climate-ref 0.6.1__py3-none-any.whl → 0.6.2__py3-none-any.whl

climate_ref/cli/__init__.py

@@ -88,7 +88,7 @@ def build_app() -> typer.Typer:
     :
         The CLI app
     """
-    app = typer.Typer(name="climate_ref", no_args_is_help=True)
+    app = typer.Typer(name="ref", no_args_is_help=True)
 
     app.command(name="solve")(solve.solve)
     app.add_typer(config.app, name="config")
@@ -136,10 +136,10 @@ def main(  # noqa: PLR0913
     ] = None,
 ) -> None:
     """
-    climate_ref: A CLI for the Assessment Fast Track Rapid Evaluation Framework
+    A CLI for the Assessment Fast Track Rapid Evaluation Framework
 
     This CLI provides a number of commands for managing and executing diagnostics.
-    """
+    """  # noqa: D401
     if quiet:
         log_level = LogLevel.Warning
     if verbose:

climate_ref/cli/config.py

@@ -20,9 +20,9 @@ def list_(ctx: typer.Context) -> None:
     print(config.dumps(defaults=True))
 
 
-@app.command()
-def update() -> None:
-    """
-    Update a configuration value
-    """
-    print("config")
+# @app.command()
+# def update() -> None:
+#     """
+#     Update a configuration value
+#     """
+#     print("config")

climate_ref/cli/datasets.py

@@ -1,5 +1,9 @@
 """
 View and ingest input datasets
+
+The metadata from these datasets are stored in the database so that they can be used to determine
+which executions are required for a given diagnostic without having to re-parse the datasets.
+
 """
 
 import errno
@@ -105,9 +109,12 @@ def ingest(  # noqa: PLR0913
     ] = False,
 ) -> None:
     """
-    Ingest a dataset
+    Ingest a directory of datasets into the database
+
+    Each dataset will be loaded and validated using the specified dataset adapter.
+    This will extract metadata from the datasets and store it in the database.
 
-    This will register a dataset in the database to be used for diagnostics calculations.
+    A table of the datasets will be printed to the console at the end of the operation.
     """
     config = ctx.obj.config
     db = ctx.obj.database

climate_ref/cli/executions.py

@@ -1,5 +1,5 @@
 """
-View diagnostic executions
+View execution groups and their results
 """
 
 import pathlib
@@ -29,11 +29,19 @@ console = Console()
 @app.command()
 def list_groups(
     ctx: typer.Context,
-    column: Annotated[list[str] | None, typer.Option()] = None,
+    column: Annotated[
+        list[str] | None,
+        typer.Option(help="Only include specified columns in the output"),
+    ] = None,
     limit: int = typer.Option(100, help="Limit the number of rows to display"),
 ) -> None:
     """
     List the diagnostic execution groups that have been identified
+
+    The data catalog is sorted by the date that the execution group was created (first = newest).
+    If the `--column` option is provided, only the specified columns will be displayed.
+
+    The output will be in a tabular format.
     """
     session = ctx.obj.database.session
 
@@ -178,6 +186,8 @@ def _log_panel(result_directory: pathlib.Path) -> Panel | None:
 def inspect(ctx: typer.Context, execution_id: int) -> None:
     """
     Inspect a specific execution group by its ID
+
+    This will display the execution details, datasets, results directory, and logs if available.
     """
     config: Config = ctx.obj.config
     session = ctx.obj.database.session

climate_ref/cli/providers.py

@@ -56,7 +56,10 @@ def create_env(
     ] = None,
 ) -> None:
     """
-    Create a virtual environment containing the provider software.
+    Create a conda environment containing the provider software.
+
+    If no provider is specified, all providers will be installed.
+    If the provider is up to date or does not use a virtual environment, it will be skipped.
     """
     config = ctx.obj.config
     db = ctx.obj.database

climate_ref/cli/solve.py

@@ -49,6 +49,10 @@ def solve(  # noqa: PLR0913
 
     This may trigger a number of additional calculations depending on what data has been ingested
     since the last solve.
+    This command will block until all executions have been solved or the timeout is reached.
+
+    Filters can be applied to limit the diagnostics and providers that are considered, see the options
+    `--diagnostic` and `--provider` for more information.
     """
     config = ctx.obj.config
     db = ctx.obj.database

climate_ref/config.py

@@ -15,6 +15,7 @@ which always take precedence over any other configuration values.
 # https://github.com/ESGF/esgf-download/blob/main/esgpull/config.py
 
 import importlib.resources
+import os
 from pathlib import Path
 from typing import TYPE_CHECKING, Any
 
