aggfly 0.1.0__tar.gz

aggfly-0.1.0/LICENSE

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aggfly-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: aggfly
+Version: 0.1.0
+Summary: Efficient spatial and temporal aggregation of gridded climate data
+Author: Dylan Hogan
+Author-email: dth2133@columbia.edu
+Requires-Python: >=3.11.6
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: dask (>=2023.11.0,<2024.0.0)
+Requires-Dist: dask-geopandas (>=0.3.1,<0.4.0)
+Requires-Dist: dill (>=0.3.8,<0.4.0)
+Requires-Dist: geopandas (>=0.14.4,<0.15.0)
+Requires-Dist: matplotlib (>=3.9.0,<4.0.0)
+Requires-Dist: netcdf4 (>=1.6.5,<2.0.0)
+Requires-Dist: numba (>=0.59.1,<0.60.0)
+Requires-Dist: numpy (>=1.26.4,<2.0.0)
+Requires-Dist: pandas (>=2.2.2,<3.0.0)
+Requires-Dist: pygeos (>=0.14,<0.15)
+Requires-Dist: pytest (>=8.2.1,<9.0.0)
+Requires-Dist: pyyaml (>=6.0.1,<7.0.0)
+Requires-Dist: rasterio (>=1.3.10,<2.0.0)
+Requires-Dist: rioxarray (>=0.15.5,<0.16.0)
+Requires-Dist: xarray (>=2024.5.0,<2025.0.0)
+Requires-Dist: zarr (>=2.18.2,<3.0.0)
+Description-Content-Type: text/markdown
+
+# aggfly
+A more permanent home for my climate data aggregation code
+
+Will add docs and instructions in the next few weeks as I have time. For questions in the meantime, feel free to email me at `dth2133@columbia.edu`.
+
+The `aggfly-dev-environment.yml` file provides the core packages you'll need to run the code. You can use this file to recreate the conda environment I use to develop the package. Check out the [conda documentation](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-from-an-environment-yml-file) if you need help using it. The following command (executed from root directory of the repository) should be sufficient for most users:
+
+```
+conda env create --file aggfly-dev-environment.yml -n aggfly-dev 
+```
+
+Once you have all the dependencies, you can install this package by running `pip install -e .` from the root directory of the repository.
+
+```
+conda activate aggfly-dev
+pip install -e .
+```
+
+Of course, please feel free to suggest changes/improvements/extensions in [Issues](https://github.com/dylanhogan/aggfly/issues) :)
+

aggfly-0.1.0/README.md

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+# aggfly
+A more permanent home for my climate data aggregation code
+
+Will add docs and instructions in the next few weeks as I have time. For questions in the meantime, feel free to email me at `dth2133@columbia.edu`.
+
+The `aggfly-dev-environment.yml` file provides the core packages you'll need to run the code. You can use this file to recreate the conda environment I use to develop the package. Check out the [conda documentation](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-from-an-environment-yml-file) if you need help using it. The following command (executed from root directory of the repository) should be sufficient for most users:
+
+```
+conda env create --file aggfly-dev-environment.yml -n aggfly-dev 
+```
+
+Once you have all the dependencies, you can install this package by running `pip install -e .` from the root directory of the repository.
+
+```
+conda activate aggfly-dev
+pip install -e .
+```
+
+Of course, please feel free to suggest changes/improvements/extensions in [Issues](https://github.com/dylanhogan/aggfly/issues) :)

aggfly-0.1.0/aggfly/__init__.py

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+from .aggregate import (
+    TemporalAggregator,
+    SpatialAggregator,
+    aggregate_dataset,
+    aggregate_time,
+    aggregate_space,
+    distributed_client,
+    is_distributed,
+    start_dask_client,
+    shutdown_dask_client
+)
+from .dataset import Dataset, Grid, dataset_from_path
+from .weights import (
+    CropWeights, 
+    PopWeights, 
+    GridWeights, 
+    SecondaryWeights,
+    weights_from_objects, 
+    pop_weights_from_path, 
+    crop_weights_from_path,
+    secondary_weights_from_path
+)
+from .regions import GeoRegions, georegions_from_path, georegions_from_name
+from .tests import (
+    georegion,
+    dataset_360,
+    secondary_weights,
+    weights,
+    test_weights,
+    test_aggregate_time,
+    test_aggregate
+)

