Merge pull request #97 from GeoscienceAustralia/NPI-NPI-4237-clean-up-deprecated-type-hinting_branch_from_NPI-4067

NPI-4237 Clean up of deprecated type hinting (PEP 585)

Author: ronaldmaj

gnssanalysis/filenames.py

@@ -7,7 +7,7 @@
 
 # The collections.abc (rather than typing) versions don't support subscripting until 3.9
 # from collections import Iterable
-from typing import Iterable, Mapping, Any, Dict, Optional, Tuple, Union, overload
+from typing import Iterable, Mapping, Any, Optional, Union, overload
 import warnings
 
 import click
@@ -99,8 +99,8 @@
 @click.option("--verbose", is_flag=True)
 def determine_file_name_main(
     files: Iterable[pathlib.Path],
-    defaults: Iterable[Tuple[str, str]],
-    overrides: Iterable[Tuple[str, str]],
+    defaults: Iterable[tuple[str, str]],
+    overrides: Iterable[tuple[str, str]],
     current_name: bool,
     delimiter: str,
     verbose: bool,
@@ -165,8 +165,8 @@ def determine_file_name(
      defined as a parameter to maintain syntactic simplicity when calling.
 
     :param pathlib.Path file_path: Path to the file for which to determine name
-    :param Dict[str, Any] defaults: Default name properties to use when properties can't be determined
-    :param Dict[str, Any] overrides: Name properties that should override anything detected in the file
+    :param dict[str, Any] defaults: Default name properties to use when properties can't be determined
+    :param dict[str, Any] overrides: Name properties that should override anything detected in the file
     :raises NotImplementedError: For files that we should support but currently don't (bia, iox, obx, sum, tro)
     :return str: Proposed IGS long filename
     """
@@ -182,7 +182,7 @@ def determine_properties_from_contents_and_filename(
     file_path: pathlib.Path,
     defaults: Optional[Mapping[str, Any]] = None,
     overrides: Optional[Mapping[str, Any]] = None,
-) -> Dict[str, Any]:
+) -> dict[str, Any]:
     """Determine the properties of a file based on its contents
 
     The function reads both the existing filename of the provided file as well as
@@ -204,8 +204,8 @@ def determine_properties_from_contents_and_filename(
      - project: str
 
     :param pathlib.Path file_path: Path to the file for which to determine properties
-    :param Dict[str, Any] defaults: Default name properties to use when properties can't be determined
-    :param Dict[str, Any] overrides: Name properties that should override anything detected in the file
+    :param dict[str, Any] defaults: Default name properties to use when properties can't be determined
+    :param dict[str, Any] overrides: Name properties that should override anything detected in the file
     :raises NotImplementedError: For files that we should support but currently don't (bia, iox, obx, sum, tro)
     :return str: Dictionary of file properties
     """
@@ -459,15 +459,15 @@ def convert_nominal_span(nominal_span: str) -> datetime.timedelta:
         return datetime.timedelta()
 
 
-def determine_clk_name_props(file_path: pathlib.Path) -> Dict[str, Any]:
+def determine_clk_name_props(file_path: pathlib.Path) -> dict[str, Any]:
     """Determine the IGS filename properties for a CLK files
 
     Like all functions in this series, the function reads both a filename and the files contents
     to determine properties that can be used to describe the expected IGS long filename. The
     function returns a dictionary with any properties it manages to successfully determine.
 
     :param pathlib.Path file_path: file for which to determine name properties
-    :return Dict[str, Any]: dictionary containing the extracted name properties
+    :return dict[str, Any]: dictionary containing the extracted name properties
     """
     name_props = {}
     try:
@@ -519,15 +519,15 @@ def determine_clk_name_props(file_path: pathlib.Path) -> Dict[str, Any]:
     return name_props
 
 
-def determine_erp_name_props(file_path: pathlib.Path) -> Dict[str, Any]:
+def determine_erp_name_props(file_path: pathlib.Path) -> dict[str, Any]:
     """Determine the IGS filename properties for a ERP files
 
     Like all functions in this series, the function reads both a filename and the files contents
     to determine properties that can be used to describe the expected IGS long filename. The
     function returns a dictionary with any properties it manages to successfully determine.
 
