Update packaging to src layout (#217)

* update to src layout

* fix lock and other elements

Author: mscheltienne

.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:

MANIFEST.in

@@ -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/

README.md

@@ -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]

pyproject.toml

@@ -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

src/template/__init__.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()

template/_commands/__init__.py src/template/_commands/__init__.pytemplate/_commands/__init__.py renamed to src/template/_commands/__init__.py

@@ -2,7 +2,7 @@
 
 import click
 
-from .. import sys_info
+from template.utils.config import sys_info
 
 
 @click.command(name="sys-info")

template/_commands/main.py src/template/_commands/main.pytemplate/_commands/main.py renamed to src/template/_commands/main.py

@@ -0,0 +1,3 @@
+"""Utilities module."""
+
+from template.utils import config, logs