Update to use python-graphblas instead of grblas. (#2)

* Update to use `python-graphblas` instead of `grblas`.

Also, add git pre-commit hooks

* New commit (trying to make coveralls happy)

* coveralls debug

* Don't upload to coveralls atm.  why broke?!

Author: eriknw

.github/workflows/test.yml

@@ -30,7 +30,7 @@ jobs:
           activate-environment: testing
       - name: Install dependencies
         run: |
-          conda install -c conda-forge grblas networkx scipy pytest coverage black flake8 coveralls
+          conda install -c conda-forge python-graphblas networkx scipy pytest coverage black flake8 coveralls
           pip install -e .
       - name: Style checks
         run: |
@@ -46,26 +46,26 @@ jobs:
           COVERALLS_PARALLEL: true
         run: |
           coverage report --show-missing
-          coveralls --service=github
+          # coveralls --service=github  # Broken :(
 
-  finish:
-    needs: test
-    if: always()
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
-    steps:
-      - name: Create env
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: "3.10"
-          activate-environment: finishing
-      - name: Update env
-        run: conda install -c conda-forge coveralls
-      - name: Coveralls finished
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          coveralls --finish
+#  finish:
+#    needs: test
+#    if: always()
+#    runs-on: ubuntu-latest
+#    defaults:
+#      run:
+#        shell: bash -l {0}
+#    steps:
+#      - name: Create env
+#        uses: conda-incubator/setup-miniconda@v2
+#        with:
+#          auto-update-conda: true
+#          python-version: "3.10"
+#          activate-environment: finishing
+#      - name: Update env
+#        run: conda install -c conda-forge coveralls
+#      - name: Coveralls finished
+#        env:
+#          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+#        run: |
+#          coveralls --finish

.pre-commit-config.yaml

@@ -0,0 +1,56 @@
+# https://pre-commit.com/
+#
+# Before first use: `pre-commit install`
+# To run: `pre-commit run --all-files`
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.2.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+  - repo: https://github.com/myint/autoflake
+    rev: v1.4
+    hooks:
+      - id: autoflake
+        args: [--in-place]
+  - repo: https://github.com/pycqa/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+        language_version: python3
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.32.0
+    hooks:
+      - id: pyupgrade
+        args: [--py38-plus]
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+        language_version: python3
+        args: [--target-version=py38]
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        additional_dependencies: &flake8_dependencies
+        - flake8==4.0.1
+        - flake8-comprehensions==3.8.0
+        - flake8-bugbear==22.3.23
+  - repo: https://github.com/asottile/yesqa
+    rev: v1.3.0
+    hooks:
+      - id: yesqa
+        additional_dependencies: *flake8_dependencies
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.1.0
+    hooks:
+      - id: codespell
+        types_or: [python, rst, markdown]
+        files: ^(graphblas_algorithms|docs)/
+        # args: ["--ignore-words-list=coo,ba"]
+# Maybe: black-jupyter, blacken-docs, blackdoc mypy, velin

CODE_OF_CONDUCT.md

@@ -36,7 +36,7 @@ This Code of Conduct applies both within project spaces and in public spaces
 when an individual is representing the project or its community.
 
 A working group of community members is committed to promptly addressing any
-reported issues. The working group is made up of Grblas and Metagraph contributors and users.
+reported issues. The working group is made up of Python-graphblas and Metagraph contributors and users.
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported by contacting the working group by e-mail ([email protected]).
 Messages sent to this e-mail address will not be publicly visible but only to

README.md

@@ -1,14 +1,14 @@
 # **GraphBLAS Algorithms**
 
 [![pypi](https://img.shields.io/pypi/v/graphblas-algorithms.svg)](https://pypi.python.org/pypi/graphblas-algorithms/)
-[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://github.com/metagraph-dev/graphblas-algorithms/blob/main/LICENSE)
-[![Tests](https://github.com/metagraph-dev/graphblas-algorithms/workflows/Tests/badge.svg?branch=main)](https://github.com/metagraph-dev/graphblas-algorithms/actions)
-[![Coverage](https://coveralls.io/repos/metagraph-dev/graphblas-algorithms/badge.svg?branch=main)](https://coveralls.io/r/metagraph-dev/graphblas-algorithms)
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://github.com/python-graphblas/graphblas-algorithms/blob/main/LICENSE)
+[![Tests](https://github.com/python-graphblas/graphblas-algorithms/workflows/Tests/badge.svg?branch=main)](https://github.com/python-graphblas/graphblas-algorithms/actions)
+[![Coverage](https://coveralls.io/repos/python-graphblas/graphblas-algorithms/badge.svg?branch=main)](https://coveralls.io/r/python-graphblas/graphblas-algorithms)
 [![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 <!--- [![conda-forge](https://img.shields.io/conda/vn/conda-forge/graphblas-algorithms.svg)](https://anaconda.org/conda-forge/graphblas-algorithms) --->
 <!--- [![Docs](https://readthedocs.org/projects/graphblas-algorithms/badge/?version=latest)](https://graphblas-algorithms.readthedocs.io/en/latest/) --->
 