     :param pathlib.Path file_path: file for which to determine name properties
-    :return Dict[str, Any]: dictionary containing the extracted name properties
+    :return dict[str, Any]: dictionary containing the extracted name properties
     """
     name_props = {}
     try:
@@ -574,15 +574,15 @@ def determine_erp_name_props(file_path: pathlib.Path) -> Dict[str, Any]:
     return name_props
 
 
-def determine_snx_name_props(file_path: pathlib.Path) -> Dict[str, Any]:
+def determine_snx_name_props(file_path: pathlib.Path) -> dict[str, Any]:
     """Determine the IGS filename properties for a SINEX files
 
     Like all functions in this series, the function reads both a filename and the files contents
     to determine properties that can be used to describe the expected IGS long filename. The
     function returns a dictionary with any properties it manages to successfully determine.
 
     :param pathlib.Path file_path: file for which to determine name properties
-    :return Dict[str, Any]: dictionary containing the extracted name properties
+    :return dict[str, Any]: dictionary containing the extracted name properties
     """
     name_props = {}
     try:
@@ -668,7 +668,7 @@ def determine_snx_name_props(file_path: pathlib.Path) -> Dict[str, Any]:
 
 def determine_sp3_name_props(
     file_path: pathlib.Path, strict_mode: type[StrictMode] = StrictModes.STRICT_WARN
-) -> Dict[str, Any]:
+) -> dict[str, Any]:
     """Determine the IGS filename properties for a SP3 files
 
     Like all functions in this series, the function reads both a filename and the files contents
@@ -678,7 +678,7 @@ def determine_sp3_name_props(
     :param pathlib.Path file_path: file for which to determine name properties
     :param type[StrictMode] strict_mode: indicates whether to raise, warn, or silently continue on errors such as
         failure to get properties from a filename.
-    :return Dict[str, Any]: dictionary containing the extracted name properties. May be empty on some errors, if
+    :return dict[str, Any]: dictionary containing the extracted name properties. May be empty on some errors, if
         strict_mode is not set to RAISE.
     :raises ValueError: if strict_mode set to RAISE, and unable to statically extract properties from a filename
     """

gnssanalysis/gn_aux.py

@@ -1,7 +1,7 @@
 """Auxiliary functions"""
 
 import logging as _logging
-from typing import overload, Tuple, Union
+from typing import overload, Union
 import numpy as _np
 import pandas as _pd
 
@@ -183,7 +183,7 @@ def rms(
 
 def get_std_bounds(
     a: _np.ndarray,
-    axis: Union[None, int, Tuple[int, ...]] = None,
+    axis: Union[None, int, tuple[int, ...]] = None,
     sigma_coeff: int = 3,
 ):
     """
@@ -287,7 +287,7 @@ def degminsec2deg(a: Union[_pd.Series, _pd.DataFrame, list, str]) -> Union[_pd.S
         assert isinstance(a_series, _pd.Series)
         return _series_str_degminsec2deg(a_series).unstack()
     else:
-        raise TypeError("Unsupported input type. Please use either of _pd.Series, _pd.DataFrame, List or str")
+        raise TypeError("Unsupported input type. Please use either of _pd.Series, _pd.DataFrame, list or str")
 
 
 def _deg2degminsec(a: _np.ndarray) -> _np.ndarray:

gnssanalysis/gn_download.py

@@ -28,7 +28,7 @@
 import ftplib as _ftplib
 from ftplib import FTP_TLS as _FTP_TLS
 from pathlib import Path as _Path
-from typing import Any, Generator, List, Literal, Optional, Tuple, Union
+from typing import Any, Generator, Literal, Optional, Union
 from urllib import request as _request
 from urllib.error import HTTPError as _HTTPError
 
@@ -391,7 +391,7 @@ def generate_product_filename(
     version: str = "0",
     project: str = "OPS",
     content_type: str = None,
-) -> Tuple[str, GPSDate, _datetime.datetime]:
+) -> tuple[str, GPSDate, _datetime.datetime]:
     """Given a reference datetime and extention of file, generate the IGS filename and GPSDate obj for use in download
 
