sequencegenerator

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Very first steps

Initialize your code

Initialize git inside your repo:

cd sequencegenerator && git init

If you don't have Poetry installed run:

make poetry-download

Initialize poetry and install pre-commit hooks:

make install
make pre-commit-install

Run the codestyle:

make codestyle

Upload initial code to GitHub:

git add .
git commit -m ":tada: Initial commit"
git branch -M main
git remote add origin https://github.com/sequencegenerator/sequencegenerator.git
git push -u origin main

Set up bots

Set up Dependabot to ensure you have the latest dependencies.
Set up Stale bot for automatic issue closing.

Poetry

Want to know more about Poetry? Check its documentation.

Details about Poetry

Poetry's [commands](https://python-poetry.org/docs/cli/#commands) are very intuitive and easy to learn, like: - `poetry add numpy@latest` - `poetry run pytest` - `poetry publish --build` etc

Building and releasing your package

Building a new version of the application contains steps:

Bump the version of your package poetry version <version>. You can pass the new version explicitly, or a rule such as major, minor, or patch. For more details, refer to the Semantic Versions standard.
Make a commit to GitHub.
Create a GitHub release.
And... publish 🙂 poetry publish --build

🎯 What's next

Well, that's up to you 💪🏻. I can only recommend the packages and articles that helped me.

Typer is great for creating CLI applications.
Rich makes it easy to add beautiful formatting in the terminal.
Pydantic – data validation and settings management using Python type hinting.
Loguru makes logging (stupidly) simple.
tqdm – fast, extensible progress bar for Python and CLI.
IceCream is a little library for sweet and creamy debugging.
orjson – ultra fast JSON parsing library.
Returns makes you function's output meaningful, typed, and safe!
Hydra is a framework for elegantly configuring complex applications.
FastAPI is a type-driven asynchronous web framework.

Articles:

Open Source Guides.
A handy guide to financial support for open source
GitHub Actions Documentation.
Maybe you would like to add gitmoji to commit names. This is really funny. 😄

🚀 Features

Development features

Supports for Python 3.9 and higher.
Poetry as the dependencies manager. See configuration in pyproject.toml and setup.cfg.
Automatic codestyle with black, isort and pyupgrade.
Ready-to-use pre-commit hooks with code-formatting.
Type checks with mypy; docstring checks with darglint; security checks with safety and bandit
Testing with pytest.
Ready-to-use .editorconfig, .dockerignore, and .gitignore. You don't have to worry about those things.

Deployment features

GitHub integration: issue and pr templates.
Github Actions with predefined build workflow as the default CI/CD.
Everything is already set up for security checks, codestyle checks, code formatting, testing, linting, docker builds, etc with Makefile. More details in makefile-usage.
Dockerfile for your package.
Always up-to-date dependencies with @dependabot. You will only enable it.
Automatic drafts of new releases with Release Drafter. You may see the list of labels in release-drafter.yml. Works perfectly with Semantic Versions specification.

Open source community features

Ready-to-use Pull Requests templates and several Issue templates.
Files such as: LICENSE, CONTRIBUTING.md, CODE_OF_CONDUCT.md, and SECURITY.md are generated automatically.
Stale bot that closes abandoned issues after a period of inactivity. (You will only need to setup free plan). Configuration is here.
Semantic Versions specification with Release Drafter.

Installation

pip install -U sequencegenerator

or install with Poetry

poetry add sequencegenerator

Then you can run

sequencegenerator --help

or with Poetry:

poetry run sequencegenerator --help

Makefile usage

Makefile contains a lot of functions for faster development.

1. Download and remove Poetry

To download and install Poetry run: ```bash make poetry-download ``` To uninstall ```bash make poetry-remove ```

2. Install all dependencies and pre-commit hooks

Install requirements: ```bash make install ``` Pre-commit hooks coulb be installed after `git init` via ```bash make pre-commit-install ```

3. Codestyle

Automatic formatting uses `pyupgrade`, `isort` and `black`. ```bash make codestyle # or use synonym make formatting ``` Codestyle checks only, without rewriting files: ```bash make check-codestyle ``` > Note: `check-codestyle` uses `isort`, `black` and `darglint` library

4. Code security

```bash make check-safety ``` This command launches `Poetry` integrity checks as well as identifies security issues with `Safety` and `Bandit`. ```bash make check-safety ```

5. Type checks

Run `mypy` static type checker ```bash make mypy ```

6. Tests

Run `pytest` ```bash make test ```

7. All linters

Of course there is a command to ~~rule~~ run all linters in one: ```bash make lint ``` the same as: ```bash make test && make check-codestyle && make mypy && make check-safety ```

8. Docker

```bash make docker-build ``` which is equivalent to: ```bash make docker-build VERSION=latest ``` Remove docker image with ```bash make docker-remove ``` More information [about docker](https://github.com/sequencegenerator/sequencegenerator/tree/master/docker).

9. Cleanup

Delete pycache files ```bash make pycache-remove ``` Remove package build ```bash make build-remove ``` Or to remove pycache, build and docker image run: ```bash make clean-all ```

📈 Releases

You can see the list of available releases on the GitHub Releases page.

We follow Semantic Versions specification.

We use Release Drafter. As pull requests are merged, a draft release is kept up-to-date listing the changes, ready to publish when you’re ready. With the categories option, you can categorize pull requests in release notes using labels.

List of labels and corresponding titles

Label	Title in Releases
`enhancement`, `feature`	🚀 Features
`bug`, `refactoring`, `bugfix`, `fix`	🔧 Fixes & Refactoring
`build`, `ci`, `testing`	📦 Build System & CI/CD
`breaking`	💥 Breaking Changes
`documentation`	📝 Documentation
`dependencies`	⬆️ Dependencies updates

You can update it in release-drafter.yml.

GitHub creates the bug, enhancement, and documentation labels for you. Dependabot creates the dependencies label. Create the remaining labels on the Issues tab of your GitHub repository, when you need them.

🛡 License

This project is licensed under the terms of the BSD-3 license. See LICENSE for more details.

📃 Citation

@misc{sequencegenerator,
  author = {sequencegenerator},
  title = {sequencegenerator},
  year = {2021},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/sequencegenerator/sequencegenerator}}
}

Credits

This project was generated with python-package-template

LondonBiofoundry / SequencePoolGenerator

readme