diff --git a/Makefile b/Makefile index 917e8f4..2d87123 100644 --- a/Makefile +++ b/Makefile @@ -4,9 +4,9 @@ export BASE_IMAGE_NAME = "${PROJECT_PREFIX}base_${IMAGE_NAME}" export JUPYTER_IMAGE_NAME = "${PROJECT_PREFIX}jupyter_${IMAGE_NAME}" export RUN_OPTIONS = -build-images: build-base-image build-jupyter-image +build-images: build-base-image build-jupyter-image ## Build both the base and jupyterlab image -build-images-no-cache: build-base-image-no-cache build-jupyter-image-no-cache +build-images-no-cache: build-base-image-no-cache build-jupyter-image-no-cache ## Build both the base and jupyterlab image without using the docker cache build-base-image: ## Build the base image for the 'vanilla' workspace (default), or the workspace specified by setting the argument, IMAGE_NAME= @cd base_images/${IMAGE_NAME}; \ @@ -46,11 +46,11 @@ help: ## (DEFAULT) This help information @echo ==================================================================== @grep -E '^## .*$$' \ $(MAKEFILE_LIST) \ - | awk 'BEGIN { FS="## " }; {printf "\033[33m%-20s\033[0m \n", $$2}' + | awk 'BEGIN { FS="## " }; {printf "\033[33m%-30s\033[0m \n", $$2}' @echo @grep -E '^[0-9a-zA-Z_-]+:.*?## .*$$' \ $(MAKEFILE_LIST) \ - | awk 'BEGIN { FS=":.*?## " }; {printf "\033[36m%-20s\033[0m %s\n", $$1, $$2}' \ + | awk 'BEGIN { FS=":.*?## " }; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}' \ # | sort .PHONY: help .DEFAULT_GOAL := help \ No newline at end of file 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/isce3/docker/Dockerfile b/base_images/isce3/docker/Dockerfile index 07f0814..a275edd 100644 --- a/base_images/isce3/docker/Dockerfile +++ b/base_images/isce3/docker/Dockerfile @@ -22,7 +22,7 @@ RUN conda env create -y -f "/tmp/environment.yml" \ SHELL ["conda", "run", "-n", "isce3", "/bin/bash", "-c"] RUN mkdir /maap-py \ - && git clone --single-branch --branch v3.1.4 https://github.com/MAAP-Project/maap-py.git /maap-py/ \ + && git clone --single-branch --branch v3.1.5 https://github.com/MAAP-Project/maap-py.git /maap-py/ \ && pip install -e /maap-py/ RUN conda list diff --git a/base_images/isce3/environment.yml b/base_images/isce3/environment.yml index f4f1316..7e7bb01 100644 --- a/base_images/isce3/environment.yml +++ b/base_images/isce3/environment.yml @@ -5,12 +5,13 @@ channels: dependencies: - awscli=2.14.1 - backoff=2.2.1 - - boto3=1.34.3 + - boto3=1.34.41 - cython=3.0.7 - earthengine-api=0.1.384 - fsspec=2023.12.2 - gdal=3.7.0 - geopandas=0.14.1 + - groff=1.22.4 - h5py=3.9.0 - hdf5=1.14.1 - httpx=0.25.2 @@ -33,7 +34,7 @@ dependencies: - requests=2.31.0 - rio-cogeo=5.1.0 - rtree=1.1.0 - - s3fs=0.4.2 + - s3fs=2023.12.2 - scikit-learn=1.3.2 - scipy=1.11.4 - seaborn=0.13.0 @@ -47,5 +48,4 @@ dependencies: - pip=23.3.2 - pip: - git+https://github.com/opera-adt/RTC.git@v0.3 -variables: - MAAP_CONF: '/maap-py/' \ No newline at end of file + - rio-tiler==6.2.8 \ No newline at end of file diff --git a/base_images/pangeo/docker/Dockerfile b/base_images/pangeo/docker/Dockerfile