Merge branch 'dev' of https://github.com/NOAA-OWP/inundation-mapping …

…into dev-catfim-v2-1

CITATION.cff

@@ -1,8 +1,8 @@
 cff-version: 1.2.0
-message: "If you use this software, please cite it as below."
+message: "If you use this software, please cite it as below. To ensure you have latest and correct version, please look at the changelog.md at 'https://github.com/NOAA-OWP/inundation-mapping/blob/dev/docs/CHANGELOG.md'"
 authors:
 - family-names: "NOAA Office of Water Prediction"
 title: "Inundation Mapping"
 url: "https://github.com/NOAA-OWP/inundation-mapping"
-version: 4.4.2.1
-date-released: 2023
+version: 4.5.10.0
+date-released: 2024

Dockerfile

@@ -1,5 +1,5 @@
 ## Temporary image to build the libraries and only save the needed artifacts
-FROM ghcr.io/osgeo/gdal:ubuntu-full-3.8.3 AS builder
+FROM ghcr.io/osgeo/gdal:ubuntu-small-3.8.4 AS builder
 WORKDIR /opt/builder
 ARG dataDir=/data
 ARG projectDir=/foss_fim
@@ -10,7 +10,7 @@ ENV taudemDir=$depDir/taudem/bin
 ENV taudemDir2=$depDir/taudem_accelerated_flowDirections/taudem/build/bin
 
 # remove reference to missing repo
-RUN rm /etc/apt/sources.list.d/apache-arrow.sources
+# RUN rm /etc/apt/sources.list.d/apache-arrow.sources
 
 RUN apt-get update && apt-get install -y git  && rm -rf /var/lib/apt/lists/*
 
@@ -45,7 +45,7 @@ RUN cd taudem_accelerated_flowDirections/taudem/build/bin && mv -t $taudemDir2 d
 
 ###############################################################################################
 # Base Image that has GDAL, PROJ, etc
-FROM ghcr.io/osgeo/gdal:ubuntu-full-3.8.3
+FROM ghcr.io/osgeo/gdal:ubuntu-small-3.8.4
 ARG dataDir=/data
 ENV projectDir=/foss_fim
 ARG depDir=/dependencies
@@ -70,20 +70,12 @@ RUN mkdir -p $depDir
 COPY --from=builder $depDir $depDir
 
 # remove reference to missing repo
-RUN rm /etc/apt/sources.list.d/apache-arrow.sources
+# RUN rm /etc/apt/sources.list.d/apache-arrow.sources
 
-RUN apt-get update --fix-missing && apt-get install -y openjdk-21-jdk && rm -rf /var/lib/apt/lists/*
+RUN apt-get update --fix-missing && rm -rf /var/lib/apt/lists/*
 RUN apt update --fix-missing
 
-# An older version of openjdk still exists on the file system but was never cleaned up
-# After research, we realized, it just needs file cleanup. Leaving it there is triggering security warnings
-# RUN apt-get remove -y openjdk-17-jdk  (not installed, just residue left)
-RUN rm -rf ./usr/lib/jvm/*java-1.17* && \
-    rm -rf ./usr/lib/jvm/.java-1.17* && \
-    rm -rdf ./usr/lib/jvm/java-17*
-
-
-RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt install -y p7zip-full python3-pip time mpich parallel libgeos-dev expect tmux rsync tzdata
+RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt install -y p7zip-full python3-pip time mpich parallel libgeos-dev expect tmux rsync tzdata wget
 
 RUN apt auto-remove
 
@@ -99,18 +91,15 @@ ENV PYTHONUNBUFFERED=TRUE
 
 ## ADD TO PATHS ##
 ENV PATH="$projectDir:${PATH}"
-#ENV PATH=${PATH}:$projectDir:$projectDir/$srcDir:$projectDir/tools
-# Jul 17, 2024: Even though PYTHONPATH isn't used, it still seems to want it.
-ENV PYTHONPATH=${PATH}:$srcDir:$projectDir/tools
+ENV PYTHONPATH="${PYTHONPATH}:${projectDir}:${srcDir}:${srcDir}/utils:${projectDir}/data:${toolsDir}"
 
 ## install python 3 modules ##
-
 COPY Pipfile .
 COPY Pipfile.lock .
 RUN pip3 install pipenv==2024.0.1 && PIP_NO_CACHE_DIR=off pipenv install --system --deploy --ignore-pipfile
 
 # ----------------------------------
-# Mar 2023
+# Mar 2023 / Sep 2024
 # There are some nuances in the whitebox python downloads in that the first time it loads
 # it goes to the internet and downloads the latest/greatest WBT (whiteboxtools) engine which is
 # required for the whitebox python library to work. We don't want to have FIM attempting a download
@@ -120,12 +109,10 @@ RUN pip3 install pipenv==2024.0.1 && PIP_NO_CACHE_DIR=off pipenv install --syste
 # We download and unzip it to the same file folder that pip deployed the whitebox library.
 # Whitebox also attempts to always download a folder called testdata regardless of use.
 # We added an empty folder to fake out whitebox_tools.py so it doesn't try to download the folder
-
-# RUN wbox_path=/usr/local/lib/python3.10/dist-packages/whitebox/WBT && \
-#     wget -P $wbox_path https://www.whiteboxgeo.com/WBT_Linux/WhiteboxTools_linux_musl.zip && \
-#     unzip -o $wbox_path/WhiteboxTools_linux_musl.zip -d $wbox_path && \
-#     cp $wbox_path/whitebox_tools $wbox_path && \
-#     mkdir $wbox_path/testdata
+ENV WBT_PATH=/usr/local/lib/python3.10/dist-packages/whitebox/WBT
+RUN wget -P $WBT_PATH https://www.whiteboxgeo.com/WBT_Linux/WhiteboxTools_linux_musl.zip && \
+    unzip -o $WBT_PATH/WhiteboxTools_linux_musl.zip -d $WBT_PATH && \
+    cp $WBT_PATH/WhiteboxTools_linux_amd64/WBT/whitebox_tools $WBT_PATH
 # ----------------------------------
 
 ## RUN UMASK TO CHANGE DEFAULT PERMISSIONS ##

Pipfile

@@ -13,15 +13,15 @@ certifi = "==2024.7.4"
 dask = "==2024.6.2"
 dask-expr = "==1.1.6"
 distributed = "==2024.6.2"
-fiona = "==1.9.6"
+fiona = "==1.10.0"
 flake8 = "==6.0.0"
 flake8-pyproject = "==1.2.3"
 geopandas = "==1.0.1"
 gval = "==0.2.7.post1"
 ipympl = "==0.9.3"
 isort = "==5.12.0"
 jupyter = "==1.0.0"
-jupyterlab = "==3.6.7"
+jupyterlab = "==3.6.8"
 lmoments3 = "==1.0.6"
 monaco = "==0.13.1"
 natsort = "==8.3.1"
@@ -50,7 +50,7 @@ seaborn = "==0.12.2"
 tables = "==3.8.0"
 tqdm = "==4.66.3"
 urllib3 = "==1.26.19"
-whitebox = "==2.3.4"
+whitebox = "==2.3.5"
 xarray = "==2024.6.0"
 zarr = "==2.18.0"