Awesome `np-validator` is a Python cli/package created with https://github.com/TezRomacH/python-package-template
Project description
np-validator
np-validator
is just a simple Python cli/package that validates data sources for the neuropixel pipline using templated workflows.
Quick overview
API
Generating validation steps
from np_validator import Processor, Validator, ValidationStep, run_validation
# make a basic filesize validator
fs_validator = Validator(
name="meets_filesize_threshold",
args={
"threshold": 10,
},
)
# add validator to a validation step
validation_step_0 = ValidationStep(
path_suffix=".mapping.pkl",
validators=[fs_validator, ],
)
# make a validation step with a processor
# processors convert the data source from it's basic state, a filepath, to an easier to use object
# unpickle, unpickles an arbitrary filepath into a python object
unpickler = Processor(
name="unpickle",
)
# has_dict_key, checks if a dict-like interface has a key at path
session_uuid_validator = Validator(
name="has_dict_key",
args={
"path": ["session_uuid", ],
}
)
# assembling it all together as a validation step
validation_step_1 = ValidationStep(
path_suffix=".behavior.pkl",
processor=unpickler,
validators=[session_uuid_validator, ],
)
# running a validation
filepaths = [
"some/sort/of/path/prefix/uuid-maybe.mapping.pkl",
"some/sort/of/path/prefix/uuid-maybe.behavior.pkl",
"this/will/be/ignored/uuid-maybe.replay.pkl",
]
results = run_validation(
filepaths,
[validation_step_0, validation_step_1, ],
)
Command-line interface
Run a validation
$ np-validator validate file_list.json validation_steps.yml output.json
Get version
$ np-validator main --version
Documentation
For more detailed documentation on using this package please refer to the docs.
Contributing
Processor
To add a new processor, add the function to np_validator/processors.py
. Ideally create a test for it in tests
. Run the tests to help ensure that no regressions have been introduced. Each processor is expected to have one required argument which is expected to be a string filepath.
Validator
To add a new validator, add the function to np_validator/validators.py
. Ideally create a test for it in tests
. Run the tests to help ensure that no regressions have been introduced.
Very first steps
Initialize your code
- Initialize
git
inside your repo:
cd np-validator && 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/np_validator/np-validator.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 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 asmajor
,minor
, orpatch
. 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 3.7
and higher. Poetry
as the dependencies manager. See configuration inpyproject.toml
andsetup.cfg
.- Automatic codestyle with
black
,isort
andpyupgrade
. - Ready-to-use
pre-commit
hooks with code-formatting. - Type checks with
mypy
; docstring checks withdarglint
; security checks withsafety
andbandit
- 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 inrelease-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
, andSECURITY.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 np-validator
or install with Poetry
poetry add np-validator
Makefile usage
Makefile
contains a lot of functions for faster development.
1. Download and remove Poetry
To download and install Poetry run:
make poetry-download
To uninstall
make poetry-remove
2. Install all dependencies and pre-commit hooks
Install requirements:
make install
Pre-commit hooks coulb be installed after git init
via
make pre-commit-install
3. Codestyle
Automatic formatting uses pyupgrade
, isort
and black
.
make codestyle
# or use synonym
make formatting
Codestyle checks only, without rewriting files:
make check-codestyle
Note:
check-codestyle
usesisort
,black
anddarglint
library
Update all dev libraries to the latest version using one comand
make update-dev-deps
4. Code security
make check-safety
This command launches Poetry
integrity checks as well as identifies security issues with Safety
and Bandit
.
make check-safety
5. Type checks
Run mypy
static type checker
make mypy
6. Tests with coverage badges
Run pytest
make test
7. All linters
Of course there is a command to rule run all linters in one:
make lint
the same as:
make test && make check-codestyle && make mypy && make check-safety
8. Docker
make docker-build
which is equivalent to:
make docker-build VERSION=latest
Remove docker image with
make docker-remove
More information about docker.
9. Cleanup
Delete pycache files
make pycache-remove
Remove package build
make build-remove
Delete .DS_STORE files
make dsstore-remove
Remove .mypycache
make mypycache-remove
Or to remove all above run:
make cleanup
📈 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 MIT
license. See LICENSE for more details.
📃 Citation
@misc{np-validator,
author = {np-validator},
title = {Awesome `np-validator` is a Python cli/package created with https://github.com/TezRomacH/python-package-template},
year = {2022},
publisher = {GitHub},
journal = {GitHub repository},
howpublished = {\url{https://github.com/np_validator/np-validator}}
}
Credits
This project was generated with python-package-template
Project details
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