CI(dependabot): Bump actions/checkout from 6 to 7

.github/ISSUE_TEMPLATE/bug_report.yaml

@@ -9,29 +9,29 @@ body:
   - type: markdown
     attributes:
       value: "
-Thanks for taking the time to fill out this bug report!
+        Thanks for taking the time to fill out this bug report!
 
 
-Before submitting, make sure you search in the [issue list](https://github.com/BlueBrain/dir-content-diff/issues) that a similar issue was not already reported.
-If it is not the case, please read the following guidelines.
+        Before submitting, make sure you search in the [issue list](https://github.com/BlueBrain/dir-content-diff/issues) that a similar issue was not already reported.
+        If it is not the case, please read the following guidelines.
 
-### GUIDELINES FOR REPORTING BUGS
+        ### GUIDELINES FOR REPORTING BUGS
 
-Bug reports that are not properly formulated and formatted or without enough details can be very hard for us to understand and fix.
-In order to ensure we can help you fixing your bug, please follow these guidelines.
+        Bug reports that are not properly formulated and formatted or without enough details can be very hard for us to understand and fix.
+        In order to ensure we can help you fixing your bug, please follow these guidelines.
 
 
-Your reports must include the following features:
+        Your reports must include the following features:
 
-1. **succinct description** of the problem - typically a line or two at most.
+        1. **succinct description** of the problem - typically a line or two at most.
 
-2. **succinct, dependency-free code** which reproduces the problem, otherwise known as a [Minimal, Complete, and Verifiable](https://stackoverflow.com/help/mcve) example.
-  IF YOU DO NOT HAVE A COMPLETE, RUNNABLE TEST CASE WRITTEN DIRECTLY IN THE TEXTAREA BELOW, YOUR ISSUE MAY BE CLOSED.
+        2. **succinct, dependency-free code** which reproduces the problem, otherwise known as a [Minimal, Complete, and Verifiable](https://stackoverflow.com/help/mcve) example.
+          IF YOU DO NOT HAVE A COMPLETE, RUNNABLE TEST CASE WRITTEN DIRECTLY IN THE TEXTAREA BELOW, YOUR ISSUE MAY BE CLOSED.
 
-3. **complete stack traces for all errors** - please avoid screenshots, use formatted text inside issues.
+        3. **complete stack traces for all errors** - please avoid screenshots, use formatted text inside issues.
 
-4. other relevant things as applicable: **dependencies**, **comparative performance timings** for performance issues, etc.
-"
+        4. other relevant things as applicable: **dependencies**, **comparative performance timings** for performance issues, etc.
+      "
 
   - type: textarea
     attributes:
@@ -45,16 +45,17 @@ Your reports must include the following features:
     attributes:
       label: Optional link from https://dir-content-diff.readthedocs.io which documents the behavior that is expected
       description: "
-Please make sure the behavior you are seeing is definitely in contradiction to what's documented as the correct behavior.
-"
+        Please make sure the behavior you are seeing is definitely in contradiction to what's documented as the correct behavior.
+      "
     validations:
       required: false
 
   - type: textarea
     attributes:
       label: To Reproduce
       description: "
-Provide your [Minimal, Complete, and Verifiable](https://stackoverflow.com/help/mcve) example here."
+        Provide your [Minimal, Complete, and Verifiable](https://stackoverflow.com/help/mcve) example here.
+      "
       placeholder: "# Insert code here (text area already python formatted)"
       render: Python
     validations:
@@ -64,9 +65,9 @@ Provide your [Minimal, Complete, and Verifiable](https://stackoverflow.com/help/
     attributes:
       label: Error
       description: "
-Provide the complete text of any errors received **including the complete stack trace**.
-If the message is a warning, run your program with the ``-Werror`` flag: ``python -Werror myprogram.py``
-"
+        Provide the complete text of any errors received **including the complete stack trace**.
+        If the message is a warning, run your program with the ``-Werror`` flag: ``python -Werror myprogram.py``
+      "
       placeholder: "# Copy the complete stack trace and error message here (text area already formatted for Python backtrace)"
       render: Python traceback
     validations:

.github/ISSUE_TEMPLATE/feature_request.yaml

@@ -9,26 +9,26 @@ body:
   - type: markdown
     attributes:
       value: "
-Thanks for taking the time to fill out this feature request!
+        Thanks for taking the time to fill out this feature request!
 
