veit / jupyter-tutorial Goto Github PK

Training materials for setting up and using a research infrastructure based on Jupyter notebooks: https://cusy.io/en/seminars

Home Page: https://jupyter-tutorial.readthedocs.io/

License: BSD 3-Clause "New" or "Revised" License

Python 100.00%

jupyter ipython ipython-widget ipywidget jupyter-notebook jupyterhub notebook

jupyter-tutorial's Introduction

Quick start

Status

Installation

Download and unpack:

$ curl -O https://codeload.github.com/veit/jupyter-tutorial/zip/main
$ unzip main
Archive:  main
…
   creating: jupyter-tutorial-main/
…

Install Python packages:

$ cd jupyter-tutorial-main
$ python3 -m venv .
$ . bin/activate
$ python -m pip install -r docs/requirements.txt

Install the Jupyter Notebook Extensions Javascript and CSS files:

$ jupyter contrib nbextension install --user
jupyter contrib nbextension install --user
Installing jupyter_contrib_nbextensions nbextension files to jupyter data directory
…
Successfully installed jupyter-contrib-core-0.3.3 jupyter-contrib-nbextensions-0.5.1
jupyter-highlight-selected-word-0.2.0 jupyter-latex-envs-1.4.6
jupyter-nbextensions-configurator-0.4.1
…
$ jupyter nbextension enable latex_envs --user --py
Enabling notebook extension latex_envs/latex_envs...
      - Validating: OK

Create HTML documentation:

Note that pandoc has to be installed. On Debian/Ubuntu you can just run
```
$  sudo apt install pandoc
```
To create the HTML documentation run these commands:
```
$ cd docs/
$ make html
```

Create a PDF:

For the creation of a PDF file you need additional packages.

For Debian/Ubuntu you get them with the following command:

$ sudo apt install texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended latexmk

or for macOS with:

$ brew cask install mactex
…
🍺  mactex was successfully installed!
$ curl --remote-name https://www.tug.org/fonts/getnonfreefonts/install-getnonfreefonts
$ sudo texlua install-getnonfreefonts
…
mktexlsr: Updating /usr/local/texlive/2020/texmf-dist/ls-R...
mktexlsr: Done.

Then you can generate a PDF with:

$ make latexpdf
…
The LaTeX files are in _build/latex.
Run 'make' in that directory to run these through (pdf)latex
…

You can find the PDF at docs/_build/latex/jupytertutorial.pdf.

Install vnd run ale to check spelling

You can install Vale with:

$ brew install vale

You can install the parser for Restructuredtext with:

$ brew install docutils

.. seealso::
   * `Vale installation <https://docs.errata.ai/vale/install>`_
   * `Vale formats <https://docs.errata.ai/vale/scoping#formats>`_

Now you can check the RestructuredText files with:

$ vale .
✔ 0 errors, 0 warnings and 0 suggestions in 201 files.

Pull-Requests

If you have suggestions for improvements and additions, I recommend that you create a Fork of my GitHub Repository and make your changes there. . You are also welcome to make a pull request. If the changes contained therein are small and atomic, I’ll be happy to look at your suggestions.

jupyter-tutorial's People

Contributors

Stargazers

Watchers

Forkers

hofmannedv rikuturkki laura1206 silke christiank97 sek012 ps491 macagua idomic kentzo theo-armour jkbgbr

jupyter-tutorial's Issues

Add ipycanvas to ipywidgets libs

Add voila-embed

github.com/mariobuikhuizen/voila-embed

Add ipympl to ipywidgets libs

Add ipympl is a Matplotlib Jupyter Extension which enables the interactive features of matplotlib in Jupyter notebooks.

Add DVC compared with git-annex

See https://discuss.dvc.org/t/comparison-to-datalad-and-git-annex/92

Add ipylayout to dashboards or sphinx third party extensions

GitHub
GoldenLayout, a multi-screen layout manager for webapps
example

Python 3.8 Notebook

Python 3.8 brings several features that are very interesting for scientific computing. They should be presented in a notebook.

Extending the tutorial for parallelisation support

ipyparallel, see also Using IPython for parallel computing
Dask Futures extends Python’s concurrent.futures
- Launch Dask from IPyParallel
- Dask-MPI

Add CML

Using img.shields.io contributors and license, readthedocs.org build

Add importnb to docs/ipython/importing.ipynb

GitHub
Docs

Automating code quality in product realisation

check-manifest
mypy for static typing
Black
- Config in pyproject.toml:
```
[tool.black]
line-length = 79
```
- Link to Craft Your Python Like Poetry.

isort

Config:

[isort]
atomic=true
force_grid_wrap=0
include_trailing_comma=true
lines_after_imports=2
lines_between_types=1
multi_line_output=3
not_skip=__init__.py
use_parentheses=true

known_first_party=attr
known_third_party=hypothesis,pytest,setuptools,six,zope

For the detection of third party packages you can use seed-isort-config.

prettier for automated formatting of other file types

pre-commit offers a framework for running hooks before committing code.

