From e2d377f2ad98e6480fbf569406b3e8beef602fbd Mon Sep 17 00:00:00 2001 From: Nathan Collier Date: Fri, 24 Jan 2025 11:10:33 -0500 Subject: [PATCH] CHANGE: switch to uv for deps/CI, pooch for data retrieval (#10) * switch to uv and pooch to fix failing tests * update to deps * removing the notion of models from ilamb * CI changes --- .github/workflows/ci.yml | 23 +- .readthedocs.yml | 13 +- ci/environment-docs.yml | 26 - ci/environment.yml | 19 - docs/jupyter.md | 14 +- ilamb3/__init__.py | 25 +- ilamb3/models/__init__.py | 5 - ilamb3/models/esgf.py | 51 - ilamb3/registry/ilamb.txt | 121 ++ ilamb3/tests/comprehensive.py | 113 -- ilamb3/tests/test_regions.py | 9 +- pyproject.toml | 35 +- uv.lock | 2373 +++++++++++++++++++++++++++++++++ 13 files changed, 2562 insertions(+), 265 deletions(-) delete mode 100644 ci/environment-docs.yml delete mode 100644 ci/environment.yml delete mode 100644 ilamb3/models/__init__.py delete mode 100644 ilamb3/models/esgf.py create mode 100644 ilamb3/registry/ilamb.txt delete mode 100644 ilamb3/tests/comprehensive.py create mode 100644 uv.lock diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7da9c28..e71ee3a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -26,29 +26,24 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.10", "3.11", "3.12", "3.13"] os: [ubuntu] #, macos, windows] steps: - uses: actions/checkout@v4 with: fetch-depth: 0 # Fetch all history for all branches and tags. - - name: Create conda environment - uses: mamba-org/setup-micromamba@v1 - with: - cache-downloads: true - environment-file: ci/environment.yml - environment-name: ilamb3-dev - create-args: >- - python=${{ matrix.python-version }} + - name: Install uv environment + uses: astral-sh/setup-uv@v4 + + - name: Set up Python ${{ matrix.python-version }} + run: uv python install ${{ matrix.python-version }} - - name: Install ilamb3 - run: | - python -m pip install -e . --no-deps --force-reinstall + - name: Install ilamb3 and dependencies + run: uv sync - name: Run Tests - run: | - python -m pytest + run: uv run pytest - name: Upload coverage reports to Codecov uses: codecov/codecov-action@v4.0.1 diff --git a/.readthedocs.yml b/.readthedocs.yml index 1aed175..6d162d4 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -1,7 +1,12 @@ version: 2 -conda: - environment: ci/environment-docs.yml + build: - os: "ubuntu-20.04" + os: "ubuntu-24.04" tools: - python: "mambaforge-4.10" + python: "3.12" + commands: + - asdf plugin add uv + - asdf install uv latest + - asdf global uv latest + - uv sync --group doc + - uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html diff --git a/ci/environment-docs.yml b/ci/environment-docs.yml deleted file mode 100644 index 81a2e7c..0000000 --- a/ci/environment-docs.yml +++ /dev/null @@ -1,26 +0,0 @@ -name: ilamb3-doc -channels: - - conda-forge - - defaults -dependencies: - - furo - - numpydoc - - numpy - - xarray - - pint-xarray - - cf_xarray - - pandas - - intake - - matplotlib - - intake-xarray - - scipy - - requests - - aiohttp - - jinja2 - - pip - - pip: - - myst_nb - - sphinx_autosummary_accessors - - sphinx_copybutton - - sphinx_autodoc_typehints - - -e .. diff --git a/ci/environment.yml b/ci/environment.yml deleted file mode 100644 index 395c083..0000000 --- a/ci/environment.yml +++ /dev/null @@ -1,19 +0,0 @@ -name: ilamb3-dev -channels: - - conda-forge - - nodefaults -dependencies: - - python>=3.9 - - numpy - - xarray - - pint-xarray - - cf_xarray - - pandas - - intake - - intake-xarray - - scipy - - pytest - - pytest-cov - - requests - - aiohttp - - jinja2 diff --git a/docs/jupyter.md b/docs/jupyter.md index 2aa40c4..c3c5402 100644 --- a/docs/jupyter.md +++ b/docs/jupyter.md @@ -12,22 +12,20 @@ kernelspec: `ilamb3` has been redesigned to allow you to import our analysis functions and run them locally on your own datasets. This means that you can apply our analysis methods in your own Jupyter notebooks and python scripts. First, we import the functionality that we will need. ```{code-cell} -import intake import matplotlib.pyplot as plt - +import xarray as xr +import ilamb3 from ilamb3.analysis import bias_analysis ``` ILAMB analysis functions are available in the `ilamb3.analysis` package. You can import just this package and browse the member functions to see what is available. In this example, we will run the ILAMB bias methodology and so we import only this function. The ILAMB analysis functions have been redesigned to take as inputs two xarray datasets, a reference and a comparison. In this example, we