Merge branch 'main' into ns-rse/748-grain-profiles-grainstats

.git-blame-ignore-revs

@@ -1,3 +1,30 @@
+# numpydoc validation - Linting docstrings with pre-commit numpydoc
+836e1bf5347eb7a9f97e784e783045c0287b3fe9
+2580811edefac867938ee0c4b705649a493e5d4f
+b35307bb55c703b44f6a28652e33dd64cc184e43
+af779c5a16c261716097573ba8cb8a5f882e04c0
+7f0818349e7a06d51654d0554e8ba8a879402ddb
+57a0c001d79c72fd459158fcec7acb27dfae2734
+7a265dab01aa661965adf7cb0c85605e08366ea8
+83649f8697746e5c839ee90d1dc04d3a96777657
+31b3c86f532ba6c276af393dc78c839b5007fe7b
+0af8d30ff4685ee721b25272b36b3652aeaeb18f
+e028184b234e50dd67abdf1cf81e40d90f72f4f1
+46e014b1b5b73d089068e81874b56d0141eec9a3
+db41c74333a5ee0fbb9758155770c282e01e7ecb
+acfc93c178c54fef30266a27c1b0d418d0c367c7
+0c4c4f7b7f448339f83af856c78979bb0c20554a
+f79295ed2fbf989c392caf554d82077bfea7756e
+119e3d989f84f6711c1140a7dd8617fbffaa39e1
+e18d311603fbf1e9c4251382dea6d11a91a2dc17
+165f5dc1688d590b326d5664c9211eb4d10dcb6a
+3fc2d275f2d354918d0c431a786ec6aac48843a9
+86bae88351eec40ad18163478f070b972231283b
+0fd0707948c1fbca47fc4e79b7a2c04b36da5c4f
+583e0e3b9edcd31d3f81c31313999ed2016ae091
+68a220ab800406a84f726a850cc0a2230f862eb3
+a0aef99cb350575e481d0d6e8c5c39e1f0704017
+
 # codespell
 e9f1c8fa0904d643285901110e7a026f3427dc15
 

.github/workflows/tests.yaml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
@@ -25,7 +25,11 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Upgrade pip and install test dependencies
         run: |
-          pip install --upgrade pip
+          pip install --upgrade virtualenv
+          pip install --upgrade pip setuptools
+          pip show pip setuptools
+          virtualenv --upgrade-embed-wheels
+          # virtualenv --reset-app-data
           pip install -e .[tests]
       - name: Test with pytest
         run: |

.pre-commit-config.yaml

@@ -25,20 +25,20 @@ repos:
         args: []
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.15.2
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.2.0
+    rev: v0.3.5
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix, --show-fixes]
 
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.1.1
+    rev: 24.3.0
     hooks:
       - id: black
         types: [python]
@@ -68,6 +68,11 @@ repos:
     hooks:
       - id: nbstripout
 
+  - repo: https://github.com/numpy/numpydoc
+    rev: v1.7.0
+    hooks:
+      - id: numpydoc-validation
+
   - repo: local
     hooks:
       - id: pylint

pyproject.toml

@@ -258,6 +258,29 @@ skip = '*.spm*,*.mplstyle'
 count = ''
 quiet-level = 3
 
+[tool.numpydoc_validation]
+checks = [
+  "all", # Perform all check except those listed below
+  "ES01",
+  "EX01",
+  "PR10", # Conflicts with black formatting
+  "SA01",
+]
+exclude = [  # don't report on objects that match any of these regex
+    "\\.undocumented_method$",
+    "\\.__repr__$",
+    "^test_",
+    "^conftest",
+    "^dnatrcing",
+    "^tracingfuncs",
+    "^conf$",
+]
+override_SS05 = [  # override SS05 to allow docstrings starting with these words
+    "^Process ",
+    "^Assess ",
+    "^Access ",
+]
+
 [project.scripts]
 topostats = "topostats.entry_point:entry_point"
 run_topostats = "topostats.entry_point:legacy_run_topostats_entry_point"

tests/conftest.py

@@ -5,6 +5,7 @@
 
 import numpy as np
 import pandas as pd
+import pySPM
 import pytest
 import yaml
 
@@ -373,6 +374,13 @@ def load_scan_spm() -> LoadScans:
     return LoadScans([RESOURCES / "minicircle.spm"], channel="Height")
 
 
+@pytest.fixture()
+def spm_channel_data() -> pySPM.SPM.SPM_image:
+    """Instantiate channel data from a LoadScans object."""
+    scan = pySPM.Bruker(RESOURCES / "minicircle.spm")
+    return scan.get_channel("Height")
+
+
 @pytest.fixture()
 def load_scan_ibw() -> LoadScans:
     """Instantiate a LoadScans object from a .ibw file."""

