Notebook `5. Point Cloud Classification` still uses `torch-cluster` instead of `pyg-lib`

Describe the bug

I'm currently learning PyG with the example notebooks, but notebook 5. Point Cloud Classification still uses torch-cluster, which is "This repository is deprecated in favor of pyg-lib>=0.7.0" (https://github.com/rusty1s/pytorch_cluster).

When I try to set up the notebook locally, running uv add torch-cluster fails with the following message:

mgros@MININT-01QHOVN:~/projects/MasterThesisGNN$ uv add torch-cluster 
  × Failed to build `torch-cluster==1.6.3`
  ├─▶ The build backend returned an error
  ╰─▶ Call to `setuptools.build_meta:__legacy__.build_wheel` failed (exit status: 1)

      [stderr]
      Traceback (most recent call last):
        File "<string>", line 14, in <module>
        File "/home/mgros/.cache/uv/builds-v0/.tmpsjGdD7/lib/python3.12/site-packages/setuptools/build_meta.py", line 333, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/home/mgros/.cache/uv/builds-v0/.tmpsjGdD7/lib/python3.12/site-packages/setuptools/build_meta.py", line 301, in _get_build_requires
          self.run_setup()
        File "/home/mgros/.cache/uv/builds-v0/.tmpsjGdD7/lib/python3.12/site-packages/setuptools/build_meta.py", line 520, in run_setup
          super().run_setup(setup_script=setup_script)
        File "/home/mgros/.cache/uv/builds-v0/.tmpsjGdD7/lib/python3.12/site-packages/setuptools/build_meta.py", line 317, in run_setup
          exec(code, locals())
        File "<string>", line 8, in <module>
      ModuleNotFoundError: No module named 'torch'

hint: `torch-cluster` (v1.6.3) was included because `masterthesisgnn` (v0.1.0) depends on `torch-cluster`
hint: This error likely indicates that `[email protected]` depends on `torch`, but doesn't declare it as a build dependency. If `torch-cluster` is a first-party package, consider adding `torch` to its `build-system.requires`. Otherwise, either add it to your `pyproject.toml` under:

[tool.uv.extra-build-dependencies]
torch-cluster = ["torch"]

or `uv pip install torch` into the environment and re-run with `--no-build-isolation`.

I'd like to create a PR that migrates the notebook 5 to pyg-lib myself, but afaik, these notebooks are only Google Drive downloads and not publicly tracked via Git/GitHub, correct? So side question: Are there any plans to add these notebooks to GitHub?

Versions

uv run python collect_env.py Collecting environment information... PyTorch version: 2.12.0+cu130 Is debug build: False CUDA used to build PyTorch: 13.0 ROCM used to build PyTorch: N/A

OS: Ubuntu 24.04.1 LTS (x86_64) GCC version: (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0 Clang version: Could not collect CMake version: version 3.28.3 Libc version: glibc-2.39

Python version: 3.12.13 (main, May 10 2026, 19:30:01) [Clang 22.1.3 ] (64-bit runtime) Python platform: Linux-5.15.167.4-microsoft-standard-WSL2-x86_64-with-glibc2.39 Is CUDA available: True CUDA runtime version: 13.0.48 CUDA_MODULE_LOADING set to: GPU models and configuration: GPU 0: NVIDIA GeForce RTX 5070 Nvidia driver version: 591.86 cuDNN version: Could not collect Is XPU available: False HIP runtime version: N/A MIOpen runtime version: N/A Is XNNPACK available: True Caching allocator config: N/A

CPU: Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Address sizes: 48 bits physical, 48 bits virtual Byte Order: Little Endian CPU(s): 16 On-line CPU(s) list: 0-15 Vendor ID: AuthenticAMD Model name: AMD Ryzen 7 9700X 8-Core Processor CPU family: 26 Model: 68 Thread(s) per core: 2 Core(s) per socket: 8 Socket(s): 1 Stepping: 0 BogoMIPS: 7599.82 Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl tsc_reliable nonstop_tsc cpuid extd_apicid pni pclmulqdq ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm cmp_legacy svm cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw topoext perfctr_core ssbd ibrs ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid avx512f avx512dq rdseed adx smap avx512ifma clflushopt clwb avx512cd sha_ni avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves avx_vnni avx512_bf16 clzero xsaveerptr arat npt nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold v_vmsave_vmload avx512vbmi umip avx512_vbmi2 gfni vaes vpclmulqdq avx512_vnni avx512_bitalg avx512_vpopcntdq rdpid fsrm avx512_vp2intersect Virtualization: AMD-V Hypervisor vendor: Microsoft Virtualization type: full L1d cache: 384 KiB (8 instances) L1i cache: 256 KiB (8 instances) L2 cache: 8 MiB (8 instances) L3 cache: 32 MiB (1 instance) Vulnerability Gather data sampling: Not affected Vulnerability Itlb multihit: Not affected Vulnerability L1tf: Not affected Vulnerability Mds: Not affected Vulnerability Meltdown: Not affected Vulnerability Mmio stale data: Not affected Vulnerability Reg file data sampling: Not affected Vulnerability Retbleed: Not affected Vulnerability Spec rstack overflow: Not affected Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl and seccomp Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization Vulnerability Spectre v2: Mitigation; Retpolines; IBPB conditional; IBRS_FW; STIBP always-on; RSB filling; PBRSB-eIBRS Not affected; BHI Not affected Vulnerability Srbds: Not affected Vulnerability Tsx async abort: Not affected

Versions of relevant libraries: [pip3] Could not collect [conda] Could not collect