     :param _datetime.datetime reference_start: Datetime of the start period of interest
@@ -405,7 +405,7 @@ def generate_product_filename(
     :param str version: Version of the file, defaults to "0"
     :param str project: IGS project descriptor, defaults to "OPS"
     :param str content_type: IGS content specifier - if None set automatically based on file_ext, defaults to None
-    :return _Tuple[str, GPSDate, _datetime.datetime]: Tuple of filename str, GPSDate and datetime obj (based on shift)
+    :return tuple[str, GPSDate, _datetime.datetime]: Tuple of filename str, GPSDate and datetime obj (based on shift)
     """
     reference_start += _datetime.timedelta(hours=shift)
     if type(reference_start == _datetime.date):
@@ -822,7 +822,7 @@ def download_product_from_cddis(
     project_type: str = "OPS",
     timespan: _datetime.timedelta = _datetime.timedelta(days=2),
     if_file_present: str = "prompt_user",
-) -> List[_Path]:
+) -> list[_Path]:
     """Download the file/s from CDDIS based on start and end epoch, to the download directory (download_dir)
 
     :param _Path download_dir: Where to download files (local directory)
@@ -838,7 +838,7 @@ def download_product_from_cddis(
     :param _datetime.timedelta timespan: Timespan of the file/s to download, defaults to _datetime.timedelta(days=2)
     :param str if_file_present: What to do if file already present: "replace", "dont_replace", defaults to "prompt_user"
     :raises FileNotFoundError: Raise error if the specified file cannot be found on CDDIS
-    :return List[_Path]: Return list of paths of downloaded files
+    :return list[_Path]: Return list of paths of downloaded files
     """
     # Download the correct IGS FIN ERP files
     if file_ext == "ERP" and analysis_center == "IGS" and solution_type == "FIN":  # get the correct start_epoch
@@ -1193,12 +1193,12 @@ def download_satellite_metadata_snx(download_dir: _Path, if_file_present: str =
     return download_filepath
 
 
-def download_yaw_files(download_dir: _Path, if_file_present: str = "prompt_user") -> List[_Path]:
+def download_yaw_files(download_dir: _Path, if_file_present: str = "prompt_user") -> list[_Path]:
     """Download yaw rate / bias files needed to for Ginan's PEA
 
     :param _Path download_dir: Where to download files (local directory)
     :param str if_file_present: What to do if file already present: "replace", "dont_replace", defaults to "prompt_user"
-    :return List[_Path]: Return list paths of downloaded files
+    :return list[_Path]: Return list paths of downloaded files
     """
     ensure_folders([download_dir])
     download_filepaths = []

gnssanalysis/gn_io/erp.py

@@ -7,7 +7,7 @@
 # from collections.abc import Callable, Iterable
 from typing import Callable, Iterable
 from io import BytesIO as _BytesIO
-from typing import List, TextIO, Union
+from typing import TextIO, Union
 from urllib import request as _rqs
 
 import numpy as _np
@@ -17,11 +17,11 @@
 from gnssanalysis import gn_io as _gn_io
 
 
-def normalise_headers(headers: Iterable[str]) -> List[str]:
+def normalise_headers(headers: Iterable[str]) -> list[str]:
     """Apply :func: `gn_io.erp.normalise_headers` to all headers in an iterable
 
     :param Iterable[str] headers: Iterable of header strings obtained from an ERP file
-    :return List[str]: List of normalised headers as per :func: `gn_io.erp.normalise_headers`
+    :return list[str]: List of normalised headers as per :func: `gn_io.erp.normalise_headers`
     """
     return [normalise_header(h) for h in headers]
 
@@ -44,15 +44,15 @@ def normalise_header(header: str) -> str:
     return get_canonical_header(header)
 
 
-def merge_hyphen_headers(raw_split_header: Iterable[str]) -> List[str]:
+def merge_hyphen_headers(raw_split_header: Iterable[str]) -> list[str]:
     """Take a list of raw headers from an ERP file and merge hyphenated headers that got split
 
     In some ERP files hyphenated headers, such as UTC-TAI, occasionally have spaces before or after
     the hyphen/minus sign. This breaks tokenisation as the header gets split into multiple parts.
     This function re-merges those header components.
 