 
-Before submitting, make sure the feature does not already exist in the [documentation](https://dir-content-diff.readthedocs.io) and that you searched in the [issue list](https://github.com/BlueBrain/dir-content-diff/issues) that a similar feature request has not already been reported.
-If it is not the case, please read the following guidelines.
+        Before submitting, make sure the feature does not already exist in the [documentation](https://dir-content-diff.readthedocs.io) and that you searched in the [issue list](https://github.com/BlueBrain/dir-content-diff/issues) that a similar feature request has not already been reported.
+        If it is not the case, please read the following guidelines.
 
-### GUIDELINES FOR REQUESTING HELP
+        ### GUIDELINES FOR REQUESTING HELP
 
-Feature requests that are not properly formulated and formatted or without enough details can be very hard for us to understand.
-In order to ensure we can help you, please follow these guidelines.
+        Feature requests that are not properly formulated and formatted or without enough details can be very hard for us to understand.
+        In order to ensure we can help you, please follow these guidelines.
 
 
-Your requests must include the following features:
+        Your requests must include the following features:
 
-1. **succinct description** of the feature - typically a line or two at most to describe what the new feature would do.
+        1. **succinct description** of the feature - typically a line or two at most to describe what the new feature would do.
 
-2. **succinct, dependency-free code** which shows how you would like to use this feature, otherwise known as a [Minimal, Complete, and Verifiable](https://stackoverflow.com/help/mcve) example.
+        2. **succinct, dependency-free code** which shows how you would like to use this feature, otherwise known as a [Minimal, Complete, and Verifiable](https://stackoverflow.com/help/mcve) example.
 
-3. Why do you need this feature? What would be the use cases?
-"
+        3. Why do you need this feature? What would be the use cases?
+      "
 
   - type: textarea
     attributes:

.github/ISSUE_TEMPLATE/how_to_use.yaml

@@ -9,31 +9,31 @@ body:
   - type: markdown
     attributes:
       value: "
-Thanks for using this package and taking the time to fill out this help request!
+        Thanks for using this package and taking the time to fill out this help request!
 
 
-Before submitting, make sure you read the [documentation](https://dir-content-diff.readthedocs.io) carefully.
-If you still have a question, you should search in the [issue list](https://github.com/BlueBrain/dir-content-diff/issues) that a similar issue has not already been reported, you might find your answer there.
-If it is not the case, please read the following guidelines.
+        Before submitting, make sure you read the [documentation](https://dir-content-diff.readthedocs.io) carefully.
+        If you still have a question, you should search in the [issue list](https://github.com/BlueBrain/dir-content-diff/issues) that a similar issue has not already been reported, you might find your answer there.
+        If it is not the case, please read the following guidelines.
 
-### GUIDELINES FOR REQUESTING HELP
+        ### GUIDELINES FOR REQUESTING HELP
 
-Questions that are not properly formulated and formatted or without enough details can be very hard for us to understand.
-In order to ensure we can help you, please follow these guidelines.
+        Questions that are not properly formulated and formatted or without enough details can be very hard for us to understand.
+        In order to ensure we can help you, please follow these guidelines.
 
 
-Your requests must include the following features:
+        Your requests must include the following features:
 
-1. **succinct description** of the problem - typically a line or two at most to describe what you want to achieve.
+        1. **succinct description** of the problem - typically a line or two at most to describe what you want to achieve.
 
-2. **succinct, dependency-free code** which shows what you tried to do, otherwise known as a [Minimal, Complete, and Verifiable Example](https://stackoverflow.com/help/mcve).
+        2. **succinct, dependency-free code** which shows what you tried to do, otherwise known as a [Minimal, Complete, and Verifiable Example](https://stackoverflow.com/help/mcve).
 
