climate-ref 0.6.1__tar.gz → 0.6.3__tar.gz

{climate_ref-0.6.1 → climate_ref-0.6.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: climate-ref
-Version: 0.6.1
+Version: 0.6.3
 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 → climate_ref-0.6.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "climate-ref"
-version = "0.6.1"
+version = "0.6.3"
 description = "Application which runs the CMIP Rapid Evaluation Framework"
 readme = "README.md"
 authors = [
@@ -16,7 +16,6 @@ license = "Apache-2.0"
 requires-python = ">=3.11"
 classifiers = [
     "Development Status :: 3 - Alpha",
-    "Operating System :: OS Independent",
     "Intended Audience :: Developers",
     "Intended Audience :: Science/Research",
     "Programming Language :: Python",
@@ -26,6 +25,8 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering",
     "License :: OSI Approved :: Apache Software License",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: POSIX :: Linux",
 ]
 dependencies = [
     "climate-ref-core",
@@ -40,7 +41,9 @@ dependencies = [
     "ecgtools>=2024.7.31",
     "platformdirs>=4.3.6",
     "tqdm>=4.67.1",
-    "parsl>=2025.5.19"
+    # parsl doesn't support Windows yet
+    # We don't target Windows either, but this __might__ allow Windows users to install the package
+    'parsl>=2025.5.19; sys_platform != "win32"'
 ]
 
 [project.optional-dependencies]

{climate_ref-0.6.1 → climate_ref-0.6.3}/src/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-0.6.1 → climate_ref-0.6.3}/src/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-0.6.1 → climate_ref-0.6.3}/src/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-0.6.1 → climate_ref-0.6.3}/src/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-0.6.1 → climate_ref-0.6.3}/src/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-0.6.1 → climate_ref-0.6.3}/src/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-0.6.1 → climate_ref-0.6.3}/src/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-0.6.1 → climate_ref-0.6.3}/src/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-0.6.1 → climate_ref-0.6.3}/src/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 → climate_ref-0.6.3}/tests/unit/cli/test_config.py

@@ -30,9 +30,9 @@ class TestConfigList:
         assert "Configuration file not found" in result.stdout
 
 
-class TestConfigUpdate:
-    def test_config_update(self, invoke_cli):
-        result = invoke_cli(["config", "update"])
-
-        # TODO: actually implement this functionality
-        assert "config" in result.stdout
+# class TestConfigUpdate:
+#     def test_config_update(self, invoke_cli):
+#         result = invoke_cli(["config", "update"])
+#
+#         # TODO: actually implement this functionality
+#         assert "config" in result.stdout

{climate_ref-0.6.1 → climate_ref-0.6.3}/tests/unit/cli/test_datasets.py

@@ -11,7 +11,7 @@ from climate_ref.models.dataset import CMIP6Dataset, DatasetFile
 def test_ingest_help(invoke_cli):
     result = invoke_cli(["datasets", "ingest", "--help"])
 
-    assert "Ingest a dataset" in result.stdout
+    assert "Ingest a directory of dataset" in result.stdout
 
 
 class TestDatasetsList:

{climate_ref-0.6.1 → climate_ref-0.6.3}/tests/unit/cli/test_executions.py

@@ -11,7 +11,7 @@ from climate_ref.models.execution import execution_datasets
 def test_execution_help(invoke_cli):
     result = invoke_cli(["executions", "--help"])
 
-    assert "View diagnostic executions" in result.stdout
+    assert "View execution groups" in result.stdout
 
 
 class TestExecutionList:

{climate_ref-0.6.1 → climate_ref-0.6.3}/tests/unit/cli/test_root.py

@@ -16,8 +16,8 @@ def escape_ansi(line):
 def test_without_subcommand(invoke_cli):
     result = invoke_cli([])
     assert "Usage:" in result.stdout
-    assert "climate_ref [OPTIONS] COMMAND [ARGS]" in result.stdout
-    assert "climate_ref: A CLI for the Assessment Fast Track Rapid Evaluation Framework" in result.stdout
+    assert "ref [OPTIONS] COMMAND [ARGS]" in result.stdout
+    assert "A CLI for the Assessment Fast Track Rapid Evaluation Framework" in result.stdout
 
 
 def test_version(invoke_cli):

