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Merge pull request #15 from pablormier/dev
post r1 improvements 1.0.0.dev5
2 parents dbac128 + a36c5db commit 6644014

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‎.github/workflows/clean-pages.yml‎

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name: Cleanup gh-pages (One-Time)
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on:
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workflow_dispatch:
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jobs:
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cleanup-gh-pages:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout gh-pages branch
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uses: actions/checkout@v4
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with:
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ref: gh-pages
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- name: Remove all files
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run: |
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git rm -rf .
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git commit -m "Cleanup gh-pages branch for new structure" || echo "Nothing to commit"
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git push origin gh-pages
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‎.github/workflows/deploy-docs.yml‎

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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Setup Graphviz
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uses: ts-graphviz/setup-graphviz@v2
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- name: Cache Poetry packages
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uses: actions/cache@v3
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with:
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path: ~/.cache/pypoetry
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key: ${{ runner.os }}-poetry-${{ hashFiles('**/poetry.lock') }}
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- name: Cache pip packages
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uses: actions/cache@v3
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ hashFiles('**/poetry.lock') }}
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- name: Install Dependencies
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run: |
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set -e
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pip install poetry
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poetry install --with dev,docs
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- name: Build Docs with sphinx-multiversion
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- name: Build Docs
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run: |
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# Create a temporary directory
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TEMP_DIR=$(mktemp -d)
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chmod 777 $TEMP_DIR
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echo "TEMP_DIR=$TEMP_DIR" >> $GITHUB_ENV
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echo "Temporary directory is $TEMP_DIR"
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poetry run sphinx-multiversion docs $TEMP_DIR
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touch $TEMP_DIR/.nojekyll
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echo '<meta http-equiv="refresh" content="0; URL='https://saezlab.github.io/corneto/main'" />' > $TEMP_DIR/index.html
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- name: Deploy to GitHub Pages
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set -e
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poetry run sphinx-build -b html docs docs/_build/html
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- name: Determine doc version
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id: set_version
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run: |
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set -e
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case "${GITHUB_REF}" in
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refs/tags/*)
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version="${GITHUB_REF#refs/tags/}"
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;;
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refs/heads/main)
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version="main"
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;;
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refs/heads/dev)
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version="dev"
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;;
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*)
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echo "Unexpected branch/ref: ${GITHUB_REF}"
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version="dev"
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;;
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esac
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echo "doc_version=${version}" >> $GITHUB_OUTPUT
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- name: Generate switcher.json
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run: |
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git config --local user.email "action@github.com"
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git config --local user.name "GitHub Action"
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# Now checkout to gh-pages
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git fetch origin gh-pages
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git checkout gh-pages || git checkout --orphan gh-pages
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# Clean existing files for the branch and copy new ones
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echo "Removing current folder content: $BRANCH_NAME"
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rm -rf "./$BRANCH_NAME"
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cp -r "$TEMP_DIR/$BRANCH_NAME" "$BRANCH_NAME"
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# Adding changes to git
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git add .
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git commit -m "Update docs for branch $BRANCH_NAME" --allow-empty
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git push -u origin gh-pages
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
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set -e
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poetry run python docs/generate_switcher.py
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- name: Create root redirect to latest
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run: |
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set -e
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mkdir -p temp_root
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cp docs/switcher.json temp_root/switcher.json
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touch temp_root/.nojekyll
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cat > temp_root/index.html << EOF
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<!DOCTYPE html>
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<html>
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<head>
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<meta charset="utf-8">
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<title>Redirecting to main documentation</title>
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<meta http-equiv="refresh" content="0; URL=./main/">
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<link rel="canonical" href="./main/">
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</head>
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<body>
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<p>Redirecting to <a href="./main/">main documentation</a>...</p>
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</body>
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</html>
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EOF
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- name: Deploy content to root
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uses: peaceiris/actions-gh-pages@v4
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./temp_root
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destination_dir: ./
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keep_files: true
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- name: Deploy versioned docs
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uses: peaceiris/actions-gh-pages@v4
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./docs/_build/html
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destination_dir: ${{ steps.set_version.outputs.doc_version }}
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keep_files: true
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- name: Deploy latest docs to root
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if: ${{ steps.set_version.outputs.doc_version == 'latest' }}
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uses: peaceiris/actions-gh-pages@v4
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./docs/_build/html
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destination_dir: ./
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keep_files: true
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- name: Clean up temporary files
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run: rm -rf temp_root

‎.gitignore‎

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[_]*.ipynb
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my_graph.pkl.gz
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*.DS_Store
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tests/_notebooks
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# Ignore any "generated" folder inside docs
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docs/**/generated/

‎corneto/__init__.py‎

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import logging
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import sys
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import warnings
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from corneto import _plotting as pl
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from corneto._constants import *
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from corneto._graph import Attr, Attributes, EdgeType, Graph
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from corneto._util import info
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from corneto._data import Data, Feature, Sample
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from corneto._util import info, suppress_output
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from corneto.backend import DEFAULT_BACKEND, DEFAULT_SOLVER, available_backends
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# from corneto.backend import DEFAULT_BACKEND as K # deprecate
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from corneto.backend._base import HammingLoss as hamming_loss
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from corneto.backend._base import Indicator, NonZeroIndicator
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#from corneto._graph import Attr, Attributes, EdgeType, Graph
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from corneto.graph import Attr, Attributes, EdgeType, Graph
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from corneto.io import load_graph_from_sif
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# from corneto._core import GReNet as Graph
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from corneto.methods import (
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create_flow_graph,
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)
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from corneto.utils import Attr, Attributes
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logger = logging.getLogger(__name__)
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logger.addHandler(logging.NullHandler())
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def get_version():
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import os
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__all__ = [
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"DEFAULT_BACKEND",
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"Attr",
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"EdgeType",
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"Attributes",
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"Data",
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"EdgeType",
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"Feature",
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"Graph",
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"info",
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"DEFAULT_BACKEND",
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"available_backends",
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"K",
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"Sample",
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"available_backends",
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"info",
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"ops",
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"suppress_output",
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]
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import_sif = Graph.from_sif
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#import_sif = Graph.from_sif
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import_sif = load_graph_from_sif
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try:
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# Python 3.8 and newer

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