🚨 Fix linter errors in line with #625 (#647)

- Fix Linter Errors in line with #625 - This PR will help review of #625 by merging minor changes from that PR. ---------- Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com>
TissueImageAnalytics · Jul 21, 2023 · 3715915 · 3715915
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commit 3715915
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diff --git a/pre-commit/notebook_markdown_format.py b/pre-commit/notebook_markdown_format.py
@@ -5,12 +5,12 @@
 import copy
 import json
 from pathlib import Path
-from typing import Any, Dict, List
+from typing import Any
 
 import mdformat
 
 
-def format_notebook(notebook: Dict[str, Any]) -> Dict[str, Any]:
+def format_notebook(notebook: dict[str, Any]) -> dict[str, Any]:
     """Format a notebook in MyST style.
 
     Args:
@@ -36,7 +36,7 @@ def format_notebook(notebook: Dict[str, Any]) -> Dict[str, Any]:
     return notebook
 
 
-def main(files: List[Path]) -> None:
+def main(files: list[Path]) -> None:
     """Check markdown cells in notebooks for common mistakes.
 
     Args:
@@ -54,21 +54,25 @@ def main(files: List[Path]) -> None:
         changed = any(
             cell != formatted_cell
             for cell, formatted_cell in zip(
-                notebook["cells"], formatted_notebook["cells"]
+                notebook["cells"],
+                formatted_notebook["cells"],
             )
         )
         if not changed:
             continue
         print("Formatting notebook", path)
-        with open(path, "w") as fh:
+        with Path.open(path, "w") as fh:
             json.dump(formatted_notebook, fh, indent=1, ensure_ascii=False)
             fh.write("\n")
 
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Lint notebook markdown files.")
     parser.add_argument(
-        "files", nargs="*", help="Notebook markdown files to lint.", type=Path
+        "files",
+        nargs="*",
+        help="Notebook markdown files to lint.",
+        type=Path,
     )
     args = parser.parse_args()
     main(sorted(args.files))
diff --git a/pre-commit/notebook_urls.py b/pre-commit/notebook_urls.py
@@ -1,12 +1,13 @@
 """Simple check to ensure each code cell in a notebook is valid Python."""
+from __future__ import annotations
+
 import argparse
 import json
 import re
 import subprocess
 import sys
 from dataclasses import dataclass
 from pathlib import Path
-from typing import List, Set, Tuple
 
 
 def git_branch_name() -> str:
@@ -18,7 +19,7 @@ def git_branch_name() -> str:
     )
 
 
-def git_branch_modified_paths(from_ref: str, to_ref: str) -> Set[Path]:
+def git_branch_modified_paths(from_ref: str, to_ref: str) -> set[Path]:
     """Get a set of file paths modified on this branch vs develop."""
     from_to = f"{from_ref}...{to_ref}"
     return {
@@ -29,20 +30,20 @@ def git_branch_modified_paths(from_ref: str, to_ref: str) -> Set[Path]:
                 "diff",
                 "--name-only",
                 from_to,
-            ]
+            ],
         )
         .decode()
         .strip()
         .splitlines()
     }
 
 
-def git_previous_commit_modified_paths() -> Set[Path]:
+def git_previous_commit_modified_paths() -> set[Path]:
     """Get a set of file paths modified in the previous commit."""
     return {
         Path(p)
         for p in subprocess.check_output(
-            ["/usr/bin/git", "diff", "--name-only", "HEAD~"]
+            ["/usr/bin/git", "diff", "--name-only", "HEAD~"],
         )
         .decode()
         .strip()
@@ -72,7 +73,7 @@ class PatternReplacement:
 MAIN_BRANCHES = ("master", "main")
 
 
-def main(files: List[Path], from_ref: str, to_ref: str) -> bool:
+def main(files: list[Path], from_ref: str, to_ref: str) -> bool:
     """Check that URLs in the notebook are relative to the current branch.
 