Config pre-commit-config.yaml:

repos:
  - repo: https://github.com/psf/black
    rev: 19.10b0
    hooks:
      - id: black
        language_version: python3.7
        # override until resolved: https://github.com/ambv/black/issues/402
    files: \.pyi?$
        types: []

  - repo: https://gitlab.com/pycqa/flake8
    rev: 3.7.9
    hooks:
      - id: flake8
        language_version: python3.7

  - repo: https://github.com/asottile/seed-isort-config
rev: v1.9.4
    hooks:
      - id: seed-isort-config

  - repo: https://github.com/pre-commit/mirrors-isort
rev: v4.3.21
    hooks:
      - id: isort
        additional_dependencies: [toml]
        language_version: python3.7

  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v2.4.0
    hooks:
      - id: trailing-whitespace
      - id: end-of-file-fixer
      - id: debug-statements

Run pre-commit run --all-files

Add ipyvuetify to ipywidgets

ipyvuetify are Jupyter widgets based on vuetify UI components. Also VuetifyTemplate can be used for the use of the Vue/Vuetify api.

Remove Bokeh and Bowtie from Dashboards

Both do not create dashboards for Jupyter notebooks.

Add Intake to docs for data collection

Create an example python package with setup.py, src, version, etc.

Add qgrid to notebook extensions

See github.com/quantopian/qgrid

Cite software

Research software citation for researchers
codemeta.json, CITATION.cff
DOI
The Open Science MOOC tutorial
Save and reference research software
Research Software Citation website
Neil Chue Hong: How to cite software: current best practice
CodeMeta
Citation File Format
Software Heritage Meta Data Support

Software Journals

Add badges for all libs

Stars
Contributors
Activity
Downloads
License

e.g.

Name	Stars	Contributors	Activity	Downloads	License
Jupyter-Tutorial

Add Atom IDE

Atom IDE
- jupyter-notebook
- GitKraken

Multilingual jupyter tutorial

The phpmyadmin docs comes with a Monorepo of Sphinx projects per language, but examples is a git submodule.
General instructions can be found in the ReadTheDocs docs: Localization.

Add orjson to data chapter

github.com/ijl/orjson

Add fbprophet for forecasting time series

Add hvPlot

hvPlot

Check out Guix-Jupyter

Add VisPy

VisPy

Update packaging docs to pep517 builds

See Do not use python setup.py ….
If you are invoking setup.py, you should be looking for the alternatives:

python setup.py upload → pipenv run twine
python setup.py install → pipenv install
python setup.py test → pipenv run tox
python setup.py sdist bdist_wheel → python -m pep517.build -s -b

Add link to binder in visualisation overview

Generate custom launch badges for your Binder repository

Alternativ oder zusätzlich könnte ein Badge generiert werden für die Pipenv-Environments.

Define audience in the documentation

At least one of the following audiences should be specified for each document:

data scientists
data engineers
data analysts
systems engineers

Add Mayavi to 3D visualisation docs

Mayavi now have limited support for Jupyter notebooks.

Add readthedocs badge to visualisation overview

Badges

Add Pangeo packages

Add «Connected papers in a visual graph»

Connected papers in a visual graph

Add widget-ts-cookiecutter

Add widget-ts-cookiecutter focused on TypeScript to custom widgets.

Add voila-material

PyPI
GitHub

Add pdvega and hvPlot

See

pdvega
hvPlot
In the overview link to pandas.DataFrame.plot API
Add to requirements for docs
Add to Python-374 kernel
Add notebooks to docs

pip-tools for dependency management including automation of updates.
venv, possibly supplemented by pex or shiv.
pipdeptree print the dependency tree of the installed packages

Unfortunately, Poetry can’t install packages along with their dependencies in an explicitly specified virtual environment. However, this makes CI much easier.

Manage npm

npm init

Lock dependencies: .npmrc

$ npm config set save=true
$ npm config set save-exact=true

Secure your projects and tokens
Don’t store the token directly in .npmrc but in .profile and then link to it:
```
//registry.npmjs.org/:_authToken=${NPM_TOKEN}
```
See Deploying with npm private modules
Check for outdated dependencies
```
$ npm outdated
```
See also Greenkeeper
preinstall, postinstall and test scripts
NODE_ENV environment variables
```
console.log("Node environment :"  + process.env.NODE_ENV);
```
See also:
- https://github.com/indexzero/nconf
- https://github.com/motdotla/dotenv
Avoid devDependencies in production
To install production dependencies, run
```
$ npm install --production
```
or
```
$ NODE_ENV=production npm install
```
See also Specifying dependencies and devDependencies in a package.json file