climate-ref 0.5.0__tar.gz

climate_ref-0.5.0/.gitignore

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+# Notebooks
+*.ipynb
+
+# Databases
+*.db
+
+# Jupyter cache
+.jupyter_cache
+
+# IDE stuff
+.idea/
+
+# Ruff cache
+.ruff_cache
+
+# Licence check
+licence-check.txt
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# Mac stuff
+*.DS_Store
+
+# Esgpull
+.esgpull
+
+# Generated output
+out
+.ref
+
+# Ignore copied LICENCE/NOTICE files
+packages/*/LICENCE
+packages/*/NOTICE
+
+# Local directory for data
+/data

climate_ref-0.5.0/Dockerfile

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+# Build the container for the the REF compute engine
+# This docker container packages up the REF cli tool with the default set of diagnostic providers
+# used as part of the CMIP7 FastTrack process.
+
+FROM ghcr.io/astral-sh/uv:python3.11-bookworm-slim AS build
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    git \
+    && rm -rf /var/lib/apt/lists/*
+
+# Enable bytecode compilation
+ENV UV_COMPILE_BYTECODE=1
+
+# Copy from the cache instead of linking since it's a mounted volume
+ENV UV_LINK_MODE=copy
+
+WORKDIR /app
+
+# Install the project's dependencies using the lockfile and settings
+RUN --mount=type=cache,target=/root/.cache/uv \
+    --mount=type=bind,source=uv.lock,target=uv.lock \
+    --mount=type=bind,source=pyproject.toml,target=pyproject.toml \
+    uv sync --frozen --no-install-workspace --no-editable --no-dev
+
+# Then, add the rest of the project source code and install it
+# Installing separately from its dependencies allows optimal layer caching
+ADD . /app
+
+# Sync the project as non-editable installs
+RUN --mount=type=cache,target=/root/.cache/uv \
+    uv sync --frozen --no-editable --no-dev
+
+# Runtime container
+# Copy the installed packages from the build stage to decrease the size of the final image
+FROM python:3.11-slim AS runtime
+
+LABEL maintainer="Jared Lewis <jared.lewis@climate-resource.com>"
+LABEL description="Docker image for the REF compute engine"
+
+# Allow celery to run as root
+ENV C_FORCE_ROOT=false
+ENV PATH="/app/.venv/bin:${PATH}"
+
+# Copy the installed packages from the build stage
+COPY --from=build --chown=app:app /app/.venv /app/.venv
+COPY --from=build --chown=app:app /app/scripts /app/scripts
+
+# Location of the REF configuration files
+ENV REF_CONFIGURATION=/ref
+ENV REF_METRICS_ESMVALTOOL_DATA_DIR=/app/cache/esmvaltool
+
+#RUN ref datasets fetch-data --registry ilamb
+#RUN ref datasets fetch-data --registry iomb
+
+# Run the REF CLI tool by default
+ENTRYPOINT ["/app/.venv/bin/ref"]

climate_ref-0.5.0/LICENCE

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climate_ref-0.5.0/NOTICE

@@ -0,0 +1,3 @@
+Assessment Fast Track Rapid Evaluation Framework
+
+Copyright 2024- CMIP7 Assessment Fast Track REF Technical Implementation Team