-GraphBLAS algorithms written in Python with [`grblas`](https://github.com/metagraph-dev/grblas).  We are trying to target the NetworkX API algorithms where possible.
+GraphBLAS algorithms written in Python with [Python-graphblas](https://github.com/python-graphblas/python-graphblas).  We are trying to target the NetworkX API algorithms where possible.
 
 ### Installation
 ```

graphblas_algorithms/link_analysis.py

@@ -1,10 +1,10 @@
 from collections import OrderedDict
 from warnings import warn
 
-import grblas as gb
+import graphblas as gb
 import networkx as nx
-from grblas import Vector, binary, unary
-from grblas.semiring import plus_first, plus_times
+from graphblas import Vector, binary, unary
+from graphblas.semiring import plus_first, plus_times
 
 
 def pagerank_core(

graphblas_algorithms/tests/test_pagerank.py

@@ -18,4 +18,4 @@ def test_signatures():
     assert nx_sig == sig
 
 
-from networkx.algorithms.link_analysis.tests.test_pagerank import *  # isort:skip
+from networkx.algorithms.link_analysis.tests.test_pagerank import *  # noqa isort:skip

requirements.txt

@@ -1 +1 @@
-grblas >=2022.3.1
+python-graphblas >=2022.4.1

scripts/bench_pagerank.py

@@ -158,7 +158,7 @@ def main(filename, backend, time, n, verify, alpha, tol, _get_result=False):
         print()
         for k1, v1 in results.items():
             print("%5s" % k1, end="")
-            for k2, v2 in results.items():
+            for v2 in results.values():
                 print("%9.2g" % np.abs(v1 - v2).sum(), end="")
             print()
         return
@@ -172,7 +172,7 @@ def main(filename, backend, time, n, verify, alpha, tol, _get_result=False):
 
     if backend == "graphblas":
         import pandas as pd
-        from grblas import Matrix
+        from graphblas import Matrix
 
         from graphblas_algorithms.link_analysis import pagerank_core as pagerank
 
@@ -225,7 +225,7 @@ def main(filename, backend, time, n, verify, alpha, tol, _get_result=False):
     print("Load time:", stime(stop - start))
     timer = timeit.Timer(
         "pagerank(G, alpha=alpha, tol=tol)",
-        globals=dict(pagerank=pagerank, G=G, alpha=alpha, tol=tol),
+        globals={"pagerank": pagerank, "G": G, "alpha": alpha, "tol": tol},
     )
     first_time = timer.timeit(1)
     if time == 0:

setup.cfg

@@ -6,6 +6,7 @@ testpaths = graphblas_algorithms/tests
 
 [flake8]
 max-line-length = 100
+inline-quotes = "
 exclude =
     versioneer.py,
     graphblas_algorithms/tests/,

setup.py

@@ -2,6 +2,11 @@
 
 import versioneer
 
+extras_require = {
+    "test": ["pytest", "scipy"],
+}
+extras_require["complete"] = sorted({v for req in extras_require.values() for v in req})
+
 with open("README.md") as f:
     long_description = f.read()
 
@@ -14,11 +19,11 @@
     long_description_content_type="text/markdown",
     author="Jim Kitchen and Erik Welch",
     author_email="[email protected],[email protected]",
-    url="https://github.com/metagraph-dev/graphblas-algorithms",
+    url="https://github.com/python-graphblas/graphblas-algorithms",
     packages=find_packages(),
     python_requires=">=3.8",
-    install_requires=["grblas >=2022.4.0", "networkx"],
-    tests_require=["pytest", "scipy"],
+    install_requires=["python-graphblas >=2022.4.1", "networkx"],
+    extras_require=extras_require,
     include_package_data=True,
     license="Apache License 2.0",
     keywords=[