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Upgrade project to jupyterlab 4x #728

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12 changes: 6 additions & 6 deletions .github/workflows/unit.yml
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Original file line number Diff line number Diff line change
@@ -15,16 +15,16 @@ jobs:
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Set up Node.js 14.x
- name: Set up Node.js 20.x
uses: actions/setup-node@v3
with:
node-version: 14.17.4
node-version: '20.18.3'
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install wheel
pip install build hatch hatch-jupyter-builder
pip install flake8 pytest
pip install "jupyterlab>=3,<4"
pip install "jupyterlab>=4.3.5,<5"
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
- name: Lint with flake8
run: |
@@ -33,7 +33,7 @@ jobs:
flake8 ./test --max-complexity 10 --ignore E501,C901,W291 --show-source --statistics
- name: Install
run: |
python setup.py bdist_wheel
python -m build .
pip install ./dist/graph_notebook-*-py3-none-any.whl
- name: Post-install commands
run: |
@@ -43,4 +43,4 @@ jobs:
python -m graph_notebook.notebooks.install
- name: Test with pytest
run: |
pytest test/unit
pytest test/unit
Empty file removed =3,
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58 changes: 45 additions & 13 deletions README.md
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Original file line number Diff line number Diff line change
@@ -96,24 +96,24 @@ It is recommended to check the [ChangeLog.md](ChangeLog.md) file periodically to

You will need:

* [Python](https://www.python.org/downloads/) 3.9.x-3.10.14
* [Python](https://www.python.org/downloads/)
* For JupyterLab 4x Version: 3.9.x-3.11.x
* For JupyterLab 3x Version: 3.9.x-3.10.14
* A graph database that provides one or more of:
* A SPARQL 1.1 endpoint
* An Apache TinkerPop Gremlin Server compatible endpoint
* An endpoint compatible with openCypher

## Installation

Begin by installing `graph-notebook` and its prerequisites, then follow the remaining instructions for either Jupyter Classic Notebook or JupyterLab.
Follow the instructions for either Jupyter Classic Notebook or JupyterLab based on your requirements.

``` bash
# install the package
pip install graph-notebook
```

### Jupyter Classic Notebook

``` bash
pip install graph-notebook

# Enable the visualization widget
jupyter nbextension enable --py --sys-prefix graph_notebook.widgets

@@ -132,12 +132,39 @@ touch ~/.jupyter/nbconfig/notebook.json
python -m graph_notebook.start_notebook --notebooks-dir ~/notebook/destination/dir
```

### JupyterLab 3.x
### Jupyter Lab

Graph-notebook has been upgraded to support JupyterLab 4.x since version 5.0.0, featuring a modernized widget architecture and improved compatibility.

Choose your installation based on your JupyterLab version requirements.


### JupyterLab 4.x (Recommended)

``` bash
# install jupyterlab
pip install "jupyterlab>=4.3.5,<5"

# Install the latest version with JupyterLab 4.x support
pip install graph-notebook

# copy premade starter notebooks
python -m graph_notebook.notebooks.install --destination ~/notebook/destination/dir

# start jupyterlab
python -m graph_notebook.start_jupyterlab --jupyter-dir ~/notebook/destination/dir
```

### JupyterLab 3.x (Legacy)

``` bash

# install jupyterlab
pip install "jupyterlab>=3,<4"

# Install legacy version for JupyterLab 3.x compatibility
pip install "graph-notebook<5.0.0"

# copy premade starter notebooks
python -m graph_notebook.notebooks.install --destination ~/notebook/destination/dir

@@ -378,26 +405,31 @@ cd graph-notebook
# 2) Create a new virtual environment

# 2a) Option 1 - pyenv
# install pyenv - https://github.com/pyenv/pyenv?tab=readme-ov-file#installation
# install pyenv-virtualenv - https://github.com/pyenv/pyenv-virtualenv?tab=readme-ov-file#installation
pyenv install 3.10.13 # Only if not already installed; this can be any supported Python 3 version in Prerequisites
pyenv virtualenv 3.10.13 build-graph-notebook
pyenv local build-graph-notebook

# 2b) Option 2 - venv
deactivate
conda deactivate
rm -rf /tmp/venv
python3 -m venv /tmp/venv
python3 -m venv --clear /tmp/venv
source /tmp/venv/bin/activate


# 3) Install build dependencies
pip install --upgrade pip setuptools wheel twine
pip install "jupyterlab>=3,<4"
pip install --upgrade build hatch hatch-jupyter-builder
pip install "jupyterlab>=4.3.5,<5"

# 4) Build the distribution
python3 setup.py bdist_wheel
python3 -m build .
```

You should now be able to find the built distribution at

`./dist/graph_notebook-4.6.2-py3-none-any.whl`
`./dist/graph_notebook-5.0.0-py3-none-any.whl`

And use it by following the [installation](https://github.com/aws/graph-notebook#installation) steps, replacing

