Patch: Rioxarray Raster

docker/.dockerignore

@@ -0,0 +1,72 @@
+.travis.yaml
+.swagger-codegen-ignore
+README.md
+tox.ini
+git_push.sh
+test-requirements.txt
+setup.py
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+venv/
+.python-version
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+#Ipython Notebook
+.ipynb_checkpoints

docker/Dockerfile

@@ -0,0 +1,50 @@
+FROM python:3.9-slim
+
+RUN apt-get update && apt-get install -y \
+    python3 \
+    python3-dev \
+    gcc \
+    libssl-dev \
+    libjpeg-dev \
+    libjpeg62-turbo-dev \
+    zlib1g-dev \
+    libxslt1-dev \
+    libnetcdf-dev \
+    libhdf5-dev \
+    hdf5-helpers \
+    && pip3 install --upgrade pip \
+    && apt-get clean
+
+# Create a new user
+RUN adduser --quiet --disabled-password --shell /bin/sh --home /home/dockeruser --gecos "" --uid 1000 dockeruser
+USER dockeruser
+ENV HOME /home/dockeruser
+ENV PYTHONPATH "${PYTHONPATH}:/home/dockeruser/.local/bin"
+ENV PATH="/home/dockeruser/.local/bin:${PATH}"
+
+# Add artifactory as a trusted pip index
+RUN mkdir $HOME/.pip
+
+# The 'SOURCE' argument is what will be used in 'pip install'.
+ARG SOURCE
+
+# Set this argument if running the pip install on a local directory, so
+# the local dist files are copied into the container.
+ARG DIST_PATH
+
+USER root
+RUN mkdir -p /worker && chown dockeruser /worker
+USER dockeruser
+WORKDIR /worker
+
+COPY --chown=dockeruser $DIST_PATH $DIST_PATH
+USER dockeruser
+RUN pip3 install --use-feature=no-binary-enable-wheel-cache --force $SOURCE --user \
+    && rm -rf $DIST_PATH
+
+# Patch for rioxarray_raster
+COPY ../net2cog/rioxarray_raster_patch.diff /home/dockeruser/.local/lib/python3.9/site-packages/rioxarray/raster_writer.py
+
+# Run the subsetter
+#ENTRYPOINT ["netcdf_harmony"]
+CMD ["bash"]

docker/build-docker.sh

@@ -0,0 +1,73 @@
+#!/usr/bin/env bash
+
+# This script is intended to be run by the CI/CD pipeline to build a specific version of the L2SS Service application.
+
+set -Eeo pipefail
+
+LOCAL_BUILD=false
+
+POSITIONAL=()
+while [[ $# -gt 0 ]]
+do
+key="$1"
+
+case $key in
+    -n|--service-name)
+    service_name="$2"
+    shift # past argument
+    shift # past value
+    ;;
+    -v|--service-version)
+    service_version="$2"
+    shift # past argument
+    shift # past value
+    ;;
+    --local)
+    LOCAL_BUILD=true
+    shift # past argument
+    ;;
+    *)    # unknown option
+    POSITIONAL+=("$1") # save it in an array for later
+    shift # past argument
+    ;;
+esac
+done
+set -- "${POSITIONAL[@]}" # restore positional parameters
+
+USAGE="USAGE: build-docker.sh -n|--service-name service_name -v|--service-version service_version [--local]"
+
+# shellcheck disable=SC2154
+if [[ -z "${service_name}" ]]; then
+  echo "service_name required. Name of the service as found in pyproject.toml (e.g. podaac-staging)" >&2
+  echo "$USAGE" >&2
+  exit 1
+fi
+
+# shellcheck disable=SC2154
+if [[ -z "${service_version}" ]]; then
+  echo "service_version required. Version of software to install (e.g. 0.1.0-a1+12353)." >&2
+  echo "$USAGE" >&2
+  exit 1
+fi
+
+set -u
+
+SCRIPTPATH="$( cd "$(dirname "$0")" ; pwd -P )"
+PROJECT_DIR="$(dirname "${SCRIPTPATH}")"
+DIST_PATH="dist/"
+
+repositoryName=podaac/podaac-cloud/${service_name}
+
+# Docker tags can't include '+' https://github.com/docker/distribution/issues/1201
+dockerTagVersion=$(echo "${service_version}" | tr "+" _)
+
+# Build the image
+if [ "$LOCAL_BUILD" = true ] ; then
+  wheel_filename="$(echo "${service_name}" | tr "-" _)-${service_version}-py3-none-any.whl"
+  docker build -t "${repositoryName}":"${dockerTagVersion}" --build-arg DIST_PATH="${DIST_PATH}" --build-arg SOURCE="${DIST_PATH}${wheel_filename}" -f "$SCRIPTPATH"/Dockerfile "$PROJECT_DIR" 1>&2
+else
+  docker build -t "${repositoryName}":"${dockerTagVersion}" --build-arg SOURCE="${service_name}[podaac,harmony]==${service_version}" -f "$SCRIPTPATH"/Dockerfile "$SCRIPTPATH" 1>&2
+fi
+
+
+echo "${repositoryName}":"${dockerTagVersion}"

net2cog/rioxarray_raster_patch.diff

@@ -0,0 +1,12 @@
+--- /usr/local/lib/python3.8/site-packages/rioxarray/raster_writer.py	2023-10-19 11:07:08
++++ raster_writer.py	2023-10-19 11:06:12
+@@ -123,7 +123,8 @@
+     if the value of the nodata value changed.
+     """
+     # Complex-valued rasters can have real-valued nodata
+-    if str(new_dtype).startswith("c"):
++    new_dtype_str = str(new_dtype)
++    if new_dtype_str.startswith("c") or "date" in new_dtype_str or "time" in new_dtype_str:
+         nodata = original_nodata
+     else:
+         original_nodata = float(original_nodata)