Install dash (#213)

* Install dash * Force channel * Test moving to base * Move to base * Fix build * Unpin cdlib * Temporarily disable single-user * Merge all mamba installs * Make apt silent * Remove some generic stuff that may not be applicable to SBD * Try to fix installation issues * Bring back the image * Remove sobigdata image
EGI-Federation · Oct 23, 2024 · 51e6afd · 51e6afd
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diff --git a/.github/workflows/d4science-images.yml b/.github/workflows/d4science-images.yml
@@ -16,7 +16,7 @@ jobs:
       base: d4science-base/Dockerfile
       images: |
         "single-user-d4science/Dockerfile"
-        "single-user-sobigdata/Dockerfile"
+        # "single-user-sobigdata/Dockerfile"
         "single-user-3d-d4science/Dockerfile"
         "single-user-r-d4science/Dockerfile"
         "single-user-scientometrics-d4science/Dockerfile"

diff --git a/d4science-base/Dockerfile b/d4science-base/Dockerfile
@@ -5,13 +5,13 @@ ARG julia_version="1.9.3"
 
 USER root
 
-RUN apt-get update \
-    && apt-get install --no-install-recommends -y \
+RUN apt-get -qq update \
+    && apt-get -qq install --no-install-recommends -y \
         less \
         graphviz \
         vim \
         openssh-client \
-    && apt-get clean \
+    && apt-get -qq clean \
     && rm -rf /var/lib/apt/lists/*
 
 RUN curl https://raw.githubusercontent.com/kadwanev/retry/master/retry \
@@ -70,7 +70,7 @@ RUN julia -e 'import Pkg; Pkg.update()' && \
 # -----------------------------------------------------------------------------
 
 
-RUN mamba install -y -q \
+RUN mamba install --channel conda-forge -y -q \
         rdflib \
         prov \
         graphviz \
@@ -82,10 +82,29 @@ RUN mamba install -y -q \
         cartopy \
         ipyleaflet \
         nbgitpuller \
+        basemap \
+        beakerx \
+        xgboost \
+        lightgbm \
+        catboost \
+        netcdf4 \
+        aiohttp \
+        graph-tool \
+        scikit-learn \
+        scikit-mobility \
+        dask-jobqueue \
+        fs \
+        rasterio \
+        contextily \
+        nb_conda_kernels \
+        nb_conda \
+        pyophidia \
+	# bring dash extension hopefully
+	dash \
+	jupyter-server-proxy \
+    && conda clean -tipy \
     && conda clean --all
 
 RUN pip install --no-cache-dir shortid
 
 WORKDIR "${HOME}"
-
-RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-leaflet
diff --git a/single-user-d4science/Dockerfile b/single-user-d4science/Dockerfile
@@ -4,46 +4,31 @@ FROM $BASE_IMAGE
 
 USER root
 
-RUN apt-get update \
-    && apt-get install --no-install-recommends -y \
+RUN apt-get -qq update \
+    && apt-get -qq install --no-install-recommends -y \
         nco \
         cdo \
         gdal-bin \
         cmake \
         libgdal-dev \
-    && apt-get clean \
+    && apt-get -qq clean \
     && rm -rf /var/lib/apt/lists/*
 
 USER $NB_UID
 
-RUN mamba install -y --quiet \
-        basemap \
-        beakerx \
-        xgboost \
-        lightgbm \
-        catboost \
-        netcdf4 \
-        aiohttp \
-        graph-tool \
-        scikit-learn \
-        scikit-mobility \
-        dask-jobqueue \
-        fs \
-        rasterio \
-        contextily \
-        nb_conda_kernels \
-        nb_conda \
-        pyophidia \
-    && conda clean -tipy
-
 RUN conda create --quiet --yes -n java8 \
     && mamba install -n java8 --yes openjdk=8 \
     && conda clean -tipy
 
