Python Jupyter kernel using Poetry for reproducible notebooks

Last update: Jan 04, 2023

Related tags

Overview

Poetry Kernel

Use per-directory Poetry environments to run Jupyter kernels. No need to install a Jupyter kernel per Python virtual environment!

The idea behind this project is to allow you to capture the exact state of your environment. This means you can email your work to your peers, and they'll have exactly the same set of packages that you do! Reproducibility!

Why not virtual environments (venvs)?

Virtual environments were (and are) an important advancement to Python's package management story, but they have a few shortcomings:

They are not great for reproducibility. Usually, you'll create a new virtual environment using a requirements.txt which includes all the direct dependencies (numpy, pandas, etc.), but not transient dependencies (pandas depends on pytz for timezone support, for example). And usually, even the direct dependencies are specified only as minimum (or semver) ranges (e.g., numpy>=1.21) which can make it hard or impossible to accurately recreate the venv later.
With Jupyter, they usually require that the kernels be installed globally. This means you'll need need to have a separate kernelspec for every venv you want to use with Jupyter.

Poetry uses venvs transparently under the hood by constructing them from the pyproject.toml and poetry.lock files. The poetry.lock file records the exact state of dependencies (and transient dependencies) and can be used to more accurately reproduce the environment.

Additionally, Poetry Kernel means you only have to install one kernelspec. It then uses the pyproject.toml file from the directory of the notebook (or any parent directory) to choose which environment to run the notebook in.

Shameless plug

The reason we created this package was to make sure that the code environments created for running student code on Pathbird exactly match your development environment. Interested in developing interactive, engaging, inquiry-based lessons for your students? Check out Pathbird for more information!

Usage

Install Poetry if not yet installed.

Install this package:

# NOTE: Do **NOT** install this package in your Poetry project, it should be
# installed at the system or user level.
pip3 install --user poetry-kernel

Initialize a Poetry project (only required if you do not have an existing Poetry project ready to use):
```
poetry init -n
```

IMPORTANT: Add ipykernel to your project's dependencies:

# In the directory of your Poetry project
poetry add ipykernel

Start a "Poetry" Jupyter kernel and see it in action!

Troubleshooting

Kernel isn't starting ("No Kernel" message)

Pro-tip: Check the output of the terminal window where you launched Jupyter. It will usually explain why the kernel is failing to start.

Make sure that you are launching a notebook in a directory/folder that contains a Poetry project (pyproject.toml and poetry.lock files). You can turn a directory into a Poetry project by running:

poetry init -n

Make sure that you've installed ipykernel into your project:

poetry add ipykernel

Make sure the Poetry project is installed! This is especially important for projects that you have downloaded from others (warning: installing a Poetry project could run arbitrary code on your computer, make sure you trust your download first!):
```
poetry install
```
Still can't figure it out? Open an issue!

A package I added won't import properly

If you added the package after starting the kernel, you might need to restart the kernel for it to see the new package.

FAQ

See FAQ.md.

Comments

Windows Does not have SIGKILL

I believe the following line needs more attention to be compatible with Windows considering windows does not have SIGKILL: https://github.com/pathbird/poetry-kernel/blob/main/poetry_kernel/main.py#L39
bug good first issue prs accepted

opened by amirhessam88 4
FileNotFoundError: [Errno 2] No such file or directory: 'poetry'.
Hey, cool project!

I got the following error, not sure how informative it is for you. Happy to dig into logs etc. I'm using a Gitpod workspace with a public github repo too, so could potentially offer a completely reproducible clean environment.

Failed to start the Kernel. FileNotFoundError: [Errno 2] No such file or directory: 'poetry'.
opened by andrewcstewart 3
Check in parent_dirs for pyproject.toml

This now loops through parent directories to check for pyproject.toml to allow for kernel execution when running notebooks in sub directories. I used the same code from poetry itself to ensure compatibility

opened by nick-gorse 3
modified forward_signals to be compatible with windows

in regard to issue #3

removed signal.SIGTERM from forward_signals, as well as two others as they could not be used by signal.signal (ValueError: invalid signal value)

from https://docs.python.org/3/library/signal.html signal.CTRL_C_EVENT The signal corresponding to the Ctrl+C keystroke event. This signal can only be used with os.kill()

same for signal.CTRL_BREAK_EVENT

opened by gpfv 0
Check in parent_dirs for pyproject.toml

This now loops through parent directories to check for pyproject.toml to allow for kernel execution when running notebooks in sub directories. I used the same code as used poetry itself to ensure compatibility

opened by nick-gorse 0
poetry-kernel uses Jupyter env instead of notebook env

If a poetry pyproject.toml is used to create the environment for the Jupyter lab (adding poetry-kernel as a dependency), then no matter in which working directory the jupyter server is started, any notebook that is opened with the "poetry" kernel will have the Jupyter environment, not the environment of the notebook's project.

