diff --git a/base_images/build-image.sh b/base_images/build-image.sh index 16b1bdd..c0c2aa5 100755 --- a/base_images/build-image.sh +++ b/base_images/build-image.sh @@ -4,7 +4,7 @@ set -ex base_image_dir=$(dirname $0) # Check if on a branch or in a detached HEAD state get commit sha BRANCH=$(basename $(git symbolic-ref -q --short HEAD || git rev-parse --short HEAD)) -DIRS="vanilla r rgedi rsgislib" +DIRS="vanilla isce3 pangeo r" if [[ ! -z "$@" ]]; then DIRS=$@ fi diff --git a/base_images/isce2/docker/Dockerfile b/base_images/isce2/docker/Dockerfile deleted file mode 100644 index 5d12e23..0000000 --- a/base_images/isce2/docker/Dockerfile +++ /dev/null @@ -1,47 +0,0 @@ -FROM continuumio/miniconda3:22.11.1 -ENV LANG en_US.UTF-8 -ENV TZ US/Pacific -ARG DEBIAN_FRONTEND=noninteractive - -# install maap-py library -ENV MAAP_CONF='/maap-py/' -RUN git clone --single-branch --branch v3.1.3 https://github.com/MAAP-Project/maap-py.git \ - && cd maap-py \ - && pip install -e . - -RUN set -ex \ - && apt-get update \ - && apt-get install -y \ - libfftw3-3=3.3.8-2 \ - libgdal28=3.2.2+dfsg-2+deb11u2 \ - libhdf4-0=4.2.15-3 \ - libhdf5-103=1.10.6+repack-4+deb11u1 \ - libopencv-core4.5=4.5.1+dfsg-5 \ - libopencv-highgui4.5=4.5.1+dfsg-5 \ - libopencv-imgproc4.5=4.5.1+dfsg-5 \ - python3-gdal=3.2.2+dfsg-2+deb11u2 \ - python3-h5py=2.10.0-9 \ - python3-numpy=1:1.19.5-1 \ - python3-scipy=1.6.0-2 && \ - apt-get clean - - -RUN mkdir /projects -WORKDIR /projects -RUN sed -i -e 's/\/root/\/projects/g' /etc/passwd - -RUN conda install -y -c conda-forge pyOpenSSL=23.2.0 && \ - conda install -y -n base conda-libmamba-solver=23.7.0 && \ - conda config --system --set solver libmamba - -# need to uninstall jupyter_server_terminals as it conflicts with Jupyterlab 3.4.x. Doesn't seem to break anything -# but can get rid of if/when we upgrade jlab -RUN conda install -y --solver=libmamba -c conda-forge -c plant plant=0.1.89dev isce2=2.6.2 matplotlib=3.6.2 Cython=0.29.33 \ - numba=0.56.4 pygeos=0.14 pyproj=3.4.1 rasterio=1.3.4 && \ - pip uninstall -y jupyter_server_terminals && \ - find /opt/conda/ -follow -type f -name '*.a' -delete && \ - find /opt/conda/ -follow -type f -name '*.js.map' -delete && \ - /opt/conda/bin/conda clean -afy - -ARG IMAGE_REF -ENV DOCKERIMAGE_PATH=${IMAGE_REF} diff --git a/base_images/rgedi/docker/Dockerfile b/base_images/rgedi/docker/Dockerfile deleted file mode 100644 index 14d2734..0000000 --- a/base_images/rgedi/docker/Dockerfile +++ /dev/null @@ -1,27 +0,0 @@ -FROM continuumio/miniconda3:4.12.0 - -# install maap-py library -ENV MAAP_CONF='/maap-py/' -RUN git clone --single-branch --branch v3.1.3 https://github.com/MAAP-Project/maap-py.git \ - && cd maap-py \ - && pip install -e . - -RUN mkdir /projects -WORKDIR /projects -RUN sed -i -e 's/\/root/\/projects/g' /etc/passwd && echo "source activate r-with-gdal" > ~/.bashrc -RUN apt-get update && apt-get install -y libxt-dev && apt-get clean - -RUN conda install -y -c conda-forge pyOpenSSL=23.2.0 && \ - conda install -y -n base conda-libmamba-solver=23.7.0 && \ - conda config --system --set solver libmamba - -RUN conda install -y --solver=libmamba -c conda-forge nb_conda_kernels - -RUN conda create --name r-with-gdal --solver=libmamba -c conda-forge -c r -c csdms-stack gdal r-rgdal r-sf r-irkernel r-gridExtra r-tidyverse \ - r-randomForest r-raster r-data.table r-rlist r-gdalutils r-stringr r-devtools sysroot_linux-64=2.17 gcc r-lwgeom szip --yes && \ - /opt/conda/bin/conda clean -afy -RUN mkdir -p ~/.R/ && echo "LDFLAGS=-lproj" >> ~/.R/Makevars && \ - conda run --no-capture-output -n r-with-gdal Rscript -e "devtools::install_git('https://github.com/carlos-alberto-silva/rGEDI', dependencies=TRUE)" - -ARG IMAGE_REF -ENV DOCKERIMAGE_PATH=${IMAGE_REF} diff --git a/devfiles/index_example.json b/devfiles/index_example.json index 6747331..4e94f71 100644 --- a/devfiles/index_example.json +++ b/devfiles/index_example.json @@ -28,21 +28,6 @@ "self": "/devfiles/maap-vanilla/devfile_2.0.yaml" } }, - { - "displayName": "MAAP RGEDI Stable", - "description": "Latest version of MAAP RGEDI", - "tags": [ - "JupyterLab", - "Python", - "R", - "MAAP" - ], - "icon": "/images/r.png", - "globalMemoryLimit": "2710Mi", - "links": { - "self": "/devfiles/rgedi/devfile.yaml" - } - }, { "displayName": "MAAP ESA EDAV", "description": "Latest version of MAAP ESA EDAV", diff --git a/devfiles/isce2/devfile/devfile.yaml b/devfiles/isce2/devfile/devfile.yaml deleted file mode 100644 index 47bd7d3..0000000 --- a/devfiles/isce2/devfile/devfile.yaml +++ /dev/null @@ -1,95 +0,0 @@ -apiVersion: 1.0.0 -metadata: - generateName: isce2- -attributes: - editorFree: 'true' -components: - - endpoints: - - attributes: - type: ide - discoverable: 'false' - path: / - public: 'true' - protocol: http - name: jupyter - port: 3100 - referenceContent: | - kind: List - items: - - apiVersion: v1 - kind: Pod - metadata: - name: ws - labels: - ssh: enabled - spec: - volumes: - - name: ws-pvc - persistentVolumeClaim: - claimName: ws - - name: s3fs-volume - emptyDir: {} - containers: - - name: jupyter - image: 'mas.dit.maap-project.org/root/maap-workspaces/jupyterlab3/isce2:develop' - imagePullPolicy: Always - resources: - limits: - memory: 8096Mi - volumeMounts: - - name: ws-pvc - mountPath: /projects - subPath: projects - - name: s3fs-volume - mountPath: /projects/.jupyter - subPath: dotjupyter - - name: s3fs-volume - mountPath: /projects/my-private-bucket - subPath: my-private-bucket - mountPropagation: HostToContainer - - name: s3fs-volume - mountPath: /projects/my-public-bucket - subPath: my-public-bucket - mountPropagation: HostToContainer - - name: s3fs-volume - mountPath: /projects/shared-buckets - subPath: shared-buckets - mountPropagation: HostToContainer - - name: s3fs - image: 'mas.dit.maap-project.org/root/che-sidecar-s3fs:master' - imagePullPolicy: Always - resources: - limits: - memory: 256Mi - securityContext: - privileged: true - volumeMounts: - - name: s3fs-volume - mountPath: /my-public-bucket - subPath: my-public-bucket - mountPropagation: Bidirectional - - name: s3fs-volume - mountPath: /my-private-bucket - subPath: my-private-bucket - mountPropagation: Bidirectional - - name: s3fs-volume - mountPath: /shared-buckets - subPath: shared-buckets - mountPropagation: Bidirectional - - apiVersion: v1 - kind: PersistentVolumeClaim - metadata: - name: ws - spec: - storageClassName: nfs-client-che - - apiVersion: v1 - kind: Service - metadata: - generateName: sshport- - spec: - type: NodePort - ports: - - port: 22 - selector: - ssh: enabled - type: kubernetes diff --git a/devfiles/isce2/devfile/isce.png b/devfiles/isce2/devfile/isce.png