Update .pre-commit-config.yaml and Implement Suggestions

.flake8

@@ -14,3 +14,5 @@ per-file-ignores =
     __init__.py:F401,F403,
     _nx_cugraph/__init__.py:E501,
     nx_cugraph/__init__.py:E402,F401,F403,
+    benchmarks/nx-cugraph/pytest-based/create_results_summary_page.py:E501,W605,
+    docs/nx-cugraph/source/conf.py:E501

.github/workflows/pr.yaml

@@ -13,47 +13,13 @@ jobs:
   pr-builder:
     needs:
       - checks
-      - docs-build
-      - wheel-build-nx-cugraph
-      - wheel-tests-nx-cugraph
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/[email protected]
+    uses: rapidsai/shared-workflows/.github/workflows/[email protected]
+    if: always()
+    with:
+      needs: ${{ toJSON(needs) }}
   checks:
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/checks.yaml@python-3.12
+    uses: rapidsai/shared-workflows/.github/workflows/checks.yaml@branch-24.12
     with:
       enable_check_generated_files: false
-  conda-notebook-tests:
-    needs: conda-python-build
-    secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/[email protected]
-    with:
-      build_type: pull-request
-      node_type: "gpu-v100-latest-1"
-      arch: "amd64"
-      container_image: "rapidsai/ci-conda:cuda11.8.0-ubuntu22.04-py3.10"
-      run_script: "ci/test_notebooks.sh"
-  docs-build:
-    needs: conda-python-build
-    secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/[email protected]
-    with:
-      build_type: pull-request
-      node_type: "gpu-v100-latest-1"
-      arch: "amd64"
-      container_image: "rapidsai/ci-conda:cuda11.8.0-ubuntu22.04-py3.10"
-      run_script: "ci/build_docs.sh"
-  wheel-build-nx-cugraph:
-    needs: wheel-tests-pylibcugraph
-    secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/[email protected]
-    with:
-      build_type: pull-request
-      script: ci/build_wheel_nx-cugraph.sh
-  wheel-tests-nx-cugraph:
-    needs: wheel-build-nx-cugraph
-    secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/[email protected]
-    with:
-      build_type: pull-request
-      script: ci/test_wheel_nx-cugraph.sh

.pre-commit-config.yaml

@@ -1,54 +1,91 @@
 ## https://pre-commit.com/
 #
 # Before first use: `pre-commit install`
-# To run: `pre-commit run --all-files`
+# To run: `make lint`
+# To update: `make lint-update`
+#  - &flake8_dependencies below needs updated manually
 exclude: '^thirdparty'
+fail_fast: false
+default_language_version:
+    python: python3
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-ast
+      - id: check-toml
+      - id: check-yaml
       - id: debug-statements
       - id: end-of-file-fixer
+        exclude_types: [svg]
       - id: mixed-line-ending
+      - id: no-commit-to-branch
+        args: [-p, "^branch-2....$"]
       - id: trailing-whitespace
   - repo: https://github.com/PyCQA/flake8
     rev: 7.1.1
     hooks:
       - id: flake8
-        args: ["--config=.flake8"]
-        files: nx_cugraph.*$
-        types: [file]
-        types_or: [python] # TODO: Enable [python, cython]
-        additional_dependencies: ["flake8-force"]
+        args: ["--config=.flake8"] # uses config
+        additional_dependencies: &flake8_dependencies
+          # These versions need updated manually
+          - flake8==7.1.1
+          - flake8-bugbear==24.8.19
+          - flake8-simplify==0.21.0
   - repo: https://github.com/asottile/yesqa
     rev: v1.3.0
     hooks:
       - id: yesqa
-        additional_dependencies:
-          - flake8==7.1.1
-  - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v16.0.6
+        additional_dependencies: *flake8_dependencies
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.19
+    hooks:
+      - id: validate-pyproject
+        name: Validate pyproject.toml
+  - repo: https://github.com/PyCQA/autoflake
+    rev: v2.3.1
+    hooks:
+      - id: autoflake
+        args: [--in-place]
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
     hooks:
-      - id: clang-format
-        types_or: [c, c++, cuda]
-        args: ["-fallback-style=none", "-style=file", "-i"]
+      - id: isort
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.17.0
+    hooks:
+      - id: pyupgrade
+        args: [--py310-plus]
+  - repo: https://github.com/psf/black
+    rev: 24.8.0
+    hooks:
+      - id: black
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        types_or: [python, rst, markdown]
+        additional_dependencies: [tomli]
+        files: ^(nx_cugraph|docs)/
+        args: ["-L thirdparty,coo,COO,numer"]
   - repo: https://github.com/rapidsai/pre-commit-hooks
     rev: v0.4.0
     hooks:
       - id: verify-copyright
         files: |
           (?x)
-              [.](cmake|cpp|cu|cuh|h|hpp|sh|pxd|py|pyx)$|
-              CMakeLists[.]txt$|
-              CMakeLists_standalone[.]txt$|
+              [.](sh|py)$|
               [.]flake8[.]cython$|
               meta[.]yaml$|
               setup[.]cfg$
       - id: verify-alpha-spec
         args: ["--fix"]
   - repo: https://github.com/rapidsai/dependency-file-generator
-    rev: v1.13.11
+    rev: v1.16.0
     hooks:
         - id: rapids-dependency-file-generator
           args: ["--clean"]
@@ -61,7 +98,7 @@ repos:
         types: [python]
         language: python
         pass_filenames: false
-        additional_dependencies: ["networkx>=3.3"]
+        additional_dependencies: ["networkx>=3.4"]
   - repo: local
     hooks:
       - id: nx-cugraph-readme-update

