Pip refactor #31
Pip refactor #31
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This looks like a lot of comments, but is really only two different points. One is that since your functions are coming from ponyo you can remove a bunch of pythonpath tinkering.
The second is that you don't currently have ponyo in your environment file so this PR breaks your code
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This isn't a criticism so much as something I'm curious about: why did you decide to add a shebang line here? I don't see it very frequently for python scripts, though I imagine there's a reason for you adding it
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Is it something that nbconvert started doing?
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I hadn't noticed that before. It does look like its something that is added when you nbconvert: jupyter/nbconvert#690
Pseudo_experiments/nbconverted/generate_E_GEOD_51409_template_experiment.py
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Validate_simulations/nbconverted/test_reduced_expression_variance.py
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Validate_simulations/nbconverted/viz_Pa_simulated_experiment_compendium.py
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| - conda-forge::libiconv=1.15 | ||
| - conda-forge::joblib=0.13.2 | ||
| - pip=9.0 | ||
| - anaconda::protobuf | ||
| - pip=19.2.1 | ||
| - pip: | ||
| - torch>=0.4.0 | ||
| - matplotlib==3.0.0 |
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Don't forget to add ponyo to your environment file. You could do a pip install pointing to a github link for now, then update it once ponyo is added to pypi
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Currently I am manually pip installing ponyo into this conda environment because ponyo is not uploaded to pypi just yet. I plan to add ponyo to this yml file once it is.
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Let me know if the changes look ok |
This PR updates the notebooks to import ponyo modules (https://github.com/ajlee21/ponyo), which contains all the functions from this repository and modularizes them.
This PR also updates the environment file to automatically install R packages.
All notebooks were re-run on a small test dataset to make sure everything runs as expected. Test datasets and outputs are not seen in this PR.