chore: library upgrade (#251)

Co-authored-by: Noe Thalheim <[email protected]> Co-authored-by: Lorenzo Cavazzi <[email protected]>
SwissDataScienceCenter · Jul 27, 2022 · 9c452bf · 9c452bf
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diff --git a/.github/workflows/build_and_push_to_docker.yml b/.github/workflows/build_and_push_to_docker.yml
@@ -24,7 +24,7 @@ jobs:
         - docker/qgis/Dockerfile
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2 
+    - uses: actions/checkout@v2
     - uses: hadolint/[email protected]
       with:
         dockerfile: ${{ matrix.DOCKERFILE_PATH }}
@@ -38,8 +38,8 @@ jobs:
       fail-fast: true
       matrix:
         BASE_IMAGE_TAG:
-          - lab-3.2.1
-          - python-3.9.7
+          - lab-3.4.0
+          - python-3.9.12
           - python-3.8.8
           - python-3.7.6
 
@@ -62,7 +62,7 @@ jobs:
 
         # This ensures the same image tags as before are built, in addition to new ones
         if [[ "${{ matrix.BASE_IMAGE_TAG }}" == lab-* ]]; then
-          export LABEL_PREFIX=3.9
+          export LABEL_PREFIX=3.10
         else
           export LABEL_PREFIX=${{ matrix.BASE_IMAGE_TAG }}
         fi
@@ -114,7 +114,7 @@ jobs:
         fi
 
         docker build docker/$EXTENSION \
-          --build-arg BASE_IMAGE="$DOCKER_NAME-py:3.9-$LABEL" \
+          --build-arg BASE_IMAGE="$DOCKER_NAME-py:3.10-$LABEL" \
           --tag $DOCKER_NAME-$EXTENSION:$LABEL
         docker push $DOCKER_NAME-$EXTENSION:$LABEL
       env:
@@ -142,25 +142,25 @@ jobs:
             CUDA_COMPAT_PACKAGE: "cuda-compat-11-1"
             LIBCUDNN_PACKAGE: "libcudnn8=8.0.5.39-1+cuda11.1"
           - CUDA_VERSION: "11.2"
-            PYTHON_VERSION: "3.9.7"
+            PYTHON_VERSION: "3.9.12"
             EXTRA_LIBRARIES: ""
             CUDA_CUDART_PACKAGE: "cuda-cudart-11-2=11.2.152-1"
             CUDA_COMPAT_PACKAGE: "cuda-compat-11-2"
             LIBCUDNN_PACKAGE: "libcudnn8=8.1.1.33-1+cuda11.2"
           - CUDA_VERSION: "11.3"
-            PYTHON_VERSION: "3.9.7"
+            PYTHON_VERSION: "3.9.12"
             EXTRA_LIBRARIES: ""
             CUDA_CUDART_PACKAGE: "cuda-cudart-11-3=11.3.109-1"
             CUDA_COMPAT_PACKAGE: "cuda-compat-11-3"
             LIBCUDNN_PACKAGE: "libcudnn8=8.2.1.32-1+cuda11.3"
           - CUDA_VERSION: "11.4"
-            PYTHON_VERSION: "3.9.7"
+            PYTHON_VERSION: "3.9.12"
             EXTRA_LIBRARIES: ""
             CUDA_CUDART_PACKAGE: "cuda-cudart-11-4=11.4.148-1"
             CUDA_COMPAT_PACKAGE: "cuda-compat-11-4"
             LIBCUDNN_PACKAGE: "libcudnn8=8.2.4.15-1+cuda11.4"
           - CUDA_VERSION: "11.5"
-            PYTHON_VERSION: "3.9.7"
+            PYTHON_VERSION: "3.9.12"
             EXTRA_LIBRARIES: ""
             CUDA_CUDART_PACKAGE: "cuda-cudart-11-5=11.5.117-1"
             CUDA_COMPAT_PACKAGE: "cuda-compat-11-5"
@@ -298,7 +298,7 @@ jobs:
       env:
         EXTENSION: ${{ matrix.VNC-EXTENSIONS }}
         DOCKER_NAME: "renku/renkulab"
-  
+
   build-py-batch:
     needs: build-py
     runs-on: ubuntu-latest
@@ -320,8 +320,8 @@ jobs:
         fi
 
         docker build docker/batch \
-          --build-arg RENKU_BASE="$DOCKER_NAME-py:3.9-$LABEL" \
-          --build-arg BASE_IMAGE="python:3.9-slim-buster" \
+          --build-arg RENKU_BASE="$DOCKER_NAME-py:3.10-$LABEL" \
+          --build-arg BASE_IMAGE="python:3.10-slim-buster" \
           --tag $DOCKER_NAME-batch:$LABEL
         docker push $DOCKER_NAME-batch:$LABEL
       env:
@@ -356,7 +356,7 @@ jobs:
 