     :param Iterable[str] raw_split_header: ERP header line that has been split/tokenized
-    :return List[str]: List of ERP headers with hyphen-separated headers merged
+    :return list[str]: List of ERP headers with hyphen-separated headers merged
     """
     # Copy to avoid mutating input list
     headers = list(raw_split_header)

gnssanalysis/gn_io/igslog.py

@@ -4,7 +4,7 @@
 import glob as _glob
 import re as _re
 from multiprocessing import Pool as _Pool
-from typing import Union, List, Tuple
+from typing import Union
 
 import numpy as _np
 import pandas as _pd
@@ -169,7 +169,7 @@ def determine_log_version(data: bytes) -> str:
 
 def extract_id_block(
     data: bytes, file_path: str, file_code: str, version: Union[str, None] = None
-) -> Union[List[str], _np.ndarray]:
+) -> Union[list[str], _np.ndarray]:
     """Extract the site ID block given the bytes object read from an IGS site log file
 
     :param bytes data: The bytes object returned from an open() call on a IGS site log in "rb" mode
@@ -229,12 +229,12 @@ def extract_location_block(data: bytes, file_path: str, version: Union[str, None
     return location_block
 
 
-def extract_receiver_block(data: bytes, file_path: str) -> Union[List[Tuple[bytes]], _np.ndarray]:
+def extract_receiver_block(data: bytes, file_path: str) -> Union[list[tuple[bytes]], _np.ndarray]:
     """Extract the location block given the bytes object read from an IGS site log file
 
     :param bytes data: The bytes object returned from an open() call on a IGS site log in "rb" mode
     :param str file_path: The path to the file from which the "data" bytes object was obtained
-    :return List[Tuple[bytes]] or _np.ndarray: The receiver block of the data. Each list element specifies an receiver.
+    :return list[tuple[bytes]] or _np.ndarray: The receiver block of the data. Each list element specifies an receiver.
         If regex doesn't match, an empty numpy NDArray is returned instead.
     """
     receiver_block = _REGEX_REC.findall(data)
@@ -244,12 +244,12 @@ def extract_receiver_block(data: bytes, file_path: str) -> Union[List[Tuple[byte
     return receiver_block
 
 
-def extract_antenna_block(data: bytes, file_path: str) -> Union[List[Tuple[bytes]], _np.ndarray]:
+def extract_antenna_block(data: bytes, file_path: str) -> Union[list[tuple[bytes]], _np.ndarray]:
     """Extract the antenna block given the bytes object read from an IGS site log file
 
     :param bytes data: The bytes object returned from an open() call on a IGS site log in "rb" mode
     :param str file_path: The path to the file from which the "data" bytes object was obtained
-    :return List[Tuple[bytes]] or _np.ndarray: The antenna block of the data. Each list element specifies an antenna.
+    :return list[tuple[bytes]] or _np.ndarray: The antenna block of the data. Each list element specifies an antenna.
         If regex doesn't match, an empty numpy NDArray is returned instead.
     """
     antenna_block = _REGEX_ANT.findall(data)
@@ -397,13 +397,13 @@ def translate_series(series: _pd.Series, translation: dict) -> _pd.Series:
 
 def gather_metadata(
     logs_glob_path: str = "/data/station_logs/station_logs_IGS/*/*.log", rnx_glob_path: str = None, num_threads: int = 1
-) -> List[_pd.DataFrame]:
+) -> list[_pd.DataFrame]:
     """Parses log files found with glob expressions into pd.DataFrames
 
     :param str logs_glob_path: A glob expression for log files, defaults to "/data/station_logs_IGS/*/*.log"
     :param str rnx_glob_path: A glob expression for rnx files, e.g. /data/pea/exs/data/*.rnx, defaults to None
     :param int num_threads: Number of threads to run, defaults to 1
-    :return List[_pd.DataFrame]: List of DataFrames with [ID, Receiver, Antenna] data
+    :return list[_pd.DataFrame]: List of DataFrames with [ID, Receiver, Antenna] data
     """
     parsed_filenames = find_recent_logs(logs_glob_path=logs_glob_path, rnx_glob_path=rnx_glob_path).values