@@ -408,7 +440,7 @@ pip install graph-notebook
with

``` python
pip install ./dist/graph_notebook-4.6.2-py3-none-any.whl
pip install ./dist/graph_notebook-5.0.0-py3-none-any.whl --force-reinstall
```

## Contributing Guidelines
18 changes: 6 additions & 12 deletions additional-databases/sagemaker/sagemaker-notebook-lifecycle/install-graph-notebook-lc.sh
View file
Original file line number Diff line number Diff line change
@@ -19,17 +19,6 @@ python3 -m ipykernel install --sys-prefix --name python3 --display-name "Python
echo "installing python dependencies..."
pip uninstall NeptuneGraphNotebook -y # legacy uninstall when we used to install from source in s3

pip install "jupyter_core<=5.3.2"
pip install "jupyter_server<=2.7.3"
pip install "jupyter-console<=6.4.0"
pip install "jupyter-client<=6.1.12"
pip install "ipywidgets==7.7.2"
pip install "jupyterlab_widgets==1.1.1"
pip install "notebook==6.4.12"
pip install "nbclient<=0.7.0"
pip install "itables<=1.4.2"
pip install awswrangler

if [[ ${NOTEBOOK_VERSION} == "" ]]; then
pip install --upgrade graph-notebook
else
@@ -47,11 +36,14 @@ if [[ ${NOTEBOOK_VERSION//./} < 330 ]] && [[ ${NOTEBOOK_VERSION} != "" ]]; then
jupyter nbextension install --py --sys-prefix graph_notebook.widgets
fi
jupyter nbextension enable --py --sys-prefix graph_notebook.widgets
echo "enabled visualization..."

echo "Copying starter notebooks..."
mkdir -p ~/SageMaker/Neptune
cd ~/SageMaker/Neptune || exit
python -m graph_notebook.notebooks.install
chmod -R a+rw ~/SageMaker/Neptune/*
echo "Copied starter notebooks..."

source ~/.bashrc || exit
HOST=${GRAPH_NOTEBOOK_HOST}
@@ -89,7 +81,9 @@ else
echo "Skipping, unsupported on graph-notebook<=3.4.1"
fi

conda /home/ec2-user/anaconda3/bin/deactivate
echo "graph-notebook installation complete."

conda deactivate || echo "Already deactivated or not in an environment."
echo "done."

EOF
130 changes: 130 additions & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,130 @@
[build-system]
requires = [
"hatchling>=1.5.0",
"jupyterlab>=4.0.0,<5.0.0",
"hatch-nodejs-version",
"hatch-jupyter-builder>=0.5"
]
build-backend = "hatchling.build"

[project]
name = "graph-notebook"
version = "5.0.0"
description = "Jupyter notebook extension to connect to graph databases"
readme = "README.md"
license = { file = "LICENSE" }
requires-python = ">=3.9,<3.12"
authors = [
{ name = "amazon-neptune", email = "amazon-neptune-pypi@amazon.com" },
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"License :: OSI Approved :: Apache Software License"
]
keywords = ["jupyter", "neptune", "gremlin", "sparql", "opencypher"]
dependencies = [
# Jupyter ecosystem
'ipyfilechooser==0.6.0',
'ipykernel>=6.5.0',
'ipython>=7.16.1,<=8.10.0',
'ipywidgets>=8.0.0,<9.0.0',
'jupyter-server>=2.0.0,<3.0.0',
'jupyter-server-proxy>=4.0.0,<5.0.0',
'jupyter_client>=8.0.0,<9.0.0',
'jupyterlab>=4.3.5,<5.0.0',
'jupyterlab-widgets>=3.0.0,<4.0.0',
'nbclient>=0.7.3',
'nbconvert>=6.3.0,<=7.2.8',
# Pinned for compatibility with custom nbextensions and Jupyter classic notebooks.
# JupyterLab 7+ removed support for nbextensions as part of modernizing the extension system.
# Our project uses custom nbextensions (setup in src/graph_notebook/nbextensions/install.py)
# that need to work with Jupyter classic.
# See: https://github.com/ipython-contrib/jupyter_contrib_nbextensions/issues/1661
# Will require migration work to support JupyterLab 7+ in the future.
'notebook==6.4.2',

# Data processing and visualization
'itables>=2.0.0,<=2.1.0',
'networkx==2.4',
'numpy>=1.23.5,<1.24.0',
'pandas>=2.1.0,<=2.2.2',

# Graph databases and query languages
'gremlinpython>=3.5.1,<=3.7.2',
'neo4j>=5.0.0,<=5.23.1',
'rdflib==7.0.0',
'SPARQLWrapper==2.0.0',

# AWS SDK
'boto3>=1.34.74',
'botocore>=1.34.74',

# Utilities
'async-timeout>=4.0,<5.0',
'jedi>=0.18.1,<=0.18.2',
'Jinja2>=3.0.3,<=3.1.4',
'json-repair==0.29.2',
'nest_asyncio>=1.5.5,<=1.6.0',
'requests>=2.32.0,<=2.32.2'
]

