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Merged
eriknw merged 2 commits intopython-graphblas:mainfromeriknw:blacken_docs_sort_of
May 19, 2023
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7 changes: 5 additions & 2 deletions.github/workflows/test_and_build.yml
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Expand Up@@ -17,6 +17,10 @@ on:
branches:
- main

concurrency:
group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
cancel-in-progress: true

jobs:
rngs:
# To achieve consistent coverage, we need a little bit of correlated collaboration.
Expand DownExpand Up@@ -248,8 +252,7 @@ jobs:
fi
echo "versions: np${npver} sp${spver} pd${pdver} ak${akver} nx${nxver} numba${numbaver} yaml${yamlver} sparse${sparsever} psgver${psgver}"

# TODO: remove `-c numba` when numba 0.57 is properly released on conda-forge
$(command -v mamba || command -v conda) install -c numba packaging pytest coverage coveralls=3.3.1 pytest-randomly cffi donfig tomli \
$(command -v mamba || command -v conda) install packaging pytest coverage coveralls=3.3.1 pytest-randomly cffi donfig tomli \
pyyaml${yamlver} ${sparse} pandas${pdver} scipy${spver} numpy${npver} ${awkward} \
networkx${nxver} ${numba} ${fmm} ${psg} \
${{ matrix.slowtask == 'pytest_bizarro' && 'black' || '' }} \
Expand Down
28 changes: 20 additions & 8 deletions.pre-commit-config.yaml
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Expand Up@@ -5,10 +5,12 @@
# To update: `pre-commit autoupdate`
# - &flake8_dependencies below needs updated manually
ci:
# See: https://pre-commit.ci/#configuration
autofix_prs: false
autoupdate_schedule: monthly
skip: [pylint, no-commit-to-branch]
# See: https://pre-commit.ci/#configuration
autofix_prs: false
autoupdate_schedule: monthly
autoupdate_commit_msg: "chore: update pre-commit hooks"
autofix_commit_msg: "style: pre-commit fixes"
skip: [pylint, no-commit-to-branch]
fail_fast: true
default_language_version:
python: python3
Expand All@@ -17,15 +19,21 @@ repos:
rev: v4.4.0
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: trailing-whitespace
- id: name-tests-test
args: ["--pytest-test-first"]
- repo: https://github.com/abravalheri/validate-pyproject
rev: v0.12.2
rev: v0.13
hooks:
- id: validate-pyproject
name: Validate pyproject.toml
Expand DownExpand Up@@ -58,7 +66,7 @@ repos:
- id: black
- id: black-jupyter
- repo: https://github.com/charliermarsh/ruff-pre-commit
rev: v0.0.267
rev: v0.0.269
hooks:
- id: ruff
args: [--fix-only, --show-fixes]
Expand DownExpand Up@@ -86,7 +94,7 @@ repos:
additional_dependencies: [tomli]
files: ^(graphblas|docs)/
- repo: https://github.com/charliermarsh/ruff-pre-commit
rev: v0.0.267
rev: v0.0.269
hooks:
- id: ruff
- repo: https://github.com/sphinx-contrib/sphinx-lint
Expand All@@ -101,6 +109,10 @@ repos:
hooks:
- id: pyroma
args: [-n, "10", .]
- repo: https://github.com/shellcheck-py/shellcheck-py
rev: "v0.9.0.2"
hooks:
- id: shellcheck
- repo: local
hooks:
# Add `--hook-stage manual` to pre-commit command to run (very slow)
Expand DownExpand Up@@ -137,4 +149,4 @@ repos:
# hooks:
# - id: bandit
#
# blacken-docs, blackdoc mypy, pydocstringformatter, velin, flynt, yamllint
# blacken-docs, blackdocprettier,mypy, pydocstringformatter, velin, flynt, yamllint
7 changes: 4 additions & 3 deletionsREADME.md
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Expand Up@@ -176,8 +176,9 @@ use as well as the blocking/non-blocking mode. If the context is not initialized
be performed automatically.
```python
import graphblas as gb

# Context initialization must happen before any other imports
gb.init('suitesparse', blocking=True)
gb.init("suitesparse", blocking=True)

# Now we can import other items from graphblas
from graphblas import binary, semiring
Expand All@@ -195,7 +196,7 @@ def force_odd_func(x):
return x + 1
return x

unary.register_new('force_odd', force_odd_func)
unary.register_new("force_odd", force_odd_func)

v = Vector.from_coo([0, 1, 3], [1, 2, 3])
w = v.apply(unary.force_odd).new()
Expand All@@ -210,7 +211,7 @@ import graphblas as gb

# scipy.sparse matrices
A = gb.io.from_scipy_sparse(m)
m = gb.io.to_scipy_sparse(m, format='csr')
m = gb.io.to_scipy_sparse(m, format="csr")

# networkx graphs
A = gb.io.from_networkx(g)
Expand Down
31 changes: 10 additions & 21 deletionsdocs/getting_started/primer.rst
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Expand Up@@ -89,26 +89,13 @@ makes for faster graph algorithms.

# networkx-style storage of an undirected graph
G = {
0: {1: {'weight': 5.6},
2: {'weight': 2.3},
3: {'weight': 4.6}},
1: {0: {'weight': 5.6},
2: {'weight': 1.9},
3: {'weight': 6.2}},
2: {0: {'weight': 2.3},
1: {'weight': 1.9},
3: {'weight': 3.0}},
3: {0: {'weight': 4.6},
1: {'weight': 6.2},
2: {'weight': 3.0},
4: {'weight': 1.4}},
4: {3: {'weight': 1.4},
5: {'weight': 4.4},
6: {'weight': 1.0}},
5: {4: {'weight': 4.4},
6: {'weight': 2.8}},
6: {4: {'weight': 1.0},
5: {'weight': 2.8}}
0: {1: {"weight": 5.6}, 2: {"weight": 2.3}, 3: {"weight": 4.6}},
1: {0: {"weight": 5.6}, 2: {"weight": 1.9}, 3: {"weight": 6.2}},
2: {0: {"weight": 2.3}, 1: {"weight": 1.9}, 3: {"weight": 3.0}},
3: {0: {"weight": 4.6}, 1: {"weight": 6.2}, 2: {"weight": 3.0}, 4: {"weight": 1.4}},
4: {3: {"weight": 1.4}, 5: {"weight": 4.4}, 6: {"weight": 1.0}},
5: {4: {"weight": 4.4}, 6: {"weight": 2.8}},
6: {4: {"weight": 1.0}, 5: {"weight": 2.8}},
}

An alternative way to store a graph is as an adjacency matrix. Each node becomes both a row
Expand DownExpand Up@@ -240,7 +227,9 @@ node 0.
[0, 0, 1, 1, 2],
[1, 2, 2, 3, 3],
[2.0, 5.0, 1.5, 4.25, 0.5],
nrows=4, ncols=4)
nrows=4,
ncols=4
)
v = Vector.from_coo([start_node], [0.0], size=4)

# Compute SSSP
Expand Down
3 changes: 2 additions & 1 deletiondocs/user_guide/init.rst
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Expand Up@@ -8,8 +8,9 @@ GraphBLAS must be initialized before it can be used. This is done with the
.. code-block:: python

import graphblas as gb

# Context initialization must happen before any other imports
gb.init('suitesparse', blocking=False)
gb.init("suitesparse", blocking=False)

# Now we can import other items from graphblas
from graphblas import binary, semiring
Expand Down
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