feat: add ERA5 download and aggregation (#61)

* feat: add era5 download modules

* feat: add era5 sync function

* fix: update package dependencies

* fix: add json file as package data

* fix: do not move tmp file before closing

* fix: infinite loop in sync function

* fix: better log message

* fix: better log message

* fix: infinite loop in sync function

* fix: infinite loop in sync function

* feat(era5): download all CDS products for a given period

* fix(era5): do not download daily data if monthly file is present

* fix(era5): compatibility with cads_api_client>=1.4.5

* fix(era5): make datetime unaware of timezones for comparability

* feat(era5): add era5 aggregate module

* docs(era5): add era5 README

* docs(era5): update era5 README

openhexa/toolbox/era5/README.md

@@ -0,0 +1,180 @@
+# OpenHEXA Toolbox ERA5
+
+The package contains ETL classes and functions to acquire and process ERA5-Land data. ERA5-Land
+provides hourly information of surface variables from 1950 to 5 days before the current date, with
+a ~9 km spatial resolution. See [ERA5-Land: data
+documentation](https://confluence.ecmwf.int/display/CKB/ERA5-Land%3A+data+documentation) for more
+information.
+
+Available variables include:
+* 2 metre temperature
+* Wind components
+* Leaf area index
+* Volumetric soil water layer
+* Total precipitation
+
+See [ERA5-Land data
+documentation](https://confluence.ecmwf.int/display/CKB/ERA5-Land%3A+data+documentation#ERA5Land:datadocumentation-parameterlistingParameterlistings)
+for a full list of available parameters.
+
+In addition to download clients for the Copernicus [Climate Data Store](https://cds.climate.copernicus.eu/datasets/reanalysis-era5-land?tab=overview) and [Google Public Datasets](https://cloud.google.com/storage/docs/public-datasets/era5), the package includes an `aggregate` module to aggregate ERA5 measurements in space (geographic boundaries) and time (hourly to daily).
+
+## Usage
+
+The package contains 3 modules:
+* `openhexa.toolbox.era5.cds`: download ERA5-land products from the Copernicus [Climate Data Store](https://cds.climate.copernicus.eu/datasets/reanalysis-era5-land?tab=overview)
+* `openhexa.toolbox.era5.google`: download ERA5 products from Google Cloud [Public Datasets](https://cloud.google.com/storage/docs/public-datasets/era5)
+* `openhexa.toolbox.era5.aggregate`: aggregate ERA5 data in space and time
+
+### Download from CDS
+
+To download products from the Climate Data Store, you will need to create an account and generate an API key in ECMWF (see [CDS](https://cds.climate.copernicus.eu/)).
+
+```python
+from openhexa.toolbox.era5.cds import Client
+
+cds = Client(key="<cds_api_key>")
+
+request = cds.build_request(
+    variable="2m_temperature",
+    year=2024,
+    month=4
+)
+
+cds.download(
+    request=request,
+    dst_file="data/product.grib"
+)
+```
+
+The module also contains helper functions to use bounds from a geoparquet file as an area of
+interest. Source bounds are buffered and rounded by default to make sure the required data is
+downloaded.
+
+```python
+bounds = bounds_from_file(fp=Path("data/districts.parquet"), buffer=0.5)
+
+request = cds.build_request(
+    variable="total_precipitation",
+    year=2023,
+    month=10,
+    days=[1, 2, 3, 4, 5],
+    area=bounds
+)
+
+cds.download(
+    request=request,
+    dst_file="data/product.grib"
+)
+```
+
+To download multiple products for a given period, use `Client.download_between()`:
+
+```python
+cds.download_between(
+    variable="2m_temperature",
+    start=datetime(2020, 1, 1),
+    end=datetime(2021, 6, 1),
+    dst_dir="data/raw/2m_temperature",
+    area=bounds