tests/test_entry_point.py

@@ -68,42 +68,49 @@ def test_entry_point_subprocess_help(capsys, argument: str, option: str) -> None
 @pytest.mark.parametrize(
     ("options", "expected_function", "expected_arg_name", "expected_arg_value"),
     [
-        (
+        pytest.param(
             [
                 "process",
-                "-c dummy/config/dir/config.yaml",
+                "-c",
+                "dummy/config/dir/config.yaml",
             ],
             run_topostats,
             "config_file",
-            " dummy/config/dir/config.yaml",
+            Path("dummy/config/dir/config.yaml"),
+            id="Process with config file argument",
         ),
-        (
+        pytest.param(
             [
                 "process",
-                "-b /tmp/",
+                "-b",
+                "/tmp/",  # noqa: S108
             ],
             run_topostats,
             "base_dir",
-            " /tmp/",
+            Path("/tmp/"),  # noqa: S108
+            id="Process with base dir argument",
         ),
-        (
+        pytest.param(
             [
                 "create-config",
                 "--filename",
                 "dummy/config/dir/config.yaml",
             ],
             write_config_with_comments,
             "filename",
-            "dummy/config/dir/config.yaml",
+            Path("dummy/config/dir/config.yaml"),
+            id="Create config with output filename",
         ),
-        (
+        pytest.param(
             [
                 "summary",
-                "-l dummy/config/dir/var_to_label.yaml",
+                "-l",
+                "dummy/config/dir/var_to_label.yaml",
             ],
             run_toposum,
             "var_to_label",
-            " dummy/config/dir/var_to_label.yaml",
+            Path("dummy/config/dir/var_to_label.yaml"),
+            id="Summary with label file.",
         ),
     ],
 )
@@ -114,10 +121,8 @@ def test_entry_point(
     returned_args = entry_point(options, testing=True)
     # convert argparse's Namespace object to dictionary
     returned_args_dict = vars(returned_args)
-
     # check that the correct function is collected
     assert returned_args.func == expected_function
-
     # check that the argument has successfully been passed through into the dictionary
     assert returned_args_dict[expected_arg_name] == expected_arg_value
 
@@ -133,28 +138,30 @@ def test_entry_point_create_config_file(tmp_path: Path) -> None:
             f"{tmp_path}",
         ]
     )
-
     assert Path(f"{tmp_path}/test_create_config.yaml").is_file()
 
 
 # Test that the right functions are returned with the right arguments
 @pytest.mark.parametrize(
     ("options", "expected_arg_name", "expected_arg_value"),
     [
-        (
+        pytest.param(
             [
-                "-c dummy/config/dir/config.yaml",
+                "-c",
+                "dummy/config/dir/config.yaml",
             ],
             "config_file",
-            " dummy/config/dir/config.yaml",
+            Path("dummy/config/dir/config.yaml"),
+            id="Test using -c flag for config file",
         ),
-        (
+        pytest.param(
             [
                 "--config",
                 "dummy/config/dir/config.yaml",
             ],
             "config_file",
-            "dummy/config/dir/config.yaml",
+            Path("dummy/config/dir/config.yaml"),
+            id="Test using --config flag for config file",
         ),
     ],
 )

tests/test_io.py

@@ -4,10 +4,12 @@
 import logging
 from datetime import datetime
 from pathlib import Path
+from unittest.mock import patch
 
 import h5py
 import numpy as np
 import pandas as pd
+import pySPM
 import pytest
 
 from topostats.io import (
@@ -605,20 +607,31 @@ def test_gwy_read_component(load_scan_dummy: LoadScans) -> None:
         assert list(test_dict.values()) == [{"test nested component": 3}]
 