index 653d6de..fcf6fae 100644 --- a/base_images/pangeo/docker/Dockerfile +++ b/base_images/pangeo/docker/Dockerfile @@ -20,7 +20,7 @@ SHELL ["conda", "run", "-n", "pangeo", "/bin/bash", "-c"] # Install maap-py library RUN mkdir /maap-py \ - && git clone --single-branch --branch v3.1.4 https://github.com/MAAP-Project/maap-py.git /maap-py/ \ + && git clone --single-branch --branch v3.1.5 https://github.com/MAAP-Project/maap-py.git /maap-py/ \ && pip install -e /maap-py/ RUN conda list diff --git a/base_images/pangeo/environment.yml b/base_images/pangeo/environment.yml index eeecb06..4d3326d 100644 --- a/base_images/pangeo/environment.yml +++ b/base_images/pangeo/environment.yml @@ -7,9 +7,11 @@ dependencies: - backoff=2.2.1 - basemap=1.3.7 - bokeh=3.3.3 - - boto3=1.33.13 + - boto3=1.34.41 - bottleneck=1.3.7 - cartopy=0.22.0 + - cdsapi=0.6.1 + - cf_xarray=0.9.0 - cfgrib=0.9.10.4 - cython=3.0.7 - dask-ml=2023.3.24 @@ -20,48 +22,58 @@ dependencies: - eofs=1.4.0 - erddapy=2.2.0 - esmpy=8.4.2 + - fastjmd95=0.2.1 - flox=0.8.6 - fsspec=2023.12.2 - gcm_filters=0.3.0 - gdal=3.7.0 - geocube=0.4.2 + - geogif=0.1.5 - geopandas=0.14.2 + - geopy=2.4.1 - geoviews-core=1.11.0 + - groff=1.22.4 - h5netcdf=1.3.0 - h5py=3.9.0 - hdf5=1.14.0 - holoviews=1.18.1 - httpx=0.26.0 - hvplot=0.9.1 - - intake=0.7.0 + - intake-esm=2024.2.6 - intake-geopandas=0.4.0 - intake-stac=0.4.0 - intake-xarray=0.7.0 + - intake=0.7.0 - kerchunk=0.2.2 + - line_profiler=4.1.1 - lxml=4.9.3 - lz4=4.3.2 - mapclassify=2.6.1 - matplotlib=3.7.3 + - memory_profiler=0.61.0 + - metpy=1.6.1 - mizani=0.10.0 - mpl-scatter-density=0.7 - nc-time-axis=1.4.1 - netcdf4=1.6.4 - numba=0.58.1 + - numbagg=0.8.0 - numcodecs=0.11.0 - numpy=1.26.3 - odc-stac=0.3.8 - - pandas=2.1.4 - pandarallel=1.6.5 + - pandas=2.1.4 - pyarrow=14.0.1 + - pycamhd=0.7.0 - pycurl=7.45.1 - pydap=3.4.0 - pygeos=0.14 - pyogrio=0.6.0 - pyproj=3.5.0 - - pystac=1.9.0 - pystac-client=0.6.1 - - python=3.10.13 + - pystac=1.9.0 - python-blosc=1.10.6 + - python=3.10.13 - rasterio=1.3.7 - rasterstats=0.19.0 - rechunker=0.5.2 @@ -70,6 +82,7 @@ dependencies: - rioxarray=0.15.0 - rtree=1.1.0 - s3fs=2023.12.2 + - satpy=0.47.0 - scikit-image=0.22.0 - scikit-learn=1.3.2 - scipy=1.11.4 @@ -79,18 +92,29 @@ dependencies: - sparse=0.15.0 - stackstac=0.5.0 - statsmodels=0.14.1 + - tiledb-py=0.19.1 + - timezonefinder=6.4.1 - tqdm=4.66.1 - unidecode=1.3.7 - - xarray=2023.12.0 - xarray-datatree=0.0.13 - xarray-spatial=0.3.5 + - xarray=2023.12.0 - xarrayutils=2.0.0 + - xbatcher=0.3.0 + - xcape=0.1.4 + - xclim=0.46.0 + - xcube=0.9.1 - xesmf=0.8.2 + - xgboost=2.0.3 + - xgcm=0.8.1 - xhistogram=0.3.2 + - xmip=0.7.2 + - xmitgcm=0.5.2 - xmltodict=0.13.0 + - xpublish=0.3.3 + - xrft=1.0.1 - zarr=2.16.1 - pip=23.3.2 - pip: - morecantile==5.1.0 -variables: - MAAP_CONF: '/maap-py/' \ No newline at end of file + - rio-tiler==6.2.8 \ No newline at end of file diff --git a/base_images/r/docker/Dockerfile b/base_images/r/docker/Dockerfile index 