     Args:
@@ -150,7 +151,7 @@ def main(files: List[Path], from_ref: str, to_ref: str) -> bool:
         # Write the file if it has changed
         if changed:
             print(f"Updating {path}")
-            with open(path, "w", encoding="utf-8") as fh:
+            with Path.open(path, "w", encoding="utf-8") as fh:
                 json.dump(notebook, fh, indent=1, ensure_ascii=False)
                 fh.write("\n")
         else:
@@ -159,8 +160,10 @@ def main(files: List[Path], from_ref: str, to_ref: str) -> bool:
 
 
 def check_notebook(
-    path: Path, to_ref: str, replacements: List[PatternReplacement]
-) -> Tuple[bool, dict]:
+    path: Path,
+    to_ref: str,
+    replacements: list[PatternReplacement],
+) -> tuple[bool, dict]:
     """Check the notebook for URL replacements.
 
     Args:
@@ -183,7 +186,7 @@ def check_notebook(
         return changed, None
 
     # Load the notebook
-    with open(path, encoding="utf-8") as fh:
+    with Path.open(path, encoding="utf-8") as fh:
         notebook = json.load(fh)
         # Check each cell
     for cell_num, cell in enumerate(notebook["cells"]):
@@ -197,7 +200,7 @@ def check_notebook(
     return changed, notebook
 
 
-def replace_line(line: str, to_ref: str, replacements: List[PatternReplacement]) -> str:
+def replace_line(line: str, to_ref: str, replacements: list[PatternReplacement]) -> str:
     """Perform pattern replacements in the line.
 
     Args:
@@ -230,7 +233,11 @@ def replace_line(line: str, to_ref: str, replacements: List[PatternReplacement])
         default=list(Path.cwd().rglob("*.ipynb")),
     )
     parser.add_argument(
-        "-f", "--from-ref", help="Reference to diff from", type=str, default="develop"
+        "-f",
+        "--from-ref",
+        help="Reference to diff from",
+        type=str,
+        default="develop",
     )
     parser.add_argument(
         "-t",

diff --git a/setup.py b/setup.py
@@ -6,10 +6,10 @@
 
 from setuptools import find_packages, setup
 
-with open("README.md") as readme_file:
+with Path("README.md").open() as readme_file:
     readme = readme_file.read()
 
-with open("HISTORY.md") as history_file:
+with Path("HISTORY.md").open() as history_file:
     history = history_file.read()
 
 install_requires = [

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -19,6 +19,7 @@
 
 
 def pytest_configure(config):
+    """Perform initial configuration for TIAToolbox tests."""
     logger.info(
         "🏁 Starting tests. TIAToolbox Version: %s. CI: %s",
         tiatoolbox.__version__,
@@ -79,6 +80,7 @@ def __remote_sample(key: str) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def sample_ndpi(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for ndpi images.
+
     Download ndpi image for pytest.
 
     """
@@ -99,6 +101,7 @@ def sample_ndpi2(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def sample_svs(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for svs images.
+
     Download svs image for pytest.
 
     """
@@ -108,6 +111,7 @@ def sample_svs(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def sample_ome_tiff(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for ome-tiff (brightfield pyramid) images.
+
     Download ome-tiff image for pytest.
 
     """
@@ -117,6 +121,7 @@ def sample_ome_tiff(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def sample_jp2(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for JP2 images.
+
     Download jp2 image for pytest.
 
     """
@@ -183,6 +188,7 @@ def sample_svs_ndpi_wsis(sample_ndpi2, sample_svs, tmpdir_factory):
 @pytest.fixture(scope="session")
 def source_image(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for source image.
+
     Download stain normalization source image for pytest.
 
     """
@@ -192,6 +198,7 @@ def source_image(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def norm_macenko(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for norm_macenko image.
+
     Download norm_macenko image for pytest.
 
     """
@@ -201,6 +208,7 @@ def norm_macenko(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def norm_reinhard(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for norm_reinhard image.
+
     Download norm_reinhard image for pytest.
 
     """
@@ -210,6 +218,7 @@ def norm_reinhard(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def norm_ruifrok(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for norm_ruifrok image.
+
     Download norm_ruifrok image for pytest.
 
