add cursor file, upgrade version, add a more complete file structure

.cursorignore

@@ -0,0 +1,21 @@
+*.json
+*.csv
+*.txt
+*.md
+*.ipynb
+*.Rmd
+*.Rproj
+*.Rproj.user
+*.parquet
+*.ckpt
+*.h5ad
+site/
+*.lamindb
+*.lndb
+*.out
+*.html
+*.pdf
+*.npy
+*.npz
+*.whl
+*.gz

.github/workflows/main.yml

@@ -18,12 +18,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.9]
+        python-version: [3.11]
         os: [ubuntu-latest]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install UV
@@ -38,12 +38,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.9]
+        python-version: [3.11]
         os: [ubuntu-latest]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install UV
@@ -54,6 +54,9 @@ jobs:
         run: uv run task test
       - name: "Upload coverage to Codecov"
         uses: codecov/codecov-action@v3
+        with:
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
         # with:
         #   fail_ci_if_error: true
 
@@ -62,12 +65,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.9]
+        python-version: [3.11]
         os: [macos-latest]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install UV
@@ -82,12 +85,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.9]
+        python-version: [3.11]
         os: [windows-latest]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install Pip

.github/workflows/release.yml

@@ -18,7 +18,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           # by default, it uses a depth of 1
           # this fetches all history so that we can read each commit
@@ -32,21 +32,19 @@ jobs:
 
   deploy:
     needs: release
-    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: ["3.11"]
+        os: [ubuntu-latest]
+    runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: __token__
-        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Build and publish
+        run: |
+          uv build && uv publish -u __token__ -p ${{ secrets.POETRY_TOKEN }}

