Merge remote-tracking branch 'origin/add-better-error-messege-edges-g…

…etitem' into add-better-error-messege-edges-getitem

.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/nightly.yml

@@ -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/

.pre-commit-config.yaml

@@ -2,10 +2,6 @@
 # pre-commit install
 
 repos:
-  - repo: https://github.com/adamchainz/blacken-docs
-    rev: 1.16.0
-    hooks:
-      - id: blacken-docs
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v3.1.0
     hooks:

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
 

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))

doc/conf.py

@@ -22,10 +22,10 @@
     "sphinx.ext.todo",
     "sphinx.ext.viewcode",
     "sphinx_gallery.gen_gallery",
-    "nb2plots",
     "texext",
     "numpydoc",
     "matplotlib.sphinxext.plot_directive",
+    "myst_nb",
 ]
 
 # https://github.com/sphinx-gallery/sphinx-gallery
@@ -77,8 +77,9 @@
 # The encoding of source files.
 source_encoding = "utf-8"
 
-# Do not include release announcement template
-exclude_patterns = ["release/release_template.rst"]
+# Items to exclude during source collection, including release announcement
+# template, build outputs, and READMEs (markdown only)
+exclude_patterns = ["release/release_template.rst", "build/*", "README.md"]
 
 # General substitutions.
 project = "NetworkX"
@@ -258,6 +259,9 @@
 def setup(app):
     app.add_css_file("custom.css")
     app.add_js_file("copybutton.js")
+    # Workaround to prevent duplicate file warnings from sphinx w/ myst-nb.
+    # See executablebooks/MyST-NB#363
+    app.registry.source_suffix.pop(".ipynb")
 
 
 # Monkeypatch numpydoc to show "Backends" section

doc/developer/deprecations.rst

@@ -70,3 +70,6 @@ Version 3.5
   to return a dict. See #6527
 * Change ``shortest_path`` in ``algorithms/shortest_path/generic.py``
   to return a iterator. See #6527
+* Remove ``total_spanning_tree_weight`` from ``linalg/laplacianmatrix.py``
+* Remove ``create`` keyword argument from ``nonisomorphic_trees`` in 
+  ``generators/nonisomorphic_trees``.

doc/reference/algorithms/assortativity.rst

@@ -6,6 +6,8 @@ Assortativity
 .. autosummary::
    :toctree: generated/
 
+.. _networkx.algorithms.assortativity.correlation:
+
 Assortativity
 -------------
 .. autosummary::
@@ -16,13 +18,16 @@ Assortativity
    numeric_assortativity_coefficient
    degree_pearson_correlation_coefficient
 
+.. _networkx.algorithms.assortativity.neighbor_degree:
+
 Average neighbor degree
 -----------------------
 .. autosummary::
    :toctree: generated/
 
    average_neighbor_degree
 
+.. _networkx.algorithms.assortativity.connectivity:
 
 Average degree connectivity
 ---------------------------
@@ -31,6 +36,7 @@ Average degree connectivity
 
    average_degree_connectivity
 
+.. _networkx.algorithms.assortativity.mixing:
 
 Mixing
 ------
@@ -43,6 +49,8 @@ Mixing
    degree_mixing_dict
    mixing_dict
 
+.. _networkx.algorithms.assortativity.pairs:
+
 Pairs
 -----
 .. autosummary::