Chore: Bump Copier template

.copier-answers.yml

@@ -1,6 +1,6 @@
 # Changes here will be overwritten by Copier
 
-_commit: 0.1.57
+_commit: 0.1.63
 _src_path: [email protected]:neuromath/python-template.git
 author_email: ''
 author_name: Blue Brain Project, EPFL

.github/workflows/commitlint.yml

@@ -8,6 +8,8 @@ jobs:
   check-pr-title:
     name: Check PR title
     runs-on: ubuntu-latest
+    env:
+      PR_TITLE: ${{ github.event.pull_request.title }}
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-node@v4
@@ -16,4 +18,4 @@ jobs:
       - run: npm install -g --force commitlint @commitlint/cli commitlint-plugin-cleanfeet
       - run: npm install conventional-changelog-conventionalcommits
       - run: touch .git/COMMIT_EDITMSG
-      - run: echo "${{ github.event.pull_request.title }}" | commitlint
+      - run: echo "$PR_TITLE" | commitlint

.github/workflows/publish-sdist.yml

@@ -11,10 +11,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.8
+      - name: Set up Python 3.10
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: "3.10"
       - name: Build a wheel and a source tarball
         run: |
           pip install setuptools>=42 build setuptools_scm[toml]>=3.4

.github/workflows/run-tox.yml

@@ -13,12 +13,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         min_versions: ["min_versions", "latest_versions"]
         exclude:
           - min_versions: "min_versions"
         include:
-          - python-version: "3.8"
+          - python-version: "3.9"
             min_versions: "min_versions"
 
     steps:

.pre-commit-config.yaml

@@ -1,8 +1,6 @@
-default_language_version:
-  python: python3.8
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
@@ -13,22 +11,22 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/alessandrojcm/commitlint-pre-commit-hook
-    rev: v9.5.0
+    rev: v9.17.0
     hooks:
         - id: commitlint
           stages:
             - commit-msg
           additional_dependencies: ['conventional-changelog-conventionalcommits']
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 24.8.0
     hooks:
       - id: black
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.3.0
     hooks:
       - id: codespell
         args: ["-x", ".codespellignorelines"]
@@ -38,6 +36,6 @@ repos:
       - id: pydocstyle
         additional_dependencies: ["tomli"]
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.1.1
     hooks:
       - id: flake8

.pylintrc

@@ -4,7 +4,8 @@ disable=
 	invalid-name,
 	len-as-condition,
 	no-else-return,
-    broad-exception-raised
+	broad-exception-raised,
+	too-many-positional-arguments
 
 [FORMAT]
 # Regexp for a line that is allowed to be longer than the limit.

CONTRIBUTING.md

@@ -59,7 +59,7 @@ When you wish to contribute to the code base, please consider the following guid
   or
 
   ```shell
-  tox -e py38 -e lint -e docs -e check-packaging
+  tox -e py39 -e lint -e docs -e check-packaging
   ```
 
 * Commit your changes using a descriptive commit message.

neurots/generate/grower.py

@@ -179,9 +179,11 @@ def _post_grow(self):
         self.neuron = Morphology(self.neuron)
 
         self.apical_sections = [
-            point_to_section_segment(self.neuron, apical_point)[0]
-            if apical_point is not None
-            else None
+            (
+                point_to_section_segment(self.neuron, apical_point)[0]
+                if apical_point is not None
+                else None
+            )
             for apical_point in apical_points
         ]
 

pyproject.toml

@@ -10,10 +10,10 @@ build-backend = "setuptools.build_meta"
 [tool.black]
 line-length = 100
 target-version = [
-    "py38",
     "py39",
     "py310",
     "py311",
+    "py312",
 ]
 
 [tool.pydocstyle]

setup.py

@@ -15,7 +15,7 @@
     "matplotlib>=3.4",
     "morphio>=3.3.6,<4.0",
     "neurom>=3.0,<4.0",
-    "numpy>=1.22.0",
+    "numpy>=1.22.0,<2",
     "packaging>=20",
     "scipy>=1.6",
     "tmd>=2.3.0",
@@ -35,10 +35,10 @@
     "dictdiffer>=0.5",
     "mock>=3",
     "morph-tool>=2.9",
-    "pytest>=6",
-    "pytest-cov>=3",
-    "pytest-html>=2",
+    "pytest-cov>=4.1",
+    "pytest-html>=3.2",
     "pytest-xdist>=2",
+    "pytest>=6.1",
     "tqdm>=4.8.4",
 ]
 
@@ -55,7 +55,7 @@
     },
     license="Apache License 2.0",
     packages=find_namespace_packages(include=["neurots*"]),
-    python_requires=">=3.8",
+    python_requires=">=3.9",
     use_scm_version=True,
     setup_requires=[
         "setuptools_scm",
@@ -72,10 +72,10 @@
         "License :: OSI Approved :: Apache Software License",
         "Programming Language :: Python",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
 )

tests/astrocyte/test_space_colonization.py

@@ -209,13 +209,13 @@ def test_colonization_split():
 
     module = "neurots.astrocyte.space_colonization."
 