 
-# FIXME : Get this test working
-# @pytest.mark.parametrize(
-#     "unit, x, y, expected",
-#     [
-#         ("um", 100, 100, 97.65625),
-#         ("nm", 50, 50, 0.048828125),
-#     ],
-# )
-# def test_extract_pixel_to_nm_scaling(load_scan: LoadScans, unit, x, y, expected) -> None:
-#     """Test extraction of pixels to nanometer scaling."""
-#     load_scan.load_spm()
-#     load_scan._spm_pixel_to_nm_scaling() {"unit": unit, "x": x, "y": y}
-#     test_filters_random.extract_pixel_to_nm_scaling()
-#     assert test_filters_random.pixel_to_nm_scaling == expected
+@patch("pySPM.SPM.SPM_image.pxs")
+@pytest.mark.parametrize(
+    ("unit", "x", "y", "expected_px2nm"),
+    [
+        pytest.param("mm", 0.01, 0.01, 10000, id="mm units; square"),
+        pytest.param("um", 1.5, 1.5, 1500, id="um units; square"),
+        pytest.param("nm", 50, 50, 50, id="nm units; square"),
+        pytest.param("pm", 233, 233, 0.233, id="pm units; square"),
+        pytest.param("pm", 1, 512, 0.001, id="pm units; rectangular (thin)"),
+        pytest.param("pm", 512, 1, 0.512, id="pm units; rectangular (tall)"),
+    ],
+)
+def test__spm_pixel_to_nm_scaling(
+    mock_pxs,
+    load_scan_spm: LoadScans,
+    spm_channel_data: pySPM.SPM.SPM_image,
+    unit: str,
+    x: int,
+    y: int,
+    expected_px2nm: float,
+) -> None:
+    """Test extraction of pixels to nanometer scaling."""
+    mock_pxs.return_value = [(x, unit), (y, unit)]  # issue is that pxs is a func that returns the data
+    result = load_scan_spm._spm_pixel_to_nm_scaling(spm_channel_data)
+    assert result == expected_px2nm
 
 
 @pytest.mark.parametrize(

tests/test_plottingfuncs.py

@@ -8,7 +8,6 @@
 import pytest
 from matplotlib.axes import Axes
 from matplotlib.figure import Figure
-from skimage import io
 
 from topostats.grains import Grains
 from topostats.io import LoadScans
@@ -108,29 +107,17 @@ def test_save_figure(
     assert isinstance(ax, Axes)
 
 
-def test_save_array_figure(tmp_path: Path):
-    """Tests that the image array is saved."""
-    rng2 = np.random.default_rng()
-    Images(
-        data=rng2.random((10, 10)),
-        output_dir=tmp_path,
-        filename="result",
-    ).save_array_figure()
-    assert Path(tmp_path / "result.png").exists()
-
-
 @pytest.mark.mpl_image_compare(baseline_dir="resources/img/")
-def test_plot_and_save_no_colorbar(load_scan_data: LoadScans, tmp_path: Path) -> None:
+def test_plot_and_save_no_colorbar(load_scan_data: LoadScans, plotting_config: dict, tmp_path: Path) -> None:
     """Test plotting without colorbar."""
+    plotting_config["colorbar"] = False
     fig, _ = Images(
         data=load_scan_data.image,
         output_dir=tmp_path,
         filename="01-raw_heightmap",
         pixel_to_nm_scaling=load_scan_data.pixel_to_nm_scaling,
         title="Raw Height",
-        colorbar=False,
-        axes=True,
-        image_set="all",
+        **plotting_config,
     ).plot_and_save()
     return fig
 
@@ -145,17 +132,15 @@ def test_plot_histogram_and_save(load_scan_data: LoadScans, tmp_path: Path) -> N
 
 
 @pytest.mark.mpl_image_compare(baseline_dir="resources/img/")
-def test_plot_and_save_colorbar(load_scan_data: LoadScans, tmp_path: Path) -> None:
-    """Test plotting with colorbar."""
+def test_plot_and_save_colorbar_and_axes(load_scan_data: LoadScans, plotting_config: dict, tmp_path: Path) -> None:
+    """Test plotting with colorbar and axes (True in default_config.yaml)."""
     fig, _ = Images(
         data=load_scan_data.image,
         output_dir=tmp_path,
         filename="01-raw_heightmap",
         pixel_to_nm_scaling=load_scan_data.pixel_to_nm_scaling,
         title="Raw Height",
-        colorbar=True,
-        axes=True,
-        image_set="all",
+        **plotting_config,
     ).plot_and_save()
     return fig
 
@@ -174,20 +159,19 @@ def test_plot_and_save_no_axes(load_scan_data: LoadScans, plotting_config: dict,
     return fig
 
 
+@pytest.mark.mpl_image_compare(baseline_dir="resources/img/")
 def test_plot_and_save_no_axes_no_colorbar(load_scan_data: LoadScans, plotting_config: dict, tmp_path: Path) -> None:
     """Test plotting without axes and without the colourbar."""
     plotting_config["axes"] = False
     plotting_config["colorbar"] = False
-    Images(
+    fig, _ = Images(
         data=load_scan_data.image,
         output_dir=tmp_path,
         filename="01-raw_heightmap",
         title="Raw Height",
         **plotting_config,
     ).plot_and_save()
-    img = io.imread(tmp_path / "01-raw_heightmap.png")
-    assert np.sum(img) == 1535334
-    assert img.shape == (64, 64, 4)
+    return fig
 
 
 @pytest.mark.mpl_image_compare(baseline_dir="resources/img/")