Merge pull request #12 from guimou/dev

Release 0.0.12

CHANGELOG.md

@@ -7,6 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+- Monai notebook in the `notebook-controller-images` line. As it's not thoroughly tested it's still not officially released.
+
+## [0.0.12] - 2022-08-04
+
+### Added
+
 - New organization of images for upcoming Kubeflow Notebook Controller
 - Base, Minimal, Data Science, Code-Server and RStudio images available in the new `notebook-controller-images` line
 

jupyterhub-images/monai-notebook/README.md

@@ -13,4 +13,4 @@ Project MONAI also includes MONAI Label, an intelligent open source image labeli
 
 Streamlit turns data scripts into shareable web apps in minutes.
 All in pure Python. No front‑end experience required.
-See [details on Streamlit implementation](../streamlit-notebook/README.md).
+See [details on Streamlit implementation](../streamlit-notebook/README.md).

notebook-controller-images/s2i-monai/Makefile

@@ -0,0 +1,13 @@
+.PHONY: default ubi9-py39
+
+TAG ?= $(shell git describe --tags --always --dirty)
+
+default:
+	@echo "Options are:"
+	@echo "ubi9-py39 : builds an image based on UBI9 with Python 3.9"
+	@echo "---"
+	@echo "Please specify the base image with BASE_IMAGE=..."
+	@echo "Please specify the image tag with TAG=..."
+
+ubi9-py39:
+	cd container && podman build --build-arg=BASE_IMAGE=${BASE_IMAGE} --build-arg=UBI_VERSION=ubi9 --build-arg=PYTHON_VERSION=py39 --build-arg=PYTHON_VERSION_LONG="Python 3.9" -t s2i-monai-notebook-ubi9-py39:${TAG} .

notebook-controller-images/s2i-monai/README.md

@@ -0,0 +1,22 @@
+# S2I Monai image
+
+Notebook based on the Data Science notebook, adding:
+
+* [Monai](https://monai.io/) ([Github repo](https://github.com/Project-MONAI))
+
+MONAI is a freely available, community-supported, PyTorch-based framework for deep learning in healthcare imaging. It provides domain-optimized foundational capabilities for developing healthcare imaging training workflows in a native PyTorch paradigm.
+Project MONAI also includes MONAI Label, an intelligent open source image labeling and learning tool that helps researchers and clinicians collaborate, create annotated datasets, and build AI models in a standardized MONAI paradigm.
+
+NOTE: CUDA is a requirement for Monai. However PyTorch is also a requirement, which comes with it own embedded CUDA when installed from PyPi (or Conda), so we can start from a standard image.
+
+* [Streamlit](https://streamlit.io/) ([Github repo](https://github.com/streamlit/streamlit))
+
+Streamlit turns data scripts into shareable web apps in minutes.
+All in pure Python. No front‑end experience required.
+See [details on Streamlit implementation](../streamlit-notebook/README.md).
+
+Build example from UBI9 with Python 3.9:
+
+```bash
+make ubi9-py39 BASE_IMAGE=localhost/s2i-datascience-notebook-ubi9-py39:0.0.1 TAG=0.0.1
+```

notebook-controller-images/s2i-monai/container/Dockerfile

@@ -0,0 +1,36 @@
+ARG BASE_IMAGE
+FROM ${BASE_IMAGE}
+
+ARG CODESERVER_VERSION=v4.5.1
+
+ARG UBI_VERSION
+ARG PYTHON_VERSION
+ARG PYTHON_VERSION_LONG
+
+LABEL name="s2i-code-server-${UBI_VERSION}-${PYTHON_VERSION}:latest" \
+    summary="S2I Code-Server with ${PYTHON_VERSION_LONG} image based on ${UBI_VERSION}" \
+    description="Code-Server notebook with ${PYTHON_VERSION_LONG}, Source-to-Image from ${UBI_VERSION}" \
+    io.k8s.description="Code-Server notebook with ${PYTHON_VERSION_LONG}, Source-to-Image from ${UBI_VERSION}" \
+    io.k8s.display-name="S2I Code-Server notebook with ${PYTHON_VERSION_LONG} ${UBI_VERSION} image" \
+    authoritative-source-url="https://github.com/guimou/custom-notebooks" \
+    io.openshift.s2i.build.commit.ref="main" \
+    io.openshift.s2i.build.source-location="https://github.com/guimou/custom-notebooks/notebook-controller-images/s2i-code-server" \
+    io.openshift.s2i.build.image="https://quay.io/guimou/s2i-code-server-${UBI_VERSION}-${PYTHON_VERSION}"
+
+####################
+# Monai            #
+####################
+
+USER 0
+
+WORKDIR /tmp
+
+# Copying custom packages
+COPY Pipfile Pipfile.lock /tmp/
+RUN micropipenv install --deploy && \
+    rm -rf /opt/app-root/lib/python3.9/site-packages/~*
+
+WORKDIR /opt/app-root/src
+USER 1001
+
+CMD /opt/app-root/bin/start-singleuser.sh

notebook-controller-images/s2i-monai/container/Pipfile

@@ -0,0 +1,63 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[[source]]
+url = "https://download.pytorch.org/whl/cu116"
+verify_ssl = true
+name = "pytorch"
+
+[packages]
+aiohttp = "~=3.8.1"
+beautifulsoup4 = "==4.11.1"
+black = "==21.12b0"
+bokeh = "~=2.4.3"
+boto3 = "==1.24.39"
+cloudpickle = "~=2.1.0"
+cython = "==0.29.31"
+dask = "==2022.7.1"
+dill = "~=0.3.5.1"
+distributed = "2022.7.1"
+elyra-python-editor-extension = "==3.10.1"
+greenlet = "~=1.1.2"
+h5py = "~=3.7.0"
+ipywidgets = "~=7.7.1"
+jupyter-bokeh = "~=3.0.4"
+jupyter-contrib-nbextensions = "~=0.5.1"
+jupyter-server-proxy = "~=3.2.1"
+jupyterlab = "~=3.4.4"
+jupyterlab-git = "~=0.37.1"
+jupyterlab-spellchecker = "~=0.7.2"
+jupyterlab-tabnine = "==0.0.24"
+kafka-python = "~=2.0.2"
+matplotlib = "~=3.5.2"
+monai = "~=0.9.1"
+monai-deploy-app-sdk = "~=0.4.0"
+nbgitpuller = "~=1.1.0"
+notebook = "~=6.4.12"
+numpy = "~=1.23.1"
+pandas = "~=1.4.3"
+pip = "==22.2.1"
+plotly = "~=5.9.0"
+pre-commit = "~=2.20.0"
+pyarrow = "~=8.0.0"
+pylint = "~=2.14.5"
+rope = "~=1.1.1"
+scikit-image = "~=0.19.3"
+scikit-learn = "~=1.1.1"
+scipy = "~=1.8.1"
+seaborn = "~=0.11.2"
+send2trash = "==1.8.0"
+sqlalchemy = "~=1.4.39"
+statsmodels = "~=0.13.2"
+streamlit = "~=1.11.1"
+streamlit-option-menu = "~=0.3.2"
+torch = {version="~=1.12.0", index="pytorch"}
+torchvision = "~=0.13.0"
+
+
+[dev-packages]
+
+[requires]
+python_version = "3.9"