diff --git a/.github/scripts/retry.sh b/.github/scripts/retry.sh new file mode 100755 index 0000000..5905f5c --- /dev/null +++ b/.github/scripts/retry.sh @@ -0,0 +1,20 @@ +#!/bin/bash + +DT=${2:-${RETRY_TIME:-5m}} +MAX=${3:-${MAX_RETRIES:-3}} + +for N in `seq 1 $MAX`; do + echo "Attempt $N/$MAX: $1" + eval $1; + RESULT=$? + if [[ $RESULT -eq 0 ]]; then + exit 0 + fi + if [[ $N -lt $MAX ]]; then + echo "Failed attempt $N/$MAX. Waiting $DT" + sleep $DT + else + echo "Failed attempt $N/$MAX." + exit $RESULT + fi +done diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml new file mode 100644 index 0000000..5e3fde2 --- /dev/null +++ b/.github/workflows/check.yml @@ -0,0 +1,46 @@ +name: check +on: + push: + branches: + - main + - master + - develop + - 'feature/**' +env: + PROJECT_NAME: my_project + WORKFLOW: check +jobs: + run-unit-tests: + strategy: + fail-fast: false + matrix: + os: + - ubuntu-latest + - windows-latest + - macos-latest + python-version: + - '3.8' + - '3.9' + - '3.10' + - '3.11' + runs-on: ${{ matrix.os }} + name: Run tests on Python ${{ matrix.python-version }}, on ${{ matrix.os }} + timeout-minutes: 45 + concurrency: + group: ${{ github.workflow }}-run-unit-tests-${{ matrix.python-version }}-${{ matrix.os }}-${{ github.event.number || github.ref }} + cancel-in-progress: true + steps: + - name: Setup Python + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + + - name: Checkout code + uses: actions/checkout@v3 + + - name: Restore Python dependencies + run: | + pip install -r requirements.txt + + - name: Test + run: python -m unittest discover -s test -t . diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml new file mode 100644 index 0000000..8748d90 --- /dev/null +++ b/.github/workflows/deploy.yml @@ -0,0 +1,76 @@ +name: deploy +on: + workflow_run: + workflows: + - check + types: + - completed + branches: + - master + - main + - develop +env: + PROJECT_NAME: my_project + WORKFLOW: deploy +jobs: + deploy: + runs-on: ubuntu-latest + if: ${{ github.event.workflow_run.conclusion == 'success' }} + name: Deploy on PyPI and create release + steps: + - name: Checkout code + uses: actions/checkout@v2 + with: + fetch-depth: 0 # all history + + - name: Get All Tags + run: git fetch --tags -f + + - name: Get Python Version + id: get-python-version + run: echo ::set-output name=version::$(cat .python-version) + + - name: Setup Python + uses: actions/setup-python@v2 + with: + python-version: ${{ steps.get-python-version.outputs.version }} + + - name: Restore Python dependencies + run: pip install -r requirements.txt + + - name: Change default logging level + run: sed -i -e 's/DEBUG/WARN/g' my_project/__init__.py + + - name: Pack + run: python -m build + + - name: Archive Dist Artifacts + if: failure() || success() + uses: actions/upload-artifact@v2 + with: + name: dist + path: './dist' + + - name: Upload + run: python -m twine upload dist/* + env: + PYPI_USERNAME: ${{ secrets.PYPI_USERNAME }} + PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }} + + - name: Get Version + id: get-version + run: echo ::set-output name=version::$(python setup.py get_project_version | tail -n 1) + + - name: Release Assets + id: upload-release-assets + run: | + set -x + ASSETS=() + for A in dist/*; do + ASSETS+=("-a" "$A") + echo "Releasing $A" + done + RELEASE_TAG='${{ steps.get-version.outputs.version }}' + hub release create "${ASSETS[@]}" -m "$RELEASE_TAG" "$RELEASE_TAG" + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/dockerify.yml b/.github/workflows/dockerify.yml new file mode 100644 index 0000000..390ec0d --- /dev/null +++ b/.github/workflows/dockerify.yml @@ -0,0 +1,46 @@ +name: dockerify +on: + workflow_run: + workflows: + - deploy + types: + - completed + branches: + - main + - master + - develop +env: + PROJECT_NAME: my_project + WORKFLOW: dockerify + RETRY_TIME: 5m + MAX_RETRIES: 3 +jobs: + dockerify: + runs-on: ubuntu-latest + if: ${{ github.event.workflow_run.conclusion == 'success' }} + name: Dockerify with Jupyter support + steps: + - name: Docker Login + run: docker login -u ${{ secrets.DOCKERHUB_USERNAME }} -p ${{ secrets.DOCKERHUB_PASSWORD }} + + - name: Checkout code + uses: actions/checkout@v3 + with: + fetch-depth: 0 # all history + submodules: recursive + + - name: Get All Tags + run: git fetch --tags -f + + - name: Get Version + id: get-version + run: echo ::set-output name=version::$(python