Upgrade to Python 3.12 and Qiskit 1.0 (#31)

- Upgrade to Python 3.12
- Drop cuQuantum due to NVIDIA CUDA requirement
- Upgrade packages
- Fix #30

Check list:

- [X] PR description is meaningful.
- [X] `./generate_requirements.sh` has been executed (when appropriate).
- [X] `./check_docker.sh` executes successfully locally.
- [x] `./build_docker.sh` executes successfully locally.
- [x] Zoose version in `.env` has been updated appropriately.
- [X] Commit has been tagged `git tag X.Y.Z` with `X.Y.Z` as in `.env`.
- [x] `README` has been updated (if applicable).

.env

@@ -1,3 +1,3 @@
 PREFIX=databaseline/zoose
 BASE=databaseline/zoose-base
-TAG=4.4.0
+TAG=5.0.0

.github/PULL_REQUEST_TEMPLATE.md

@@ -4,6 +4,6 @@ Check list:
 - [ ] `./generate_requirements.sh` has been executed (when appropriate).
 - [ ] `./check_docker.sh` executes successfully locally.
 - [ ] `./build_docker.sh` executes successfully locally.
-- [ ] Zoose version in `.env` has been updated appropriately.
+- [ ] Zoose version in .env has been updated appropriately.
 - [ ] Commit has been tagged `git tag X.Y.Z` with `X.Y.Z` as in `.env`.
 - [ ] `README` has been updated (if applicable).

README.md

@@ -32,65 +32,64 @@ In Gitpod, you have two options for Zoose notebooks:
 2. JupyterLab, which you can start from the Gitpod workspace terminal with `/jupyter.sh`.
 
 ### Zoose Base
-- Python 3.10
-- JupyterLab 3.6 with extensions
+- Python 3.12
+- JupyterLab 4.3 with extensions
 
 Python packages:
 - Beautiful Soup 4.12
 - Gower 0.1
-- Keras 2.12
+- Keras 3.5
 - LIME 0.2
-- Matplotlib 3.7
-- NLTK 3.8
-- Numpy 1.24
-- Pandas 2.0
-- Prince 0.10
-- Requests 2.31
-- Scikit-learn 1.2
-- SciPy 1.10
-- Scrapy 2.9
-- Seaborn 0.12
-- SHAP 0.41
-- spaCy 3.5
+- Matplotlib 3.9
+- NLTK 3.9
+- Numpy 1.26
+- Pandas 2.2
+- Prince 0.13
+- Requests 2.32
+- scikit-learn 1.5
+- SciPy 1.14
+- Scrapy 2.11
+- Seaborn 0.13
+- SHAP 0.46
+- spaCy 3.7
 - StatsModels 0.14
-- thefuzz 0.20
+- thefuzz 0.22
 
 ### Zoose Neo4j
 Zoose Neo4j includes everything from Zoose Base as well as:
 - Neo4j Community Edition 4.4
-- py2neo 2021.2.4
+- neomodel 5.3.2
 
 ### Zoose PyTorch
 Zoose PyTorch includes everything from Zoose Base as well as:
-- Captum 0.6
-- PyTorch 2.0
-- PyTorch Audio 2.0 (CPU)
-- PyTorch Text 0.15 (CPU)
-- PyTorch Vision 0.15 (CPU)
-- Transformers 4.29
+- Captum 0.7
+- PyTorch 2.4
+- PyTorch Audio 2.4 (CPU)
+- PyTorch Text 0.18 (CPU)
+- PyTorch Vision 0.19 (CPU)
+- Transformers 4.44
 
 ### Zoose Quantum
 Zoose Quantum includes everything from Zoose Base as well as:
-- Amazon Braket SDK 1.41
-- Cirq 1.1
-- cuQuantum 23.3
-- OpenFermion 1.5
-- PennyLane 0.30 with plugins for Cirq, Stawberry Fields, Qiskit
-- pytket 1.15
-- Qiskit 0.43
-- QuTiP 4.7
+- Amazon Braket SDK 1.57
+- Cirq 1.4
+- OpenFermion 1.6
+- PennyLane 0.38 with plugins for Cirq, Stawberry Fields, Qiskit
+- pytket 1.32
+- Qiskit 1.2
+- QuTiP 5.0
 - Strawberry Fields 0.23
 
 ### Zoose Geo
 Zoose Geo includes everything from Zoose Base as well as:
-- Geopandas 0.13
+- Geopandas 1.0
 - Geoplot 0.5
 - h3 3.7
-- h5py 3.8
-- netCDF4 1.6
+- h5py 3.11
+- netCDF4 1.7
 - shapely 2.0
-- xarray 2023.5
-- zarr 2.14
+- xarray 2024.9
+- zarr 2.18
 
 # How to use?
 Execute `./zoose.sh`, which launches a Jupyter notebooks session.

base/Dockerfile

@@ -1,11 +1,10 @@
-ARG SOURCE
+FROM ubuntu:24.04
 
-FROM ${SOURCE}
 LABEL org.opencontainers.image.authors="Ian Hellström" \
       org.opencontainers.image.source="https://github.com/ianhellstrom/zoose" \
-      org.opencontainers.image.vendor="Databaseline"
+      org.opencontainers.image.vendor="ianhellstrom.org"
 
-ENV PYTHON_VERSION="3.10"
+ENV PYTHON_VERSION="3.12"
 ARG DEBIAN_FRONTEND="noninteractive"
 ARG TZ="Europe/Berlin"
 
@@ -23,13 +22,10 @@ RUN apt-get update && apt-get -y upgrade && \
         openjdk-11-jre \
         python${PYTHON_VERSION} \
         python${PYTHON_VERSION}-dev \
-        python${PYTHON_VERSION}-distutils \
         libzmq3-dev \
         libcurl4-openssl-dev \
         libssl-dev \
         libopenblas0-pthread \
-        jupyter-core \
-        jupyter-client \
         git \
         sudo \
         libgdal-dev 
@@ -40,7 +36,7 @@ RUN add-apt-repository -y universe && apt-get update && \
 
 WORKDIR /setup
 COPY requirements.txt /setup/requirements.txt
-RUN pip install --no-cache-dir -r /setup/requirements.txt
+RUN pip install --no-cache-dir --break-system-packages --ignore-installed -r /setup/requirements.txt
 
 COPY dictionaries /usr/local/share/jupyter/dictionaries/
 COPY config/extensions.json /root/.jupyter/lab/user-settings/@jupyterlab/extensionmanager-extension/plugin.jupyterlab-settings

base/constraints.txt

@@ -1,2 +1,2 @@
 # Because of quantum libraries
-networkx==2.8.8
+# networkx==2.8.8