climate_ref-0.5.0/PKG-INFO

@@ -0,0 +1,97 @@
+Metadata-Version: 2.4
+Name: climate-ref
+Version: 0.5.0
+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: Apache-2.0
+License-File: LICENCE
+License-File: NOTICE
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.11
+Requires-Dist: alembic>=1.13.3
+Requires-Dist: attrs>=24.2.0
+Requires-Dist: cattrs>=24.1.2
+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: platformdirs>=4.3.6
+Requires-Dist: setuptools>=75.8.0
+Requires-Dist: sqlalchemy>=2.0.36
+Requires-Dist: tomlkit>=0.13.2
+Requires-Dist: typer>=0.12.5
+Provides-Extra: celery
+Requires-Dist: climate-ref-celery>=0.5.0; extra == 'celery'
+Provides-Extra: metrics
+Requires-Dist: climate-ref-esmvaltool>=0.5.0; extra == 'metrics'
+Requires-Dist: climate-ref-ilamb>=0.5.0; extra == 'metrics'
+Requires-Dist: climate-ref-pmp>=0.5.0; extra == 'metrics'
+Provides-Extra: postgres
+Requires-Dist: psycopg2-binary>=2.9.2; extra == 'postgres'
+Description-Content-Type: text/markdown
+
+# Climate REF (Rapid Evaluation Framework)
+
+[![PyPI version](https://badge.fury.io/py/climate-ref.svg)](https://badge.fury.io/py/climate-ref)
+[![Documentation Status](https://readthedocs.org/projects/climate-ref/badge/?version=latest)](https://climate-ref.readthedocs.io/en/latest/?badge=latest)
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![Python Version](https://img.shields.io/badge/python-3.11%2B-blue)](https://www.python.org/downloads/)
+
+**Status**: This project is in active development. We expect to be ready for beta releases in Q2 2025.
+
+The Rapid Evaluation Framework (REF) is a set of Python packages that provide the ability to manage the execution of calculations against climate datasets.
+The aim is to be able to evaluate climate data against a set of reference data in near-real time as datasets are published,
+and to update any produced data and figures as new datasets become available.
+This is somewhat analogous to a CI/CD pipeline for climate data.
+
+## Installation
+
+```bash
+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[metrics]
+```
+
+## Quick Start
+
+```bash
+# Ingest some observation datasets
+ref datasets fetch-data --registry obs4ref --output-dir datasets/obs4ref
+ref datasets fetch-data --registry sample-data --output-dir datasets/sample-data
+
+# Run metrics against your climate data
+ref solve
+```
+
+## Features
+
+- Real-time evaluation of climate datasets
+- Support for multiple metrics providers (PMP, ILAMB, ESMValTool)
+- Distributed processing capabilities
+- Extensible architecture for adding new metrics providers
+- Command-line interface for easy interaction
+
+## Documentation
+
+For detailed documentation, please visit [https://climate-ref.readthedocs.io/](https://climate-ref.readthedocs.io/)
+
+## Contributing
+
+REF is a community project, and we welcome contributions from anyone. Please see our [Contributing Guide](https://climate-ref.readthedocs.io/en/latest/contributing/) for more information.
+
+## License
+
+This project is licensed under the Apache License 2.0 - see the [LICENSE](LICENSE) file for details.

climate_ref-0.5.0/README.md

@@ -0,0 +1,56 @@
+# Climate REF (Rapid Evaluation Framework)
+
+[![PyPI version](https://badge.fury.io/py/climate-ref.svg)](https://badge.fury.io/py/climate-ref)
+[![Documentation Status](https://readthedocs.org/projects/climate-ref/badge/?version=latest)](https://climate-ref.readthedocs.io/en/latest/?badge=latest)
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![Python Version](https://img.shields.io/badge/python-3.11%2B-blue)](https://www.python.org/downloads/)
+
+**Status**: This project is in active development. We expect to be ready for beta releases in Q2 2025.
+
+The Rapid Evaluation Framework (REF) is a set of Python packages that provide the ability to manage the execution of calculations against climate datasets.
+The aim is to be able to evaluate climate data against a set of reference data in near-real time as datasets are published,
+and to update any produced data and figures as new datasets become available.
+This is somewhat analogous to a CI/CD pipeline for climate data.
+
+## Installation
+
+```bash
+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[metrics]
+```
+
+## Quick Start
+
+```bash
+# Ingest some observation datasets
+ref datasets fetch-data --registry obs4ref --output-dir datasets/obs4ref
+ref datasets fetch-data --registry sample-data --output-dir datasets/sample-data
+
+# Run metrics against your climate data
+ref solve
+```
+
+## Features
+
+- Real-time evaluation of climate datasets
+- Support for multiple metrics providers (PMP, ILAMB, ESMValTool)
+- Distributed processing capabilities
+- Extensible architecture for adding new metrics providers
+- Command-line interface for easy interaction
+
+## Documentation
+
+For detailed documentation, please visit [https://climate-ref.readthedocs.io/](https://climate-ref.readthedocs.io/)
+
+## Contributing
+
+REF is a community project, and we welcome contributions from anyone. Please see our [Contributing Guide](https://climate-ref.readthedocs.io/en/latest/contributing/) for more information.
+
+## License
+
+This project is licensed under the Apache License 2.0 - see the [LICENSE](LICENSE) file for details.