setup.py get_project_version | tail -n 1) + + - name: Create Docker Image + run: ./.github/scripts/retry.sh "docker build -t aequitas-aod/$PROJECT_NAME:$VERSION --build-arg VERSION=$VERSION ." + shell: bash + env: + VERSION: '${{ steps.get-version.outputs.version }}' + + - name: Push Image on Docker Hub + run: docker push pikalab/$PROJECT_NAME:${{ steps.get-version.outputs.version }} diff --git a/.github/workflows/todos.yml b/.github/workflows/todos.yml new file mode 100644 index 0000000..a733198 --- /dev/null +++ b/.github/workflows/todos.yml @@ -0,0 +1,16 @@ +name: "TODOs finder" +on: + push: + branches-ignore: + - 'autodelivery**' + - 'bump-**' + - 'renovate/**' + - 'dependabot/**' +jobs: + build: + runs-on: "ubuntu-latest" + steps: + - uses: "actions/checkout@master" + - name: "TODO to Issue" + uses: "alstr/todo-to-issue-action@v4.6.6" + id: "todo" diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..0ee1237 --- /dev/null +++ b/.gitignore @@ -0,0 +1,142 @@ +VERSION + +tmp/ +.idea/ +.vscode/ +.DS_Store +*.data +demo/ + +*~ +*.jar + +### Python ### +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..7a82656 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.11.1 \ No newline at end of file diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..a5917ce --- /dev/null +++ b/Dockerfile @@ -0,0 +1,13 @@ +FROM python:latest +ARG VERSION +EXPOSE 8888 +RUN apt update; apt install -y -q openjdk-17-jdk +RUN pip install jupyter +RUN pip install my_project==$VERSION +RUN mkdir -p /root/.jupyter +ENV JUPYTER_CONF_FILE /root/.jupyter/jupyter_notebook_config.py +RUN echo "c.NotebookApp.allow_origin = '*'" > $JUPYTER_CONF_FILE +RUN echo "c.NotebookApp.ip = '0.0.0.0'" >> $JUPYTER_CONF_FILE +RUN mkdir -p /notebook +WORKDIR /notebook +CMD jupyter notebook --allow-root --no-browser diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..c654e3d --- /dev/null +++ b/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright 2021 PIKA-lab / eXplanable AI + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. \ No newline at end of file diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..96c23fe --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,3 @@ +include VERSION +include requirements.txt +exclude test/* diff --git a/README.md b/README.md new file mode 100644 index 0000000..d8d280b --- /dev/null +++ b/README.md @@ -0,0 +1,28 @@ +# Python project template + +A simple template of a Python project, with a rigid file structure, and predisposition for unit testing and release on PyPi. + +## Project structure + +Overview: +```bash + +├── my_project/ # main package (should be named after your project) +│ ├── __init__.py # python package marker +│ └── __main__.py # application entry point +├── test/ # test package (should contain unit tests) +├── .github/ # configuration of GitHub CI +│ ├── scripts/ # contains bash script to be used in CI +│ │ └── retry.sh # script automating timed retry of release operations +│ └── workflows/ # configuration of GitHub Workflows +│ ├── check.yml # runs tests on multiple OS and versions of Python +│ ├── deploy.yml # if check succeeds, and the current branch is one of {main, master, develop}, triggers automatic releas on PyPi +│ └── dockerify.yml # if deploy succeeds, builds a Docker image and pushes it on DockerHub +├── MANIFEST.in # file stating what to include/exclude in releases +├── LICENSE # license file (Apache 2.0 by default) +├── pyproject.toml # declares build dependencies +├── renovate.json # configuration of Renovate bot, for automatic dependency updates +├── requirements.txt # declares development dependencies +├── setup.py # configuration of the package to be released on Pypi +└── Dockerfile # configuration of the Docker image to be realsed on Dockerhub +``` diff --git a/my_project/__init__.py b/my_project/__init__.py new file mode 100644 index 0000000..83b19f2 --- /dev/null +++ b/my_project/__init__.py @@ -0,0 +1,16 @@ +import logging + + +logging.basicConfig(level=logging.DEBUG) +logger = logging.getLogger('my_project') + +# this is the initial module of your app +# this is executed whenever some client-code is calling `import my_project` or `from my_project import ...