will load two of our biomass reference data products and use the ILAMB bias methodology to compare them. -ILAMB reference datasets are available through an [intake](https://github.com/intake/intake) catalog. To use it, you only need to install the `intake` package and then add the following call to `open_catalog()`. We will use the catalog to load the biomass products from [Xu & Saatchi, 2021](https://zenodo.org/records/4161694) and [ESACCI](https://climate.esa.int/en/projects/biomass/). +ILAMB reference datasets are available through an [pooch](https://github.com/fatiando/pooch) registry available via `ilamb3.open_catalog()`. We will use the catalog to load the biomass products from [Xu & Saatchi, 2021](https://zenodo.org/records/4161694) and [ESACCI](https://climate.esa.int/en/projects/biomass/). ```{code-cell} -cat = intake.open_catalog( - "https://raw.githubusercontent.com/nocollier/intake-ilamb/main/ilamb.yaml" -) -ds_xusaatchi = cat["biomass | XuSaatchi2021"].read() -ds_esacci = cat["biomass | ESACCI"].read() +cat = ilamb3.ilamb_catalog() +ds_xusaatchi = xr.open_dataset(cat.fetch("biomass/XuSaatchi2021/XuSaatchi.nc")) +ds_esacci = xr.open_dataset(cat.fetch("biomass/ESACCI/biomass.nc")) ``` Now that this data is loaded into memory as xarray datasets, we can initialize an ILAMB bias analysis. diff --git a/ilamb3/__init__.py b/ilamb3/__init__.py index a50fab1..545c643 100644 --- a/ilamb3/__init__.py +++ b/ilamb3/__init__.py @@ -2,8 +2,10 @@ # import these packages so that units via pint will be possible once anything # from ilamb is imported. -import intake +import importlib + import pint_xarray # noqa +import pooch import xarray as xr from cf_xarray.units import units @@ -15,18 +17,29 @@ units.define("Pg = 1e15 * g") -def ilamb_catalog() -> intake.Catalog: +def ilamb_catalog() -> pooch.Pooch: """ - Return the intake ilamb reference data catalog. + Return the pooch ilamb reference data catalog. Returns ------- - intake.Catalog + pooch.Pooch The intake ilamb reference data catalog. """ - return intake.open_catalog( - "https://raw.githubusercontent.com/nocollier/intake-ilamb/main/ilamb.yaml" + + _ILAMB_DATA_VERSION = ( + "0.1" # we don't really have data versions for the collection :/ + ) + registry = pooch.create( + path=pooch.os_cache("ilamb3"), + base_url="https://www.ilamb.org/ILAMB-Data/DATA", + version=_ILAMB_DATA_VERSION, + env="ILAMB_ROOT", + ) + registry.load_registry( + importlib.resources.open_binary("ilamb3.registry", "ilamb.txt") ) + return registry __all__ = ["dataset", "compare", "analysis", "regions", "ilamb_catalog"] diff --git a/ilamb3/models/__init__.py b/ilamb3/models/__init__.py deleted file mode 100644 index 6b615f1..0000000 --- a/ilamb3/models/__init__.py +++ /dev/null @@ -1,5 +0,0 @@ -"""Model abstractions used in ILAMB.""" - -from ilamb3.models.esgf import ModelESGF - -__all__ = ["ModelESGF"] diff --git a/ilamb3/models/esgf.py b/ilamb3/models/esgf.py deleted file mode 100644 index 755e17f..0000000 --- a/ilamb3/models/esgf.py +++ /dev/null @@ -1,51 +0,0 @@ -import xarray as xr -from intake_esgf import ESGFCatalog -from intake_esgf.exceptions import NoSearchResults - -from ilamb3.exceptions import VarNotInModel - - -def _create_cell_measures(ds: xr.Dataset, variable_id: str) -> xr.Dataset: - """Create cell measures from the areacella/sftlf or areacello/sftof information.""" - da = ds[variable_id] - if "cell_measures" not in da.attrs: - return ds - cm = da.attrs["cell_measures"].replace("area: ", "") - ds = ds.rename({cm: "cell_measures"}) - if "cell_methods" not in da.attrs: - return ds - for domain, frac in zip(["land", "ocean"], ["sftlf", "sftof"]): - if domain in da.attrs["cell_methods"] and frac in ds: - fr = ds["sftlf"] - if fr.max() > 50.0: - fr = fr * 0.01 - ds["cell_measures"] *= fr - ds = ds.drop_vars(frac) - return ds - - -class ModelESGF: - def __init__(self, source_id: str, variant_label: str, grid_label: str): - self.search = dict( - source_id=source_id, - variant_label=variant_label, - grid_label=grid_label, - experiment_id="historical", - frequency="mon", - ) - - def __repr__(self): - return f"{self.search['source_id']}|{self.search['variant_label']}|{self.search['grid_label']}" - - def get_variable(self, variable_id: str, quiet: bool = True) -> xr.Dataset: - search = self.search.copy() - search.update({"variable_id": variable_id}) - try: - cat = ESGFCatalog().search(quiet=quiet, **search) - except NoSearchResults: - raise VarNotInModel(f"{variable_id} not in {self.