     """
@@ -219,6 +228,7 @@ def norm_ruifrok(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def norm_vahadane(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for norm_vahadane image.
+
     Download norm_vahadane image for pytest.
 
     """
@@ -256,6 +266,7 @@ def sample_visual_fields(
 @pytest.fixture(scope="session")
 def patch_extr_vf_image(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for a visual field image.
+
     Download TCGA-HE-7130-01Z-00-DX1 image for pytest.
 
     """
@@ -265,6 +276,7 @@ def patch_extr_vf_image(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def patch_extr_csv(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch extraction csv.
+
     Download sample patch extraction csv for pytest.
 
     """
@@ -274,6 +286,7 @@ def patch_extr_csv(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def patch_extr_json(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch extraction json.
+
     Download sample patch extraction json for pytest.
 
     """
@@ -283,6 +296,7 @@ def patch_extr_json(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def patch_extr_npy(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch extraction npy.
+
     Download sample patch extraction npy for pytest.
 
     """
@@ -292,6 +306,7 @@ def patch_extr_npy(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def patch_extr_csv_noheader(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch extraction noheader csv.
+
     Download sample patch extraction noheader csv for pytest.
 
     """
@@ -301,6 +316,7 @@ def patch_extr_csv_noheader(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def patch_extr_2col_json(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch extraction 2col json.
+
     Download sample patch extraction 2col json for pytest.
 
     """
@@ -310,6 +326,7 @@ def patch_extr_2col_json(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def patch_extr_2col_npy(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch extraction 2col npy.
+
     Download sample patch extraction 2col npy for pytest.
 
     """
@@ -319,6 +336,7 @@ def patch_extr_2col_npy(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def patch_extr_jp2_csv(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch extraction jp2 csv.
+
     Download sample patch extraction jp2 csv for pytest.
 
     """
@@ -328,6 +346,7 @@ def patch_extr_jp2_csv(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def patch_extr_jp2_read(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch extraction jp2 read npy.
+
     Download sample patch extraction jp2 read npy for pytest.
 
     """
@@ -337,6 +356,7 @@ def patch_extr_jp2_read(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def patch_extr_npy_read(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch extraction read npy.
+
     Download sample patch extraction read npy for pytest.
 
     """
@@ -346,6 +366,7 @@ def patch_extr_npy_read(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def patch_extr_svs_csv(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch extraction svs csv.
+
     Download sample patch extraction svs csv for pytest.
 
     """
@@ -355,6 +376,7 @@ def patch_extr_svs_csv(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def patch_extr_svs_header(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch extraction svs_header csv.
+
     Download sample patch extraction svs_header csv for pytest.
 
     """
@@ -364,6 +386,7 @@ def patch_extr_svs_header(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def patch_extr_svs_npy_read(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch extraction svs_read npy.
+
     Download sample patch extraction svs_read npy for pytest.
 
     """
@@ -373,6 +396,7 @@ def patch_extr_svs_npy_read(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def sample_patch1(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch 1.
+
     Download sample patch 1 (Kather100K) for pytest.
 
     """
@@ -382,6 +406,7 @@ def sample_patch1(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def sample_patch2(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch 2.
+
     Download sample patch 2 (Kather100K) for pytest.
 
     """
@@ -391,6 +416,7 @@ def sample_patch2(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def sample_patch3(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch 3.
+
     Download sample patch 3 (PCam) for pytest.
 
     """
@@ -400,6 +426,7 @@ def sample_patch3(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def sample_patch4(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch 4.
+
     Download sample patch 4 (PCam) for pytest.
 
     """
@@ -424,6 +451,7 @@ def dir_sample_patches(sample_patch1, sample_patch2, tmpdir_factory):
 @pytest.fixture(scope="session")
 def sample_wsi_dict(remote_sample):
     """Sample pytest fixture for torch wsi dataset.
+
     Download svs image for pytest.
 
     """