Merge pull request #1 from spatial-data-lab/knime5.3.2-geospatial1.2

Knime5.3.2 geospatial1.2

Dockerfile

@@ -1,30 +1,45 @@
 # Define the base image
-FROM registry.hub.knime.com/knime/knime-full:r-5.1.2-433
+FROM knime/knime-full:r-5.3.2-564
+# registry.hub.knime.com/knime/knime-full:r-5.3.1-498
+# knime/knime-full:r-5.3.2-563
 # Define the list of update sites and features
-# Optional, the default is the KNIME Analytics Platform update site (first entry in the list below)
-ENV KNIME_UPDATE_SITES=https://update.knime.com/analytics-platform/5.1,https://update.knime.com/community-contributions/trusted/5.1
-# Install a feature from the Community Trusted update site
-# ENV KNIME_FEATURES="sdl.harvard.features.geospatial.feature.group"
-ENV KNIME_FEATURES="sdl.harvard.features.geospatial.feature.group"
+
 
 # Change to the root user
 USER root
 # Install the ca-certificates package to avoid SSL certificate issues
-RUN apt update && apt install -y ca-certificates curl
+# RUN apt update && apt install -y ca-certificates curl
+# Update/upgrade package manager and install ca-certificates to enable ca certificates that micromamba (for python) is asking for
+RUN apt-get update && \
+    apt-get upgrade -yq && \
+    apt-get install -yq \
+        ca-certificates curl && \
+    # cleanup
+    rm -rf /var/lib/apt/lists/*
+
 # Change back to the knime user
 USER knime
 
+
+ENV KNIME_UPDATE_SITES=https://update.knime.com/analytics-platform/5.2,https://update.knime.com/community-contributions/trusted/5.2
+# Install a feature from the Community Trusted update site
+ENV KNIME_FEATURES="sdl.harvard.features.geospatial.feature.group"
+
 # Execute extension installation script 
 RUN ./install-extensions.sh
 
+# set up the Python environment
+
 # Install Python 3.9
-RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" 
-# /home/knime/
-RUN bash -c "bash Miniforge3-$(uname)-$(uname -m).sh -b -p /home/knime/condaforge"
-RUN rm -rf Miniforge3-$(uname)-$(uname -m).sh
-ENV PATH="/home/knime/condaforge/bin:$PATH"
-
-# Install Python packages
-COPY knime_py39.yml /home/knime/knime_py39.yml
-RUN /home/knime/condaforge/bin/conda env create -f /home/knime/knime_py39.yml
-RUN rm -rf /home/knime/knime_py39.yml
+# RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" 
+# # /home/knime/
+# RUN bash -c "bash Miniforge3-$(uname)-$(uname -m).sh -b -p /home/knime/condaforge"
+# RUN rm -rf Miniforge3-$(uname)-$(uname -m).sh
+# ENV PATH="/home/knime/condaforge/bin:$PATH"
+
+# # Install Python packages
+COPY py3_knime.yml /home/knime/py3_knime.yml
+RUN /home/knime/miniconda3/condabin/conda env create -f /home/knime/py3_knime.yml
+COPY knime_dl_cpu.yml /home/knime/knime_dl_cpu.yml
+RUN /home/knime/miniconda3/condabin/conda env create -f /home/knime/knime_dl_cpu.yml
+# RUN rm -rf /home/knime/py3_knime.yml

executor.epf

@@ -1,14 +1,14 @@
 
 # add python path here
-/instance/org.knime.conda/condaDirectoryPath=/home/knime/condaforge
+/instance/org.knime.conda/condaDirectoryPath=/home/knime/miniconda3
 
