From 8b159d20cc63c93af7fd37e6f634a744777f2ad4 Mon Sep 17 00:00:00 2001
From: Guillaume Moutier <guillaume.moutier@gmail.com>
Date: Thu, 4 Aug 2022 16:06:56 -0400
Subject: [PATCH] Release

pre-release CHANGELOG

Auto stash before rebase of "refs/heads/dev"
---
 CHANGELOG.md                                  |    6 +
 jupyterhub-images/monai-notebook/README.md    |    2 +-
 notebook-controller-images/s2i-monai/Makefile |   13 +
 .../s2i-monai/README.md                       |   22 +
 .../s2i-monai/container/Dockerfile            |   36 +
 .../s2i-monai/container/Pipfile               |   63 +
 .../s2i-monai/container/Pipfile.lock          | 3436 +++++++++++++++++
 .../s2i-rstudio/rstudio-example.yaml          |    2 +-
 8 files changed, 3578 insertions(+), 2 deletions(-)
 create mode 100644 notebook-controller-images/s2i-monai/Makefile
 create mode 100644 notebook-controller-images/s2i-monai/README.md
 create mode 100644 notebook-controller-images/s2i-monai/container/Dockerfile
 create mode 100644 notebook-controller-images/s2i-monai/container/Pipfile
 create mode 100644 notebook-controller-images/s2i-monai/container/Pipfile.lock

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9c13606..d05c72c 100644
--- a/CHANGELOG.md
+++ b/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
 
