adding tree broadcast algorithm

.circleci/config.yml

@@ -44,6 +44,8 @@ jobs:
             pip install git+https://github.com/rapidsai/cugraph.git#subdirectory=python/nx-cugraph --no-deps
             # Development version of GraphBLAS backend
             pip install git+https://github.com/python-graphblas/graphblas-algorithms.git@main --no-deps
+            # Development version of nx-parallel backend
+            pip install git+https://github.com/networkx/nx-parallel.git@main --no-deps
             pip list
 
       - save_cache:

.git-blame-ignore-revs

@@ -12,3 +12,4 @@ be23fa0e422b51f4526828cb19b8105c89e5dcbb
 5c0b11afb4c0882a070d522ef3fa41482ba935d3
 5fcf01b9a43a097c4f579486023d1279b2b88619
 7297ae8a37dd3356b64d383cb0c55735a6364bcc
+3c0f096f66ab352cfaf8dbe2d5fc5731cbbc4338

.github/dependabot.yml

@@ -4,6 +4,10 @@ updates:
     directory: "/"
     schedule:
       interval: "monthly"
+    groups:
+      actions:
+        patterns:
+          - "*"
     labels:
       - "type: Maintenance"
   - package-ecosystem: "pip"

.github/workflows/benchmark.yml

@@ -0,0 +1,117 @@
+### Inspired from https://github.com/scikit-image/scikit-image/blob/main/.github/workflows/benchmarks.yml
+
+name: Benchmark PR
+on:
+  pull_request:
+    types: [labeled, synchronize]
+
+jobs:
+  ## This code below is to make sure a new commit on a PR with the label
+  ## retriggers the benchmark, otherwise the label needs to be removed and
+  ## applied again to run the benchmark.
+  check:
+    runs-on: ubuntu-latest
+    outputs:
+      result: ${{ steps.check.outputs.result }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/github-script@v7
+        name: Check for benchmark label and new commit
+        id: check
+        with:
+          script: |
+            const { owner, repo, number: pull_number } = context.issue;
+
+            // Check for label
+            const { data: pullRequest } = await github.rest.pulls.get({ owner, repo, pull_number });
+            if (!pullRequest.labels.some(({ name }) => name === 'run:benchmark')) {
+              return false;
+            }
+
+            // Check for repo name and organization name
+            const { data: repository } = await github.rest.repos.get({ owner, repo });
+            return repository.name === 'networkx' && repository.owner.login === 'networkx';
+  benchmark:
+    needs: check
+    if: ${{ needs.check.outputs.result == 'true' }}
+    # if: contains(github.event.pull_request.labels.*.name, 'run:benchmark') || ${{ github.event.label.name == 'run:benchmark' }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Setup some dependencies
+        shell: bash -l {0}
+        run: |
+          sudo apt-get update -y && sudo apt-get install -y ccache
+          # Make gcc/gxx symlinks first in path
+          sudo /usr/sbin/update-ccache-symlinks
+          echo "/usr/lib/ccache" >> $GITHUB_PATH
+
+      - name: "Prepare ccache"
+        id: prepare-ccache
+        shell: bash -l {0}
+        run: |
+          echo "key=benchmark-$RUNNER_OS" >> $GITHUB_OUTPUT
+          echo "timestamp=$(date +%Y%m%d-%H%M%S)" >> $GITHUB_OUTPUT
+          ccache -p
+          ccache -z
+
+      - name: "Restore ccache"
+        uses: actions/cache@v3
+        with:
+          path: .ccache
+          key: ccache-${{ secrets.CACHE_VERSION }}-${{ steps.prepare-ccache.outputs.key }}-${{ steps.prepare-ccache.outputs.timestamp }}
+          restore-keys: |
+            ccache-${{ secrets.CACHE_VERSION }}-${{ steps.prepare-ccache.outputs.key }}-
+
+      - name: Install packages
+        run: |
+          pip install --upgrade pip
+          pip install -r requirements/default.txt
+          pip install .
+          pip list
+
+      - name: Run benchmarks
+        shell: bash -l {0}
+        id: benchmark
+        env:
+          ASV_FACTOR: 1.5
+          ASV_SKIP_SLOW: 1
+        run: |
+          set -x
+          python -m pip install asv virtualenv packaging
+          cd benchmarks/
+
+          # ID this runner
+          python -m asv machine --yes --conf asv.conf.json
+
+          echo "Baseline:  ${{ github.event.pull_request.base.sha }} (${{ github.event.pull_request.base.label }})"
+
+          echo "Contender: ${GITHUB_SHA} (${{ github.event.pull_request.head.label }})"
+
+          # Run benchmarks for current commit against base
+          ASV_OPTIONS="--split --show-stderr --factor $ASV_FACTOR --conf asv.conf.json"
+          python -m asv continuous $ASV_OPTIONS ${{ github.event.pull_request.base.sha }} ${GITHUB_SHA} \
+              | sed "/Traceback \|failed$\|PERFORMANCE DECREASED/ s/^/::error::/" \
+              | tee benchmarks.log
+
+          # Report and export results for subsequent steps
+          if grep "Traceback \|failed\|PERFORMANCE DECREASED" benchmarks.log > /dev/null ; then
+             exit 1
+          fi
+
+      - name: "Check ccache performance"
+        shell: bash -l {0}
+        run: ccache -s
+        if: always()
+
+      - uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: asv-benchmark-results-${{ runner.os }}
+          path: benchmarks.log

.github/workflows/coverage.yml

@@ -19,7 +19,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/deploy-docs.yml