@@ -64,6 +65,7 @@ def ensure_absolute_path(path: str | Path) -> Path:
     """
     if isinstance(path, str):
         path = Path(path)
+    path = Path(*[os.path.expandvars(p) for p in path.parts])
     return path.resolve()
 
 

climate_ref/executor/hpc.py

@@ -7,9 +7,14 @@ If you want to
 
 """
 
+try:
+    import parsl
+except ImportError:  # pragma: no cover
+    raise ImportError("The HPCExecutor requires the `parsl` package")
+
 import os
 import time
-from typing import Any, cast
+from typing import Any
 
 import parsl
 from loguru import logger
@@ -41,7 +46,7 @@ def _process_run(definition: ExecutionDefinition, log_level: str) -> ExecutionRe
     except DiagnosticError as e:  # pragma: no cover
         # any diagnostic error will be caught here
         logger.exception("Error running diagnostic")
-        return cast(ExecutionResult, e.result)
+        raise e
 
 
 def _to_float(x: Any) -> float | None:
@@ -264,20 +269,27 @@ class HPCExecutor:
                 # Iterate over a copy of the list and remove finished tasks
                 for result in results[:]:
                     if result.future.done():
-                        try:
-                            execution_result = result.future.result(timeout=0)
-                        except Exception as e:
-                            # Something went wrong when attempting to run the execution
-                            # This is likely a failure in the execution itself not the diagnostic
-                            raise ExecutionError(
-                                f"Failed to execute {result.definition.execution_slug()!r}"
-                            ) from e
+                        # Cannot catch the execption raised by result.future.result
+                        if result.future.exception() is None:
+                            try:
+                                execution_result = result.future.result(timeout=0)
+                            except Exception as e:
+                                # Something went wrong when attempting to run the execution
+                                # This is likely a failure in the execution itself not the diagnostic
+                                raise ExecutionError(
+                                    f"Failed to execute {result.definition.execution_slug()!r}"
+                                ) from e
+                        else:
+                            err = result.future.exception()
+                            if isinstance(err, DiagnosticError):
+                                execution_result = err.result
+                            else:
+                                execution_result = None
 
                         assert execution_result is not None, "Execution result should not be None"
                         assert isinstance(execution_result, ExecutionResult), (
                             "Execution result should be of type ExecutionResult"
                         )
-
                         # Process the result in the main process
                         # The results should be committed after each execution
                         with self.database.session.begin():
@@ -286,7 +298,7 @@ class HPCExecutor:
                                 if result.execution_id
                                 else None
                             )
-                            process_result(self.config, self.database, result.future.result(), execution)
+                            process_result(self.config, self.database, execution_result, execution)
                         logger.debug(f"Execution completed: {result}")
                         t.update(n=1)
                         results.remove(result)

climate_ref/slurm.py

@@ -1,4 +1,5 @@
 import importlib.util
+import os
 from typing import Any
 
 HAS_REAL_SLURM = importlib.util.find_spec("pyslurm") is not None
@@ -85,10 +86,13 @@ class SlurmChecker:
             return False
 
         sample_acc = account_info[0]
-        for acc in account_info:
-            if acc.user == "minxu":
-                sample_acc = acc
-                break
+        user_name = os.environ["USER"]
+
+        if user_name:
+            for acc in account_info:
+                if acc.user == user_name:
+                    sample_acc = acc
+                    break
 
         allowed_qoss = sample_acc.qos
         if allowed_qoss is None:

{climate_ref-0.6.1.dist-info → climate_ref-0.6.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: climate-ref
-Version: 0.6.1
+Version: 0.6.2
 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
@@ -10,7 +10,8 @@ Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: Apache Software License
-Classifier: Operating System :: OS Independent
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: POSIX :: Linux
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
@@ -25,7 +26,7 @@ Requires-Dist: climate-ref-core
 Requires-Dist: ecgtools>=2024.7.31
 Requires-Dist: environs>=11.0.0
 Requires-Dist: loguru>=0.7.2
-Requires-Dist: parsl>=2025.5.19
+Requires-Dist: parsl>=2025.5.19; sys_platform != 'win32'
 Requires-Dist: platformdirs>=4.3.6
 Requires-Dist: sqlalchemy>=2.0.36
 Requires-Dist: tomlkit>=0.13.2

