EOSC image

.github/workflows/egi-images.yml

@@ -15,6 +15,7 @@ jobs:
       base: base/Dockerfile
       images: |
         "single-user/Dockerfile"
+        "single-user-eosc/Dockerfile"
         "single-user-panosc/Dockerfile"
         "single-user-ai4pp/Dockerfile"
         "single-user-ai/Dockerfile"

.github/workflows/lint.yml

@@ -30,3 +30,6 @@ jobs:
           VALIDATE_DOCKERFILE_HADOLINT: false
           # disable this as well
           VALIDATE_CHECKOV: false
+          # Not linting the CSS from Jupyter as we don't want to modify this
+          # (so it's easy to track changes in casse it's needed)
+          FILTER_REGEX_EXCLUDE: "single-user-eosc/eosc/custom.css"

single-user-eosc/Dockerfile

@@ -0,0 +1,83 @@
+ARG BASE_IMAGE=eginotebooks/base:latest
+# hadolint ignore=DL3006
+FROM $BASE_IMAGE
+
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
+RUN mamba install -y --quiet \
+        cftime \
+        ipympl \
+        jmespath \
+	psycopg2 \
+	boto3 \
+	folium \
+	tensorflow \
+	tqdm \
+	lxml \
+	pymongo \
+	rasterstats \
+	geopandas \
+	ipywidgets \
+	matplotlib \
+	scipy \
+	lightgbm \
+	plotly \
+	graphviz \
+	jq \
+	nb_conda_kernels \
+        # resource usage info in GUI
+        jupyter-resource-usage \
+    && conda clean --all
+
+# Octave, install on a different environment
+# Octave from conda won't build packages
+# see https://discourse.jupyter.org/t/installing-octave-packages-with-binder/4206
+USER root
+
+RUN apt-get update \
+    && apt-get install --install-recommends -y \
+        octave octave-signal gnuplot\
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+USER $NB_UID
+
+RUN mamba install -y --quiet octave_kernel=0.32.0 \
+    && conda clean --all
+
+# Rstudio
+USER root
+RUN apt-get update \
+    && apt-get install -y gdebi-core \
+    && wget -q https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2022.07.2-576-amd64.deb \
+    && gdebi -n rstudio-server-2022.07.2-576-amd64.deb \
+    && rm rstudio-server-2022.07.2-576-amd64.deb \
+    && apt-get remove -y gdebi \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+USER $NB_UID
+
+RUN mamba install -y --quiet \
+       -c conda-forge jupyter-rsession-proxy \
+    && conda clean --all
+
+# packages not in conda
+RUN pip install --no-cache-dir \
+        h5glance \
+        nbtop \
+        panel
+
+# EOSC customisation
+COPY eosc /opt/conda/share/eosc
+RUN set -x \
+    && export PKG_PATH="$(python -c 'import jupyter_server; print(jupyter_server.__path__[0])')" \
+    && mkdir -p "$PKG_PATH/static/custom/logo" \
+    && ln -s /opt/conda/share/eosc/custom.css "$PKG_PATH/static/custom/" \
+    && ln -s /opt/conda/share/eosc/eosc-ntb-logo.svg "$PKG_PATH/static/custom/logo" \
+    && mkdir -p /opt/conda/share/jupyter/lab/settings/ \
+    && ln -s /opt/conda/share/eosc/overrides.json /opt/conda/share/jupyter/lab/settings/overrides.json
+
+RUN jupyter lab build
+
+RUN rmdir work