mscheltienne · mscheltienne · Jan 2, 2026 · Jan 2, 2026 · Jan 2, 2026
diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml
@@ -36,7 +36,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - run: uv sync -q --no-default-groups --group test
       - run: template sys-info --developer
-      - run: pytest template --cov=template --cov-report=xml --cov-config=pyproject.toml
+      - run: pytest tests --cov=template --cov-report=xml --cov-config=pyproject.toml
       - uses: codecov/codecov-action@v5
         if: ${{ github.repository == 'mscheltienne/template-python' }}
         with:
@@ -63,7 +63,7 @@ jobs:
           uv sync -q --no-default-groups --group test
           uv pip install -q --upgrade --prerelease allow --only-binary :all: -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy
       - run: template sys-info --developer
-      - run: pytest template --cov=template --cov-report=xml --cov-config=pyproject.toml
+      - run: pytest tests --cov=template --cov-report=xml --cov-config=pyproject.toml
       - uses: codecov/codecov-action@v5
         if: ${{ github.repository == 'mscheltienne/template-python' }}
         with:

diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@
 Template python repository. To bootstrap a project from this template, the
 following steps are required:
 
-- [ ] Rename the folder `template` to the package name
+- [ ] Rename the folder `src/template` to the package name and update imports
 - [ ] Edit `pyproject.toml` and all the `template` entries
 - [ ] Edit the GitHub workflows in `.github`
 - [ ] Enable `pre-commit.ci` on https://pre-commit.ci/

diff --git a/pyproject.toml b/pyproject.toml
@@ -19,6 +19,7 @@ doc = [
 ]
 ide = [
   'ipykernel',
+  'ipympl',
   'ipython',
 ]
 style = [
@@ -99,14 +100,15 @@ branch = true
 cover_pylib = false
 omit = [
   '**/__init__.py',
-  '**/conftest.py',
   '**/template/_version.py',
   '**/template/utils/_fixes.py',
-  '**/tests/**',
 ]
 
 [tool.pytest.ini_options]
 addopts = ['--color=yes', '--cov-report=', '--durations=20', '--junit-xml=junit-results.xml', '--strict-config', '--tb=short', '-ra', '-v']
+filterwarnings = [
+  'error',
+]
 junit_family = 'xunit2'
 minversion = '8.0'
 
@@ -120,7 +122,10 @@ line-ending = "lf"
 
 [tool.ruff.lint]
 ignore = []
-select = ['A', 'B', 'C4', 'D', 'E', 'F', 'G', 'I', 'LOG', 'NPY', 'PERF', 'PIE', 'PT', 'T20', 'UP', 'W']
+select = ['A', 'B', 'C4', 'D', 'E', 'F', 'G', 'I', 'LOG', 'NPY', 'PERF', 'PIE', 'PT', 'T20', 'TID', 'UP', 'W']
+
+[tool.ruff.lint.flake8-tidy-imports]
+ban-relative-imports = "all"
 
 [tool.ruff.lint.per-file-ignores]
 '*' = [
@@ -129,7 +134,6 @@ select = ['A', 'B', 'C4', 'D', 'E', 'F', 'G', 'I', 'LOG', 'NPY', 'PERF', 'PIE',
   'D104',  # 'Missing docstring in public package'
   'D107',  # 'Missing docstring in __init__'
 ]
-'*.pyi' = ['E501']
 '__init__.py' = ['F401']
 'tutorials/*' = ['D205', 'D400', 'T201']
 
@@ -141,11 +145,11 @@ ignore-decorators = ["template.utils._docs.copy_doc"]
 include-package-data = false
 
 [tool.setuptools.packages.find]
-exclude = ['template*tests']
 include = ['template*']
+where = ['src']
 
 [tool.setuptools_scm]
-version_file = "template/_version.py"
+version_file = "src/template/_version.py"
 version_scheme = "release-branch-semver"
 
 [tool.tomlsort]

diff --git a/src/template/__init__.py b/src/template/__init__.py
@@ -0,0 +1,4 @@
+from template import utils
+from template._version import __version__
+from template.utils.config import sys_info
+from template.utils.logs import add_file_handler, set_log_level
diff --git a/template/_commands/__init__.py → src/template/_commands/__init__.py b/template/_commands/__init__.py → src/template/_commands/__init__.py
diff --git a/template/_commands/main.py → src/template/_commands/main.py b/template/_commands/main.py → src/template/_commands/main.py
@@ -2,7 +2,7 @@
 
 import click
 
-from .sys_info import run as sys_info
+from template._commands.sys_info import run as sys_info
 
 
 @click.group()

diff --git a/template/_commands/sys_info.py → src/template/_commands/sys_info.py b/template/_commands/sys_info.py → src/template/_commands/sys_info.py
@@ -2,7 +2,7 @@
 
 import click
 
-from .. import sys_info
+from template.utils.config import sys_info
 
 
 @click.command(name="sys-info")

diff --git a/src/template/utils/__init__.py b/src/template/utils/__init__.py
@@ -0,0 +1,3 @@
+"""Utilities module."""
+
+from template.utils import config, logs
diff --git a/template/utils/_checks.py → src/template/utils/_checks.py b/template/utils/_checks.py → src/template/utils/_checks.py
diff --git a/template/utils/_docs.py → src/template/utils/_docs.py b/template/utils/_docs.py → src/template/utils/_docs.py
diff --git a/template/utils/_fixes.py → src/template/utils/_fixes.py b/template/utils/_fixes.py → src/template/utils/_fixes.py
diff --git a/template/utils/_imports.py → src/template/utils/_imports.py b/template/utils/_imports.py → src/template/utils/_imports.py
diff --git a/template/utils/config.py → src/template/utils/config.py b/template/utils/config.py → src/template/utils/config.py
@@ -12,7 +12,7 @@
 import psutil
 from packaging.requirements import Requirement
 
