2 update template

.github/workflows/tests.yml

@@ -11,11 +11,12 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os: [ubuntu-latest] #, windows-latest, macos-latest] # Extend to your needs
+        python-version: ["3.9", "3.10", "3.11", "3.12"] # Extend to your needs
 
     steps:
       - uses: actions/checkout@v4
@@ -27,14 +28,22 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install flake8 pytest
+          python -m pip install flake8 pytest pytest-cov
           pip install -e .
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      # TODO adapt package_name to the name of your package
       - name: Test with pytest
         run: |
-          pytest
+          pytest --cov package_name
+      # Add the following block to upload coverage to Codecov, requires a CODECOV_TOKEN secret to be set in the repository
+      # - name: Upload results to Codecov
+      #   # Only upload to Codecov after a merge to the main branch
+      #   if: github.ref == 'refs/heads/main' && github.event_name == 'push'
+      #   uses: codecov/codecov-action@v4
+      #   with:
+      #     token: ${{ secrets.CODECOV_TOKEN }}

CONTRIBUTING.md

@@ -0,0 +1,22 @@
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+# Contributing to BraTS
+
+First off, thanks for taking the time to contribute! 🎉
+
+
+## Contribute Code 
+Fork the repository, clone it and implement your contribution.
+
+**Setup:**
+- We use [poetry](https://python-poetry.org/), make sure it is installed: `pip install poetry`
+- Install dependencies by running: `poetry install`
+
+**Requirements:**
+- Our project follows the [black code style](https://github.com/psf/black). Make sure your code is formatted accordingly.
+- Please add _meaningful_ docstring for your functions and annotate types
+- Please add _meaningful_ tests for your contribution in `/tests` and make sure _all_ tests are passing by running `python -m pytest`
+
+
+
+Once done, create a Pull Request to integrate the code into our project!

README.md

@@ -1,2 +1,52 @@
-# brainles-template
-Template for new BrainLes repositories
+# PACKAGE_NAME
+
+[![Python Versions](https://img.shields.io/pypi/pyversions/PACKAGE_NAME)](https://pypi.org/project/PACKAGE_NAME/)
+[![Stable Version](https://img.shields.io/pypi/v/PACKAGE_NAME?label=stable)](https://pypi.python.org/pypi/PACKAGE_NAME/)
+[![Documentation Status](https://readthedocs.org/projects/PACKAGE_NAME/badge/?version=latest)](http://PACKAGE_NAME.readthedocs.io/?badge=latest)
+[![tests](https://github.com/BrainLesion/PACKAGE_NAME/actions/workflows/tests.yml/badge.svg)](https://github.com/BrainLesion/PACKAGE_NAME/actions/workflows/tests.yml)
+[![codecov](https://codecov.io/gh/BrainLesion/PACKAGE_NAME/graph/badge.svg?token=A7FWUKO9Y4)](https://codecov.io/gh/BrainLesion/PACKAGE_NAME)
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+
+Description 
+## Features
+
+
+## Installation
+
+With a Python 3.8+ environment, you can install `PACKAGE_NAME` directly from [PyPI](https://pypi.org/project/brats/):
+
+```bash
+pip install PACKAGE_NAME
+```
+
+
+## Use Cases and Tutorials
+
+A minimal example to create a segmentation could look like this:
+
+```python
+    # example
+```
+
+<!-- For more examples and details please refer to our extensive Notebook tutorials here [NBViewer](https://nbviewer.org/github/BrainLesion/tutorials/blob/main/PACKAGE_NAME/tutorial.ipynb) ([GitHub](https://github.com/BrainLesion/tutorials/blob/main/PACKAGE_NAME/tutorial.ipynb)). For the best experience open the notebook in Colab. -->
+
+
+## Citation
+
+If you use PACKAGE_NAME in your research, please cite it to support the development!
+
+```
+TODO: citation will be added asap
+```
+
+## Contributing
+
+We welcome all kinds of contributions from the community!
+
+### Reporting Bugs, Feature Requests and Questions
+
+Please open a new issue [here](https://github.com/BrainLesion/PACKAGE_NAME/issues).
+
+### Code contributions
+
+Nice to have you on board! Please have a look at our [CONTRIBUTING.md](CONTRIBUTING.md) file.