aggfly-0.1.0/aggfly/aggregate/__init__.py

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+from .aggregate_utils import *
+from .aggregate import aggregate_dataset, aggregate_time, aggregate_space
+from .temporal import TemporalAggregator
+from .spatial import SpatialAggregator
+

aggfly-0.1.0/aggfly/aggregate/aggregate.py

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+"""
+This module contains functions for aggregating datasets over time and space.
+
+Functions:
+- transform_dataset(dataset: Dataset, key: str, **kwargs: Union[int, List[int]]) -> Dict[str, Dataset]:
+    Transform a given dataset by raising it to a power or interacting with another dataset.
+
+- aggregate_time(dataset: Dataset, aggregator_dict: Dict[str, Union[List[Tuple], TemporalAggregator]] = None, weights: GridWeights = None, **kwargs) -> Dict[str, Dataset]:
+    Aggregate a dataset over time using the specified temporal aggregators.
+
+- aggregate_space(dataset_dict: Dict[str, Dataset], weights: GridWeights) -> pd.DataFrame:
+    Aggregate a dictionary of datasets over space.
+
+- aggregate_dataset(dataset: Dataset, weights: GridWeights, aggregator_dict: Dict[str, Union[List[Tuple], TemporalAggregator]] = None, **kwargs) -> pd.DataFrame:
+    Aggregate a dataset over time and space.
+"""
+
+from typing import List, Dict, Union, Tuple
+import pandas as pd
+import dask
+from dask.distributed import LocalCluster, Client, progress
+
+from .temporal import TemporalAggregator
+from .spatial import SpatialAggregator
+from ..dataset import Dataset
+from ..weights import GridWeights
+from .aggregate_utils import distributed_client, is_distributed, start_dask_client, shutdown_dask_client
+
+
+from dask.diagnostics import ProgressBar
+ProgressBar().register()
+
+
+def transform_dataset(
+    dataset: Dataset, key: str, **kwargs: Union[int, List[int]]
+) -> Dict[str, Dataset]:
+    """
+    Transform a given dataset by raising it to a power or interacting with another dataset.
+
+    Args:
+        dataset (Dataset): The dataset to transform.
+        key (str): The name of the dataset.
+        **kwargs:   Keyword arguments for the transformation.
+                    If 'exp' is provided, raise the dataset to the power of the provided exponent(s).
+                    If 'inter' is provided, interact the dataset with another dataset.
+
+    Returns:
+        dict: A dictionary containing the transformed dataset(s).
+    """
+
+    if "exp" in kwargs:
+        if not isinstance(kwargs["exp"], list):
+            kwargs["exp"] = [kwargs["exp"]]
+        dataset = [dataset.power(exp) for exp in kwargs["exp"][0]]
+        new_keys = [f"{key}_{exp}" for exp in kwargs["exp"][0]]
+        output_dict = dict(zip(new_keys, dataset))
+    elif "inter" in kwargs:
+        dataset = dataset.interact(kwargs["inter"])
+        output_dict = {key: dataset}
+    else:
+        raise ValueError("No valid transform argument provided.")
+    return output_dict.values(), output_dict.keys()
+
+
+def aggregate_time(
+    dataset: Dataset,
+    weights: GridWeights = None,
+    aggregator_dict: Dict[str, Union[List[Tuple], TemporalAggregator]] = None,
+    **kwargs,
+) -> Dict[str, Dataset]:
+    """
+    Aggregate a dataset over time using the specified temporal aggregators.
+
+    Args:
+        dataset (Dataset): The dataset to aggregate.
+        weights (GridWeights, optional): The weights to use for aggregation. Defaults to None.
+        aggregator_dict (Dict[str, Union[List[Tuple], TemporalAggregator]], optional): A dictionary of temporal aggregators to apply to the dataset. Defaults to None.
+        **kwargs: Additional keyword arguments to use if `aggregator_dict` is not provided.
+
+    Returns:
+        Dict[str, Dataset]: A dictionary of aggregated datasets, with keys corresponding to the keys in `aggregator_dict`.
+    """
+
+
+def aggregate_time(
+    dataset: Dataset,
+    weights: GridWeights = None,
+    aggregator_dict: Dict[str, Union[List[Tuple], TemporalAggregator]] = None,
+    **kwargs,
+) -> Dict[str, Dataset]:
+    if aggregator_dict is None:
+        if kwargs is None:
+            raise ValueError("No arguments provided.")
+        else:
+            aggregator_dict = kwargs
+    out_dict = {}
+    for key, value in aggregator_dict.items():
+        keys = [key]
+        data = [dataset.deepcopy()]
+        for key2, value2 in value:
+            if key2 == "aggregate":
+                if not isinstance(value2, TemporalAggregator):
+                    value2 = TemporalAggregator(**value2)