-    with patch(module + "_repulsion") as repulsion, patch(
-        module + "upper_half_ball_query"
-    ) as half_ball_query, patch(module + "_fallback_strategy") as fallback_strategy, patch(
-        module + "_colonization_strategy_primary"
-    ) as primary_strategy, patch(
-        module + "_colonization_strategy_secondary"
-    ) as secondary_strategy:
+    with (
+        patch(module + "_repulsion") as repulsion,
+        patch(module + "upper_half_ball_query") as half_ball_query,
+        patch(module + "_fallback_strategy") as fallback_strategy,
+        patch(module + "_colonization_strategy_primary") as primary_strategy,
+        patch(module + "_colonization_strategy_secondary") as secondary_strategy,
+    ):
         repulsion.return_value = np.array([3.0, 2.0, 1.0])
         half_ball_query.return_value = []
 
@@ -344,13 +344,12 @@ def test_colonization_split_with_target_influence():
 
     module = "neurots.astrocyte.space_colonization."
 
-    with patch(module + "_colonization_split") as mock_colonization_split, patch(
-        module + "in_squared_proximity"
-    ) as mock_in_squared_proximity, patch(
-        module + "_add_attraction_bias"
-    ) as mock_add_attraction_bias, patch(
-        module + "_majorize_process"
-    ) as mock_majorize_process:
+    with (
+        patch(module + "_colonization_split") as mock_colonization_split,
+        patch(module + "in_squared_proximity") as mock_in_squared_proximity,
+        patch(module + "_add_attraction_bias") as mock_add_attraction_bias,
+        patch(module + "_majorize_process") as mock_majorize_process,
+    ):
         mock_colonization_split.return_value = (
             np.array([0.0, 0.0, 1.0]),
             None,

tests/test_preprocess.py

@@ -1,4 +1,5 @@
 """Test the neurots.preprocess functions."""
+
 # pylint: disable=redefined-outer-name
 # pylint: disable=unused-argument
 import json

tox.ini

@@ -8,7 +8,7 @@ envlist =
     lint
     docs
     min_versions
-    py{38,39,310,311}
+    py{39,310,311,312}
     coverage
 
 minversion = 3.18
@@ -18,12 +18,7 @@ extras =
     test
 setenv =
     COVERAGE_FILE = {env:COVERAGE_FILE:.coverage-{envname}}
-deps =
-    min_versions: Requirements-Builder
 commands =
-    min_versions: requirements-builder --level=min --extras=test -o {envtmpdir}/requirements_min.txt setup.py
-    min_versions: pip install -r {envtmpdir}/requirements_min.txt
-    min_versions: pip freeze
     pytest \
         -n {env:PYTEST_NPROCS:4} \
         --basetemp={envtmpdir} \
@@ -58,10 +53,16 @@ commands =
     twine check {envtmpdir}/dist/*
 
 [testenv:min_versions]
-basepython = python3.8
+basepython = python3.9
+deps =
+    Requirements-Builder
+commands_pre =
+    requirements-builder --level=min --extras=test -o {envtmpdir}/requirements_min.txt setup.py
+    pip install -r {envtmpdir}/requirements_min.txt
+    pip freeze
 
 [testenv:lint]
-basepython = python3.8
+basepython = python3.9
 deps =
     pre-commit
     pylint
@@ -70,7 +71,7 @@ commands =
     pylint -j {env:PYLINT_NPROCS:1} {[base]files}
 
 [testenv:format]
-basepython = python3.8
+basepython = python3.9
 skip_install = true
 deps =
     codespell
@@ -91,7 +92,7 @@ commands =
 
 [gh-actions]
 python =
-  3.8: py38, lint
-  3.9: py39, docs
+  3.9: py39, lint
   3.10: py310, check-packaging
-  3.11: py311
+  3.11: py311, docs
+  3.12: py312

validation/boxplot_comparison.py

@@ -1,5 +1,6 @@
 """Example for comparing a neuron to a population
    using their morphometrics"""
+
 import neurom as nm
 import numpy as np
 import pylab as plt

validation/violin_comparison.py

@@ -1,5 +1,6 @@
 """Example for comparing two populations using
    the violin plots from their morphometrics"""
+
 import neurom as nm
 import numpy as np
 import pandas