-3. **expected results**
+        3. **expected results**
 
-4. **complete stack traces for all errors** if you have any - please avoid screenshots, use formatted text inside issues.
+        4. **complete stack traces for all errors** if you have any - please avoid screenshots, use formatted text inside issues.
 
-5. other relevant things: **dependencies**, **operating system**, **comparative performance timings** for performance issues.
-"
+        5. other relevant things: **dependencies**, **operating system**, **comparative performance timings** for performance issues.
+      "
 
   - type: textarea
     attributes:
@@ -46,7 +46,8 @@ Your requests must include the following features:
     attributes:
       label: Show what you tried to do.
       description: "
-Provide your [Minimal, Complete, and Verifiable Example](https://stackoverflow.com/help/mcve) here."
+        Provide your [Minimal, Complete, and Verifiable Example](https://stackoverflow.com/help/mcve) here.
+      "
       placeholder: "# Insert code here (text area already python formatted)"
       render: Python
     validations:
@@ -63,9 +64,9 @@ Provide your [Minimal, Complete, and Verifiable Example](https://stackoverflow.c
     attributes:
       label: Error
       description: "
-If you are facing an arror, provide the complete text of any errors received **including the complete stack trace**.
-If the message is a warning, run your program with the ``-Werror`` flag: ``python -Werror myprogram.py``
-"
+        If you are facing an arror, provide the complete text of any errors received **including the complete stack trace**.
+        If the message is a warning, run your program with the ``-Werror`` flag: ``python -Werror myprogram.py``
+      "
       placeholder: "# Copy the complete stack trace and error message here (text area already formatted for Python backtrace)"
       render: Python traceback
     validations:

.github/workflows/commitlint.yml

@@ -11,7 +11,7 @@ jobs:
     env:
       PR_TITLE: ${{ github.event.pull_request.title }}
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: actions/setup-node@v6
         with:
           node-version: '20'

.github/workflows/publish-sdist.yml

@@ -10,7 +10,7 @@ jobs:
     name: Build and publish on PyPI
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - name: Set up Python 3.10
         uses: actions/setup-python@v6
         with:

.github/workflows/run-tox.yml

@@ -15,16 +15,16 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
         min_versions: ["min_versions", "latest_versions"]
         exclude:
           - min_versions: "min_versions"
         include:
-          - python-version: "3.9"
+          - python-version: "3.10"
             min_versions: "min_versions"
 
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v6
       with:
@@ -35,27 +35,27 @@ jobs:
     - name: Install APT Packages
       run: |
         sudo apt-get install -y poppler-utils imagemagick
-    - name: Cache tox and precommit environments
+    - name: Cache tox and prek environments
       uses: actions/cache@v5
       with:
         path: |
           .tox
-          ~/.cache/pre-commit
-        key: ${{ runner.os }}-${{ matrix.python-version }}-${{ steps.date.outputs.date }}-${{ hashFiles('setup.py') }}-${{ hashFiles('.pre-commit-config.yaml') }}
+          ~/.cache/prek
+        key: ${{ runner.os }}-${{ matrix.python-version }}-${{ steps.date.outputs.date }}-${{ hashFiles('setup.py', 'pyproject.toml', 'tox.ini', 'dir_content_diff/comparators/dependencies.json', '.pre-commit-config.yaml') }}
     - name: Clear results in tox environments
       run: |
         rm -rf .tox/*/tmp
     - name: Run tox with latest versions
       if: ${{ matrix.min_versions == 'latest_versions' }}
       run: |
         python -m pip install --upgrade pip setuptools
-        pip install tox-gh-actions
+        pip install tox-uv tox-gh-actions
         tox
     - name: Run tox with min versions
       if: ${{ matrix.min_versions == 'min_versions' }}
       run: |
         python -m pip install --upgrade pip setuptools
-        pip install tox
+        pip install tox-uv
         tox run -e min_versions
     - name: JUnit Report Action
       uses: mikepenz/action-junit-report@v6

.pre-commit-config.yaml

@@ -1,3 +1,7 @@
+default_install_hook_types:
+  - pre-commit
+  - commit-msg
+
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.7.0

