From 610bfe0ac2f868797da0b173850eedce2b3e41c1 Mon Sep 17 00:00:00 2001 From: Elaine Ho <49234946+elainehoml@users.noreply.github.com> Date: Thu, 12 Dec 2024 10:31:25 +0000 Subject: [PATCH] Initial commit --- .github/workflows/python-package.yml | 48 +++++++ .gitignore | 166 ++++++++++++++++++++++ .pre-commit-config.yaml | 43 ++++++ CODE_OF_CONDUCT.md | 70 ++++++++++ CONTRIBUTING.md | 113 +++++++++++++++ LICENSE | 201 +++++++++++++++++++++++++++ README.md | 37 +++++ pyproject.toml | 108 ++++++++++++++ src/template/__init__.py | 28 ++++ src/template/command_line.py | 33 +++++ tests/__init__.py | 0 tests/test_template.py | 18 +++ 12 files changed, 865 insertions(+) create mode 100644 .github/workflows/python-package.yml create mode 100644 .gitignore create mode 100644 .pre-commit-config.yaml create mode 100644 CODE_OF_CONDUCT.md create mode 100644 CONTRIBUTING.md create mode 100644 LICENSE create mode 100644 README.md create mode 100644 pyproject.toml create mode 100644 src/template/__init__.py create mode 100644 src/template/command_line.py create mode 100644 tests/__init__.py create mode 100644 tests/test_template.py diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml new file mode 100644 index 0000000..f8c500c --- /dev/null +++ b/.github/workflows/python-package.yml @@ -0,0 +1,48 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python + +name: Python package + +on: + push: + branches: [ "main" ] + pull_request: + branches: [ "main" ] + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ["3.8", "3.9", "3.10", "3.11"] + + steps: + - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v3 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + python -m pip install flake8 black pytest pytest-cov + if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + - name: Install package + run: | + python -m pip install -e . + - name: Run black --check + run: black --check src tests + - name: Lint with flake8 + run: | + # stop the build if there are Python syntax errors or undefined names + flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + - name: Test with pytest + run: | + pytest diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..a5ea299 --- /dev/null +++ b/.gitignore @@ -0,0 +1,166 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +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/ +cover/ + +# 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 +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .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 + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__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/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ + +# Ignore ctags +tags + +# Ignore setuptools-scm version file +_version.py diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..87411ac --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,43 @@ +repos: +- repo: https://github.com/ambv/black + rev: 23.10.1 + hooks: + - id: black + args: [--safe] + language_version: python3 +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v2.1.0 + hooks: + - id: check-added-large-files + - id: trailing-whitespace + - id: end-of-file-fixer + - id: debug-statements + - id: name-tests-test + - id: requirements-txt-fixer + - id: flake8 + args: ['--max-line-length=88', '--select=W291,W292,W293,F401'] + language_version: python3 +- repo: https://github.com/pycqa/pydocstyle + rev: 6.3.0 + hooks: + - id: pydocstyle + exclude: tests + args: + - --convention=google + - --add-ignore=D100,D104,D212,D200,D415 +- repo: https://github.com/pre-commit/mirrors-mypy + rev: v1.3.0 + hooks: + - id: mypy + exclude: tests + args: ["--ignore-missing-imports", "--implicit-optional", "--follow-imports=skip"] +- repo: https://github.com/pycqa/isort + rev: 5.12.0 + hooks: + - id: isort + args: ["--profile", "black"] +- repo: https://github.com/rubik/xenon + rev: v0.9.0 + hooks: + - id: xenon + args: [ --max-absolute A, --max-modules A, --max-average A ] \ No newline at end of file diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..bbcd2fb --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,70 @@ +# Code of Conduct - python-template + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as +contributors and maintainers pledge to make participation in our project and +our community a harassment-free experience for everyone, regardless of age, body +size, disability, ethnicity, sex characteristics, gender identity and expression, +level of experience, education, socio-economic status, nationality, personal +appearance, race, religion, or sexual identity and orientation. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the + overall community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or + advances +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email + address, without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, or to ban +temporarily or permanently any contributor for other behaviors that they deem +inappropriate, threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant](https://contributor-covenant.org/), version +[1.4](https://www.contributor-covenant.org/version/1/4/code-of-conduct/code_of_conduct.md) and +[2.0](https://www.contributor-covenant.org/version/2/0/code_of_conduct/code_of_conduct.md), +and was generated by [contributing-gen](https://github.com/bttger/contributing-gen). diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..8d50580 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,113 @@ + +# Contributing to python-template + +First off, thanks for taking the time to contribute! ❤️ + +All types of contributions are encouraged and valued. See the [Table of Contents](#table-of-contents) for different ways to help and details about how this project handles them. Please make sure to read the relevant section before making your contribution. It will make it a lot easier for us maintainers and smooth out the experience for all involved. The community looks forward to your contributions. 