Minimal example: https://github.com/drakesiardxy/poetry-kernel-bug To replicate: Create the jupyer-base env and the kernel_a env separately, then start the jupyter server with the first environment and attempt to run kernel_a.ipynb using the "Poetry" kernel. pandas will be missing, because the notebook will have been launched with the environment of the server, not the environment belonging to the notebook's project.

opened by drakesiardxy 0

Is it possible to make poetry-kernel work with JupyterHub?

Hi!

We have a multi-user JupyterHub instance and we would like to use your library. So far we have only been able to see the poetry-kernel button in the kernel selection screen by installing poetry kernel at the user level (if we install poetry kernel from the user that launches JupyterHub, the root user, the button does not show). But the problem that we have is that when we press the poetry button and create a new notebook in a folder with a poetry project (and ipykernel installed), the kernel is never connected so no code can be executed. The generated logs are the following:

Apr 26 15:30:26 labs-ubuntu-20-04 python3[446728]: [I 2022-04-26 15:30:26.298 SingleUserLabApp restarter:66] AsyncIOLoopKernelRestarter: restarting kernel (2/5), new random ports
Apr 26 15:30:26 labs-ubuntu-20-04 python3[1028846]: Traceback (most recent call last):
Apr 26 15:30:26 labs-ubuntu-20-04 python3[1028846]:   File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main
Apr 26 15:30:26 labs-ubuntu-20-04 python3[1028846]:     return _run_code(code, main_globals, None,
Apr 26 15:30:26 labs-ubuntu-20-04 python3[1028846]:   File "/usr/lib/python3.8/runpy.py", line 87, in _run_code
Apr 26 15:30:26 labs-ubuntu-20-04 python3[1028846]:     exec(code, run_globals)
Apr 26 15:30:26 labs-ubuntu-20-04 python3[1028846]:   File "/home/marta/.local/lib/python3.8/site-packages/poetry_kernel/__main__.py", line 68, in <module>
Apr 26 15:30:26 labs-ubuntu-20-04 python3[1028846]:     main()
Apr 26 15:30:26 labs-ubuntu-20-04 python3[1028846]:   File "/home/marta/.local/lib/python3.8/site-packages/poetry_kernel/__main__.py", line 37, in main
Apr 26 15:30:26 labs-ubuntu-20-04 python3[1028846]:     proc = subprocess.Popen(cmd)
Apr 26 15:30:26 labs-ubuntu-20-04 python3[1028846]:   File "/usr/lib/python3.8/subprocess.py", line 858, in __init__
Apr 26 15:30:26 labs-ubuntu-20-04 python3[1028846]:     self._execute_child(args, executable, preexec_fn, close_fds,
Apr 26 15:30:26 labs-ubuntu-20-04 python3[1028846]:   File "/usr/lib/python3.8/subprocess.py", line 1704, in _execute_child
Apr 26 15:30:26 labs-ubuntu-20-04 python3[1028846]:     raise child_exception_type(errno_num, err_msg, err_filename)
Apr 26 15:30:26 labs-ubuntu-20-04 python3[1028846]: FileNotFoundError: [Errno 2] No such file or directory: 'poetry'

This looks like poetry is not being found by the library although it is indeed installed both at the root and user level. Is there a way to solve this? Or is this case out of the scope of the library for now?

opened by MsLimon 2

Releases(v0.1.2)

v0.1.2(Mar 30, 2022)
What's Changed

modified forward_signals to be compatible with windows by @gpfv in https://github.com/pathbird/poetry-kernel/pull/4

New Contributors

@gpfv made their first contribution in https://github.com/pathbird/poetry-kernel/pull/4

Full Changelog: https://github.com/pathbird/poetry-kernel/compare/v0.1.1...v0.1.2
Source code(tar.gz)
Source code(zip)
v0.1.0(Aug 26, 2021)

Source code(tar.gz)
Source code(zip)

Owner

Pathbird

Pathbird is a platform for instructors to build interactive, engaging, inquiry-based lessons for computational courses.

GitHub Repository

Forecasting with Gradient Boosted Time Series Decomposition

ThymeBoost ThymeBoost combines time series decomposition with gradient boosting to provide a flexible mix-and-match time series framework for spicy fo

131 Jan 08, 2023

PyTorch ,ONNX and TensorRT implementation of YOLOv4

4.2k Jan 01, 2023

Rapid experimentation and scaling of deep learning models on molecular and crystal graphs.