-from ._checks import check_type
+from template.utils._checks import check_type
 
 if TYPE_CHECKING:
     from collections.abc import Callable
@@ -110,7 +110,14 @@ def sys_info(
             pyproject_data = tomllib.load(fid)
         dependency_groups = pyproject_data.get("dependency-groups", {})
         for key in sorted(dependency_groups):
-            dependencies = [Requirement(dep) for dep in dependency_groups[key]]
+            # Skip include-group references (dicts), only parse string dependencies
+            dependencies = [
+                Requirement(dep)
+                for dep in dependency_groups[key]
+                if isinstance(dep, str)
+            ]
+            if len(dependencies) == 0:
+                continue
             out(f"\nDeveloper '{key}' dependencies\n")
             _list_dependencies_info(out, ljust, package, dependencies)
 

diff --git a/template/utils/logs.py → src/template/utils/logs.py b/template/utils/logs.py → src/template/utils/logs.py
@@ -8,8 +8,8 @@
 from typing import TYPE_CHECKING
 from warnings import warn_explicit
 
-from ._checks import ensure_verbose
-from ._fixes import WrapStdOut
+from template.utils._checks import ensure_verbose
+from template.utils._fixes import WrapStdOut
 
 if TYPE_CHECKING:
     from collections.abc import Callable

diff --git a/template/__init__.py b/template/__init__.py
diff --git a/template/conftest.py b/template/conftest.py
diff --git a/template/utils/__init__.py b/template/utils/__init__.py
diff --git a/template/_commands/tests/__init__.py → tests/__init__.py b/template/_commands/tests/__init__.py → tests/__init__.py
diff --git a/template/utils/tests/__init__.py → tests/_commands/__init__.py b/template/utils/tests/__init__.py → tests/_commands/__init__.py
diff --git a/template/_commands/tests/test_main.py → tests/_commands/test_main.py b/template/_commands/tests/test_main.py → tests/_commands/test_main.py
@@ -2,7 +2,7 @@
 
 from click.testing import CliRunner
 
-from ..main import run
+from template._commands.main import run
 
 
 def test_main() -> None:

diff --git a/template/_commands/tests/test_sys_info.py → tests/_commands/test_sys_info.py b/template/_commands/tests/test_sys_info.py → tests/_commands/test_sys_info.py
@@ -3,7 +3,7 @@
 import pytest
 from click.testing import CliRunner
 
-from ..sys_info import run
+from template._commands.sys_info import run
 
 
 @pytest.mark.parametrize("developer", [False, True])

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -0,0 +1,13 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+from template.utils.logs import logger
+
+if TYPE_CHECKING:
+    import pytest
+
+
+def pytest_configure(config: pytest.Config) -> None:
+    """Configure pytest options."""
+    logger.propagate = True  # setup logging
diff --git a/tests/utils/__init__.py b/tests/utils/__init__.py
diff --git a/template/utils/tests/test_checks.py → tests/utils/test_checks.py b/template/utils/tests/test_checks.py → tests/utils/test_checks.py
@@ -6,7 +6,13 @@
 import numpy as np
 import pytest
 
-from .._checks import check_type, check_value, ensure_int, ensure_path, ensure_verbose
+from template.utils._checks import (
+    check_type,
+    check_value,
+    ensure_int,
+    ensure_path,
+    ensure_verbose,
+)
 
 
 def test_ensure_int() -> None:

diff --git a/template/utils/tests/test_config.py → tests/utils/test_config.py b/template/utils/tests/test_config.py → tests/utils/test_config.py
@@ -4,7 +4,7 @@
 
 import pytest
 
-from ..config import _get_gpu_info, sys_info
+from template.utils.config import _get_gpu_info, sys_info
 
 
 def test_sys_info() -> None:

diff --git a/template/utils/tests/test_docs.py → tests/utils/test_docs.py b/template/utils/tests/test_docs.py → tests/utils/test_docs.py
@@ -2,8 +2,8 @@
 
 import pytest
 
-from .._docs import copy_doc
-from ..logs import verbose
+from template.utils._docs import copy_doc
+from template.utils.logs import verbose
 
 
 def test_copy_doc_function() -> None:

diff --git a/template/utils/tests/test_imports.py → tests/utils/test_imports.py b/template/utils/tests/test_imports.py → tests/utils/test_imports.py
@@ -2,7 +2,7 @@
 
 import pytest
 
-from .._imports import import_optional_dependency
+from template.utils._imports import import_optional_dependency
 
 
 def test_import_optional_dependency() -> None:

diff --git a/template/utils/tests/test_logs.py → tests/utils/test_logs.py b/template/utils/tests/test_logs.py → tests/utils/test_logs.py
@@ -5,7 +5,7 @@
 
 import pytest
 
-from ..logs import _use_log_level, add_file_handler, logger, verbose, warn
+from template.utils.logs import _use_log_level, add_file_handler, logger, verbose, warn
 
 if TYPE_CHECKING:
     from pathlib import Path
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		"""Utilities module."""

		from template.utils import config, logs