+                data = [value2.execute(x, weights) for x in data]
+
+                if value2.multi_dd:
+                    if len(data) > 1:
+                        raise ValueError(
+                            "Cannot aggregate multiple datasets with multiple ddargs, e.g., multiple polynomials for multiple bins"
+                        )
+                    data, keys = multi_dd_to_dict(data[0], key, value2.ddargs)
+
+            elif key2 == "transform":
+                transformed_data, transformed_keys = [], []
+                for d, k in zip(data, keys):
+                    d2, k2 = transform_dataset(d, k, **value2)
+                    transformed_data.extend(d2)
+                    transformed_keys.extend(k2)
+                data, keys = transformed_data, transformed_keys
+
+        data_dict = dict(zip(keys, data))
+        out_dict = out_dict | data_dict
+    return out_dict
+
+
+def aggregate_space(
+    dataset_dict: Dict[str, Dataset], weights: GridWeights,
+    npartitions=None, **kwargs
+) -> pd.DataFrame:
+    """
+    Aggregate a dictionary of datasets over space.
+
+    Args:
+        dataset_dict (dict): A dictionary containing the datasets to aggregate, where
+                            the keys are the names of the datasets and the values are the datasets themselves.
+        weights (GridWeights): The weights to use for aggregation.
+
+    Returns:
+        df: A dataframe containing the aggregated data.
+    """
+    
+    
+    dataset_list = list(dataset_dict.values())
+    
+    # client = distributed_client()
+    # if client is None and npartitions is None:
+    #     npartitions=1
+    # else:
+        # npartitions=len(client.scheduler_info()["workers"])
+        # da_list = dask.persist([x.da for x in dataset_list])[0]
+        # progress(da_list)
+        # for i, dataset in enumerate(dataset_list):
+        #     dataset.da = da_list[i]
+    df = SpatialAggregator(
+        dataset_list, weights, names=list(dataset_dict.keys()),
+    ).compute(npartitions=npartitions)
+    return df
+
+
+def aggregate_dataset(
+    weights: GridWeights,
+    dataset: Dataset = None,
+    aggregator_dict: Dict[str, Union[List[Tuple], TemporalAggregator]] = None,
+    dataset_dict = None,
+    n_workers = 50,
+    threads_per_worker = 1,
+    processes = True,
+    memory_limit=None,
+    cluster_args = {},
+    **kwargs,
+) -> pd.DataFrame:
+    """
+    Aggregate a dataset over time and space.
+
+    Args:
+        dataset (Dataset): The dataset to aggregate.
+        weights (GridWeights): The weights to use for aggregation.
+        agg_dict (dict): A dictionary containing the arguments for creating TemporalAggregator objects.
+                        The keys of the dictionary are names, and the values are a list of either tuples or TemporalAggregator objects.
+                        If the list contains tuples, use them as arguments to instantiate a temporal aggregator.
+
+    Returns:
+        df: A dataframe containing the aggregated data.
+    """
+
+    if dataset is None:
+        raise ValueError("No dataset provided.")
+    
+    if aggregator_dict is None and kwargs is not None:
+        aggregator_dict = kwargs
+    
+    if aggregator_dict is not None:
+        dataset_dict = aggregate_time(dataset, weights, aggregator_dict)
+    elif dataset_dict is None:
+        dataset_dict = {"variable": dataset}
+        if dataset_dict is None and dataset is None:
+            raise ValueError("No aggregator dict or dataset dict provided.")
+
+    df = aggregate_space(dataset_dict, weights)
+    df = (
+        weights.georegions.shp[[weights.georegions.regionid]].merge(
+            df, left_index=True, right_on="region_id"
+        )
+    ).drop(columns="region_id")
+    
+    # client.shutdown()
+
+    # _ = shutdown_dask_client()
+    
+    return df
+
+
+def multi_dd_to_dict(data, key, ddargs):
+    """
+    Converts a multi-variable list of datasets to a dictionary with keys
+    generated from the given key and ddargs.
+
+    Args:
+        data (list): The list of Datasets to convert to a dictionary.
+        key (str): The base key to use for generating the dictionary keys.
+        ddargs (list): A list of tuples representing the dimensions of the array.
+
+    Returns:
+        dict: A dictionary with keys generated from the given key and ddargs, and values from the list of datasets.
+    """
+    keys = [f"{key}_{x[0]}_{x[1]}" for x in ddargs]
+    # data_dict = dict(zip(keys, data))
+    return data, keys