deleted file mode 100644 index a7f9859..0000000 Binary files a/devfiles/isce2/devfile/isce.png and /dev/null differ diff --git a/devfiles/isce2/devfile/meta.yaml b/devfiles/isce2/devfile/meta.yaml deleted file mode 100644 index 200158c..0000000 --- a/devfiles/isce2/devfile/meta.yaml +++ /dev/null @@ -1,6 +0,0 @@ ---- -displayName: "MAAP ISCE2/PLAnT" -description: Latest version of MAAP ISCE2/PLAnT -tags: ["JupyterLab", "Python", "MAAP", "ISCE2", "PLAnT"] -icon: /devfiles/isce2/devfile/isce.png -globalMemoryLimit: 2710Mi diff --git a/devfiles/rgedi/devfile/devfile.yaml b/devfiles/rgedi/devfile/devfile.yaml deleted file mode 100644 index 920321d..0000000 --- a/devfiles/rgedi/devfile/devfile.yaml +++ /dev/null @@ -1,95 +0,0 @@ -apiVersion: 1.0.0 -metadata: - generateName: rgedi- -attributes: - editorFree: 'true' -components: - - endpoints: - - attributes: - type: ide - discoverable: 'false' - path: / - public: 'true' - protocol: http - name: jupyter - port: 3100 - referenceContent: | - kind: List - items: - - apiVersion: v1 - kind: Pod - metadata: - name: ws - labels: - ssh: enabled - spec: - volumes: - - name: ws-pvc - persistentVolumeClaim: - claimName: ws - - name: s3fs-volume - emptyDir: {} - containers: - - name: jupyter - image: 'mas.dit.maap-project.org/root/maap-workspaces/jupyterlab3/rgedi:develop' - imagePullPolicy: Always - resources: - limits: - memory: 8096Mi - volumeMounts: - - name: ws-pvc - mountPath: /projects - subPath: projects - - name: s3fs-volume - mountPath: /projects/.jupyter - subPath: dotjupyter - - name: s3fs-volume - mountPath: /projects/my-private-bucket - subPath: my-private-bucket - mountPropagation: HostToContainer - - name: s3fs-volume - mountPath: /projects/my-public-bucket - subPath: my-public-bucket - mountPropagation: HostToContainer - - name: s3fs-volume - mountPath: /projects/shared-buckets - subPath: shared-buckets - mountPropagation: HostToContainer - - name: s3fs - image: 'mas.dit.maap-project.org/root/che-sidecar-s3fs:master' - imagePullPolicy: Always - resources: - limits: - memory: 256Mi - securityContext: - privileged: true - volumeMounts: - - name: s3fs-volume - mountPath: /my-public-bucket - subPath: my-public-bucket - mountPropagation: Bidirectional - - name: s3fs-volume - mountPath: /my-private-bucket - subPath: my-private-bucket - mountPropagation: Bidirectional - - name: s3fs-volume - mountPath: /shared-buckets - subPath: shared-buckets - mountPropagation: Bidirectional - - apiVersion: v1 - kind: PersistentVolumeClaim - metadata: - name: ws - spec: - storageClassName: nfs-client-che - - apiVersion: v1 - kind: Service - metadata: - generateName: sshport- - spec: - type: NodePort - ports: - - port: 22 - selector: - ssh: enabled - type: kubernetes diff --git a/devfiles/rgedi/devfile/meta.yaml b/devfiles/rgedi/devfile/meta.yaml deleted file mode 100644 index a6adeaf..0000000 --- a/devfiles/rgedi/devfile/meta.yaml +++ /dev/null @@ -1,6 +0,0 @@ ---- -displayName: "MAAP RGEDI Stable" -description: Latest version of MAAP RGEDI -tags: ["Python", "R", "JupyterLab", "MAAP"] -icon: /devfiles/rgedi/devfile/r.png -globalMemoryLimit: 2710Mi diff --git a/devfiles/rgedi/devfile/r.png b/devfiles/rgedi/devfile/r.png deleted file mode 100644 index bcbd6df..0000000 Binary files a/devfiles/rgedi/devfile/r.png and /dev/null differ