Bug thrown in LabelModel after I upgrade to Catalina and had to change Snorkel environment.

[wimurr]

Snorkel Upgrade bug 2020-08-19_16-25-41.pdf

Issue description

A clear and concise description of what the bug is.

The LabelModel throws an error saying that the 'Graph' object has no attribute 'node' in graph_utils.py in get_clique_tree.

The only changes I made in my code were:

1. I had to upgrade to Mac OS Catalina.
2. I had to create a new Snorkel virtual environment (0.90).
3. The code to import LabelModel seemed to no longer work as it seemed to now been in a different place, a submodule. Previously, I had:

from snorkel.labeling.model import LabelModel

What I changed it to, as I saw LabelModel had moved:

from snorkel.labeling.model.label_model import LabelModel

Code example/repro steps

Expected behavior

I just expected it to create a labeling model, as before.

Screenshots

See PDF.

System info

• How you installed Snorkel (conda, pip, source): conda
• OS: Catalina
• Python version: 3.7
• Snorkel version: 0.90 Add any other context about the problem here. Just upgraded to Catalina on Mac

[paroma]

The specific error message is due to network changing their syntax between minor versions. You may find #1491 and #1494 relevant. Our Python requirements currently upperbound networkx to be <2.4.

[wimurr]

Thanks! Yes, I keep forgetting when I rebuild my Snorkel environment that it is crucially important that I run:

pip install -r requirements.txt

and not just rely on conda install snorkel. This time I wrote notes for the next time I have to go through an Apple major software upgrade.

I also had to rebuild scikit-learn following the instructions for MacOS at https://scikit-learn.org/0.21/developers/advanced_installation.html, specifically:

brew install libomp export CC=/usr/bin/clang export CXX=/usr/bin/clang++ export CPPFLAGS="$CPPFLAGS -Xpreprocessor -fopenmp" export CFLAGS="$CFLAGS -I/usr/local/opt/libomp/include" export CXXFLAGS="$CXXFLAGS -I/usr/local/opt/libomp/include" export LDFLAGS="$LDFLAGS -L/usr/local/opt/libomp/lib -lomp" export DYLD_LIBRARY_PATH=/usr/local/opt/libomp/lib

before trying

pip install -r requirements.txt

again which failed the first time on sklearn and an issue with OpenMP. Thanks!