 # B - KNIME Python Integration - Default options for Python Integration. By default KNIME uses the bundled environment (shipped with KNIME) if no Conda Environment Propagation node is used.
 # Line below can be set to either "bundled" (default), "conda" or "manual"
 /instance/org.knime.python3.scripting.nodes/pythonEnvironmentType=conda
 /instance/org.knime.python3.scripting.nodes/bundledCondaEnvPath=org_knime_pythonscripting
 # Following rows are only required if "bundled" value above is replaced with "conda"
 /instance/org.knime.python3.scripting.nodes/python2CondaEnvironmentDirectoryPath=<path to default conda environment dir>
-/instance/org.knime.python3.scripting.nodes/python3CondaEnvironmentDirectoryPath=/home/knime/condaforge/envs/knime_py39
+/instance/org.knime.python3.scripting.nodes/python3CondaEnvironmentDirectoryPath=/home/knime/miniconda3/envs/py3_knime
 # Following rows are only required if "bundled" value above is replaced with "manual"
 /instance/org.knime.python3.scripting.nodes/python2Path=<path to python2 env>
 /instance/org.knime.python3.scripting.nodes/python3Path=<path to python3 env>
@@ -20,7 +20,7 @@
 /instance/org.knime.python2/serializerId=org.knime.python2.serde.arrow
 # Following rows are only required if "conda" is set above
 /instance/org.knime.python2/python2CondaEnvironmentDirectoryPath=<path to default conda environment dir>
-/instance/org.knime.python2/python3CondaEnvironmentDirectoryPath=/home/knime/condaforge/envs/knime_py39
+/instance/org.knime.python2/python3CondaEnvironmentDirectoryPath=/home/knime/miniconda3/envs/py3_knime
 # Following rows are only required if "conda" value above is replaced with "manual"
 /instance/org.knime.python2/python2Path=<path to python2 env>
 /instance/org.knime.python2/python3Path=<path to python3 env>
@@ -30,12 +30,12 @@
 # Select either "python" or "dl" (without quotation marks) in next row. If "python" is used, the configuration of section B above is reused. If "dl" is used, a custom config for Deep Learning can be provided.
 /instance/org.knime.dl.python/pythonConfigSelection=dl
 # Following rows only required if row above is set to "dl"
-/instance/org.knime.dl.python/kerasCondaEnvironmentDirectoryPath=/home/knime/condaforge/envs/knime_dl_cpu
+/instance/org.knime.dl.python/kerasCondaEnvironmentDirectoryPath=/home/knime/miniconda3/envs/knime_dl_cpu
 /instance/org.knime.dl.python/librarySelection=keras
 /instance/org.knime.dl.python/manualConfig=python3
 /instance/org.knime.dl.python/pythonEnvironmentType=conda
 /instance/org.knime.dl.python/serializerId=org.knime.python2.serde.arrow
-/instance/org.knime.dl.python/tf2CondaEnvironmentDirectoryPath=/home/knime/condaforge/envs/knime_dl_cpu
+/instance/org.knime.dl.python/tf2CondaEnvironmentDirectoryPath=/home/knime/miniconda3/envs/knime_dl_cpu
 /instance/org.knime.dl.python/tf2ManualConfig=python3
 
 # R home

knime_dl_cpu.yml

@@ -0,0 +1,16 @@
+name: knime_dl_cpu
+channels:
+  - conda-forge
+  - knime
+  - anaconda
+dependencies:
+  - python=3.6
+  - h5py=2.8
+  - tensorflow-mkl=1.12
+  - keras=2.2.4
+  - pandas=0.25.3
+  - py-xgboost-cpu
+  # - scikit-learn
+  # - geopandas
+  # - scipy
+prefix: /home/knime/miniconda3/envs/knime_dl_cpu

py3_knime.yml

@@ -0,0 +1,31 @@
+name: py3_knime
+channels:
+  - conda-forge
+  - knime
+dependencies:
+  - python=3.11
+  - geopandas
+  - pyarrow
+  - knime-python-scripting=5.3
+  - matplotlib
+  - earthengine-api
+  - geemap
+  - folium
+  - mapclassify
+  - keplergl
+  - h3-py
+  - geopy
+  - esda
+  - libpysal
+  - mgwr
+  - osmnx
+  - polyline
+  - pulp
+  - pysal
+  - rasterio
+  - seaborn
+  - sympy
+  - pointpats
+  - scipy
+  - scikit-learn
+prefix: /home/knime/miniconda3/envs/py3_knime