LitMatter A template for rapid experimentation and scaling deep learning models on molecular and crystal graphs. How to use Clone this repository and

32 Dec 06, 2022

tensorrt int8 量化yolov5 4.0 onnx模型

onnx模型转换为 int8 tensorrt引擎

123 Dec 28, 2022

Using Convolutional Neural Networks (CNN) for Semantic Segmentation of Breast Cancer Lesions (BRCA)

Using Convolutional Neural Networks (CNN) for Semantic Segmentation of Breast Cancer Lesions (BRCA). Master's thesis documents. Bibliography, experiments and reports.

73 Dec 04, 2022

Official PyTorch code of DeepPanoContext: Panoramic 3D Scene Understanding with Holistic Scene Context Graph and Relation-based Optimization (ICCV 2021 Oral).

DeepPanoContext (DPC) [Project Page (with interactive results)][Paper] DeepPanoContext: Panoramic 3D Scene Understanding with Holistic Scene Context G

66 Nov 16, 2022

Reimplementation of NeurIPS'19: "Meta-Weight-Net: Learning an Explicit Mapping For Sample Weighting" by Shu et al.

[Re] Meta-Weight-Net: Learning an Explicit Mapping For Sample Weighting Reimplementation of NeurIPS'19: "Meta-Weight-Net: Learning an Explicit Mapping

1 Mar 13, 2020

Head and Neck Tumour Segmentation and Prediction of Patient Survival Project

Head-and-Neck-Tumour-Segmentation-and-Prediction-of-Patient-Survival Welcome to the Head and Neck Tumour Segmentation and Prediction of Patient Surviv

5 Oct 20, 2022

A vision library for performing sliced inference on large images/small objects

SAHI: Slicing Aided Hyper Inference A vision library for performing sliced inference on large images/small objects Overview Object detection and insta

2.3k Jan 04, 2023

This code is an unofficial implementation of HiFiSinger.

HiFiSinger This code is an unofficial implementation of HiFiSinger. The algorithm is based on the following papers: Chen, J., Tan, X., Luan, J., Qin,

87 Dec 23, 2022

This repo contains implementation of different architectures for emotion recognition in conversations.

Emotion Recognition in Conversations Updates 🔥 🔥 🔥 Date Announcements 03/08/2021 🎆 🎆 We have released a new dataset M2H2: A Multimodal Multiparty

1k Dec 30, 2022

Pathdreamer: A World Model for Indoor Navigation

Pathdreamer: A World Model for Indoor Navigation This repository hosts the open source code for Pathdreamer, to be presented at ICCV 2021. Paper | Pro

122 Jan 04, 2023

3D cascade RCNN for object detection on point cloud

3D Cascade RCNN This is the implementation of 3D Cascade RCNN: High Quality Object Detection in Point Clouds. We designed a 3D object detection model

22 Dec 02, 2022

Official code for "Decoupling Zero-Shot Semantic Segmentation"

Decoupling Zero-Shot Semantic Segmentation This is the official code for the arxiv. ZegFormer is the first framework that decouple the zero-shot seman

108 Dec 30, 2022

Python scripts form performing stereo depth estimation using the HITNET model in ONNX.

ONNX-HITNET-Stereo-Depth-estimation Python scripts form performing stereo depth estimation using the HITNET model in ONNX. Stereo depth estimation on

30 Nov 08, 2022

Object-Centric Learning with Slot Attention

Slot Attention This is a re-implementation of "Object-Centric Learning with Slot Attention" in PyTorch (https://arxiv.org/abs/2006.15055). Requirement

72 Jan 02, 2023

UniLM AI - Large-scale Self-supervised Pre-training across Tasks, Languages, and Modalities

Pre-trained (foundation) models across tasks (understanding, generation and translation), languages (100+ languages), and modalities (language, image, audio, vision + language, audio + language, etc.

7.6k Jan 01, 2023

😇A pyTorch implementation of the DeepMoji model: state-of-the-art deep learning model for analyzing sentiment, emotion, sarcasm etc

------ Update September 2018 ------ It's been a year since TorchMoji and DeepMoji were released. We're trying to understand how it's being used such t

865 Dec 24, 2022

Visual odometry package based on hardware-accelerated NVIDIA Elbrus library with world class quality and performance.

Isaac ROS Visual Odometry This repository provides a ROS2 package that estimates stereo visual inertial odometry using the Isaac Elbrus GPU-accelerate

343 Jan 03, 2023

Jax/Flax implementation of Variational-DiffWave.

jax-variational-diffwave Jax/Flax implementation of Variational-DiffWave. (Zhifeng Kong et al., 2020, Diederik P. Kingma et al., 2021.) DiffWave with

37 Dec 16, 2022