.gitignore

@@ -130,3 +130,5 @@ dmypy.json
 
 # templates
 .github/templates/*
+
+.DS_Store

CONTRIBUTING.md

@@ -87,7 +87,6 @@ clean:            ## Clean unused files.
 virtualenv:       ## Create a virtual environment.
 release:          ## Create a new tag for release.
 docs:             ## Build the documentation.
-switch-to-poetry: ## Switch to poetry package manager.
 init:             ## Initialize the project based on an application template.
 ```
 

Containerfile

@@ -1,5 +1,5 @@
-FROM python:3.7-slim
+FROM python:3.11-slim
 COPY . /app
 WORKDIR /app
-RUN pip install .
+RUN uv sync --all-extras --dev
 CMD ["project_name"]

LICENSE

@@ -1,24 +1,21 @@
-This is free and unencumbered software released into the public domain.
+MIT License
 
-Anyone is free to copy, modify, publish, use, compile, sell, or
-distribute this software, either in source code form or as a compiled
-binary, for any purpose, commercial or non-commercial, and by any
-means.
+Copyright (c) 2024 jérémie kalfon, laura cantini, gabriel peyré
 
-In jurisdictions that recognize copyright laws, the author or authors
-of this software dedicate any and all copyright interest in the
-software to the public domain. We make this dedication for the benefit
-of the public at large and to the detriment of our heirs and
-successors. We intend this dedication to be an overt act of
-relinquishment in perpetuity of all present and future rights to this
-software under copyright law.
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
-OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
-ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-OTHER DEALINGS IN THE SOFTWARE.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
 
-For more information, please refer to <https://unlicense.org>
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -3,10 +3,6 @@
 
 A low dependency and really simple to start project template for Python Projects.
 
-See also 
-- [Flask-Project-Template](https://github.com/rochacbruno/flask-project-template/) for a full feature Flask project including database, API, admin interface, etc.
-- [FastAPI-Project-Template](https://github.com/rochacbruno/fastapi-project-template/) The base to start an openapi project featuring: SQLModel, Typer, FastAPI, JWT Token Auth, Interactive Shell, Management Commands.
-
 ### HOW TO USE THIS TEMPLATE
 
 > **DO NOT FORK** this is meant to be used from **[Use this template](https://github.com/rochacbruno/python-project-template/generate)** feature.
@@ -25,28 +21,19 @@ See also
 
 ### What is included on this template?
 
-- 🖼️ Templates for starting multiple application types:
-  * **Basic low dependency** Python program (default) [use this template](https://github.com/rochacbruno/python-project-template/generate)
-  * **Flask** with database, admin interface, restapi and authentication [use this template](https://github.com/rochacbruno/flask-project-template/generate).
-  **or Run `make init` after cloning to generate a new project based on a template.**
-- 📦 A basic [setup.py](setup.py) file to provide installation, packaging and distribution for your project.  
+- 📦 A basic [pyproject.toml](pyproject.toml) file to provide installation, packaging and distribution for your project.  
   Template uses setuptools because it's the de-facto standard for Python packages, you can run `make switch-to-poetry` later if you want.
-- 🤖 A [Makefile](Makefile) with the most useful commands to install, test, lint, format and release your project.
 - 📃 Documentation structure using [mkdocs](http://www.mkdocs.org)
 - 💬 Auto generation of change log using **gitchangelog** to keep a HISTORY.md file automatically based on your commit history on every release.
 - 🐋 A simple [Containerfile](Containerfile) to build a container image for your project.  
   `Containerfile` is a more open standard for building container images than Dockerfile, you can use buildah or docker with this file.
 - 🧪 Testing structure using [pytest](https://docs.pytest.org/en/latest/)
-- ✅ Code linting using [flake8](https://flake8.pycqa.org/en/latest/)
+- ✅ Code linting using [ruff]()
 - 📊 Code coverage reports using [codecov](https://about.codecov.io/sign-up/)
-- 🛳️ Automatic release to [PyPI](https://pypi.org) using [twine](https://twine.readthedocs.io/en/latest/) and github actions.
+- 🛳️ Automatic release to [PyPI](https://pypi.org) using [uv] and github actions.
 - 🎯 Entry points to execute your program using `python -m <project_name>` or `$ project_name` with basic CLI argument parsing.
 - 🔄 Continuous integration using [Github Actions](.github/workflows/) with jobs to lint, test and release your project on Linux, Mac and Windows environments.
 
-> Curious about architectural decisions on this template? read [ABOUT_THIS_TEMPLATE.md](ABOUT_THIS_TEMPLATE.md)  
-> If you want to contribute to this template please open an [issue](https://github.com/rochacbruno/python-project-template/issues) or fork and send a PULL REQUEST.
-
-[❤️ Sponsor this project](https://github.com/sponsors/rochacbruno/)
 
 <!--  DELETE THE LINES ABOVE THIS AND WRITE YOUR PROJECT README BELOW -->
 

makefile

@@ -0,0 +1,89 @@
+.ONESHELL:
+ENV_PREFIX=$(shell python -c "if __import__('pathlib').Path('.venv/bin/pip').exists(): print('.venv/bin/')")
+USING_POETRY=$(shell grep "tool.poetry" pyproject.toml && echo "yes")
+
+.PHONY: help
+help:             ## Show the help.
+	@echo "Usage: make <target>"
+	@echo ""
+	@echo "Targets:"
+	@fgrep "##" Makefile | fgrep -v fgrep
+
+
+.PHONY: show
+show:             ## Show the current environment.
+	@echo "Current environment:"
+	@echo "Running using $(ENV_PREFIX)"
+	@$(ENV_PREFIX)python -V
+	@$(ENV_PREFIX)python -m site
+
+.PHONY: install
+install:          ## Install the project in dev mode.
+	$(ENV_PREFIX)uv sync --all-extras --dev
+
+.PHONY: fmt
+fmt:              ## Format code using black & isort.
+	$(ENV_PREFIX)uv run ruff format project_name/ tests/
+
+.PHONY: lint
+lint:             ## Run pep8, black, mypy linters.
+#most are due to flashattention...
+	$(ENV_PREFIX)uv run ruff check --fix project_name/ tests/
+
+.PHONY: test
+test: lint        ## Run tests and generate coverage report.
+	$(ENV_PREFIX)uv run pytest -v --cov-config .coveragerc --cov=project_name -l --tb=short --maxfail=1 tests/
+	$(ENV_PREFIX)uv run coverage xml
+	$(ENV_PREFIX)uv run coverage html
+
+.PHONY: clean
+clean:            ## Clean unused files.
+	@find ./ -name '*.pyc' -exec rm -f {} \;
+	@find ./ -name '__pycache__' -exec rm -rf {} \;
+	@find ./ -name 'Thumbs.db' -exec rm -f {} \;
+	@find ./ -name '*~' -exec rm -f {} \;
+	@rm -rf .cache
+	@rm -rf .pytest_cache
+	@rm -rf .mypy_cache
+	@rm -rf build
+	@rm -rf dist
+	@rm -rf *.egg-info
+	@rm -rf htmlcov
+	@rm -rf .tox/
+	@rm -rf docs/_build
+
+.PHONY: virtualenv
+virtualenv:       ## Create a virtual environment.
+	@echo "creating virtualenv ..."
+	@rm -rf .venv
+	@uv venv
+	@source .venv/bin/activate
+	@make install
+	@echo "!!! Please run 'source .venv/bin/activate' to enable the environment !!!"
+
+.PHONY: release
+release:          ## Create a new tag for release.
+	@echo "WARNING: This operation will create s version tag and push to github"
+	@read -p "Version? (provide the next x.y.z semver) : " TAG
+	@echo "$${TAG}" > project_name/VERSION
+	@sed -i 's/^version = .*/version = "'$${TAG}'"/' pyproject.toml
+	@sed -i 's/__version__ = .*/__version__ = "'$${TAG}'"/' project_name/__init__.py
+	@$(ENV_PREFIX)gitchangelog > HISTORY.md
+	@git add project_name/VERSION HISTORY.md pyproject.toml
+	@git commit -m "release: version $${TAG} 🚀"
+	@echo "creating git tag : $${TAG}"
+	@git tag $${TAG}
+	@git push -u origin HEAD --tags
+	@echo "Github Actions will detect the new tag and release the new version."
+	@mkdocs gh-deploy
+	@echo "Documentation deployed to https://author_name.github.io/project_name/"
+
+.PHONY: docs
+docs:             ## Build the documentation.
+	@echo "building documentation ..."
+	@$(ENV_PREFIX)mkdocs build
+	URL="site/index.html"; xdg-open $$URL || sensible-browser $$URL || x-www-browser $$URL || gnome-open $$URL || open $$URL
+
+.PHONY: init
+init:             ## Initialize the project based on an application template.
+	@./.github/init.sh

notebooks/test_notebooks/test.ipynb

@@ -0,0 +1,10 @@
+{
+ "cells": [],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

project_name/__init__.py

@@ -0,0 +1,3 @@
+from importlib.metadata import version
+
+__version__ = version("project_name")