fix(doc): compilation dependencies (#205)

* fix(doc): compilation dependencies

* style: lint

* update .gitignore for pyenv

.gitignore

@@ -24,6 +24,7 @@ __pycache__/
 
 # Distribution / packaging
 .Python
+.python-version
 build/
 develop-eggs/
 dist/

disdrodb/configs.py

@@ -5,7 +5,6 @@
 @author: ghiggi
 """
 import os
-from typing import Dict
 
 from disdrodb.utils.yaml import read_yaml, write_yaml
 
@@ -66,7 +65,7 @@ def define_disdrodb_configs(base_dir: str = None, zenodo_token: str = None, zeno
     return
 
 
-def read_disdrodb_configs() -> Dict[str, str]:
+def read_disdrodb_configs() -> dict[str, str]:
     """
     Reads the DISDRODB configuration file and returns a dictionary with the configuration settings.
 

disdrodb/data_transfer/download_data.py

@@ -20,7 +20,7 @@
 
 import os
 import shutil
-from typing import List, Optional, Union
+from typing import Optional, Union
 
 import click
 import pooch
@@ -97,9 +97,9 @@ def click_download_options(function: object):
 
 
 def download_archive(
-    data_sources: Optional[Union[str, List[str]]] = None,
-    campaign_names: Optional[Union[str, List[str]]] = None,
-    station_names: Optional[Union[str, List[str]]] = None,
+    data_sources: Optional[Union[str, list[str]]] = None,
+    campaign_names: Optional[Union[str, list[str]]] = None,
+    station_names: Optional[Union[str, list[str]]] = None,
     force: bool = False,
     base_dir: Optional[str] = None,
 ):
@@ -222,7 +222,7 @@ def _has_disdrodb_data_url(metadata_filepath):
     return _is_valid_disdrodb_data_url(disdrodb_data_url)
 
 
-def _select_metadata_with_remote_data_url(metadata_filepaths: List[str]) -> List[str]:
+def _select_metadata_with_remote_data_url(metadata_filepaths: list[str]) -> list[str]:
     """Select metadata files that have a remote data url specified."""
     return [fpath for fpath in metadata_filepaths if _has_disdrodb_data_url(fpath)]
 

disdrodb/data_transfer/upload_data.py

@@ -18,7 +18,7 @@
 # -----------------------------------------------------------------------------.
 """Routines to upload data to the DISDRODB Decentralized Data Archive."""
 
-from typing import List, Optional
+from typing import Optional
 
 import click
 
@@ -95,7 +95,7 @@ def _check_if_upload(metadata_filepath: str, force: bool):
             raise ValueError(f"'force' is False and {metadata_filepath} has already a 'disdrodb_data_url' specified.")
 
 
-def _filter_already_uploaded(metadata_filepaths: List[str], force: bool) -> List[str]:
+def _filter_already_uploaded(metadata_filepaths: list[str], force: bool) -> list[str]:
     """Filter metadata files that already have a remote url specified."""
     filtered = []
     for metadata_filepath in metadata_filepaths:

disdrodb/data_transfer/zenodo.py

@@ -20,7 +20,6 @@
 
 import json
 import os
-from typing import Tuple
 
 import requests
 
@@ -52,7 +51,7 @@ def _check_http_response(
     raise ValueError(error_message)
 
 
-def _create_zenodo_deposition(sandbox) -> Tuple[int, str]:
+def _create_zenodo_deposition(sandbox) -> tuple[int, str]:
     """Create a new Zenodo deposition and get the deposit information.
 
