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4 changes: 2 additions & 2 deletions .github/workflows/build.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -15,10 +15,10 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python 3.10
- name: Set up Python 3.11
uses: actions/setup-python@v5
with:
python-version: "3.10"
python-version: "3.11"
cache: "pip"
cache-dependency-path: "**/pyproject.toml"
- name: Install build dependencies
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14 changes: 5 additions & 9 deletions .github/workflows/test.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -23,22 +23,18 @@ jobs:
fail-fast: false
matrix:
include:
- os: ubuntu-latest
python: "3.10"
- os: ubuntu-latest
python: "3.11"
- os: ubuntu-latest
python: "3.12"
- os: ubuntu-latest
python: "3.12"
python: "3.13"
- os: ubuntu-latest
python: "3.14"
- os: ubuntu-latest
python: "3.14"
pip-flags: "--pre"
name: PRE-RELEASE DEPENDENCIES
# - os: ubuntu-latest
# python: "3.13"
# - os: ubuntu-latest
# python: "3.13"
# pip-flags: "--pre"
# name: PRE-RELEASE DEPENDENCIES

name: ${{ matrix.name }} Python ${{ matrix.python }}

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6 changes: 3 additions & 3 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -11,19 +11,19 @@ repos:
hooks:
- id: prettier
- repo: https://github.com/tox-dev/pyproject-fmt
rev: "2.2.3"
rev: "v2.16.1"
hooks:
- id: pyproject-fmt
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.6.5
rev: v0.15.0
hooks:
- id: ruff
types_or: [python, pyi, jupyter]
args: [--fix, --exit-non-zero-on-fix]
- id: ruff-format
types_or: [python, pyi, jupyter]
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.6.0
rev: v6.0.0
hooks:
- id: detect-private-key
- id: check-ast
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2 changes: 1 addition & 1 deletion .python-version
Original file line number Diff line number Diff line change
@@ -1 +1 @@
3.12
Python 3.11.13
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7 changes: 6 additions & 1 deletion .vscode/settings.json
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,12 @@
"notebook.cellFocusIndicator": "gutter",
"notebook.lineNumbers": "on",
"files.watcherExclude": {
"**/.venv/**": true
"**/.venv/**": true,
"**/__pycache__/**": true,
"**/.pytest_cache/**": true,
"**/.ruffle_cache/**": true,
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Copilot AI Mar 11, 2026

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files.watcherExclude contains "**/.ruffle_cache/**", but Ruff’s cache directory is .ruff_cache. This typo means the cache won’t be excluded from the file watcher.

Suggested change
"**/.ruffle_cache/**": true,
"**/.ruff_cache/**": true,

Copilot uses AI. Check for mistakes.
"**/data/**": true,
"**/dist/**": true
},
"githubPullRequests.ignoredPullRequestBranches": ["main"]
}
69 changes: 62 additions & 7 deletions docs/source/example.ipynb
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python-igraph is deprecated, should now use igraph

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igraph is a dev dependency. I resolve the deprecation by adding "scanpy[leiden]".

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