Merge pull request #143 from AFM-SPM/ns-rse/142-drop-python-3-9

Author: ns-rse

.github/workflows/pypi.yaml

@@ -22,7 +22,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.11
       - name: Installing the package
         run: |
           pip3 install .

.github/workflows/tests.yaml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12']
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python

AFMReader/asd.py

@@ -1,6 +1,5 @@
 """For decoding and loading .asd AFM file format into Python Numpy arrays."""
 
-from __future__ import annotations
 import errno
 import os
 from pathlib import Path
@@ -232,8 +231,7 @@ def load_asd(file_path: str | Path, channel: str):
             header_dict = read_header_file_version_2(open_file)
         else:
             raise ValueError(
-                f"File version {file_version} unknown. Please add support if you "
-                "know how to decode this file version."
+                f"File version {file_version} unknown. Please add support if you know how to decode this file version."
             )
         logger.debug(f"header dict: \n{header_dict}")
 
@@ -250,7 +248,7 @@ def load_asd(file_path: str | Path, channel: str):
         if channel == header_dict["channel1"]:
             logger.info(f"Requested channel {channel} matches first channel in file: {header_dict['channel1']}")
         elif channel == header_dict["channel2"]:
-            logger.info(f"Requested channel {channel} matches second channel in file: " f"{header_dict['channel2']}")
+            logger.info(f"Requested channel {channel} matches second channel in file: {header_dict['channel2']}")
 
             # Skip first channel data
             _size_of_frame_header = header_dict["frame_header_length"]
@@ -818,7 +816,7 @@ def create_analogue_digital_converter(
         )
     else:
         raise ValueError(
-            f"Analogue to digital range hex value {analogue_digital_range} has no known " "analogue-digital mapping."
+            f"Analogue to digital range hex value {analogue_digital_range} has no known analogue-digital mapping."
         )
     logger.info(f"Analogue to digital mapping | Range: {analogue_digital_range} -> {mapping}")
     logger.info(f"Converter: {converter}")

AFMReader/general_loader.py

@@ -1,6 +1,5 @@
 """Switchboard for input files."""
 
-from __future__ import annotations
 from pathlib import Path
 
 import numpy.typing as npt

AFMReader/gwy.py

@@ -1,6 +1,5 @@
 """For decoding and loading .gwy AFM file format into Python Numpy arrays."""
 
-from __future__ import annotations
 from pathlib import Path
 import re
 from typing import Any, BinaryIO
@@ -11,7 +10,7 @@
 from AFMReader.io import read_uint32, read_null_terminated_string, read_char, read_double
 
 
-def load_gwy(file_path: Path | str, channel: str) -> tuple[np.ndarray[Any, np.dtypes.Float64DType], float]:
+def load_gwy(file_path: Path | str, channel: str) -> tuple[np.ndarray[Any, np.float64], float]:
     """
     Extract image and pixel to nm scaling from the .gwy file.
 

AFMReader/ibw.py

@@ -1,6 +1,5 @@
 """For decoding and loading .ibw AFM file format into Python Numpy arrays."""
 
-from __future__ import annotations
 import errno
 import os
 from pathlib import Path

AFMReader/io.py

@@ -1,6 +1,5 @@
 """For reading and writing data from / to files."""
 
-from __future__ import annotations
 from pathlib import Path
 
 import struct

AFMReader/jpk.py

@@ -1,6 +1,5 @@
 """For decoding and loading .jpk AFM file format into Python Numpy arrays."""
 
-from __future__ import annotations
 from importlib import resources
 from pathlib import Path
 
@@ -12,6 +11,8 @@
 
 logger.enable(__package__)
 
+# pylint: disable=too-many-locals
+
 
 def _jpk_pixel_to_nm_scaling(tiff_page: tifffile.tifffile.TiffPage, jpk_tags: dict[str, int]) -> float:
     """
@@ -141,11 +142,13 @@ def _get_z_scaling(tif: tifffile.tifffile, channel_idx: int, jpk_tags: dict[str,
         for value in values:
             if tif.pages[channel_idx].tags[str(value)].value == default_slot.value:
                 _default_slot = slot
-
+    # pylint: disable=possibly-used-before-assignment
     # Determine if the default slot requires scaling and find scaling and offset values
     scaling_type = _get_tag_value(
-        tif.pages[channel_idx], str(int(jpk_tags["first_scaling_type"]) + (jpk_tags["slot_size"] * (_default_slot)))
+        tif.pages[channel_idx],
+        str(int(jpk_tags["first_scaling_type"]) + (jpk_tags["slot_size"] * (_default_slot))),
     )
+    # pylint: enable=possibly-used-before-assignment
     if scaling_type == "LinearScaling":
         scaling_name = (
             tif.pages[channel_idx]
@@ -203,7 +206,9 @@ def load_jpk(
     Load height trace channel from the .jpk file. 'height_trace' is the default channel name.
 
     >>> from AFMReader.jpk import load_jpk
-    >>> image, pixel_to_nanometre_scaling_factor = load_jpk(file_path="./my_jpk_file.jpk", channel="height_trace", flip_image=True)
+    >>> image, pixel_to_nanometre_scaling_factor = load_jpk(file_path="./my_jpk_file.jpk",
+    >>>                                                     channel="height_trace",
+    >>>                                                     flip_image=True)
     """
     logger.info(f"Loading image from : {file_path}")
     file_path = Path(file_path)

AFMReader/spm.py

@@ -1,6 +1,5 @@
 """For decoding and loading .spm AFM file format into Python Numpy arrays."""
 
-from __future__ import annotations
 from pathlib import Path
 
 import pySPM

AFMReader/stp.py

@@ -1,6 +1,5 @@
 """For decoding and loading .stp AFM file format into Python Numpy arrays."""
 
-from __future__ import annotations
 from pathlib import Path
 import re