[project.optional-dependencies]
test = [
"pytest==6.2.5"
]

[project.entry-points]
"ipython" = { "graph_notebook_magics" = "graph_notebook.magics:load_ipython_extension" }
"notebook.extensions" = { "graph_notebook_widgets" = "graph_notebook.widgets:_jupyter_nbextension_paths" }
"jupyter_labextension" = { "graph_notebook_widgets" = "graph_notebook.widgets:_jupyter_labextension_paths" }

[tool.hatch.build.hooks.jupyter-builder]
dependencies = ["hatch-jupyter-builder>=0.5"]
build-function = "hatch_jupyter_builder.npm_builder"
ensured-targets = [
"src/graph_notebook/widgets/labextension/package.json",
"src/graph_notebook/widgets/labextension/static/style.js",
"src/graph_notebook/widgets/nbextension/index.js",
]
skip-if-exists = ["src/graph_notebook/widgets/labextension/static/style.js"]

[tool.hatch.build.hooks.jupyter-builder.build-kwargs]
build_cmd = "build:prod"
npm = ["npm", "--prefix", "src/graph_notebook/widgets"]
source_dir = "src/graph_notebook/widgets"
build_dir = "src/graph_notebook/widgets/lib"

[tool.hatch.build]
artifacts = [
"src/graph_notebook/widgets/labextension",
"src/graph_notebook/widgets/nbextension",
]

[tool.hatch.build.targets.wheel.shared-data]
"src/graph_notebook/widgets/labextension" = "share/jupyter/labextensions/graph_notebook_widgets"
"src/graph_notebook/widgets/nbextension" = "share/jupyter/nbextensions/graph_notebook_widgets"
"src/graph_notebook/widgets/graph_notebook_widgets.json" = "etc/jupyter/nbconfig/notebook.d/graph_notebook_widgets.json"

[tool.hatch.build.targets.sdist]
exclude = [
"/.github",
"/docs",
"node_modules",
]

[tool.hatch.build.targets.wheel]
packages = ["src/graph_notebook"]
include = [
"src/graph_notebook/**/*.py",
"src/graph_notebook/**/*.ipynb",
"src/graph_notebook/**/*.json",
"src/graph_notebook/**/*.txt",
"src/graph_notebook/**/*.html",
"src/graph_notebook/**/*.css",
"src/graph_notebook/**/*.js",
"src/graph_notebook/**/*.yaml",
"src/graph_notebook/**/*.csv"
]
58 changes: 31 additions & 27 deletions requirements.txt
View file
Original file line number Diff line number Diff line change
@@ -1,33 +1,37 @@
SPARQLWrapper==2.0.0
networkx==2.4
Jinja2>=3.0.3,<=3.1.4
jupyter==1.0.0
notebook>=6.1.5,<7.0.0
ipywidgets==7.7.2
jupyterlab_widgets>=1.0.0,<=1.1.10
nbclient<=0.7.0
jupyter-contrib-nbextensions<=0.7.0
widgetsnbextension<=3.6.1
gremlinpython>=3.5.1,<=3.7.2
requests>=2.32.0,<=2.32.2
ipython>=7.16.1,<=8.10.0
ipykernel==5.3.4
# Jupyter ecosystem
ipyfilechooser==0.6.0
neo4j>=5.0.0,<=5.23.1
rdflib==7.0.0
setuptools>=70.0.0,<=70.0.3
ipykernel>=6.5.0
ipython>=7.16.1,<=8.10.0
ipywidgets>=8.0.0,<9.0.0
jupyter-server>=2.0.0,<3.0.0
jupyter-server-proxy>=4.0.0,<5.0.0
jupyter_client>=8.0.0,<9.0.0
jupyterlab>=4.3.5,<5.0.0
jupyterlab-widgets>=3.0.0,<4.0.0
nbclient>=0.7.3
nbconvert>=6.3.0,<=7.2.8
jedi>=0.18.1,<=0.18.2
markupsafe<2.1.0
notebook==6.4.2

# Data processing and visualization
itables>=2.0.0,<=2.1.0
networkx==2.4
numpy>=1.23.5,<1.24.0
pandas>=2.1.0,<=2.2.2
numpy<1.24.0
nest_asyncio>=1.5.5,<=1.6.0

# Graph databases and query languages
gremlinpython>=3.5.1,<=3.7.2
neo4j>=5.0.0,<=5.23.1
rdflib==7.0.0
SPARQLWrapper==2.0.0

# AWS SDK
boto3>=1.34.74
botocore>=1.34.74

# Utilities
async-timeout>=4.0,<5.0
jedi>=0.18.1,<=0.18.2
Jinja2>=3.0.3,<=3.1.4
json-repair==0.29.2

# requirements for testing
botocore~=1.34.74
boto3~=1.34.74
pytest==6.2.5
parameterized==0.8.1
nest_asyncio>=1.5.5,<=1.6.0
requests>=2.32.0,<=2.32.2
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