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tests: added py313 #105

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Merged
canergen merged 3 commits into from
Mar 1, 2026
Merged

tests: added py313 #105

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1ed44fa
Updated to py313
ori-kron-wis Nov 6, 2025
693bd68
Updated minimal versions
ori-kron-wis Nov 6, 2025
4be3424
Updated minimal versions
ori-kron-wis Nov 6, 2025
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4 changes: 2 additions & 2 deletions .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,12 +24,12 @@ 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: "3.13"

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

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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -13,8 +13,14 @@ to several million cells on workstations with 128 GB of RAM
and enable more GPU-accelerated
functions.

## Version 0.6

### 0.6.0

## Version 0.5

### 0.5.3

### 0.5.2

#### Fixed
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8 changes: 6 additions & 2 deletions pyproject.toml
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Expand Up @@ -13,7 +13,7 @@ name = "popV"
version = "0.6.0"
description = "Consensus prediction of cell type labels with popV"
readme = "README.md"
requires-python = ">=3.10"
requires-python = ">=3.11"
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Copilot AI Mar 1, 2026

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Raising the minimum supported Python to >=3.11 makes the existing runtime version warning in popv/init.py (it currently checks sys.version_info[:2] != (3, 10) while mentioning Python 3.11) trigger on every supported Python version. Please update/remove that warning (e.g., check for != (3, 11) or format the f-string correctly) so users on supported versions don’t always see a misleading warning.

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Copilot AI Mar 1, 2026

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PR title suggests this is only adding Python 3.13 to the test matrix, but this diff also changes the package’s supported Python range (drops 3.10 by setting requires-python to >=3.11) and adds new runtime dependencies. Please update the PR title/description to reflect the full scope, or split the support/dependency changes into a separate PR for clearer review.

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license = {file = "LICENSE"}
authors = [
{name = "Can Ergen"},
Expand All @@ -28,9 +28,9 @@ classifiers = [
"Development Status :: 4 - Beta",
"Intended Audience :: Science/Research",
"Natural Language :: English",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"Operating System :: MacOS :: MacOS X",
"Operating System :: Microsoft :: Windows",
"Operating System :: POSIX :: Linux",
Expand All @@ -54,6 +54,10 @@ dependencies = [
"faiss-cpu",
"leidenalg",
"cellxgene_census",
"torch>=2.4",
"transformers>=4.35.0",
"sentence-transformers>=2.3.1",
"tokenizers>=0.14.0",
Comment on lines +57 to +60
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Copilot AI Mar 1, 2026

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These newly-added heavyweight NLP deps (torch/transformers/sentence-transformers/tokenizers) significantly increase install size/time and may not be needed for typical popV usage (they appear to be required mainly for create_ontology_resources -> SentenceTransformer). Consider moving them into an optional extra (e.g., nlp) and raising a clear ImportError with install instructions when the feature is used without the extra, instead of making them unconditional core dependencies.

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]

[project.optional-dependencies]
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