8f98a98..3c9d8b4 100644 --- a/base_images/r/docker/Dockerfile +++ b/base_images/r/docker/Dockerfile @@ -21,7 +21,7 @@ RUN apt-get clean && apt-get update && \ libhdf4-alt-dev=4.2.15-3 \ libhdf5-dev=1.10.6+repack-4+deb11u1 \ libjq-dev=1.6-2.1 \ - libpq-dev=13.13-0+deb11u1 \ + libpq-dev=13.14-0+deb11u1 \ libproj-dev=7.2.1-1 \ libprotobuf-dev=3.12.4-1+deb11u1 \ libnetcdf-dev=1:4.7.4-1 \ @@ -54,7 +54,7 @@ RUN /scripts/install_cran_packages_r.sh # Install maap-py library RUN mkdir /maap-py \ - && git clone --single-branch --branch v3.1.4 https://github.com/MAAP-Project/maap-py.git /maap-py/ \ + && git clone --single-branch --branch v3.1.5 https://github.com/MAAP-Project/maap-py.git /maap-py/ \ && pip install -e /maap-py/ RUN conda list diff --git a/base_images/r/environment.yml b/base_images/r/environment.yml index 7a1e13e..6685bae 100644 --- a/base_images/r/environment.yml +++ b/base_images/r/environment.yml @@ -5,14 +5,18 @@ channels: - nodefaults dependencies: - awscli=2.14.1 + - boto3=1.34.41 - earthaccess=0.8.2 + - groff=1.22.4 - parallel=20231122 - perl=5.32.1 - postgis=3.4.0 - python=3.10.13 - r=4.2 + - r-arrow=14.0.1 - r-aws.s3=0.3.22 - r-base=4.2.3 + - r-BiocManager=1.30.22 - r-broom=1.0.5 - r-car=3.1_2 - r-chron=2.3_61 @@ -104,5 +108,4 @@ dependencies: - pip: - ff==0.0.10 - grid==0.7.1 -variables: - MAAP_CONF: '/maap-py/' \ No newline at end of file + - rio-tiler==6.2.8 \ No newline at end of file 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/base_images/vanilla/docker/Dockerfile b/base_images/vanilla/docker/Dockerfile index 8b49f89..2175387 100644 --- a/base_images/vanilla/docker/Dockerfile +++ b/base_images/vanilla/docker/Dockerfile @@ -20,7 +20,7 @@ SHELL ["conda", "run", "-n", "vanilla", "/bin/bash", "-c"] # Install maap-py library RUN mkdir /maap-py \ - && git clone --single-branch --branch v3.1.4 https://github.com/MAAP-Project/maap-py.git /maap-py/ \ + && git clone --single-branch --branch v3.1.5 https://github.com/MAAP-Project/maap-py.git /maap-py/ \ && pip install -e /maap-py/ RUN conda list diff --git a/base_images/vanilla/environment.yml b/base_images/vanilla/environment.yml index d89bea8..d5f7b83 100644 --- a/base_images/vanilla/environment.yml +++ b/base_images/vanilla/environment.yml @@ -6,12 +6,13 @@ dependencies: - awscli=2.14.1 - backoff=2.2.1 - basemap=1.3.7 - - boto3=1.34.15 + - boto3=1.34.41 - cython=3.0.7 - earthengine-api=0.1.384 - gdal=3.7.0 - geocube=0.4.2 - geopandas=0.14.2 + - groff=1.22.4 - h5py=3.9.0 - hdf5=1.14.0 - httpx=0.26.0 @@ -34,7 +35,7 @@ dependencies: - requests=2.31.0 - rio-cogeo=5.1.1 - rtree=1.1.0 - - s3fs=0.4.2 + - s3fs=2023.12.2 - scikit-learn=1.3.2 - scipy=1.11.4 - seaborn=0.13.1 @@ -47,5 +48,4 @@ dependencies: - pip=23.3.2 - pip: - morecantile==5.1.0 -variables: - MAAP_CONF: '/maap-py/' \ No newline at end of file + - rio-tiler==6.2.8 \ No newline at end of file diff --git a/devfiles/edav/devfile/devfile.yaml b/devfiles/edav/devfile/devfile.yaml index 89bedf3..6c78aab 100644 --- a/devfiles/edav/devfile/devfile.yaml +++ b/devfiles/edav/devfile/devfile.yaml @@ -56,7 +56,7 @@ components: subPath: shared-buckets mountPropagation: HostToContainer - name: s3fs - image: 'mas.ops.maap-project.org/root/che-sidecar-s3fs:master' + image: 'mas.dit.maap-project.org/root/che-sidecar-s3fs:master' imagePullPolicy: Always resources: limits: 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 06de73b..