Add files

.gitignore

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+*~
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

TODO.txt

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+* Create plant geometry with more leaves
+* Add slide on results when comparing different geometries
+* Add images of plant geometries to slides
+* Push and verify binder works

environment.yml

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+name: CiS2021-hackathon-environment
+channels:
+  - conda-forge
+dependencies:
+  - python=3.9
+  - yggdrasil=1.6.3
+  - trimesh
+  - networkx
+  - pygments
+  - notebook
+  - ipykernel

launch_local.sh

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+#!/bin/bash
+set -e
+source /opt/conda/etc/profile.d/conda.sh
+conda activate CiS2021-hackathon-environment
+jupyter notebook --no-browser --ip=0.0.0.0 --NotebookApp.token='' --NotebookApp.password='' --allow-root

local.Docker

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+FROM jupyter/minimal-notebook
+
+SHELL ["/bin/bash", "--login", "-c"]
+
+# Create output director
+RUN mkdir "output"
+
+# Create the environment:
+COPY environment.yml .
+RUN conda env create --file environment.yml
+
+# Make RUN commands use the new environment:
+RUN source /opt/conda/etc/profile.d/conda.sh && \
+    conda activate CiS2021-hackathon-environment && \
+    yggconfig && \
+    ygginfo --verbose && \
+    yggcompile c cpp fortran
+
+RUN echo "source activate CiS2021-hackathon-environment" > ~/.bashrc
+
+VOLUME /home/${NB_USER}/work
+
+# Copy the files
+WORKDIR /home/${NB_USER}/work
+COPY input /home/${NB_USER}/work/input
+COPY meshes /home/${NB_USER}/work/meshes
+COPY models /home/${NB_USER}/work/models
+COPY yamls /home/${NB_USER}/work/yamls
+COPY solutions /home/${NB_USER}/work/solutions
+COPY *.ipynb /home/${NB_USER}/work
+RUN mkdir "/home/${NB_USER}/work/output"
+RUN fix-permissions "/home/${NB_USER}/work/output" && fix-permissions "/home/${NB_USER}/work/models"
+COPY launch_local.sh .
+
+# /home/${NB_USER}/work
+
+
+EXPOSE 8888
+ENTRYPOINT ["/bin/bash", "launch_local.sh"]