@@ -14,7 +14,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
@@ -38,6 +38,8 @@ jobs:
           pip install git+https://github.com/rapidsai/cugraph.git#subdirectory=python/nx-cugraph --no-deps
           # Development version of GraphBLAS backend
           pip install git+https://github.com/python-graphblas/graphblas-algorithms.git@main --no-deps
+          # Development version of nx-parallel backend
+          pip install git+https://github.com/networkx/nx-parallel.git@main --no-deps
           pip list
 
       # To set up a cross-repository deploy key:

.github/workflows/lint.yml

@@ -17,7 +17,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/mypy.yml

@@ -17,7 +17,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/nightly-release-test.yml

@@ -14,7 +14,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/nightly.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: Install Python requirements
@@ -27,7 +27,7 @@ jobs:
       - name: List contents of wheel
         run: python -m zipfile --list dist/networkx-*.whl
       - name: Upload nighlty wheel
-        uses: scientific-python/upload-nightly-action@5fb764c5bce1ac2297084c0f7161b1919f17c74f # 0.2.0
+        uses: scientific-python/upload-nightly-action@b67d7fcc0396e1128a474d1ab2b48aa94680f9fc # 0.5.0
         with:
           anaconda_nightly_upload_token: ${{ secrets.ANACONDA_NIGHTLY }}
           artifacts_path: dist/

.github/workflows/pytest-randomly.yml

@@ -11,7 +11,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
 

.github/workflows/release.yml

@@ -19,7 +19,7 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: "3.11"

.github/workflows/test.yml

@@ -16,7 +16,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -40,7 +40,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -66,7 +66,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -90,7 +90,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -150,7 +150,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 

.pre-commit-config.yaml

@@ -2,26 +2,19 @@
 # pre-commit install
 
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.9.1
-    hooks:
-      - id: black
-  - repo: https://github.com/adamchainz/blacken-docs
-    rev: 1.16.0
-    hooks:
-      - id: blacken-docs
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.3
+    rev: v3.1.0
     hooks:
       - id: prettier
         files: \.(html|md|toml|yml|yaml)
         args: [--prose-wrap=preserve]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.291
+    rev: v0.1.8
     hooks:
       - id: ruff
         args:
           - --fix
+      - id: ruff-format
   - repo: local
     hooks:
       - id: generate_requirements.py

CONTRIBUTING.rst

@@ -78,8 +78,8 @@ Development Workflow
          # Test your installation
          pytest --pyargs networkx
 
-   * Finally, we recommend you use a pre-commit hook, which runs black when
-     you type ``git commit``::
+   * Finally, we recommend you install pre-commit which checks
+     that your code matches formatting guidelines::
 
        pre-commit install
 

LICENSE.txt

@@ -2,7 +2,7 @@ NetworkX is distributed with the 3-clause BSD license.
 
 ::
 
-   Copyright (C) 2004-2023, NetworkX Developers
+   Copyright (C) 2004-2024, NetworkX Developers
    Aric Hagberg <hagberg@lanl.gov>
    Dan Schult <dschult@colgate.edu>
    Pieter Swart <swart@lanl.gov>

README.rst

@@ -67,7 +67,7 @@ License
 
 Released under the 3-Clause BSD license (see `LICENSE.txt`)::
 
-   Copyright (C) 2004-2023 NetworkX Developers
+   Copyright (C) 2004-2024 NetworkX Developers
    Aric Hagberg <hagberg@lanl.gov>
    Dan Schult <dschult@colgate.edu>
    Pieter Swart <swart@lanl.gov>

benchmarks/benchmarks/benchmark_neighbors.py

@@ -0,0 +1,51 @@
+import networkx as nx
+
+
+# NOTE: explicit set construction in benchmarks is required for meaningful
+# comparisons due to change in return type from generator -> set. See gh-7244.
+class NonNeighbors:
+    param_names = ["num_nodes"]
+    params = [10, 100, 1000]
+
+    def setup(self, num_nodes):
+        self.star_graph = nx.star_graph(num_nodes)
+        self.complete_graph = nx.complete_graph(num_nodes)
+        self.path_graph = nx.path_graph(num_nodes)
+
+    def time_star_center(self, num_nodes):
+        set(nx.non_neighbors(self.star_graph, 0))
+
+    def time_star_rim(self, num_nodes):
+        set(nx.non_neighbors(self.star_graph, 5))
+
+    def time_complete(self, num_nodes):
+        set(nx.non_neighbors(self.complete_graph, 0))
+
+    def time_path_first(self, num_nodes):
+        set(nx.non_neighbors(self.path_graph, 0))
+
+    def time_path_last(self, num_nodes):
+        set(nx.non_neighbors(self.path_graph, num_nodes - 1))
+
+    def time_path_center(self, num_nodes):
+        set(nx.non_neighbors(self.path_graph, num_nodes // 2))
+
+
+# NOTE: explicit set construction in benchmarks is required for meaningful
+# comparisons due to change in return type from generator -> set. See gh-7244.
+class CommonNeighbors:
+    param_names = ["num_nodes"]
+    params = [10, 100, 1000]
+
+    def setup(self, num_nodes):
+        self.star_graph = nx.star_graph(num_nodes)
+        self.complete_graph = nx.complete_graph(num_nodes)
+
+    def time_star_center_rim(self, num_nodes):
+        set(nx.common_neighbors(self.star_graph, 0, num_nodes // 2))
+
+    def time_star_rim_rim(self, num_nodes):
+        set(nx.common_neighbors(self.star_graph, 4, 5))
+
+    def time_complete(self, num_nodes):
+        set(nx.common_neighbors(self.complete_graph, 0, num_nodes // 2))