Environment bug identified by Fatemeh

[amyheather]

Fatemeh identified an issue with missing dependencies for sim-tools.

Issue

I have encountered an error for running codes related to number of replications. Not sure what the problem is, it might be some interdependencies for the packages or with my environment.

Following is an snapshot of the error:

And the following is my environment:

My suggested solution

Looking at the issue, it looks like sim-tools expects matplotlib to be installed, and is complaining because it can't find it. Your environment matches the one used when building and running the code in the book, so this is probably due to operating system differences in whether they found and installed certain "hidden" dependencies like this, I would guess.

Could you try adding matplotlib to your environment and re-running? You can edit the environment.yaml file then run conda env update --file environment.yml --prune. Alternatively you can run conda install matplotlib but it is still best to record this in the YAML file so the environment is fully specified.

To do

If this does solve the issue, then I should add matplotlib as a dependency in the book's environment.yaml.

I should also check sim-tools dependencies - maybe matplotlib needs to be moved from optional to required?

[amyheather]

Solution did not resolve. Confirmed matplotlib present in environment. From this stackoverflow post, looks like could be issue of being outdated, issue with the install, or conflict between versions. Though trying these did not resolve:

pip uninstall matplotlib
pip install --no-cache-dir matplotlib

Pip uninstall matplotlib
Pip install --force-reinstall --no-deps matplotlib

More screenshots from Fatemeh:

[amyheather]

This error disappeared when re-ran jupyter book as mentioned in #144:

"When I run the first block for the first time in a new jupyterbook I encounter following comment, though running for the second time is error-free"

I am guessing that it maybe was an issue with a dodgy install of matplotlib and was resolved when environment remade and reset the notebook, so will close this issue for now, as don't think there is anything further here to address.

[amyheather]

Fatemeh notes in #144 that it might be good to document some of these errors and provide readers with some possible solutions. Not sure there is anything specific to mention here, as seems an individual issue with matplotlib.