updating Anaconda dependencies (#476)

* updating Anaconda dependencies

* add line to EOF

* removing references for elyra

* removing 1 more elyra

* updated for yaml linting

Author: trujillm

base/anaconda-python-3.8/environment.yml

@@ -5,7 +5,7 @@ channels:
 dependencies:
   - _libgcc_mutex=0.1=main
   - _openmp_mutex=5.1=1_gnu
-  - ca-certificates=2023.08.22=h06a4308_0
+  - ca-certificates=2024.3.11=h06a4308_0
   - icu=73.1=h6a678d5_0
   - ld_impl_linux-64=2.38=h1181459_1
   - libffi=3.4.4=h6a678d5_0
@@ -14,15 +14,15 @@ dependencies:
   - libstdcxx-ng=11.2.0=h1234567_1
   - libuv=1.44.2=h5eee18b_0
   - ncurses=6.4=h6a678d5_0
-  - nodejs=18.16.0=h2d74bed_1
-  - openssl=3.0.12=h7f8727e_0
+  - nodejs=18.18.2=h2d74bed_0
+  - openssl=3.0.13=h7f8727e_0
   - pip=23.3.1=py38h06a4308_0
   - python=3.8.18=h955ad1f_0
   - readline=8.2=h5eee18b_0
-  - setuptools=68.0.0=py38h06a4308_0
+  - setuptools=68.2.2=py38h06a4308_0
   - sqlite=3.41.2=h5eee18b_0
   - tk=8.6.12=h1ccaba5_0
   - wheel=0.41.2=py38h06a4308_0
-  - xz=5.4.2=h5eee18b_0
+  - xz=5.4.6=h5eee18b_0
   - zlib=1.2.13=h5eee18b_0
 prefix: /opt/app-root

jupyter/datascience/anaconda-python-3.8/Dockerfile

@@ -26,28 +26,28 @@ COPY utils utils/
 # Install Python packages and Jupyterlab extensions from conda environment file
 COPY environment.yml start-notebook.sh ./
 # Copy Elyra setup to utils so that it's sourced at startup
-COPY jupyter_elyra_config.py setup-elyra.sh pipeline-flow.svg ./utils/
+#COPY jupyter_elyra_config.py setup-elyra.sh pipeline-flow.svg ./utils/
 
 RUN echo "Installing softwares and packages" && \
     /opt/anaconda3/bin/conda env update -p "${APP_ROOT}" --file environment.yml && \
     rm -f ./environment.yml && \
     # setup path for runtime configuration \
     mkdir /opt/app-root/runtimes && \
     # switch to Data Science Pipeline \
-    cp utils/pipeline-flow.svg /opt/app-root/lib/python3.8/site-packages/elyra/static/icons/kubeflow.svg && \
-    sed -i "s/Kubeflow Pipelines/Data Science/g" /opt/app-root/lib/python3.8/site-packages/elyra/pipeline/runtime_type.py && \
-    sed -i "s/Kubeflow Pipelines/Data Science Pipelines/g" /opt/app-root/lib/python3.8/site-packages/elyra/metadata/schemas/kfp.json && \
-    sed -i "s/\"default\": \"Argo\",/\"default\": \"Tekton\",/g" /opt/app-root/lib/python3.8/site-packages/elyra/metadata/schemas/kfp.json && \
+    # cp utils/pipeline-flow.svg /opt/app-root/lib/python3.8/site-packages/elyra/static/icons/kubeflow.svg && \
+    # sed -i "s/Kubeflow Pipelines/Data Science/g" /opt/app-root/lib/python3.8/site-packages/elyra/pipeline/runtime_type.py && \
+    # sed -i "s/Kubeflow Pipelines/Data Science Pipelines/g" /opt/app-root/lib/python3.8/site-packages/elyra/metadata/schemas/kfp.json && \
+    # sed -i "s/\"default\": \"Argo\",/\"default\": \"Tekton\",/g" /opt/app-root/lib/python3.8/site-packages/elyra/metadata/schemas/kfp.json && \
     # Replace Notebook's launcher, "(ipykernel)" with Python's version 3.x.y \
     sed -i -e "s/Python.*/$(python --version)\",/" /opt/app-root/share/jupyter/kernels/python3/kernel.json && \
     # Remove default Elyra runtime-images \
-    rm /opt/app-root/share/jupyter/metadata/runtime-images/*.json && \
+    # rm /opt/app-root/share/jupyter/metadata/runtime-images/*.json && \
     # Fix permissions to support pip in Openshift environments \
     chmod -R g+w /opt/app-root/lib/python3.8/site-packages && \
     fix-permissions /opt/app-root -P
 
 # Copy Elyra runtime-images definitions and set the version
-COPY runtime-images/ /opt/app-root/share/jupyter/metadata/runtime-images/
+# COPY runtime-images/ /opt/app-root/share/jupyter/metadata/runtime-images/
 
 USER root
 RUN mkdir /etc/conda

jupyter/datascience/anaconda-python-3.8/environment.in

@@ -1,27 +1,25 @@
-boto3~=1.28
+boto3~=1.34
 kafka-python~=2.0
-matplotlib~=3.6
+matplotlib~=3.7
 numpy~=1.24
-pandas~=1.5
-plotly~=5.16
+pandas~=2.0
+plotly~=5.20
 scikit-learn~=1.3
 scipy~=1.10
-skl2onnx~=1.15
-pymongo~=4.5
+skl2onnx~=1.16
+onnxconverter-common~=1.13
+pymongo~=4.6
 psycopg~=3.1
-pyodbc~=4.0
-mysql-connector-python~=8.0
-elyra-pipeline-editor-extension>=3.15
-elyra-python-editor-extension>=3.15
-elyra-code-snippet-extension>=3.15
+pyodbc~=5.1
+mysql-connector-python~=8.3
 jupyterlab~=3.6
 jupyter_bokeh~=3.0
-jupyter_server~=2.7
+jupyter_server~=2.13
 jupyter-server-proxy~=4.0
-jupyter_server_terminals~=0.4
-jupyterlab-git~=0.42
+jupyter_server_terminals~=0.5
+jupyterlab-git~=0.44
 jupyterlab-lsp~=4.2
 jupyterlab_widgets~=3.0
-jupyter-resource-usage~=0.6
+jupyter-resource-usage~=0.7
 nbdime~=3.2
 nbgitpuller~=1.2