` +# put your main classes here, eg: +class MyClass: + def my_method(self): + return "Hello World" + + +# let this be the last line of this file +logger.info("my_project loaded") diff --git a/my_project/__main__.py b/my_project/__main__.py new file mode 100644 index 0000000..d022fa0 --- /dev/null +++ b/my_project/__main__.py @@ -0,0 +1,7 @@ +import my_project + +# this is the main module of your app +# it is only required if your project must be runnable +# this is the script to be executed whenever some users writes `python -m my_project` on the command line, eg. +x = my_project.MyClass().my_method() +print(x) diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..9787c3b --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,3 @@ +[build-system] +requires = ["setuptools", "wheel"] +build-backend = "setuptools.build_meta" diff --git a/renovate.json b/renovate.json new file mode 100644 index 0000000..39a2b6e --- /dev/null +++ b/renovate.json @@ -0,0 +1,6 @@ +{ + "$schema": "https://docs.renovatebot.com/renovate-schema.json", + "extends": [ + "config:base" + ] +} diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..4bf8ca3 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,4 @@ +build>=0.6.0 +twine>=3.4.2 +scikit-learn==1.0.2 +pandas==1.4.2 diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..8183c7a --- /dev/null +++ b/setup.py @@ -0,0 +1,103 @@ +from setuptools import setup, find_packages +import pathlib +import subprocess +import distutils.cmd + +# current directory + +here = pathlib.Path(__file__).parent.resolve() + +version_file = here / 'VERSION' + +# Get the long description from the README file +long_description = (here / 'README.md').read_text(encoding='utf-8') + + +def format_git_describe_version(version): + if '-' in version: + splitted = version.split('-') + tag = splitted[0] + index = f"dev{splitted[1]}" + return f"{tag}.{index}" + else: + return version + + +def get_version_from_git(): + try: + process = subprocess.run(["git", "describe"], cwd=str(here), check=True, capture_output=True) + version = process.stdout.decode('utf-8').strip() + version = format_git_describe_version(version) + with version_file.open('w') as f: + f.write(version) + return version + except subprocess.CalledProcessError: + if version_file.exists(): + return version_file.read_text().strip() + else: + return '0.1.0' + + +version = get_version_from_git() + + +print(f"Detected version {version} from git describe") + + +class GetVersionCommand(distutils.cmd.Command): + """A custom command to get the current project version inferred from git describe.""" + + description = 'gets the project version from git describe' + user_options = [] + + def initialize_options(self): + pass + + def finalize_options(self): + pass + + def run(self): + print(version) + +setup( + name='my_project', # Required + version=version, + description='description here', + license='Apache 2.0 License', + long_description=long_description, + long_description_content_type='text/markdown', + url='https://github.com/aequitas-aod/my_project', + author='Name Surname', + author_email='name.surname@organization.domain', + classifiers=[ + 'Development Status :: 3 - Alpha', + 'Intended Audience :: Developers', + 'Topic :: Software Development :: Libraries', + 'Topic :: Scientific/Engineering :: Artificial Intelligence', + 'License :: OSI Approved :: Apache Software License', + 'Programming Language :: Python :: 3', + 'Programming Language :: Python :: 3.9', + 'Programming Language :: Python :: 3 :: Only', + 'Programming Language :: Prolog' + ], + keywords='aeuitas, horizon2020, xai, bias', # Optional + # package_dir={'': 'src'}, # Optional + packages=find_packages(), # Required + include_package_data=True, + python_requires='>=3.9.0, <3.10', + install_requires=[ + 'scikit-learn>=1.0.2', + 'pandas>=1.4.2', + ], # Optional + zip_safe = False, + platforms = "Independant", + project_urls={ # Optional + 'Bug Reports': 'https://github.com/aequitas-aod/my_project/issues', + # 'Funding': 'https://donate.pypi.org', + # 'Say Thanks!': 'http://saythanks.io/to/example', + 'Source': 'https://github.com/aequitas-aod/my_project', + }, + cmdclass={ + 'get_project_version': GetVersionCommand, + }, +) diff --git a/test/__init__.py b/test/__init__.py new file mode 100644 index 0000000..3bfdb2b --- /dev/null +++ b/test/__init__.py @@ -0,0 +1,8 @@ +import unittest +from my_project import MyClass + +class TestMyClass(unittest.TestCase): + # test methods' names should begin with `test_` + def test_my_method(self): + x = MyClass().my_method() + self.assertEqual("Hello World", x)