🎉 + +> And if you like the project, but just don't have time to contribute, that's fine. There are other easy ways to support the project and show your appreciation, which we would also be very happy about: +> - Star the project +> - Tweet about it +> - Refer this project in your project's readme +> - Mention the project at local meetups and tell your friends/colleagues + + +## Table of Contents + +- [Code of Conduct](#code-of-conduct) +- [I Have a Question](#i-have-a-question) +- [I Want To Contribute](#i-want-to-contribute) + - [Reporting Bugs](#reporting-bugs) + - [Suggesting Enhancements](#suggesting-enhancements) + - [Your First Code Contribution](#your-first-code-contribution) + - [Improving The Documentation](#improving-the-documentation) +- [Styleguides](#styleguides) + - [Commit Messages](#commit-messages) +- [Join The Project Team](#join-the-project-team) + + +## Code of Conduct + +This project and everyone participating in it is governed by the python-template [Code of Conduct](CODE_OF_CONDUCT.md). +By participating, you are expected to uphold this code. Please report unacceptable behavior +to <>. + + +## I Have a Question + +> If you want to ask a question, we assume that you have read the available [Documentation](https://github.com/rosalindfranklininstitute/python-template). + +Before you ask a question, it is best to search for existing [Issues](https://github.com/rosalindfranklininstitute/python-template/issues) that might help you. In case you have found a suitable issue and still need clarification, you can write your question in this issue. It is also advisable to search the internet for answers first. + +If you then still feel the need to ask a question and need clarification, we recommend the following: + +- Open an [Issue](https://github.com/rosalindfranklininstitute/python-template/issues/new). +- Provide as much context as you can about what you're running into. +- Provide project and platform versions (nodejs, npm, etc), depending on what seems relevant. + +We will then take care of the issue as soon as possible. + +## I Want To Contribute + +> ### Legal Notice +> When contributing to this project, you must agree that you have authored 100% of the content, that you have the necessary rights to the content and that the content you contribute may be provided under the project license. + +### Reporting Bugs + + +#### Before Submitting a Bug Report + +A good bug report shouldn't leave others needing to chase you up for more information. Therefore, we ask you to investigate carefully, collect information and describe the issue in detail in your report. Please complete the following steps in advance to help us fix any potential bug as fast as possible. + +- Make sure that you are using the latest version. +- Determine if your bug is really a bug and not an error on your side e.g. using incompatible environment components/versions (Make sure that you have read the [documentation](https://github.com/rosalindfranklininstitute/python-template). If you are looking for support, you might want to check [this section](#i-have-a-question)). +- To see if other users have experienced (and potentially already solved) the same issue you are having, check if there is not already a bug report existing for your bug or error in the [bug tracker](https://github.com/rosalindfranklininstitute/python-template/issues?q=label%3Abug). +- Also make sure to search the internet (including Stack Overflow) to see if users outside of the GitHub community have discussed the issue. +- Collect information about the bug: + - Stack trace (Traceback) + - OS, Platform and Version (Windows, Linux, macOS, x86, ARM) + - Version of the interpreter, compiler, SDK, runtime environment, package manager, depending on what seems relevant. + - Possibly your input and the output + - Can you reliably reproduce the issue? And can you also reproduce it with older versions? + + +#### How Do I Submit a Good Bug Report? + +We use GitHub issues to track bugs and errors. If you run into an issue with the project: + +- Open an [Issue](https://github.com/rosalindfranklininstitute/python-template/issues/new). (Since we can't be sure at this point whether it is a bug or not, we ask you not to talk about a bug yet and not to label the issue.) +- Explain the behavior you would expect and the actual behavior. +- Please provide as much context as possible and describe the *reproduction steps* that someone else can follow to recreate the issue on their own. This usually includes your code. For good bug reports you should isolate the problem and create a reduced test case. +- Provide the information you collected in the previous section. + +Once it's filed: + +- The project team will label the issue accordingly. +- A team member will try to reproduce the issue with your provided steps. If there are no reproduction steps or no obvious way to reproduce the issue, the team will ask you for those steps and mark the issue as `needs-repro`. Bugs with the `needs-repro` tag will not be addressed until they are reproduced. +- If the team is able to reproduce the issue, it will be marked `needs-fix`, as well as possibly other tags (such as `critical`), and the issue will be left to be [implemented by someone](#your-first-code-contribution). + +### Suggesting Enhancements + +This section guides you through submitting an enhancement suggestion for python-template, **including completely new features and minor improvements to existing functionality**. Following these guidelines will help maintainers and the community to understand your suggestion and find related suggestions. + + +#### Before Submitting an Enhancement + +- Make sure that you are using the latest version. +- Read the [documentation](https://github.com/rosalindfranklininstitute/python-template) carefully and find out if the functionality is already covered. +- Perform a [search](https://github.com/rosalindfranklininstitute/python-template/issues) to see if the enhancement has already been suggested. If it has, add a comment to the existing issue instead of opening a new one. +- Find out whether your idea fits with the scope and aims of the project. It's up to you to make a strong case to convince the project's developers of the merits of this feature. Keep in mind that we want features that will be useful to the