         export DOCKER_TAG="${{ matrix.JULIAVERSIONS }}-$LABEL"
         docker build docker/julia \
-          --build-arg BASE_IMAGE="$DOCKER_NAME-py:3.9-$LABEL" \
+          --build-arg BASE_IMAGE="$DOCKER_NAME-py:3.10-$LABEL" \
           --tag $DOCKER_NAME-julia:$DOCKER_TAG
         echo "::set-output name=IMAGE_NAME::$DOCKER_NAME-julia:$DOCKER_TAG"
     - name: Image Acceptance Tests
@@ -408,11 +408,11 @@ jobs:
 
         export DOCKER_TAG="${{ matrix.RVERSION }}-$LABEL"
         docker build docker/r \
-          --build-arg RENKU_BASE="$DOCKER_NAME-py:3.9-$LABEL" \
+          --build-arg RENKU_BASE="$DOCKER_NAME-py:3.10-$LABEL" \
           --build-arg BASE_IMAGE="rocker/verse:${{ matrix.RVERSION }}" \
           --build-arg RSTUDIO_VERSION_OVERRIDE="${{ matrix.RSTUDIO_VERSION }}" \
           --tag $DOCKER_NAME-r:$DOCKER_TAG
-        
+
         echo "::set-output name=IMAGE_NAME::$DOCKER_NAME-r:$DOCKER_TAG"
     - name: Image Acceptance Tests
       uses: cypress-io/github-action@v2
@@ -462,7 +462,7 @@ jobs:
 
         export DOCKER_TAG="${{ matrix.RELEASE }}-$LABEL"
         docker build docker/r \
-          --build-arg RENKU_BASE="$DOCKER_NAME-py:3.9-$LABEL" \
+          --build-arg RENKU_BASE="$DOCKER_NAME-py:3.10-$LABEL" \
           --build-arg BASE_IMAGE=bioconductor/bioconductor_docker:${{ matrix.RELEASE }} \
           --tag $DOCKER_NAME-bioc:$DOCKER_TAG
         docker push $DOCKER_NAME-bioc:$DOCKER_TAG

diff --git a/README.md b/README.md
@@ -87,7 +87,7 @@ pipx install --force renku==<version>
 | [renku/renkulab-cuda-tf](https://hub.docker.com/r/renku/renkulab-cuda-tf/tags) | Cuda image with Python and Tensorflow           | [renku/renkulab-cuda](https://hub.docker.com/r/renku/renkulab-cuda/tags)                           |
 | [renku/renkulab-vnc](https://hub.docker.com/r/renku/renkulab-vnc/tags)         | VNC Image with Python                           | [renku/renkulab-py](https://hub.docker.com/r/renku/renkulab-py/tags)                               |
 
-Please refer to the [release notes](https://github.com/SwissDataScienceCenter/renkulab-docker/releases) 
+Please refer to the [release notes](https://github.com/SwissDataScienceCenter/renkulab-docker/releases)
 for more detailed lists of released images and specific links to Dockerhub.
 
 ### py
@@ -148,7 +148,9 @@ https://hub.docker.com/r/renku/renkulab-vnc/tags
 ## Development
 
 Build with Docker by running `docker build -t <name:tag> .` in the directory
-of the image you would like to build.
+of the image you would like to build. Note that on arm-based systems (e.g.
+Apple M1/M2) you may need to use the flag `--platform=linux/amd64` for the
+build because `git-lfs 3.2.0` is not available for the arm architecture.
 
 ## Adding renku to your own images
 

diff --git a/docker/py/Dockerfile b/docker/py/Dockerfile
@@ -1,5 +1,5 @@
-ARG BASE_IMAGE=jupyter/base-notebook:lab-3.2.1
-ARG RENKU_VERSION=1.4.0
+ARG BASE_IMAGE=jupyter/base-notebook:lab-3.4.0
+ARG RENKU_VERSION=1.6.0
 FROM $BASE_IMAGE as base
 
 LABEL maintainer="Swiss Data Science Center <[email protected]>"

diff --git a/docker/py/requirements.txt b/docker/py/requirements.txt
@@ -1,10 +1,8 @@
-jupyter-server-proxy~=3.2.1
-jupyterlab-git==0.30.1
+jupyter-server-proxy==3.2.1
+jupyterlab-git==0.37.1
 jupyterlab-system-monitor~=0.8.0
-jupyterlab~=3.0.0
 papermill~=2.3.0
 powerline-shell~=0.7.0
 requests>=2.20.0
-setuptools==57.5.0
 virtualenv>=20.7.2
 mistune>=2.0.1 # not directly required, pinned by Snyk to avoid a vulnerability