Add tempsed wadden sea flavor

flavors/tempsed-wadden-sea/cell-build.Dockerfile

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+FROM mambaorg/micromamba:2.0.7
+
+RUN micromamba install -y -n base -c conda-forge conda-pack && \
+    micromamba clean --all --yes
+
+ARG CONDA_ENV_FILE
+COPY --chown=mambauser:mambauser ${CONDA_ENV_FILE?} environment.yaml
+RUN micromamba create -y -n venv -f environment.yaml && \
+    micromamba clean --all --yes
+
+COPY ./flavors/tempsed-wadden-sea/install_packages.R .
+RUN micromamba run -n venv bash -c "Rscript install_packages.R"

flavors/tempsed-wadden-sea/environment.yaml

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+name: tempsed-wadden-sea
+channels:
+  - conda-forge
+dependencies:
+  # naavre-fl-*-cell-build
+  - r-jsonlite=1.9.1
+  - r-optparse=1.7.5
+  # naavre-fl-*-jupyter
+  - ipykernel=6.29.5
+  - r-irkernel=1.3.2
+  # user packages for all flavors
+  - git=2.49.0
+  - jq>=1.8
+  - minio=7.2.15
+  - pip=25.0.1
+  - python>=3.8
+  - r=4.4
+  - r-secretsprovider
+  - r-getpass
+  - r-aws.s3
+  # user packages for this flavor
+  - r-dplyr
+  - r-tidyr
+  - r-purrr
+  - r-lubridate
+  - r-ggplot2
+  - r-sf
+  - r-terra
+  - r-zoo
+  - r-data.table
+  - r-fasttime
+  - r-rcpp
+  - r-rcpproll
+  - r-ggrepel
+  - r-generics
+  - r-cli
+  - r-rcpparmadillo
+  - r-pak
+  - r-devtools
+  - r-remotes
+  - pandas
+  - geopandas
+  - matplotlib
+  - rasterio
+  # Dependencies for TempSED
+  - r-desolve
+  - r-rootsolve
+  - r-plot3d
+  - r-shape
+  - pip:
+    # user packages for all flavors
+    - SecretsProvider
+    # user packages for this flavor
+    - rws-ddlpy
+

flavors/tempsed-wadden-sea/flavor_config.yaml

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+flavor_name: tempsed-wadden-sea
+build_jupyter: True
+build_cell_base: True
+free_disk_space: False
+aliases: []

flavors/tempsed-wadden-sea/install_packages.R

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+install.packages("ReacTran", repos="https://cran.r-project.org", dependencies = FALSE)
+library("ReacTran")
+
+install.packages("grDevices", repos="https://cran.r-project.org", dependencies = FALSE)
+library("grDevices")
+
+install.packages("heatwaveR", repos="https://cran.r-project.org", dependencies = FALSE)
+library("heatwaveR")
+
+install.packages("tidyterra", repos="https://cran.r-project.org", dependencies = FALSE)
+library("tidyterra")
+
+devtools::install_github('TempSED/TempSED', build_vignettes = TRUE, dependencies = FALSE)
+require('TempSED')
+

flavors/tempsed-wadden-sea/jupyter.Dockerfile

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+FROM quay.io/jupyter/minimal-notebook:lab-4.3.6
+
+COPY --chown=jovyan:jovyan ./docker/jupyter.requirements.txt requirements.txt
+RUN pip install -r requirements.txt
+
+# nb_conda_kernels for auto-discovery of kernels in other conda environments
+RUN mamba install --yes "nb_conda_kernels>=2.5.0" && \
+    mamba clean --all --yes
+
+# Disable "Would you like to get notified about official Jupyter news?"
+# https://jupyterlab.readthedocs.io/en/stable/user/announcements.html
+RUN jupyter labextension disable "@jupyterlab/apputils-extension:announcements"
+
+ARG CONDA_ENV_FILE
+COPY --chown=jovyan:jovyan ${CONDA_ENV_FILE?} environment.yaml
+RUN mamba env create --yes -f environment.yaml && \
+    mamba clean --all --yes
+RUN echo '{"CondaKernelSpecManager": {"env_filter": "/opt/conda$", "conda_only": true}}' >> /home/jovyan/.jupyter/jupyter_config.json
+
+RUN mkdir -p /tmp/data
+
+COPY ./flavors/tempsed-wadden-sea/install_packages.R .
+RUN mamba run -n tempsed-wadden-sea bash -c "Rscript install_packages.R"

flavors/tempsed-wadden-sea/tests/tests.sh

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+#!/bin/bash
+set -e
+# activate environment in cell-test or in jupyter image
+source /venv/bin/activate || eval "$(conda shell.bash activate tempsed-wadden-sea)"
+dir="${0%/*}"
+find "$dir" -name "*.py" -print0 | xargs --null -I "{}" python "{}"
+find "$dir" -name "*.R" -print0 | xargs --null -I "{}" Rscript "{}"