     At every function call, the deposit_id and bucket url will change !

disdrodb/l0/check_configs.py

@@ -19,7 +19,7 @@
 """Check configuration files."""
 
 import os
-from typing import List, Optional, Union
+from typing import Optional, Union
 
 import numpy as np
 from pydantic import BaseModel, ValidationError, field_validator, model_validator
@@ -134,7 +134,7 @@ class L0BEncodingSchema(BaseModel):
     shuffle: bool
     fletcher32: bool
     _FillValue: Optional[Union[int, float]]
-    chunksizes: Optional[Union[int, List[int]]]
+    chunksizes: Optional[Union[int, list[int]]]
 
     # if contiguous=False, chunksizes specified, otherwise should be not !
     @model_validator(mode="before")
@@ -212,10 +212,10 @@ class RawDataFormatSchema(BaseModel):
     n_characters: Optional[int]
     n_decimals: Optional[int]
     n_naturals: Optional[int]
-    data_range: Optional[List[float]]
+    data_range: Optional[list[float]]
     nan_flags: Optional[Union[int, str]] = None
-    valid_values: Optional[List[float]] = None
-    dimension_order: Optional[List[str]] = None
+    valid_values: Optional[list[float]] = None
+    dimension_order: Optional[list[str]] = None
     n_values: Optional[int] = None
     field_number: Optional[str] = None
 

disdrodb/tests/test_l0/test_config_files.py

@@ -18,7 +18,7 @@
 # -----------------------------------------------------------------------------.
 """Check DISDRODB L0 configuration files."""
 import os
-from typing import Dict, Union
+from typing import Union
 
 import pytest
 import yaml
@@ -30,7 +30,7 @@
 CONFIG_FOLDER = os.path.join(__root_path__, "disdrodb", "l0", "configs")
 
 
-def read_yaml_file(filepath: str) -> Dict:
+def read_yaml_file(filepath: str) -> dict:
     """Read a YAML file and return a dictionary.
 
     Parameters

disdrodb/utils/netcdf.py

@@ -19,7 +19,6 @@
 """DISDRODB netCDF utility."""
 
 import logging
-from typing import Tuple
 
 import numpy as np
 import pandas as pd
@@ -31,7 +30,7 @@
 
 
 ####---------------------------------------------------------------------------.
-def _sort_datasets_by_dim(list_ds: list, filepaths: str, dim: str = "time") -> Tuple[list, list]:
+def _sort_datasets_by_dim(list_ds: list, filepaths: str, dim: str = "time") -> tuple[list, list]:
     """Sort a list of xarray.Dataset and corresponding file paths by the starting value of a specified dimension.
 
     Parameters
@@ -55,7 +54,7 @@ def _sort_datasets_by_dim(list_ds: list, filepaths: str, dim: str = "time") -> T
     return sorted_list_ds, sorted_filepaths
 
 
-def _get_dim_values_index(list_ds: list, dim: str) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
+def _get_dim_values_index(list_ds: list, dim: str) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
     """Get list and dataset indices associated to the dimension values."""
     dim_values = np.concatenate([ds[dim].values for ds in list_ds])
     list_index = np.concatenate([np.ones(len(ds[dim])) * i for i, ds in enumerate(list_ds)])
@@ -129,7 +128,7 @@ def _get_bad_info_dict(
     list_index: np.ndarray,
     dim_values: np.ndarray,
     ds_index: np.ndarray,
-) -> Tuple[dict, dict]:
+) -> tuple[dict, dict]:
     """Return two dictionaries mapping, for each dataset, the bad values and indices to remove.
 
     Parameters

docs/requirements.txt

@@ -2,6 +2,7 @@ cftime==1.6.1
 click==8.1.3
 cloudpickle==2.1.0
 colorama==0.4.5
+donfig==0.8.1.post0
 fsspec==2022.11.0
 locket==1.0.0
 netCDF4==1.6.2
@@ -19,14 +20,14 @@ nbsphinx==0.8.9
 jupyter==1.0.0
 h5py==3.7.0
 setuptools==65.5.1
-dask[distributed]==2022.9.1
+dask[distributed]==2023.11.0
 pre-commit==2.20.0
 importlib==1.0.4
 importlib-metadata==5.1.0
 trollsift==0.5.0
 coverage==7.2.2
 pooch==1.7.0
-pydantic==1.10.4
+pydantic==2.5.2
 pytest-cov==4.0.0
 pytest-mock==3.10.0
 pytest==7.2.0

pyproject.toml

@@ -18,7 +18,7 @@ classifiers = [
 	"Operating System :: MacOS :: MacOS X",
 	"Operating System :: Microsoft :: Windows",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dependencies = [
 	"click",
 	"tqdm",