_utils.py

@@ -5,6 +5,59 @@ from rich.console import Console
 from rich.table import Table
 
 
+def parse_facet_filters(filters: list[str] | None) -> dict[str, str]:
+    """
+    Parse facet filters from key=value format into a dictionary.
+
+    Parameters
+    ----------
+    filters
+        List of filter strings in 'key=value' format
+
+    Returns
+    -------
+    dict[str, str]
+        Dictionary mapping facet keys to values
+
+    Raises
+    ------
+    ValueError
+        If a filter string is not in valid 'key=value' format
+
+    Examples
+    --------
+    >>> parse_facet_filters(["source_id=GFDL-ESM4", "variable_id=tas"])
+    {'source_id': 'GFDL-ESM4', 'variable_id': 'tas'}
+    """
+    if not filters:
+        return {}
+
+    parsed: dict[str, str] = {}
+    for filter_str in filters:
+        if "=" not in filter_str:
+            raise ValueError(
+                f"Invalid filter format: '{filter_str}'. "
+                f"Expected format: 'key=value' or 'dataset_type.key=value' "
+                f"(e.g., 'source_id=GFDL-ESM4' or 'cmip6.source_id=GFDL-ESM4')"
+            )
+
+        key, value = filter_str.split("=", 1)
+        key = key.strip()
+        value = value.strip()
+
+        if not key:
+            raise ValueError(f"Empty key in filter: '{filter_str}'")
+        if not value:
+            raise ValueError(f"Empty value in filter: '{filter_str}'")
+
+        if key in parsed:
+            logger.warning(f"Filter key '{key}' specified multiple times. Using last value: '{value}'")
+
+        parsed[key] = value
+
+    return parsed
+
+
 def df_to_table(df: pd.DataFrame, max_col_count: int = -1) -> Table:
     """
     Convert a DataFrame to a rich Table instance
@@ -32,7 +85,7 @@ def df_to_table(df: pd.DataFrame, max_col_count: int = -1) -> Table:
 
     table = Table(*[str(column) for column in df.columns])
 
-    for index, value_list in enumerate(df.values.tolist()):
+    for value_list in df.values.tolist():
         row = [str(x) for x in value_list]
         table.add_row(*row)
 
@@ -59,7 +112,8 @@ def pretty_print_df(df: pd.DataFrame, console: Console | None = None) -> None:
     # Drop duplicates as they are not informative to CLI users.
     df = df.drop_duplicates()
 
-    if console is None:
+    if console is None:  # pragma: no branch
+        logger.debug("Creating new console for pretty printing")
         console = Console()
 
     max_col_count = console.width // 10

{climate_ref-0.6.5 → climate_ref-0.7.0}/src/climate_ref/cli/datasets.py

@@ -15,9 +15,9 @@ from typing import Annotated
 
 import typer
 from loguru import logger
-from rich.console import Console
 
 from climate_ref.cli._utils import pretty_print_df
+from climate_ref.database import ModelState
 from climate_ref.datasets import get_dataset_adapter
 from climate_ref.models import Dataset
 from climate_ref.provider_registry import ProviderRegistry
@@ -27,7 +27,6 @@ from climate_ref_core.dataset_registry import dataset_registry_manager, fetch_al
 from climate_ref_core.datasets import SourceDatasetType
 
 app = typer.Typer(help=__doc__)
-console = Console()
 
 
 @app.command(name="list")
@@ -70,7 +69,7 @@ def list_(
             raise typer.Exit(code=1)
         data_catalog = data_catalog[column].sort_values(by=column)
 
-    pretty_print_df(data_catalog, console=console)
+    pretty_print_df(data_catalog, console=ctx.obj.console)
 
 
 @app.command()
@@ -97,7 +96,7 @@ def list_columns(
 
 
 @app.command()
-def ingest(  # noqa: PLR0913
+def ingest(  # noqa
     ctx: typer.Context,
     file_or_directory: list[Path],
     source_type: Annotated[SourceDatasetType, typer.Option(help="Type of source dataset")],
@@ -106,7 +105,7 @@ def ingest(  # noqa: PLR0913
     n_jobs: Annotated[int | None, typer.Option(help="Number of jobs to run in parallel")] = None,
     skip_invalid: Annotated[
         bool, typer.Option(help="Ignore (but log) any datasets that don't pass validation")
-    ] = False,
+    ] = True,
 ) -> None:
     """
     Ingest a directory of datasets into the database
@@ -118,6 +117,7 @@ def ingest(  # noqa: PLR0913
     """
     config = ctx.obj.config
     db = ctx.obj.database
+    console = ctx.obj.console
 
     kwargs = {}
 
@@ -135,14 +135,33 @@ def ingest(  # noqa: PLR0913
             logger.error(f"File or directory {_dir} does not exist")
             raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), _dir)
 
-        data_catalog = adapter.find_local_datasets(_dir)
-        data_catalog = adapter.validate_data_catalog(data_catalog, skip_invalid=skip_invalid)
+        # TODO: This assumes that all datasets are nc files.
+        # THis is true for CMIP6 and obs4MIPs but may not be true for other dataset types in the future.
+        if not _dir.rglob("*.nc"):
+            logger.error(f"No .nc files found in {_dir}")
+            continue
+
+        try:
+            data_catalog = adapter.find_local_datasets(_dir)
+            data_catalog = adapter.validate_data_catalog(data_catalog, skip_invalid=skip_invalid)
+        except Exception as e:
+            logger.error(f"Error ingesting datasets from {_dir}: {e}")
+            continue
 
         logger.info(
             f"Found {len(data_catalog)} files for {len(data_catalog[adapter.slug_column].unique())} datasets"
         )
         pretty_print_df(adapter.pretty_subset(data_catalog), console=console)
 
+        # track stats for a given directory
+        num_created_datasets = 0
+        num_updated_datasets = 0
+        num_unchanged_datasets = 0
+        num_created_files = 0
+        num_updated_files = 0
+        num_removed_files = 0
+        num_unchanged_files = 0
+
         for instance_id, data_catalog_dataset in data_catalog.groupby(adapter.slug_column):
             logger.debug(f"Processing dataset {instance_id}")
             with db.session.begin():
@@ -154,9 +173,29 @@ def ingest(  # noqa: PLR0913
                     )
                     if not dataset:
                         logger.info(f"Would save dataset {instance_id} to the database")
-                        continue
                 else:
-                    adapter.register_dataset(config, db, data_catalog_dataset)
+                    results = adapter.register_dataset(config, db, data_catalog_dataset)
+
+                    if results.dataset_state == ModelState.CREATED:
+                        num_created_datasets += 1
+                    elif results.dataset_state == ModelState.UPDATED:
+                        num_updated_datasets += 1
+                    else:
+                        num_unchanged_datasets += 1
+                    num_created_files += len(results.files_added)
+                    num_updated_files += len(results.files_updated)
+                    num_removed_files += len(results.files_removed)
+                    num_unchanged_files += len(results.files_unchanged)
+
+        if not dry_run:
+            ingestion_msg = (
+                f"Datasets: {num_created_datasets}/{num_updated_datasets}/{num_unchanged_datasets}"
+                " (created/updated/unchanged), "
+                f"Files: "
+                f"{num_created_files}/{num_updated_files}/{num_removed_files}/{num_unchanged_files}"
+                " (created/updated/removed/unchanged)"
+            )
+            logger.info(ingestion_msg)
 
     if solve:
         solve_required_executions(