__repr__()}") - if len(cat.df) > 1: - cat.df = cat.df.iloc[0] - ds = cat.to_dataset_dict(quiet=quiet)[variable_id] - ds = _create_cell_measures(ds, variable_id) - return ds diff --git a/ilamb3/registry/ilamb.txt b/ilamb3/registry/ilamb.txt new file mode 100644 index 0000000..7c2ca76 --- /dev/null +++ b/ilamb3/registry/ilamb.txt @@ -0,0 +1,121 @@ +hfss/FLUXNET2015/hfss.nc sha1:a4952cbd4735c8a13e53ee979bfe382e3db09034 +hfss/WECANN/hfss.nc sha1:66aef4700703b28a5a18e8454757e0e2dbe67a17 +hfss/FLUXCOM/sh.nc 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comprehensive tests of ilamb3. -""" - -import logging -from traceback import format_exc - -import intake_esgf -import pandas as pd -import xarray as xr -from intake_esgf import ESGFCatalog -from tqdm import tqdm - -from ilamb3.analysis.base import ILAMBAnalysis -from ilamb3.models.esgf import ModelESGF - - -def get_logger() -> logging.Logger: - """ - Setup the location and logging for this package. - - Returns - ------- - logginer.Logger - The logging object configured for use in the tests. - """ - - # We need a named logger to avoid other packages that use the root logger - logger = logging.getLogger("ilamb3") - if not logger.handlers: - # Now setup the file into which we log relevant information - file_handler = logging.FileHandler("test.log") - file_handler.setFormatter( - logging.Formatter( - "%(asctime)s %(message)s", - datefmt="%Y-%m-%d %H:%M:%S", - ) - ) - file_handler.setLevel(logging.DEBUG) - logger.addHandler(file_handler) - logger.setLevel(logging.DEBUG) - - # This is probably wrong, but when I log from my logger it logs from parent also - logger.parent.handlers = [] - return logger - - -def get_ilamb_models() -> pd.Series: - """ - Return the model groups present in ESGF which are applicable to ilamb. - - Returns - ------- - pd.Series - The series whose index consists of `source_id`, `member_id`, and `grid_label`. - """ - variables = ["cSoil", "cVeg", "gpp", "lai", "nbp"] - with intake_esgf.conf.set(additional_df_cols=[]): - cat = ( - ESGFCatalog() - .search( - experiment_id="historical", - frequency="mon", - variable_id=variables, - ) - .remove_incomplete( - lambda df: ( - False - if (set(variables) - set(df["variable_id"].unique())) - else True - ) - ) - .remove_ensembles() - ) - return cat.model_groups() - - -def comprehensive_test_harness( - ref: xr.Dataset, - model_groups: pd.Series, - analysis: ILAMBAnalysis, - **analysis_kwargs: dict, -) -> pd.DataFrame: - - logger = get_logger() - dfs = [] - for model, variant, grid in tqdm(model_groups.index, desc=" Confronting models"): - try: - com = xr.merge( - [ - ModelESGF(model, variant, grid).get_variable(var) - for var in analysis.required_variables() - ] - ) - except Exception: - logger.debug( - f"({model}, {variant}, {grid}) model initialization failure\n{format_exc()}" - ) - continue - try: - df, _, _ = analysis(ref, com, **analysis_kwargs) - except Exception: - logger.debug( - f"({model}, {variant}, {grid}) analysis method failure\n{format_exc()}" - ) - continue - logger.info(f"({model}, {variant}, {grid}) completed") - df["source"] = df["source"].apply( - lambda c: model if c == "Comparison" else "Reference" - ) - dfs.append(df) - df = pd.concat(dfs).set_index(["source", "name"]).drop_duplicates() - return df diff --git a/ilamb3/tests/test_regions.py b/ilamb3/tests/test_regions.py index ead9fa1..fe4a196 100644 --- a/ilamb3/tests/test_regions.py +++ b/ilamb3/tests/test_regions.py @@ -1,8 +1,9 @@ from pathlib import Path -import intake import numpy as np +import xarray as xr +import ilamb3 from ilamb3.regions import Regions from ilamb3.tests.test_dataset import generate_test_dset @@ -15,10 +16,8 @@ def test_basic(): def test_netcdf(): # can we add regions via a dataset? - cat = intake.open_catalog( - "https://raw.githubusercontent.com/nocollier/intake-ilamb/main/ilamb.yaml" - ) - dsr = cat["regions_global_land | ILAMB"].read() + cat = ilamb3.ilamb_catalog() + dsr = xr.open_dataset(cat.fetch("regions/GlobalLand.nc")) reg = Regions() lbl = reg.add_netcdf(dsr) assert "global" in lbl diff --git a/pyproject.toml b/pyproject.toml index c7e1425..829996d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,4 +1,3 @@ - [project] authors = [ {name = "Nathan Collier", email = "nathaniel.collier@gmail.com"}, @@ -21,27 +20,35 @@ dynamic = ["version"] license = {text = "BSD-3-Clause"} name = "ilamb3" readme = "README.md" -requires-python = ">=3.9" +requires-python = ">=3.10" dependencies = [ - "numpy", - "xarray", - "pint-xarray", - "cf_xarray", - 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