Makefile

@@ -2,15 +2,7 @@
 SHELL= /bin/bash
 
 .PHONY: all
-all: plugin-info lint readme
-
-.PHONY: lint
-lint:
-	git ls-files | xargs pre-commit run --config lint.yaml --files || true
-
-.PHONY: lint-update
-lint-update:
-	pre-commit autoupdate --config lint.yaml
+all: plugin-info readme
 
 .PHONY: plugin-info
 plugin-info:

benchmarks/nx-cugraph/pytest-based/bench_algos.py

@@ -11,12 +11,11 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import random
-
 import networkx as nx
 import pandas as pd
 import pytest
 from cugraph import datasets
+
 import nx_cugraph as nxcg
 
 # Attempt to import the NetworkX dispatching module, which is only needed when

benchmarks/nx-cugraph/pytest-based/create_results_summary_page.py

@@ -12,17 +12,17 @@
 # limitations under the License.
 
 
-import re
-import pathlib
 import json
+import pathlib
 import platform
-import psutil
+import re
 import socket
 import subprocess
 
+import psutil
+
 
 def get_formatted_time_value(time):
-    res = ""
     if time < 1:
         if time < 0.001:
             units = "us"
@@ -40,7 +40,8 @@ def get_all_benchmark_info():
     # Populate benchmarks dir from .json files
     for json_file in logs_dir.glob("*.json"):
         try:
-            data = json.loads(open(json_file).read())
+            with open(json_file) as file:
+                data = json.loads(file.read())
         except json.decoder.JSONDecodeError:
             continue
 
@@ -155,8 +156,8 @@ def get_system_info():
 if __name__ == "__main__":
     logs_dir = pathlib.Path("logs")
 
-    dataset_patt = re.compile(".*ds=([\w-]+).*")
-    backend_patt = re.compile(".*backend=(\w+).*")
+    dataset_patt = re.compile(r".*ds=([\w-]+).*")
+    backend_patt = re.compile(r".*backend=(\w+).*")
     k_patt = re.compile(".*k=(10*).*")
 
     # Organize all benchmark runs by the following hierarchy: algo -> backend -> dataset
@@ -266,7 +267,7 @@ def get_system_info():
                         f"      <td>{nx_formatted} / {cg_formatted}<br>{speedup}<br>{runtime_delta}</td>"
                     )
                 else:
-                    print(f"      <td></td>")
+                    print("      <td></td>")
 
         # If a comparison between cugraph and NX cannot be made, output empty cells
         # for each dataset

benchmarks/nx-cugraph/pytest-based/get_graph_bench_dataset.py

@@ -18,14 +18,14 @@
 
 Positional Arguments:
     1) dataset name (e.g. 'email_Eu_core', 'cit-patents')
-       available datasets can be found here: `python/cugraph/cugraph/datasets/__init__.py`
+       available datasets can be found here:
+        - `python/cugraph/cugraph/datasets/__init__.py`
 """
 
 import sys
 
 import cugraph.datasets as cgds
 
-
 if __name__ == "__main__":
     # download and store dataset (csv) by using the Datasets API
     dataset = sys.argv[1].replace("-", "_")

dependencies.yaml

@@ -36,15 +36,15 @@ files:
       - test_notebook
   py_build_nx_cugraph:
     output: pyproject
-    pyproject_dir: python/nx-cugraph
+    pyproject_dir: .
     extras:
       table: build-system
     includes:
       - python_build_rapids
       - python_build_wheel
   py_run_nx_cugraph:
     output: pyproject
-    pyproject_dir: python/nx-cugraph
+    pyproject_dir: .
     extras:
       table: project
     includes:
@@ -53,7 +53,7 @@ files:
       - python_run_nx_cugraph
   py_test_nx_cugraph:
     output: pyproject
-    pyproject_dir: python/nx-cugraph
+    pyproject_dir: .
     extras:
       table: project.optional-dependencies
       key: test