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

@@ -0,0 +1,49 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+import os
+import sys
+from subprocess import run
+
+
+sys.path.insert(0, os.path.abspath("../../"))
+
+
+run(["python", "preprocess_readme.py"])
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "PACKAGE_NAME"
+copyright = "2024, Marcel Rosier et al."
+author = "Marcel Rosier, Florian Kofler"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx_copybutton",
+    "myst_parser",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "furo"
+# html_static_path = ["_static"]
+
+autodoc_default_options = {
+    "members": True,
+    "undoc-members": True,
+    "private-members": False,
+    "show-inheritance": True,
+}

docs/source/index.rst

@@ -0,0 +1,22 @@
+PACKAGE_NAME documentation
+===================
+
+.. include:: ../README_preprocessed.md
+   :parser: myst_parser.sphinx_
+
+
+Sections
+===================
+
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Getting Started:
+
+   readme
+
+.. toctree::
+   :maxdepth: 2
+   :caption: API Reference:
+

docs/source/preprocess_readme.py

@@ -0,0 +1,36 @@
+import re
+
+
+def preprocess_readme(input_file: str, output_file: str) -> None:
+    """Preprocess a README file to replace GitHub admonitions with Sphinx-style admonitions.
+
+    Args:
+        input_file (str): original README file
+        output_file (str): processed README file
+
+    """
+    with open(input_file, "r") as file:
+        content = file.read()
+
+    admonition_types = ["IMPORTANT", "NOTE", "TIP", "WARNING", "CAUTION"]
+
+    for ad_type in admonition_types:
+        # Replace > [!ad_type] with Sphinx admonition syntax
+        content = re.sub(
+            r"> \[!"
+            + ad_type
+            + "\]\s*\n((?:> .*\n)*)",  # Match the > [!ad_type] and subsequent lines
+            lambda m: "```{"
+            + ad_type
+            + "}\n"
+            + m.group(1).replace("> ", "").strip()
+            + "\n```",  # Replace with MyST syntax
+            content,
+        )
+    # Write the transformed content to the output file
+    with open(output_file, "w") as file:
+        file.write(content)
+
+
+if __name__ == "__main__":
+    preprocess_readme("../../README.md", "../README_preprocessed.md")

docs/source/readme.rst

@@ -0,0 +1,6 @@
+Readme 
+==============
+
+
+.. include:: ../README_preprocessed.md
+   :parser: myst_parser.sphinx_

pyproject.toml

@@ -6,31 +6,32 @@ build-backend = "poetry_dynamic_versioning.backend"
 enable = true
 
 [tool.poetry]
-name = ""
+name = "package_name"
 version = "0.0.0"
 description = ""
 authors = ["Florian Kofler <[email protected]>"]
-repository = ""
-homepage = ""
-documentation = ""
+repository = "https://www.TODO.com"
+homepage = "https://www.TODO.com"
+documentation = "https://www.TODO.com"
 readme = "README.md"
 
 
 # Add the exclude field directly under [tool.poetry]
 exclude = ["examples", "benchmark"]
 
 [tool.poetry.dependencies]
-python = "^3.10"
+python = ">=3.9"
 
 
 [tool.poetry.dev-dependencies]
-pytest = "^6.2.5"
+pytest = ">=8.0.0"
+pytest-cov = ">=5.0.0"
 
 [tool.poetry.group.docs]
 optional = true
 
 [tool.poetry.group.docs.dependencies]
-Sphinx  = ">=7.0.0"
+Sphinx = ">=7.0.0"
 sphinx-copybutton = ">=0.5.2"
-sphinx-rtd-theme = ">=1.3.0"
-myst-parser = ">=2.0.0"
+furo = ">=2024.8.6"
+myst-parser = ">=2.0.0"