{climate_ref-0.6.1 → climate_ref-0.6.3}/tests/unit/executor/test_hpc_executor.py

@@ -8,7 +8,7 @@ from parsl.dataflow import futures
 from climate_ref.executor.hpc import HPCExecutor, execute_locally
 from climate_ref.executor.local import ExecutionFuture
 from climate_ref_core.diagnostics import ExecutionResult
-from climate_ref_core.exceptions import DiagnosticError, ExecutionError
+from climate_ref_core.exceptions import DiagnosticError
 from climate_ref_core.executor import Executor
 
 
@@ -74,12 +74,37 @@ class TestHPCExecutor:
 
         assert len(executor.parsl_results) == 0
 
-    def test_join_exception(self, metric_definition, tmp_path):
+    def test_join_diagnostic_exception(self, metric_definition, tmp_path):
+        executor = HPCExecutor(log_dir=tmp_path / "parsl_runinfo")
+        future = futures.AppFuture(1)
+        executor.parsl_results = [ExecutionFuture(future, definition=metric_definition, execution_id=None)]
+
+        execution_result = ExecutionResult(
+            definition=metric_definition,
+            successful=False,
+            output_bundle_filename=None,
+            metric_bundle_filename=None,
+        )
+
+        future.set_exception(DiagnosticError("Some thing bad went wrong", execution_result))
+        err_result = executor.parsl_results[0].future.exception().result
+
+        executor.join(0.1)
+
+        assert err_result == ExecutionResult(
+            definition=metric_definition,
+            successful=False,
+            output_bundle_filename=None,
+            metric_bundle_filename=None,
+        )
+        assert len(executor.parsl_results) == 0
+
+    def test_join_other_exception(self, metric_definition, tmp_path):
         executor = HPCExecutor(log_dir=tmp_path / "parsl_runinfo")
         future = futures.AppFuture(1)
         executor.parsl_results = [ExecutionFuture(future, definition=metric_definition, execution_id=None)]
 
         future.set_exception(ValueError("Some thing bad went wrong"))
 
-        with pytest.raises(ExecutionError, match=re.escape("Failed to execute 'mock_provider/mock/key'")):
+        with pytest.raises(AssertionError, match=re.escape("Execution result should not be None")):
             executor.join(0.1)

{climate_ref-0.6.1 → climate_ref-0.6.3}/tests/unit/test_config.py

@@ -183,6 +183,14 @@ filename = "sqlite://climate_ref.db"
         assert config_new.paths.log == Path("/my/test/logs")
         assert config_new.paths.results == Path("/my/test/executions")
 
+    def test_custom_env_variable(self, monkeypatch, tmp_path, config):
+        monkeypatch.setenv("ABC", "/my")
+        config.paths.results = "${ABC}/test/executions"
+        # Environment variables are only expanded when loading from file.
+        config.save(tmp_path / "ref.toml")
+        config_new = Config.load(tmp_path / "ref.toml")
+        assert config_new.paths.results == Path("/my/test/executions")
+
     def test_executor_build(self, config, db):
         executor = config.executor.build(config, db)
         assert executor.name == "synchronous"

{climate_ref-0.6.1 → climate_ref-0.6.3}/tests/unit/test_slurm.py

@@ -1,3 +1,4 @@
+import os
 from unittest.mock import MagicMock
 
 import pytest
@@ -343,6 +344,9 @@ def test_slurm_checker(
     assert checker.can_account_use_qos("climate_ref1", "normal") is True
     assert checker.can_account_use_qos("climate_ref3", "normal") is False
 
+    os.environ["USER"] = "test_user"
+    assert checker.can_account_use_qos("climate_ref1", "normal") is True
+
     assert checker.get_partition_limits("cpu") == {
         "max_time_minutes": 7200,
         "default_time_minutes": 720,