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.ops.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/isce3/devfile/devfile.yaml b/devfiles/isce3/devfile/devfile.yaml index 9c4b6ee..502a3a1 100644 --- a/devfiles/isce3/devfile/devfile.yaml +++ b/devfiles/isce3/devfile/devfile.yaml @@ -55,8 +55,12 @@ components: mountPath: /projects/shared-buckets subPath: shared-buckets mountPropagation: HostToContainer + - name: s3fs-volume + mountPath: /projects/triaged-jobs + subPath: triaged-jobs + mountPropagation: HostToContainer - name: s3fs - image: 'mas.ops.maap-project.org/root/che-sidecar-s3fs:master' + image: 'mas.dit.maap-project.org/root/che-sidecar-s3fs:master' imagePullPolicy: Always resources: limits: @@ -76,6 +80,10 @@ components: mountPath: /shared-buckets subPath: shared-buckets mountPropagation: Bidirectional + - name: s3fs-volume + mountPath: /triaged-jobs + subPath: triaged-jobs + mountPropagation: Bidirectional - apiVersion: v1 kind: PersistentVolumeClaim metadata: diff --git a/devfiles/isce3/devfile/meta.yaml b/devfiles/isce3/devfile/meta.yaml index 46ed876..c5c3ac9 100644 --- a/devfiles/isce3/devfile/meta.yaml +++ b/devfiles/isce3/devfile/meta.yaml @@ -1,6 +1,6 @@ --- displayName: "MAAP ISCE3" -description: Latest version of MAAP ISCE3 +description: "MAAP ISCE3 Version: 3.1.5" tags: ["JupyterLab", "Python", "MAAP", "ISCE3"] icon: /devfiles/isce3/devfile/isce.png globalMemoryLimit: 2710Mi diff --git a/devfiles/pangeo/devfile/devfile.yaml b/devfiles/pangeo/devfile/devfile.yaml index d256bec..b30c43d 100644 --- a/devfiles/pangeo/devfile/devfile.yaml +++ b/devfiles/pangeo/devfile/devfile.yaml @@ -55,8 +55,12 @@ components: mountPath: /projects/shared-buckets subPath: shared-buckets mountPropagation: HostToContainer + - name: s3fs-volume + mountPath: /projects/triaged-jobs + subPath: triaged-jobs + mountPropagation: HostToContainer - name: s3fs - image: 'mas.ops.maap-project.org/root/che-sidecar-s3fs:master' + image: 'mas.dit.maap-project.org/root/che-sidecar-s3fs:master' imagePullPolicy: Always resources: limits: @@ -76,6 +80,10 @@ components: mountPath: /shared-buckets subPath: shared-buckets mountPropagation: Bidirectional + - name: s3fs-volume + mountPath: /triaged-jobs + subPath: triaged-jobs + mountPropagation: Bidirectional - apiVersion: v1 kind: PersistentVolumeClaim metadata: diff --git a/devfiles/pangeo/devfile/meta.yaml b/devfiles/pangeo/devfile/meta.yaml index 6b4dd28..c0e8f90 100644 --- a/devfiles/pangeo/devfile/meta.yaml +++ b/devfiles/pangeo/devfile/meta.yaml @@ -1,6 +1,6 @@ --- displayName: "Pangeo" -description: "Version: 2023.04.15" +description: "MAAP Pangeo version: 3.1.5" tags: ["Pangeo", "JupyterLab", "MAAP"] icon: /devfiles/pangeo/devfile/pangeo_simple_logo.svg globalMemoryLimit: 2710Mi diff --git a/devfiles/r/devfile/devfile.yaml b/devfiles/r/devfile/devfile.yaml index e23e6ba..4e14ea3 100644 --- a/devfiles/r/devfile/devfile.yaml +++ b/devfiles/r/devfile/devfile.yaml @@ -55,8 +55,12 @@ components: mountPath: /projects/shared-buckets subPath: shared-buckets mountPropagation: HostToContainer + - name: s3fs-volume + mountPath: /projects/triaged-jobs + subPath: triaged-jobs + mountPropagation: HostToContainer - name: s3fs - image: 'mas.ops.maap-project.org/root/che-sidecar-s3fs:master' + image: 'mas.dit.maap-project.org/root/che-sidecar-s3fs:master' imagePullPolicy: Always resources: limits: @@ -76,6 +80,10 @@ components: mountPath: /shared-buckets subPath: shared-buckets mountPropagation: Bidirectional + - name: s3fs-volume + mountPath: /triaged-jobs + subPath: triaged-jobs + mountPropagation: Bidirectional - apiVersion: v1 kind: PersistentVolumeClaim metadata: diff --git a/devfiles/r/devfile/meta.yaml b/devfiles/r/devfile/meta.yaml index 0df23cd..f4f2b86 100644 --- a/devfiles/r/devfile/meta.yaml +++ b/devfiles/r/devfile/meta.yaml @@ -1,6 +1,6 @@ --- displayName: "MAAP R Stable" -description: Latest version of MAAP R +description: "MAAP R version: 3.1.5" tags: ["Python", "R", "JupyterLab", "MAAP"] icon: /devfiles/r/devfile/r.png globalMemoryLimit: 2710Mi diff --git a/devfiles/rgedi/devfile/devfile.yaml b/devfiles/rgedi/devfile/devfile.yaml deleted file mode 100644 index 8f29b1d..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.ops.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 diff --git a/devfiles/vanilla/devfile/devfile.yaml b/devfiles/vanilla/devfile/devfile.yaml index 02280e2..5ced3c3 100644 --- a/devfiles/vanilla/devfile/devfile.yaml +++ b/devfiles/vanilla/devfile/devfile.yaml @@ -55,8 +55,12 @@ components: mountPath: /projects/shared-buckets subPath: shared-buckets mountPropagation: HostToContainer + - name: s3fs-volume + mountPath: /projects/triaged-jobs + subPath: triaged-jobs + mountPropagation: HostToContainer - name: s3fs - image: 'mas.ops.maap-project.org/root/che-sidecar-s3fs:master' + image: 'mas.dit.maap-project.org/root/che-sidecar-s3fs:master' imagePullPolicy: Always resources: limits: @@ -76,6 +80,10 @@ components: mountPath: /shared-buckets subPath: shared-buckets mountPropagation: Bidirectional + - name: s3fs-volume + mountPath: /triaged-jobs + subPath: triaged-jobs + mountPropagation: Bidirectional - apiVersion: v1 kind: PersistentVolumeClaim metadata: diff --git a/devfiles/vanilla/devfile/meta.yaml b/devfiles/vanilla/devfile/meta.yaml index 5ddab6f..54d84b0 100644 --- a/devfiles/vanilla/devfile/meta.yaml +++ b/devfiles/vanilla/devfile/meta.yaml @@ -1,6 +1,6 @@ --- displayName: "Basic Stable" -description: Latest version of MAAP Basic +description: "MAAP vanilla version: 3.1.5" tags: ["JupyterLab", "Python", "MAAP"] icon: /devfiles/vanilla/devfile/jupyter.png globalMemoryLimit: 2710Mi diff --git a/jupyterlab3/docker/Dockerfile b/jupyterlab3/docker/Dockerfile index 386ff4b..af2f2d5 100644 --- a/jupyterlab3/docker/Dockerfile +++ b/jupyterlab3/docker/Dockerfile @@ -75,7 +75,7 @@ RUN jupyter labextension disable @jupyterlab/apputils-extension:announcements ############################### # PyPi packages prepended with 'maap' so they are more easily discoverable -RUN pip install maap-jupyter-server-extension==1.3.0 +RUN pip install maap-jupyter-server-extension==1.3.4 RUN jupyter server extension enable jupyter_server_extension RUN pip install maap-dps-jupyter-extension==0.7.0 diff --git a/jupyterlab3/environments.json b/jupyterlab3/environments.json index f8d5190..f4047ed 100644 --- a/jupyterlab3/environments.json +++ b/jupyterlab3/environments.json @@ -20,16 +20,6 @@ "workspace_bucket": "maap-uat-workspace", "default_host": false }, - { - "environment": "pilot-ops", - "ade_server": "ade.ops.maap-project.org", - "api_server": "api.ops.maap-project.org", - "auth_server": "auth.ops.maap-project.org", - "mas_server": "mas.ops.maap-project.org", - "edsc_server": "ade.ops.maap-project.org:30052", - "workspace_bucket": "maap-ops-workspace", - "default_host": false - }, { "environment": "ops", "ade_server": "ade.maap-project.org", diff --git a/jupyterlab3/pangeo/environment.yml b/jupyterlab3/pangeo/environment.yml index 54d1cd0..2cba7c6 100644 --- a/jupyterlab3/pangeo/environment.yml +++ b/jupyterlab3/pangeo/environment.yml @@ -3,23 +3,33 @@ channels: - conda-forge - nodefaults dependencies: + - black=24.2.0 - folium=0.15.1 - - gitpython=3.1.40 + - gh-scoped-creds=4.1 - gh=2.40.1 - git-lfs=3.4.1 + - gitpython=3.1.40 - ipyevents=2.0.2 - ipyleaflet=0.18.1 + - ipytree=0.2.2 - ipywidgets=8.0.6 - jupyter-packaging=0.12.3 - - jupyterlab=3.6.3 - - jupyterlab-git=0.34.2 + - jupyter-panel-proxy=0.1.0 - jupyterlab_widgets=3.0.7 + - jupyterlab-git=0.34.2 + - jupyterlab-s3-browser=0.12.0 + - jupyterlab=3.6.3 + - nb_conda_kernels=2.3.1 - nbstripout=0.6.1 - nodejs=18.15.0 - pangeo-notebook=2023.04.15 - plotly=5.18.0 - plotnine=0.12.2 - pydantic=2.5.2 + - python-gist=0.10.6 + - python-graphviz=0.20.1 + - rise=5.7.1 + - snakeviz=2.2.0 - xarray_leaflet=0.2.3 - pip=23.3.2 - pip: diff --git a/jupyterlab3/shared/environment.yml b/jupyterlab3/shared/environment.yml index 863796e..32f3862 100644 --- a/jupyterlab3/shared/environment.yml +++ b/jupyterlab3/shared/environment.yml @@ -16,4 +16,10 @@ dependencies: - pip=23.3.2 - pip: - jupyter-resource-usage==0.7.2 - - rio-tiler==6.2.8 + - git+https://github.com/MAAP-Project/stac_ipyleaflet.git@0.3.6#egg-info=stac_ipyleaflet +variables: + TITILER_STAC_ENDPOINT: 'https://titiler-stac.maap-project.org/' + TITILER_ENDPOINT: 'https://titiler.maap-project.org/' + STAC_CATALOG_NAME: 'MAAP STAC' + STAC_CATALOG_URL: 'https://stac.maap-project.org/' + STAC_BROWSER_URL: 'https://stac-browser.maap-project.org/'