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Support Python 3.13 #15

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Support Python 3.13 #15

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e4840cf
Support python 3.13
Dominic-DallOsto Jul 28, 2025
3586573
Add python 3.13 to tests
Dominic-DallOsto Jul 28, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/auto_test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ["3.9", "3.10", "3.11", "3.12"]
python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
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Copilot AI Feb 27, 2026

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The PR description mentions that "slow tests" could not be fully run. Before merging Python 3.13 support, it's important to verify that the slow tests (marked with the "slow" marker as seen in pyproject.toml line 153) pass with the new numba version. These tests may exercise numba-JIT compiled code paths that could have compatibility issues with the version upgrade from 0.55.2 to 0.61.2. Consider running the full test suite including slow tests, or document any known limitations with Python 3.13 support.

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steps:
- uses: actions/checkout@v3
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4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -62,7 +62,7 @@ description = "Connectome and task-constrained vision models of the fruit fly."
dynamic = ["version"]
name = "flyvis"
readme = "readme.md"
requires-python = ">=3.9,<3.13"
requires-python = ">=3.9,<3.14"
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Copilot AI Feb 27, 2026

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The documentation at docs/docs/install.md line 13 needs to be updated to include Python 3.13 in the list of tested versions. Currently it states "flyvis is tested on Linux for python 3.9, 3.10, 3.11, 3.12" but should be updated to include 3.13 to match the changes in this PR.

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[project.optional-dependencies]
dev = [
Expand Down Expand Up @@ -93,7 +93,7 @@ docs = [
examples = ["jupyter", "tabulate", "tqdm", "ipywidgets"]

pretrained = [
"numba==0.55.2",
"numba==0.61.2",
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Copilot AI Feb 27, 2026

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The main dependencies list includes "numba" without version constraints (line 39), while the pretrained optional dependencies pin numba to version 0.61.2. This could lead to version conflicts when installing the package with the pretrained extra. When a user installs with "pip install flyvis[pretrained]", pip will need to reconcile the unpinned numba in the main dependencies with the pinned version 0.61.2 in the pretrained group. Consider either removing numba from the main dependencies if it's only needed for pretrained functionality, or ensuring the version constraints are compatible across both dependency sets.

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"matplotlib==3.7.1",
"scikit-learn==1.1.1",
Comment on lines 97 to 98
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Copilot AI Feb 27, 2026

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Numba 0.61.2 may have compatibility issues with the pinned versions of other dependencies in the pretrained group. Specifically, matplotlib 3.7.1 (line 97) and scikit-learn 1.1.1 (line 98) are quite old. Numba 0.61.2 was released in late 2024 and may not have been tested with these older library versions. Additionally, numba 0.61.2 requires llvmlite 0.45.x which might conflict with these older dependencies. Consider testing the full pretrained dependency set or upgrading the other pinned versions as well.

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"matplotlib==3.7.1",
"scikit-learn==1.1.1",
"matplotlib==3.9.0",
"scikit-learn==1.4.2",

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"umap-learn==0.5.3",
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