Miscellaneous fixes

[peterdsharpe]

Summary

• add range and overflow checks around Warp-backed neighbor and mesh operations
• correct archive member filtering and improve remote artifact fetching
• tighten example dataset and experiment-logging behavior
• document reproducible checksums for externally hosted example data

Details

This collects several independent correctness and robustness fixes:

• prefix sums are accumulated in int64 and checked before conversion to the int32 offsets required by Warp kernels
• mesh face indices are validated before native SDF and raycast execution
• archive extraction accepts only contained regular files and directories
• the package filesystem supports HTTPS, response checking, atomic cache writes, and optional SHA-256 verification while retaining the existing HTTP behavior with a warning
• the diffusion example disables unnecessary object-array loading for its numeric dataset
• experiment configuration summaries redact credential-like fields, and W&B initialization now preserves configured values correctly

Established checkpoint extensibility and existing dataset/cache serialization formats remain unchanged.

Validation

• focused changed-behavior tests: 35 passed, 3 skipped
• radius-search and Poisson sampling tests: 187 passed, 4 skipped
• checkpoint, datapipe, and HEALPix compatibility tests: 75 passed, 32 skipped
• direct CUDA/Warp FigConv smoke test passed
• Ruff, Python/YAML syntax checks, and git diff --check passed

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[peterdsharpe]

/ok to test a3913f4

[github-actions]

CODEOWNERS review map

Current for commit 4cde61f55c35. An approval covers every file listed for that owner; one owner is sufficient for shared files.

✅ @CharlelieLrt — 2 file(s)

• physicsnemo/core/filesystem.py
• physicsnemo/core/module.py

⏳ @coreyjadams — 3 file(s)

• examples/cfd/external_aerodynamics/domino/README.md
• physicsnemo/models/figconvnet/warp_neighbor_search.py
• test/core/test_filesystem.py

✅ @ktangsali — 2 file(s)

• physicsnemo/core/filesystem.py
• physicsnemo/core/module.py

✅ @loliverhennigh — 4 file(s)

• physicsnemo/nn/functional/geometry/mesh_poisson_disk_sample/_warp_impl/op.py
• physicsnemo/nn/functional/geometry/sdf.py
• physicsnemo/nn/functional/neighbors/radius_search/_warp_impl.py
• physicsnemo/nn/functional/rendering/mesh_raycast/_warp_impl.py

✅ @mnabian — 7 file(s)

• examples/cfd/lagrangian_mgn/README.md
• examples/cfd/lagrangian_mgn/conf/config.yaml
• examples/cfd/lagrangian_mgn/conf/config_2d.yaml
• examples/cfd/lagrangian_mgn/conf/config_3d.yaml
• examples/cfd/lagrangian_mgn/inference.py
• examples/cfd/lagrangian_mgn/loggers.py
• examples/cfd/lagrangian_mgn/train.py

✅ @peterdsharpe — 2 file(s) (covered by co-owner)

• physicsnemo/nn/functional/geometry/sdf.py
• physicsnemo/nn/functional/neighbors/radius_search/_warp_impl.py

No CODEOWNER

• examples/cfd/flow_reconstruction_diffusion/README.md
• examples/cfd/flow_reconstruction_diffusion/generate_dfsr.py
• test/examples/test_lagrangian_mgn_loggers.py
• test/models/test_from_checkpoint.py
• test/nn/functional/geometry/test_sdf.py
• test/nn/functional/rendering/test_mesh_raycast.py

Comment /codeowners-info to refresh.

[greptile-apps]

Greptile Summary

This PR strengthens validation and integrity handling across remote artifacts, checkpoint extraction, Warp geometry operations, and example logging behavior.

• Adds HTTPS, response checking, atomic HTTP cache writes, and optional SHA-256 verification.
• Restricts checkpoint archive extraction to contained regular files and directories.
• Detects neighbor-count overflow before converting offsets required by Warp kernels.
• Validates mesh connectivity before SDF and raycast execution.
• Redacts credential-like configuration fields and corrects W&B initialization assignments.
• Tightens example dataset loading and documents externally hosted dataset checksums.

Important Files Changed

Filename	Overview
physicsnemo/core/filesystem.py	Adds secure HTTP(S) retrieval and checksum-aware caching, but checksum-failure cleanup remains racy for shared-cache callers.
physicsnemo/core/module.py	Correctly restricts archive extraction to contained regular files and directories.
physicsnemo/nn/functional/neighbors/radius_search/_warp_impl.py	Accumulates neighbor offsets in int64 and checks totals before the required int32 Warp conversion.
physicsnemo/models/figconvnet/warp_neighbor_search.py	Prevents prefix-sum overflow while preserving the existing int32 kernel interface.
physicsnemo/nn/functional/geometry/mesh_poisson_disk_sample/_warp_impl/op.py	Adds checked int64 CSR prefix accumulation before allocating and launching int32-offset kernels.
physicsnemo/nn/functional/geometry/sdf.py	Rejects invalid mesh connectivity before native execution, but scalar bounds extraction synchronizes CUDA execution.
physicsnemo/nn/functional/rendering/mesh_raycast/_warp_impl.py	Adds vertex-index bounds validation for Warp raycasting, with the same eager CUDA synchronization cost as SDF validation.
examples/cfd/lagrangian_mgn/loggers.py	Redacts credential-like configuration values and fixes W&B key and run-ID assignment precedence.
examples/cfd/flow_reconstruction_diffusion/generate_dfsr.py	Disables unnecessary pickle-backed object-array loading for the numeric reconstruction dataset.

_{Reviews (1): Last reviewed commit: "Miscellaneous fixes" | Re-trigger Greptile}

[peterdsharpe]

/ok to test 4cde61f

[mnabian]

Lagrangian MGN changes LGTM, thanks!

[ktangsali]

Changes to module.py and filesystem.py look good.

[CharlelieLrt]

LGTM

[loliverhennigh]

LGTM, no comment on my side

[coreyjadams]

/codeowners-info

[coreyjadams]

Ive reviewed my portion of the files here, thanks Peter!

[peterdsharpe]

/ok to test 98bf3f7