covid19_sir.ipynb errors on first cell

[sam-writer]

I haven't seen the dependency sunode before. It is not pip installable. I tried pip installing by pointing to the GitHub repo, and by cloning it:

git clone https://github.com/aseyboldt/sunode.git
pip install ./sunode

But they both error out. Could you explain how to install sunode? Thank you.

[twiecki]

@sam-qordoba Yes, sunode is a very alpha package and the NB is not really meant for public consumption yet. Do you just want to check it out or are you familiar with ODEs and want to extend the model?

[sam-writer]

I have a background in math and physics, so I am not new to ODEs, however, it's been a while since I have focused on them.

The motivation is: I work on chime, and we are working on improving the underlying model.

[twiecki]

What error are you getting? You need to install sunode master as well as sundials (conda-forge).

[sam-writer]

as well as sundials (conda-forge) 🙏 I will try this, and if it doesn't work, post error logs. Thank you!

[sam-writer]

ok, @twiecki here is what I have. If I start the docker container docker run -it --rm --name tf2-gpu-covid -v $(pwd):/tf -p 8888:8888 -p 8000:8000 fabiononato/covid19:latest /bin/bash, then

rm -rf /usr/local
apt-get install wget
wget -c https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
bash ./Miniconda3-latest-Linux-x86_64.sh -b -p /usr/local
conda install -y -c chogan -c conda-forge conda-build conda-verify sundials 
git clone https://github.com/aseyboldt/sunode
cd sunode
conda-build --no-test --dirty --no-verify -c conda-forge ./conda
cd ..
conda install --use-local sunode

gives a lot of output, ending with

to be incompatible with the existing python installation in your environment:

Specifications:

  - sunode -> python[version='>=3.8,<3.9.0a0']

Your python: python=3.7

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

which, I get that I can use a different docker container... it just feels like a lot? does this seem like the right track?

[twiecki]

Yeah, I think this might be a bit too rough of a ride in its current state, sorry.