feature: handle newer topostats file versions

Restructuring of TopoStats to define classes means the `TopoStats` object now holds the `topostats_version` rather than
`topostats_file_version`.

This commit allows both to be handled and switches to using
[`packging.version`](https://packaging.pypa.io/en/stable/version.html) to do so which ensures a more consistent approach
to comparing version numbers.

Yet to write a test for working with newer `.topostats` where `topostats_version >= 2.3.2` as work is still on-going but
parameterised test is in place for when work is complete.

Author: ns-rse

.pylintrc

@@ -62,7 +62,7 @@ py-version=3.9
 
 # When enabled, pylint would attempt to guess common misconfiguration and emit
 # user-friendly hints instead of false-positive error messages.
-suggestion-mode=yes
+# suggestion-mode=yes
 
 # Allow loading of arbitrary C extensions. Extensions are imported into the
 # active Python interpreter and may run arbitrary code.

AFMReader/topostats.py

@@ -5,6 +5,7 @@
 
 import h5py
 
+from packaging.version import parse as parse_version
 from AFMReader.io import unpack_hdf5
 from AFMReader.logging import logger
 
@@ -41,10 +42,17 @@ def load_topostats(file_path: Path | str) -> dict[str, Any]:
     try:
         with h5py.File(file_path, "r") as f:
             data = unpack_hdf5(open_hdf5_file=f, group_path="/")
-            if str(data["topostats_file_version"]) >= "0.2":
+            # Handle different names for variables holding the file version (<=0.3) or the newer topostats version
+            version = (
+                data["topostats_file_version"]
+                if "topostats_file_version" in data.keys()  # pylint: disable=consider-iterating-dictionary
+                else data["topostats_version"]
+            )
+            print(f"\n{str(version)=}\n")
+            print(f'\n{parse_version(str(version)) >= parse_version("0.2")=}\n')
+            if parse_version(str(version)) > parse_version("0.2"):
                 data["img_path"] = Path(data["img_path"])
-            file_version = data["topostats_file_version"]
-            logger.info(f"[{filename}] TopoStats file version : {file_version}")
+            logger.info(f"[{filename}] TopoStats file version : {version}")
 
     except OSError as e:
         if "Unable to open file" in str(e):

tests/test_topostats.py

@@ -99,7 +99,7 @@ def test_load_topostats(
     assert topostats_data["pixel_to_nm_scaling"] == pytest.approx(pixel_to_nm_scaling)
     assert topostats_data["image"].shape == image_shape
     assert topostats_data["image"].sum() == pytest.approx(image_sum)
-    if version >= "0.2":
+    if version > "0.2":
         assert isinstance(topostats_data["img_path"], Path)