{climate_ref-0.6.1.dist-info → climate_ref-0.6.2.dist-info}/RECORD

@@ -1,21 +1,21 @@
 climate_ref/__init__.py,sha256=M45QGfl0KCPK48A8MjI08weNvZHMYH__GblraQMxsoM,808
 climate_ref/_config_helpers.py,sha256=-atI5FX7SukhLE_jz_rL-EHQ7s0YYqKu3dSFYWxSyMU,6632
 climate_ref/alembic.ini,sha256=WRvbwSIFuZ7hWNMnR2-yHPJAwYUnwhvRYBzkJhtpGdg,3535
-climate_ref/config.py,sha256=SHxqdpzq-TIfAdhwk1Yt-ob96T2a3pqYcq-Wed4Ljgg,16882
+climate_ref/config.py,sha256=T1WzwFhzJ2-RKnOzyOmyUsdXrj_KDW2eycdPXZKnbf0,16954
 climate_ref/constants.py,sha256=9RaNLgUSuQva7ki4eRW3TjOKeVP6T81QNiu0veB1zVk,111
 climate_ref/database.py,sha256=b_6XHdr78Mo7KeLqQJ5DjLsySHPdQE83P8dRpdMfzfM,8661
 climate_ref/provider_registry.py,sha256=dyfj4vU6unKHNXtT03HafQtAi3LilL37uvu3paCnmNY,4159
 climate_ref/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-climate_ref/slurm.py,sha256=20of7zMEeCg8BVQmy_IjSgZ8AJlYJbb8MK2Rjuzig-U,7215
+climate_ref/slurm.py,sha256=XWXVPdXP-4BDib3bxYW9uPcAJdPpo1ixYZAI_y1cZuw,7305
 climate_ref/solver.py,sha256=T5sQjweSvpUMG4q8MfbGjljxa5kBgKxNotT78PwyxqU,16804
 climate_ref/testing.py,sha256=1b9lVCJlKxjJ7JGq6zDD2gK3BEM9ZVv1dbA-j6yb4Yk,4256
-climate_ref/cli/__init__.py,sha256=q-JAiRmwTXqapJGwtfuZ2P-L1a4XAmWj3CoZKLWlP3A,4357
+climate_ref/cli/__init__.py,sha256=fvENOeL4j7CMPANVxrDlWfaB0QUvvYgrWcm5ptbL0P8,4350
 climate_ref/cli/_utils.py,sha256=6bIb8zEVvzXyKpv8MG58T-T2L2jH-G8WNrOOGpz3uCw,1918
-climate_ref/cli/config.py,sha256=8I6CLdqKgTu6yaASy-qG0T839Fc0lDZtLSZ6YCc4wOY,520
-climate_ref/cli/datasets.py,sha256=5fEh4VnQUcQKxSsFc8u6lWkOlpv7-ix-1eccK2TET9c,7890
-climate_ref/cli/executions.py,sha256=sZXyVFYWML5mD7dE8xlsqyunsrwOIweTBDEUKCjXEpo,6798
-climate_ref/cli/providers.py,sha256=eS9IaQxW8zGxidr8TWt7thdMU5JH53u4T3xbcIe2C_E,2455
-climate_ref/cli/solve.py,sha256=qc7yalXxqdcSZsoCh2ZSV7Mt6mxTKc4lg7zKpMA55Y8,2112
+climate_ref/cli/config.py,sha256=ak4Rn9S6fH23PkHHlI-pXuPiZYOvUB4r26eu3p525-M,532
+climate_ref/cli/datasets.py,sha256=4iYQZ0ceoF-Cd8eSpS4Q8b9aLt_vEDUw5slzGw02DsY,8277
+climate_ref/cli/executions.py,sha256=2MjwxCdRB-uVJUg7RluDIf_IsoclRn22ibJjk_nhfPo,7215
+climate_ref/cli/providers.py,sha256=-5hQkJc01jON1bc1dk--tSWTesyiHOzZuYMb9Vxge9k,2613
+climate_ref/cli/solve.py,sha256=ZTXrwDFDXNrX5GLMJTN9tFnpV3zlcZbEu2aF3JDJVxI,2367
 climate_ref/dataset_registry/obs4ref_reference.txt,sha256=2zJMbsAsQ49KaWziX3CqrlILq9yN7S2ygmfV3V5rsnw,8395
