docs: Round out supported file formats

.pre-commit-config.yaml

@@ -20,20 +20,20 @@ repos:
         types: [python, yaml, markdown]
 
   - repo: https://github.com/DavidAnson/markdownlint-cli2
-    rev: v0.18.0
+    rev: v0.18.1
     hooks:
       - id: markdownlint-cli2
         args: []
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.19.1
+    rev: v3.20.0
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.11.10
+    rev: v0.11.13
     hooks:
       - id: ruff
         args: [ --fix, --exit-non-zero-on-fix ]
@@ -58,7 +58,7 @@ repos:
       - id: numpydoc-validation
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.15.0
+    rev: v1.16.0
     hooks:
       - id: mypy
         args: [--ignore-missing-imports] # default but useful to be explicit

README.md

@@ -27,17 +27,18 @@ for use with [TopoStats](https://github.com/AFM-SPM/TopoStats).
 
 Supported file formats
 
-| File format | Description    |
-|-------------|----------------|
-| `.asd`      | High-speed AFM |
-| `.ibw`      | [WaveMetrics](https://www.wavemetrics.com/)  |
-| `.spm`      | [Bruker's Format](https://www.bruker.com/)  |
-| `.jpk`      | [Bruker](https://www.bruker.com/) |
-| `.h5-jpk`   | [Bruker](https://www.bruker.com/) |
-| `.topostats`| [TopoStats](https://github.com/AFM-SPM/TopoStats)  |
-| `.gwy`      | [Gwydion](<http://gwyddion.net>) |
-| `.stp`      | [WSXM AFM software files](http://www.wsxm.eu) |
-| `.top`      | `.stp` variant  |
+| File format     | Description                                       |
+|-----------------|---------------------------------------------------|
+| `.asd`          | High-speed AFM                                    |
+| `.gwy`          | [Gwydion](<http://gwyddion.net>)                  |
+| `.h5-jpk`       | [Bruker](https://www.bruker.com/)                 |
+| `.ibw`          | [WaveMetrics](https://www.wavemetrics.com/)       |
+| `.jpk-qi-image` | [Bruker](https://www.bruker.com/)                 |
+| `.jpk`          | [Bruker](https://www.bruker.com/)                 |
+| `.spm`          | [Bruker's Format](https://www.bruker.com/)        |
+| `.stp`          | [WSXM AFM software files](http://www.wsxm.eu)     |
+| `.top`          | `.stp` variant                                    |
+| `.topostats`    | [TopoStats](https://github.com/AFM-SPM/TopoStats) |
 
 Support for the following additional formats is planned. Some of these are already supported in TopoStats and are
 awaiting refactoring to move their functionality into AFMReader these are denoted in bold below.

docs/usage.md

@@ -11,14 +11,18 @@ integrate it into your workflow.
 
 ## Supported file formats
 
-| File format  | Description                                       |
-|--------------|---------------------------------------------------|
-| `.asd`       | High-speed AFM                                    |
-| `.ibw`       | [WaveMetrics](https://www.wavemetrics.com/)       |
-| `.spm`       | [Bruker's Format](https://www.bruker.com/)        |
-| `.jpk`       | [Bruker](https://www.bruker.com/)                 |
-| `.topostats` | [TopoStats](https://github.com/AFM-SPM/TopoStats) |
-| `.gwy`       | [Gwydion](<http://gwyddion.net>)                  |
+| File format     | Description                                       |
+|-----------------|---------------------------------------------------|
+| `.asd`          | High-speed AFM                                    |
+| `.gwy`          | [Gwydion](<http://gwyddion.net>)                  |
+| `.h5-jpk`       | [Bruker](https://www.bruker.com/)                 |
+| `.ibw`          | [WaveMetrics](https://www.wavemetrics.com/)       |
+| `.jpk-qi-image` | [Bruker](https://www.bruker.com/)                |
+| `.jpk`          | [Bruker](https://www.bruker.com/)                |
+| `.spm`          | [Bruker's Format](https://www.bruker.com/)        |
+| `.stp`          | [WSXM AFM software files](http://www.wsxm.eu)     |
+| `.top`          | `.stp` variant                                    |
+| `.topostats`    | [TopoStats](https://github.com/AFM-SPM/TopoStats) |
 
 Support for the following additional formats is planned. Some of these are already supported in TopoStats and are
 awaiting refactoring to move their functionality into AFMReader these are denoted in bold below.

tests/test_h5jpk.py

@@ -5,11 +5,14 @@
 import numpy as np
 import pytest
 
-from AFMReader import h5_jpk
+from AFMReader import h5_jpk  # pylint: disable=no-name-in-module
 
 BASE_DIR = Path.cwd()
 RESOURCES = BASE_DIR / "tests" / "resources"
 
+# pylint: disable=too-many-arguments
+# pylint: disable=too-many-positional-arguments
+
 
 @pytest.mark.parametrize(
     (
@@ -128,15 +131,15 @@ def test_load_h5jpk(
         RESOURCES / file_name, channel, flip_image
     )
 
-    assert result_pixel_to_nm_scaling == pixel_to_nm_scaling
+    assert result_pixel_to_nm_scaling == pytest.approx(pixel_to_nm_scaling)
     assert isinstance(result_image, np.ndarray)
     assert result_image.shape == image_shape
     assert result_image.dtype == np.dtype(image_dtype)
     assert isinstance(results_timestamps, timestamps_dtype)
-    assert result_image.sum() == image_sum
+    assert result_image.sum() == pytest.approx(image_sum)
     assert len(results_timestamps) == result_image.shape[0]
     assert all(
-        results_timestamps[f"frame {i}"] < results_timestamps[f"frame {i+1}"]
+        results_timestamps[f"frame {i}"] < results_timestamps[f"frame {i + 1}"]
         for i in range(len(results_timestamps) - 1)
     )