climate_ref-0.5.0/conftest.py

@@ -0,0 +1,88 @@
+import importlib.resources
+import shutil
+from pathlib import Path
+from urllib import parse as urlparse
+
+import pandas as pd
+import pytest
+from climate_ref_example import provider as example_provider
+from pytest_regressions.data_regression import RegressionYamlDumper
+from yaml.representer import SafeRepresenter
+
+from climate_ref.config import Config
+from climate_ref.database import Database
+from climate_ref.datasets.cmip6 import CMIP6DatasetAdapter
+from climate_ref.datasets.obs4mips import Obs4MIPsDatasetAdapter
+from climate_ref.models.metric_value import MetricValue
+from climate_ref.provider_registry import _register_provider
+from climate_ref_core.pycmec.controlled_vocabulary import CV
+
+# Ignore the alembic folder
+collect_ignore = ["src/climate_ref/migrations"]
+
+# Add a representer for pandas Timestamps/NaT in the regression tests
+RegressionYamlDumper.add_representer(
+    pd.Timestamp, lambda dumper, data: SafeRepresenter.represent_datetime(dumper, data.to_pydatetime())
+)
+RegressionYamlDumper.add_representer(
+    type(pd.NaT), lambda dumper, data: SafeRepresenter.represent_none(dumper, data)
+)
+
+
+def _clone_db(target_db_url: str, template_db_path: Path) -> None:
+    split_url = urlparse.urlsplit(target_db_url)
+    target_db_path = Path(split_url.path[1:])
+    target_db_path.parent.mkdir(parents=True)
+
+    shutil.copy(template_db_path, target_db_path)
+
+
+@pytest.fixture
+def db(config) -> Database:
+    return Database.from_config(config, run_migrations=True)
+
+
+@pytest.fixture(scope="session")
+def cmip7_aft_cv() -> CV:
+    cv_file = str(importlib.resources.files("climate_ref_core.pycmec") / "cv_cmip7_aft.yaml")
+
+    return CV.load_from_file(cv_file)
+
+
+@pytest.fixture(scope="session")
+def prepare_db(cmip7_aft_cv):
+    MetricValue.register_cv_dimensions(cmip7_aft_cv)
+
+
+@pytest.fixture(scope="session")
+def db_seeded_template(tmp_path_session, cmip6_data_catalog, obs4mips_data_catalog, prepare_db) -> Path:
+    template_db_path = tmp_path_session / "climate_ref_template_seeded.db"
+
+    config = Config.default()  # This is just dummy config
+    database = Database(f"sqlite:///{template_db_path}")
+    database.migrate(config)
+
+    # Seed the CMIP6 sample datasets
+    adapter = CMIP6DatasetAdapter()
+    with database.session.begin():
+        for instance_id, data_catalog_dataset in cmip6_data_catalog.groupby(adapter.slug_column):
+            adapter.register_dataset(config, database, data_catalog_dataset)
+
+    # Seed the obs4MIPs sample datasets
+    adapter_obs = Obs4MIPsDatasetAdapter()
+    with database.session.begin():
+        for instance_id, data_catalog_dataset in obs4mips_data_catalog.groupby(adapter_obs.slug_column):
+            adapter_obs.register_dataset(config, database, data_catalog_dataset)
+
+    with database.session.begin():
+        _register_provider(database, example_provider)
+
+    return template_db_path
+
+
+@pytest.fixture
+def db_seeded(db_seeded_template, config) -> Database:
+    # Copy the template database to the location in the config
+    _clone_db(config.db.database_url, db_seeded_template)
+
+    return Database.from_config(config, run_migrations=True)