+)
+```
+
+Checking latest available date in the ERA5-Land dataset:
+
+```python
+cds = Client("<api_key>")
+
+cds.latest
+```
+```
+>>> datetime(2024, 10, 8)
+```
+
+NB: End dates in product requests will be automatically replaced by latest available date if they are greater.
+
+### Download from Google Cloud
+
+```python
+from openhexa.toolbox.era5.google import Client
+
+google = Client()
+
+google.download(
+    variable="2m_temperature",
+    date=datetime(2024, 6, 15),
+    dst_file="data/product.nc"
+)
+```
+
+Or to download all products for a given period:
+
+```python
+# if products are already presents in dst_dir, they will be skipped
+google.sync(
+    variable="2m_temperature",
+    start_date=datetime(2022, 1, 1),
+    end_date=datetime(2022, 6, 1),
+    dst_dir="data"
+)
+```
+
+### Aggregation
+
+```python
+from pathlib import Path
+
+import geopandas as gpd
+from openhexa.toolbox.era5.aggregate import build_masks, merge, aggregate, get_transform
+
+boundaries = gpd.read_parquet("districts.parquet")
+data_dir = Path("data/era5/total_precipitation")
+
+ds = merge(data_dir)
+
+ncols = len(ds.longitude)
+nrows = len(ds.latitude)
+transform = get_transform(ds)
+masks = build_masks(boundaries, nrows, ncols, transform)
+
+df = aggregate(
+    ds=ds,
+    var="tp",
+    masks=masks,
+    boundaries_id=[uid for uid in boundaries["district_id"]]
+)
+
+print(df)
+```
+```
+shape: (18_410, 5)
+┌─────────────┬────────────┬───────────┬──────────┬───────────┐
+│ boundary_id ┆ date       ┆ mean      ┆ min      ┆ max       │
+│ ---         ┆ ---        ┆ ---       ┆ ---      ┆ ---       │
+│ str         ┆ date       ┆ f64       ┆ f64      ┆ f64       │
+╞═════════════╪════════════╪═══════════╪══════════╪═══════════╡
+│ mPenE8ZIBFC ┆ 2024-01-01 ┆ 0.000462  ┆ 0.0      ┆ 0.00086   │
+│ TPgpGxUBU9y ┆ 2024-01-01 ┆ 0.000462  ┆ 0.0      ┆ 0.00086   │
+│ AhST5ZpuCDJ ┆ 2024-01-01 ┆ 0.000462  ┆ 0.0      ┆ 0.00086   │
+│ Lp2BjBVT63s ┆ 2024-01-01 ┆ 0.000462  ┆ 0.0      ┆ 0.00086   │
+│ EdfRX9b9vEb ┆ 2024-01-01 ┆ 0.000462  ┆ 0.0      ┆ 0.00086   │
+│ yhs1ecKsLOc ┆ 2024-01-01 ┆ 0.000462  ┆ 0.0      ┆ 0.00086   │
+│ iHSJypSwlo5 ┆ 2024-01-01 ┆ 0.000462  ┆ 0.0      ┆ 0.00086   │
+│ CTtB0TPRvWc ┆ 2024-01-01 ┆ 0.000462  ┆ 0.0      ┆ 0.00086   │
+│ eVFAuZOzogt ┆ 2024-01-01 ┆ 0.000462  ┆ 0.0      ┆ 0.00086   │
+│ WVEJjdJ2S15 ┆ 2024-01-01 ┆ 0.000462  ┆ 0.0      ┆ 0.00086   │
+│ rbYGKFgupK9 ┆ 2024-01-01 ┆ 0.000462  ┆ 0.0      ┆ 0.00086   │
+│ Nml6rVDElLh ┆ 2024-01-01 ┆ 0.000462  ┆ 0.0      ┆ 0.00086   │
+│ E0hd8TD1M0q ┆ 2024-01-01 ┆ 0.000462  ┆ 0.0      ┆ 0.00086   │
+│ PCg4pLGmKSM ┆ 2024-01-01 ┆ 0.000462  ┆ 0.0      ┆ 0.00086   │
+│ C6EBhE8OnfW ┆ 2024-01-01 ┆ 0.000462  ┆ 0.0      ┆ 0.00086   │
+│ …           ┆ …          ┆ …         ┆ …        ┆ …         │
+│ CkpfOFkMyrd ┆ 2024-10-07 ┆ 1.883121  ┆ 0.001785 ┆ 2.700447  │
+│ tMXsltjzzmR ┆ 2024-10-07 ┆ 3.579136  ┆ 0.105436 ┆ 4.702504  │
+│ F0ytkh0RExg ┆ 2024-10-07 ┆ 8.415455  ┆ 0.838535 ┆ 17.08884  │
+...
+│ TTSmaRnHa82 ┆ 2024-10-07 ┆ 1.724243  ┆ 0.007809 ┆ 5.692989  │
+│ jbmw2gdrrTV ┆ 2024-10-07 ┆ 1.176629  ┆ 0.110173 ┆ 1.582995  │
+│ eKYyXbBdvmB ┆ 2024-10-07 ┆ 0.599976  ┆ 0.037771 ┆ 1.189411  │
+└─────────────┴────────────┴───────────┴──────────┴───────────┘
+```

openhexa/toolbox/era5/__init__.py

@@ -0,0 +1,15 @@
+import logging
+
+import cdsapi
+
+logging.basicConfig(level=logging.DEBUG, format="%(name)s %(asctime)s %(levelname)s %(message)s")
+log = logging.getLogger(__name__)
+
+BASE_URL = "https://cds-beta.climate.copernicus.eu/api"
+
+
+class ERA5:
+    def __init__(self, key: str):
+        self.client = cdsapi.Client(
+            key=key,
+        )