 climate_ref/dataset_registry/sample_data.txt,sha256=3JAHy14pRbLlo9-oNxUXLgZ_QOFJXUieEftBbapSY8E,20124
 climate_ref/datasets/__init__.py,sha256=PV3u5ZmhyfcHbKqySgwVA8m4-naZgxzydLXSBqdTGLM,1171
@@ -25,7 +25,7 @@ climate_ref/datasets/obs4mips.py,sha256=CmMm4kopfb0yFsMSgUlHUm8clGJImBaodSkh6lAv
 climate_ref/datasets/pmp_climatology.py,sha256=goHDc_3B2Wdiy_hmpERNvWDdDYZACPOyFDt3Du6nGc0,534
 climate_ref/datasets/utils.py,sha256=iLJO7h4G3DWsRe9hIC4qkIyi5_zIW1ZMw-FDASLujtM,359
 climate_ref/executor/__init__.py,sha256=PYtJs3oBS_GiUHbt8BF-6wJibpF6_vREm1Cg9TxVbLI,648
-climate_ref/executor/hpc.py,sha256=2uZkSXww-oMqmzrYmh21hwJ7Mjjpojg-AhxX8eX_8Qo,11677
+climate_ref/executor/hpc.py,sha256=4o90sCyoC4jlkem3BXNo4uwFZpIvOUGfrqYucB6EtU8,12251
 climate_ref/executor/local.py,sha256=65LUl41YtURFb87YTWZQHjDpIRlIKJ5Ny51c9DZjy0s,8582
 climate_ref/executor/result_handling.py,sha256=i7ZMX5vvyPY5gW-WWd-JHLi1BLviB9FXhn4FE8C9d4w,7787
 climate_ref/executor/synchronous.py,sha256=o4TndsoKMu9AzJYLkusU9lRkgHCy6HcCP46tEs6o86U,1895
@@ -41,9 +41,9 @@ climate_ref/models/diagnostic.py,sha256=YB6xzbEXdpz2j-Ddf19RV8mAiWBrkmtRmiAEUV3t
 climate_ref/models/execution.py,sha256=lRCpaKLSR7rZbuoL94GW76tm9wLMsSDoIOA7bIa6xgY,9848
 climate_ref/models/metric_value.py,sha256=44OLcZz-qLx-p_9w7YWDKpD5S7Y9HyTKKsvSb77RBro,10190
 climate_ref/models/provider.py,sha256=RAE2qAAxwObu-72CdK4kt5ACMmKYEn07WJm7DU9hF28,990
-climate_ref-0.6.1.dist-info/METADATA,sha256=X-O5GFGtgPisrdsh0VZp4v5JgqOXF9e5Kqx1jYkxbkI,4431
-climate_ref-0.6.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-climate_ref-0.6.1.dist-info/entry_points.txt,sha256=IaggEJlDIhoYWXdXJafacWbWtCcoEqUKceP1qD7_7vU,44
-climate_ref-0.6.1.dist-info/licenses/LICENCE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-climate_ref-0.6.1.dist-info/licenses/NOTICE,sha256=4qTlax9aX2-mswYJuVrLqJ9jK1IkN5kSBqfVvYLF3Ws,128
-climate_ref-0.6.1.dist-info/RECORD,,
+climate_ref-0.6.2.dist-info/METADATA,sha256=1yFQ4n5psYiBtO6jmhhEMdWkpOhM74sD_rE92XXm3Do,4505
+climate_ref-0.6.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+climate_ref-0.6.2.dist-info/entry_points.txt,sha256=IaggEJlDIhoYWXdXJafacWbWtCcoEqUKceP1qD7_7vU,44
+climate_ref-0.6.2.dist-info/licenses/LICENCE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+climate_ref-0.6.2.dist-info/licenses/NOTICE,sha256=4qTlax9aX2-mswYJuVrLqJ9jK1IkN5kSBqfVvYLF3Ws,128
+climate_ref-0.6.2.dist-info/RECORD,,