diff --git a/jupyterhub-images/monai-notebook/README.md b/jupyterhub-images/monai-notebook/README.md
index 1826529..fa7fb29 100644
--- a/jupyterhub-images/monai-notebook/README.md
+++ b/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).
\ No newline at end of file
+See [details on Streamlit implementation](../streamlit-notebook/README.md).
diff --git a/notebook-controller-images/s2i-monai/Makefile b/notebook-controller-images/s2i-monai/Makefile
new file mode 100644
index 0000000..f2725ea
--- /dev/null
+++ b/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} .
diff --git a/notebook-controller-images/s2i-monai/README.md b/notebook-controller-images/s2i-monai/README.md
new file mode 100644
index 0000000..23b0c43
--- /dev/null
+++ b/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
+```
diff --git a/notebook-controller-images/s2i-monai/container/Dockerfile b/notebook-controller-images/s2i-monai/container/Dockerfile
new file mode 100644
index 0000000..bf008fc
--- /dev/null
+++ b/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
diff --git a/notebook-controller-images/s2i-monai/container/Pipfile b/notebook-controller-images/s2i-monai/container/Pipfile
new file mode 100644
index 0000000..500ec09
--- /dev/null
+++ b/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"
diff --git a/notebook-controller-images/s2i-monai/container/Pipfile.lock b/notebook-controller-images/s2i-monai/container/Pipfile.lock
new file mode 100644
index 0000000..a53d307
--- /dev/null
+++ b/notebook-controller-images/s2i-monai/container/Pipfile.lock
@@ -0,0 +1,3436 @@
+{
+    "_meta": {
+        "hash": {
+            "sha256": "2306a28f7736dd5b7fe0267374f0405cdc172395a7cd3abf8e18150fa02d7771"
+        },
+        "pipfile-spec": 6,
+        "requires": {
+            "python_version": "3.9"
+        },
+        "sources": [
+            {
+                "name": "pypi",
+                "url": "https://pypi.org/simple",
+                "verify_ssl": true
+            },
+            {
+                "name": "pytorch",
+                "url": "https://download.pytorch.org/whl/cu116",
+                "verify_ssl": true
+            }
+        ]
+    },
+    "default": {
+        "absl-py": {
+            "hashes": [
+                "sha256:5d15f85b8cc859c6245bc9886ba664460ed96a6fee895416caa37d669ee74a9a",
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+            ],
+            "markers": "python_version >= '3.6'",
+            "version": "==1.2.0"
+        },
+        "aiohttp": {
+            "hashes": [
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+            "index": "pypi",
+            "version": "==3.8.1"
+        },
+        "aiosignal": {
+            "hashes": [
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+            "version": "==1.2.0"
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+        "altair": {
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+            "markers": "python_version >= '3.7'",
+            "version": "==4.2.0"
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+            "hashes": [
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+                "sha256:ca0c740734cde59bf919f8ff2c386f74f9a369818cdc60efe94893d01ea8d9b7"
+            ],
+            "version": "==0.8.4"
+        },
+        "anyio": {
+            "hashes": [
+                "sha256:413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b",
+                "sha256:cb29b9c70620506a9a8f87a309591713446953302d7d995344d0d7c6c0c9a7be"
+            ],
+            "markers": "python_full_version >= '3.6.2'",
+            "version": "==3.6.1"
+        },
+        "argon2-cffi": {
+            "hashes": [
+                "sha256:8c976986f2c5c0e5000919e6de187906cfd81fb1c72bf9d88c01177e77da7f80",
+                "sha256:d384164d944190a7dd7ef22c6aa3ff197da12962bd04b17f64d4e93d934dba5b"
+            ],
+            "markers": "python_version >= '3.6'",
+            "version": "==21.3.0"
+        },
+        "argon2-cffi-bindings": {
+            "hashes": [
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+            ],
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
+            "version": "==1.14.1"
+        },
+        "yapf": {
+            "hashes": [
+                "sha256:8fea849025584e486fd06d6ba2bed717f396080fd3cc236ba10cb97c4c51cf32",
+                "sha256:a3f5085d37ef7e3e004c4ba9f9b3e40c54ff1901cd111f05145ae313a7c67d1b"
+            ],
+            "version": "==0.32.0"
+        },
+        "yarl": {
+            "hashes": [
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+                "sha256:fae37373155f5ef9b403ab48af5136ae9851151f7aacd9926251ab26b953118b"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==1.8.1"
+        },
+        "yaspin": {
+            "hashes": [
+                "sha256:c8d34eca9fda3f4dfbe59f57f3cf0f3641af3eefbf1544fbeb9b3bacf82c580a",
+                "sha256:d574cbfaf0a349df466c91f7f81b22460ae5ebb15ecb8bf9411d6049923aee8d"
+            ],
+            "markers": "python_full_version >= '3.6.2' and python_version < '4.0'",
+            "version": "==2.1.0"
+        },
+        "zict": {
+            "hashes": [
+                "sha256:d7366c2e2293314112dcf2432108428a67b927b00005619feefc310d12d833f3",
+                "sha256:dabcc8c8b6833aa3b6602daad50f03da068322c1a90999ff78aed9eecc8fa92c"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==2.2.0"
+        },
+        "zipp": {
+            "hashes": [
+                "sha256:05b45f1ee8f807d0cc928485ca40a07cb491cf092ff587c0df9cb1fd154848d2",
+                "sha256:47c40d7fe183a6f21403a199b3e4192cca5774656965b0a4988ad2f8feb5f009"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==3.8.1"
+        }
+    },
+    "develop": {}
+}
diff --git a/notebook-controller-images/s2i-rstudio/rstudio-example.yaml b/notebook-controller-images/s2i-rstudio/rstudio-example.yaml
index 198b47b..1d91e02 100644
--- a/notebook-controller-images/s2i-rstudio/rstudio-example.yaml
+++ b/notebook-controller-images/s2i-rstudio/rstudio-example.yaml
@@ -26,5 +26,5 @@ spec:
               protocol: TCP
           imagePullPolicy: Always
           serviceAccountName: default
-          image: quay.io/guimou/s2i-rstudio-c9s-py39:0.0.1
+          image: quay.io/guimou/s2i-rstudio-c9s-py39:latest
           workingDir: /opt/app-root/src
\ No newline at end of file