majority of our users and not just a small subset. If you're just targeting a minority of users, consider writing an add-on/plugin library. + + +#### How Do I Submit a Good Enhancement Suggestion? + +Enhancement suggestions are tracked as [GitHub issues](https://github.com/rosalindfranklininstitute/python-template/issues). + +- Use a **clear and descriptive title** for the issue to identify the suggestion. +- Provide a **step-by-step description of the suggested enhancement** in as many details as possible. +- **Describe the current behavior** and **explain which behavior you expected to see instead** and why. At this point you can also tell which alternatives do not work for you. +- **Explain why this enhancement would be useful** to most python-template users. You may also want to point out the other projects that solved it better and which could serve as inspiration. + + +## Attribution +This guide is based on [contributing gen](https://github.com/bttger/contributing-gen)! diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..8ccbe1e --- /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. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. 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However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "[]" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. 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 2024 Rosalind Franklin Institute + + 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. diff --git a/README.md b/README.md new file mode 100644 index 0000000..5da05cf --- /dev/null +++ b/README.md @@ -0,0 +1,37 @@ +# python-template + +This is an example python repository that can be used as a template for other projects + +![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg) +[![Building](https://github.com/rosalindfranklininstitute/python-template/actions/workflows/python-package.yml/badge.svg)](https://github.com/rosalindfranklininstitute/python-template/actions/workflows/python-package.yml) + +## Installation + +You can install the package by running the following commands: + +``` +pip install -e . +``` + +## Testing + +You can run the package tests by running the following commands: + +``` +pip install .[test] +pytest +``` + +## Issues + +Please use the [GitHub issue tracker](https://github.com/rosalindfranklininstitute/python-template/issues) to submit bugs or request features. + +## Contributions + +If you would like to help contribute to python-template, please read our [contribution](CONTRIBUTING.md) guide and [code of conduct](CODE_OF_CONDUCT.md). + +## License + +Copyright Rosalind Franklin Institute, 2024. + +Distributed under the terms of the Apache-2.0 license, python-template is free and open source software. diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..f8c4c39 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,108 @@ +# +# Build system requirements +# +[build-system] + +requires = ["setuptools", "setuptools-scm", "wheel"] +build-backend = "setuptools.build_meta" + +# +# +# Basic project metadata +# +[project] + +name = "template" + +description = "A Python project template" + +readme = "README.md" + +requires-python = ">=3.6" + +license = {file = "LICENSE"} + +keywords = [ + "template", + "python", + "project" +] + +authors = [ + {name = "Aaron A. Aaronson", email = "aaron.aaronson@example.com" } +] + +classifiers = [ + "Development Status :: 3 - Alpha", + "License :: OSI Approved :: MIT License", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", +] + +dependencies = [ + "numpy" +] + +dynamic = [ + "version" +] + +# +# Project urls +# +[project.urls] + +"Source" = "https://github.com/rosalindfranklininstitute/python-template" +"Tracker" = "https://github.com/rosalindfranklininstitute/python-template/issues" + +# +# Project additional optional dependencies +# +[project.optional-dependencies] + +test = [ + "pytest", + "pytest-cov", +] + +# +# Project command line scripts +# +[project.scripts] + +python-template = "template.command_line:main" + +# +# Configure setup tools +# +[tool.setuptools.packages.find] + +where = ["src"] + +# +# Set the package version from git tag +# +[tool.setuptools.dynamic] + +version = {attr = "template._version.__version__"} + +# +# Configure setuptools-scm to generate version file +# +[tool.setuptools_scm] + +write_to = "src/template/_version.py" + +# +# Configure pytest +# +[tool.pytest.ini_options] + +addopts = "--cov=src --cov-report term --cov-report html" + +testpaths = [ "tests" ] diff --git a/src/template/__init__.py b/src/template/__init__.py new file mode 100644 index 0000000..4d5004d --- /dev/null +++ b/src/template/__init__.py @@ -0,0 +1,28 @@ +# Copyright 2024 Rosalind Franklin Institute +# +# 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. + + +def example(a, b): + """ + This is an example function that add the values of a and b + + Args: + a: The first value + b: The second value + + Returns: + The sum of a and b + + """ + return a + b diff --git a/src/template/command_line.py b/src/template/command_line.py new file mode 100644 index 0000000..9187b03 --- /dev/null +++ b/src/template/command_line.py @@ -0,0 +1,33 @@ +# Copyright 2024 Rosalind Franklin Institute +# +# 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. + +from argparse import ArgumentParser + +import template + + +def main(args=None): + parser = ArgumentParser(description="Add two values") + + parser.add_argument( + "-a", dest="a", type=float, required=True, help="The first value" + ) + + parser.add_argument( + "-b", dest="b", type=float, required=True, help="The second value" + ) + + args = parser.parse_args(args) + + print(template.example(args.a, args.b)) diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/test_template.py b/tests/test_template.py new file mode 100644 index 0000000..68d245b --- /dev/null +++ b/tests/test_template.py @@ -0,0 +1,18 @@ +import template +import template.command_line + + +def test_example(): + """ + Test the example function + + """ + assert template.example(1, 2) == 3 + + +def test_command_line_main(): + """ + Test the command line + + """ + template.command_line.main(["-a", "1", "-b", "2"])