aggfly-0.1.0/aggfly/aggregate/aggregate_utils.py

@@ -0,0 +1,76 @@
+import dask.distributed
+from dask.distributed import Client
+import logging
+
+def is_distributed():
+    """
+    Returns True if the code is running in a distributed environment, False otherwise.
+    
+    This function checks if the code is running in a distributed environment by attempting to get the global Dask client.
+    If the client is not None, it means that the code is running in a distributed environment.
+    
+    Returns:
+        bool: True if the code is running in a distributed environment, False otherwise.
+    """
+    client = dask.distributed.client._get_global_client()
+    if client is not None:
+        return True
+    else:
+        return False
+    
+def distributed_client():
+    """
+    Returns the global Dask distributed client object.
+
+    Returns:
+    --------
+    client : dask.distributed.Client
+        The global Dask distributed client object.
+    """
+    client = dask.distributed.client._get_global_client()
+    return client 
+
+        
+def start_dask_client(n_workers: int = 2, threads_per_worker: int = 2, **kwargs):
+    """
+    Start a dask distributed cluster.
+
+    Args:
+        n_workers (int, optional): The number of workers to use. Defaults to 2.
+        threads_per_worker (int, optional): The number of threads per worker. Defaults to 2.
+        **kwargs: Additional keyword arguments to pass to the dask Client constructor.
+
+    Returns:
+        client: A dask distributed client.
+    """
+    client = Client(
+        n_workers=n_workers,
+        threads_per_worker=threads_per_worker,
+        **kwargs
+    )
+        
+    arg_dict = {
+        "n_workers": n_workers, 
+        "threads_per_worker": threads_per_worker,
+    }
+    all_dict = {**arg_dict, **kwargs}
+    for k in all_dict.keys():
+        client.set_metadata(['args', k], all_dict[k])
+    
+    return client
+
+
+def shutdown_dask_client():
+    """
+    Shutdown the global Dask distributed client object.
+    """
+    client = dask.distributed.client._get_global_client()
+    if client is not None:
+        try:
+            args = client.get_metadata('args')
+        except:
+            raise ValueError("Please start Dask client with af.start_dask_client() or run weight calculation without Dask distributed client.")
+        client.shutdown()
+        return args
+    else:
+        return None