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dhimmel / gene-ontology

User-friendly Gene Ontology annotations
https://git.dhimmel.com/gene-ontology/
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Upgrade conda environment and update 'process.ipynb' for compatibility with newer Networkx version #7

Closed NegarJanani closed 1 month ago

NegarJanani commented 1 month ago

refs https://github.com/dhimmel/gene-ontology/issues/6

This pull request includes the following updates and changes:

  1. Conda Environment Update: The environment.yml file has been upgraded to include updated packages due to availability issues. You can review the changes in the following commit:ae04e74. Updated Packages:
conda-forge::networkx=2.6
conda-forge::numpy=1.24.3
conda-forge::pandas=2.0.3
conda-forge::python=3.8.19
conda-forge::requests=2.32.3
conda-forge::notebook=7.2.1
conda-forge::nbconvert=7.16.4
Pip Packages:
obonet==1.1.0

You can view the relevant lines here.

  1. Minor Changes in process.ipynb: Small adjustments were made in the process.ipynb notebook to align with the newer version of Networkx. These changes can be seen in the following lines:

Line 390: graph.node[go_id][key].add(gene)\n changed to graph.nodes[go_id][key].add(gene)\n Lines 404 and 409 were similarly adjusted. The specific commit for these changes can be reviewed here.