 ENV CPLUS_INCLUDE_PATH=/usr/include/gdal
 ENV C_INCLUDE_PATH=/usr/include/gdal
 
-# Pinned networkx to 2.6.3 as 2.7 makes networksns fail
+# Installing torch explictly to have only CPU version
+RUN pip install --index-url https://download.pytorch.org/whl/cpu \
+	torch torchvision torchaudio
+
+
+# cdlib[C]==0.2.3 is too old for this env, so unpinning
 RUN pip install --no-cache-dir \
         bicm \
         rdp \
@@ -54,7 +39,7 @@ RUN pip install --no-cache-dir \
         ndlib \
         motuclient \
         panel==0.9.* \
-        cdlib[C]==0.2.3 \
+        cdlib[C] \
         cython \
         node_conformity \
         git+https://github.com/obidam/pyxpcm.git \
@@ -63,7 +48,6 @@ RUN pip install --no-cache-dir \
         git+https://github.com/guglielmocola/RetweetCascade.git@f96319d0107473715104acceb2ff0925d35dd9e3 \
         fast-forward-indexes \
         NEMtropy \
-        folium==0.11.0 \
         geopy==2.0.0 \
         hvplot==0.6.0 \
         intake==0.6.0 \
@@ -72,7 +56,6 @@ RUN pip install --no-cache-dir \
         seaborn==0.11.0 \
         zarr==2.5.0 \
         holoviews \
-        networkx==2.6.3 \
         networksns \
         GDAL==$(gdal-config --version) #need to match the version of gdal installed
 

diff --git a/single-user-r-d4science/Dockerfile b/single-user-r-d4science/Dockerfile
@@ -16,6 +16,8 @@ RUN curl https://raw.githubusercontent.com/kadwanev/retry/master/retry \
 
 USER $NB_UID
 
+RUN pip install --no-cache-dir shortid
+
 RUN mamba install -y -q \
         rdflib \
         prov \
@@ -28,24 +30,12 @@ RUN mamba install -y -q \
         cartopy \
         ipyleaflet \
         nbgitpuller \
-    && conda clean --all
-
-RUN pip install --no-cache-dir shortid
-
-WORKDIR "${HOME}"
-
-RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-leaflet
-
-RUN mamba install -y --quiet \
         r-plotly \
         r-gdata \
         r-rpostgres \
         r-geojsonio \
         r-rlang  \
         r-rcpp \
-    && conda clean -tipy
-
-RUN mamba install -y --quiet \
         r-vctrs \
         r-pillar \
         r-magrittr \
@@ -55,9 +45,6 @@ RUN mamba install -y --quiet \
         r-dbi \
         r-cpp11 \
         r-bh \
-    && conda clean -tipy
-
-RUN mamba install -y --quiet \
         r-tibble \
         r-hms \
         r-jsonlite \

diff --git a/single-user-sobigdata/Dockerfile b/single-user-sobigdata/Dockerfile
@@ -26,60 +26,6 @@ USER $NB_UID
 
 ARG SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True
 
-RUN mamba install -y --quiet \
-        basemap \
-        beakerx \
-        xgboost \
-        lightgbm \
-        catboost \
-        netcdf4 \
-        aiohttp \
-        graph-tool \
-        scikit-learn \
-        scikit-mobility \
-        dask-jobqueue \
-        fs \
-        rasterio \
-        contextily \
-        nb_conda_kernels \
-        nb_conda \
-    && conda clean -tipy
-
-# Pinned networkx to 2.6.3 as 2.7 makes networksns fail
-RUN pip install --no-cache-dir \
-        bicm \
-        rdp \
-        sentinelhub \
-        import_ipynb \
-        nbresuse \
-        ndlib \
-        motuclient \
-        panel==0.9.* \
-        cdlib[C]==0.2.3 \
-        cython \
-        node_conformity \
-        git+https://github.com/geopython/OWSLib.git \
-        git+https://github.com/guglielmocola/RetweetCascade.git \
-        fast-forward-indexes \
-        NEMtropy \
-        folium==0.11.0 \
-        geopy==2.0.0 \
-        hvplot==0.6.0 \
-        intake==0.6.0 \
-        intake-esm==2020.8.15 \
-        hda \
-        seaborn==0.11.0 \
-        zarr==2.5.0 \
-        holoviews \
-        networkx==2.6.3 \
-        networksns \
-        eventclf \
-        XAI-Library \
-        convrewriting \
-        git+https://github.com/guglielmocola/TwitterMonitorLib_v2.git \
-        pygm \
-        structify-net
-
 # -------------------------------
 # SoBigData ++ specific libraries
 # -------------------------------