Fix forward merge of release/25.12 into main

[alexbarghi-nv]

Fixes the forward merge.

[greptile-apps]

Greptile Overview

Greptile Summary

This PR completes the forward merge of release/25.12 into main by applying dependency version pins for Cython (<3.2.0a0) and pytest (<9.0.0a0).

• Pins Cython to versions below 3.2.0 to workaround build issues with the newly released Cython 3.2.0
• Pins pytest to versions below 9.0 to avoid compatibility issues with the recently released pytest 9
• Updates the source dependencies.yaml file and regenerates all derived environment and configuration files
• Maintains alphabetical ordering of dependencies across all 12 files (4 conda environments, 4 cugraph-pyg dev environments, 2 pyproject.toml files, 1 recipe file, 1 source dependencies file)
• All changes are consistent and properly propagated through the rapids-dependency-file-generator tool chain

Confidence Score: 5/5

• This PR is safe to merge with no risk
• The merge cleanly applies version pins to workaround known upstream issues. All 12 files are updated consistently through the standard rapids-dependency-file-generator tooling, maintaining proper alphabetical ordering and formatting conventions throughout.
• No files require special attention

Important Files Changed

File Analysis

Filename	Score	Overview
conda/environments/all_cuda-129_arch-x86_64.yaml	5/5	Updated Cython pin to <3.2.0a0 and moved pytest pin to maintain alphabetical ordering
conda/recipes/pylibwholegraph/recipe.yaml	5/5	Updated Cython pin to <3.2.0a0 in build requirements
dependencies.yaml	5/5	Source file for dependency changes: Cython <3.2.0a0 and pytest <9.0.0a0 pins
python/pylibwholegraph/pyproject.toml	5/5	Added Cython <3.2.0a0 pin and moved pytest pin in test dependencies

Sequence Diagram

sequenceDiagram
    participant Dev as Developer
    participant Merge as Forward Merge Process
    participant DepFile as dependencies.yaml
    participant Generator as rapids-dependency-file-generator
    participant CondaEnvs as Conda Environment Files
    participant PyProj as PyProject.toml Files
    participant Recipe as Conda Recipe Files
    
    Dev->>Merge: Initiate forward merge from release/25.12
    Merge->>DepFile: Apply Cython pin (<3.2.0a0)
    Merge->>DepFile: Apply pytest pin (<9.0.0a0)
    Note over DepFile: Source of truth for all dependencies
    
    DepFile->>Generator: Trigger dependency file generation
    Generator->>CondaEnvs: Update 4 all_cuda environment files
    Note over CondaEnvs: Update Cython and pytest pins<br/>Maintain alphabetical ordering
    
    Generator->>PyProj: Update cugraph-pyg/pyproject.toml
    Generator->>PyProj: Update pylibwholegraph/pyproject.toml
    Note over PyProj: Move pytest to maintain ordering<br/>Add Cython pin where needed
    
    Generator->>Recipe: Update pylibwholegraph/recipe.yaml
    Note over Recipe: Add Cython build requirement pin
    
    Merge->>Dev: All 12 files updated consistently

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