CONTRIBUTING.md

@@ -59,7 +59,7 @@ When you wish to contribute to the code base, please consider the following guid
   or
 
   ```shell
-  tox run -e py39,lint,docs,check-packaging
+  tox run -e py310,lint,docs,check-packaging
   ```
 
 * Commit your changes using a descriptive commit message.

dir_content_diff/comparators/dependencies.json

@@ -5,5 +5,5 @@
         "tables>=3.7"
     ],
     "morphio": ["morphio>=3.3.6", "morph_tool>=2.9"],
-    "voxcell": ["voxcell>=3.1.1", "pynrrd>=0.4,<1.1"]
+    "voxcell": ["voxcell>=3.1.1", "pynrrd>=0.4,<1.1", "nptyping>=2.5"]
 }

pyproject.toml

@@ -5,15 +5,14 @@ authors = [
 ]
 description = "Simple tool to compare directory contents."
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = { text = "Apache License 2.0" }
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Developers",
     "License :: OSI Approved :: Apache Software License",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -57,7 +56,6 @@ include = ["dir_content_diff*"]
 [tool.black]
 line-length = 100
 target-version = [
-    "py39",
     "py310",
     "py311",
     "py312",

tests/test_missing_deps.py

@@ -10,36 +10,35 @@
 # LICENSE HEADER MANAGED BY add-license-header
 
 import importlib
+import sys
 from subprocess import run
 
 import pytest
 
-import dir_content_diff.comparators
-
 
 @pytest.mark.comparators_missing_deps
 def test_missing_deps(tmp_path):
     """Test missing dependencies."""
     root_dir = importlib.resources.files("dir_content_diff")  # pylint: disable=no-member
     comparator_dir = root_dir / "comparators"
     imported_comparators = [
-        f"import dir_content_diff.comparators.{i}\n"
-        for i in dir(dir_content_diff.comparators)
-        if "_" not in i and (comparator_dir / i).with_suffix(".py").exists()
+        f"import dir_content_diff.comparators.{path.stem}\n"
+        for path in sorted(comparator_dir.glob("*.py"))
     ]
     missing_deps_file = tmp_path / "test_missing_deps.py"
     with missing_deps_file.open(mode="w", encoding="utf8") as f:
         f.writelines(imported_comparators)
         f.flush()
-    res = run(["python", str(missing_deps_file)], capture_output=True, check=True)
+    res = run([sys.executable, str(missing_deps_file)], capture_output=True, check=True)
     assert res.stderr.decode() == (
         "Loading the morphio module without the required dependencies installed "
         "(requirements are the following: morphio>=3.3.6 and morph_tool>=2.9). "
         "Will crash at runtime if the related functionalities are used. "
         "These dependencies can be installed with 'pip install dir-content-diff[morphio]'."
         "\n"
         "Loading the voxcell module without the required dependencies installed "
-        "(requirement is the following: voxcell>=3.1.1). "
+        "(requirements are the following: voxcell>=3.1.1, pynrrd<1.1,>=0.4 and "
+        "nptyping>=2.5). "
         "Will crash at runtime if the related functionalities are used. "
         "These dependencies can be installed with 'pip install dir-content-diff[voxcell]'.\n"
     )

tests/test_parallel_execution.py

@@ -187,11 +187,11 @@ def test_parallel_single_file_fallback(
         generate_test_files.create_json(empty_res_tree / "file.json")
 
         # Mock the parallel executors and configure logs
-        with patch(
-            "concurrent.futures.ThreadPoolExecutor"
-        ) as mock_thread_executor, patch(
-            "concurrent.futures.ProcessPoolExecutor"
-        ) as mock_process_executor, caplog.at_level(logging.DEBUG):
+        with (
+            patch("concurrent.futures.ThreadPoolExecutor") as mock_thread_executor,
+            patch("concurrent.futures.ProcessPoolExecutor") as mock_process_executor,
+            caplog.at_level(logging.DEBUG),
+        ):
             result = compare_trees(
                 empty_ref_tree, empty_res_tree, executor_type="thread", max_workers=4
             )