[fea] adding oss licenses#26
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NickGeneva
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Addresses Peter Sharpe's CHANGES_REQUESTED review on PR NVIDIA#1576 in full, and subsumes the 3D-UFNO portion of the planned xFNO PR into this one. Net: -139 lines despite gaining trunkless mode, time-axis-extend, multi-channel output, coord features, multi-layer lift, and 2D/3D genericity. Theme 1 — Dimensional unification (Peter NVIDIA#37, NVIDIA#47, NVIDIA#52, NVIDIA#53): - ``DeepONet`` (formerly DeepONet + DeepONet3D) takes ``dimension: int`` (2 or 3) and dispatches via ``_DIM_DEFAULTS`` and per-dim conv/spectral primitives, mirroring the ``FNO`` pattern. - ``SpatialBranch`` (formerly SpatialBranch + SpatialBranch3D) takes ``dimension`` and uses an ``_DIM_LAYERS`` lookup for ``SpectralConv``/``Conv``/``BatchNorm``/``AdaptiveAvgPool``/ ``UNetAdapter`` and the permute helpers. - ``Conv{2,3}dFCLayer`` is selected via a one-line lookup (Peter NVIDIA#45). Theme 2 — Wrappers folded into DeepONet (Peter NVIDIA#54, NVIDIA#64, NVIDIA#65): - ``wrappers.py`` deleted (``DeepONetWrapper`` and ``DeepONet3DWrapper`` removed). Padding behaviour is now a constructor flag, ``auto_pad: bool = False``, and the model dispatches to ``_forward_packed`` / ``_forward_packed_trunkless`` accordingly. - 6-cell call matrix (trunked/trunkless × packed/core × spatial/mlp) is documented in the class docstring. - The previous private ``_temporal_projection`` attribute is exposed as a public ``has_temporal_projection`` property (Peter NVIDIA#55). Theme 3 — Deduplication (Peter NVIDIA#43, NVIDIA#44, NVIDIA#50, NVIDIA#51, NVIDIA#40, related Greptile): - ``TrunkNet`` and ``MLPBranch`` deleted — both duplicated ``physicsnemo.models.mlp.FullyConnected``; users now pass any ``nn.Module`` for the trunk / branches (DI-first API). - ``_SinActivation`` deleted; the activation is registered as ``"sin"`` in ``physicsnemo.nn.module.activations.ACT2FN`` (previous commit). All ``if activation_fn.lower() == "sin"`` special-cases removed. - ``DeepONet.from_config`` and the dict-config schema removed entirely; Hydra-style ``_target_`` instantiation supersedes it. - ``count_params`` collapsed from 4 duplicate copies to 1. Theme 4 — xFNO fold-in: - ``trunk: nn.Module | None = None`` enables trunkless mode (the 3D-UFNO use case from the planned xFNO PR). - ``out_channels: int = 1`` adds multi-channel output to every path. - ``time_modes: int | None`` enables xFNO-style time-axis-extend in trunkless packed mode: replicate-pads the last spatial axis to fit ``2 * time_modes`` and crops to the requested ``target_times``. - ``coord_features`` and ``lift_layers``/``lift_hidden_width`` parameters on ``SpatialBranch`` replace the deleted dict-driven "conv encoder" option. Theme 5 — Housekeeping (Peter NVIDIA#33, NVIDIA#34, NVIDIA#38, NVIDIA#41, NVIDIA#48, NVIDIA#57, NVIDIA#58, NVIDIA#59, Charlelie NVIDIA#26, Greptile NVIDIA#5, NVIDIA#6): - ``padding.py`` renamed to private ``_padding.py``; all functions carry ``jaxtyping.Shaped`` annotations. - All public forward methods carry ``jaxtyping.Float`` annotations and ``torch.compiler.is_compiling`` shape-validation guards. - ``Literal`` type aliases for ``decoder_type`` and other enums; case-insensitive validation against ``get_args`` (Greptile NVIDIA#15). - Modern type hints throughout (``dict[str, Any] | None``, no ``Dict``/``Optional``). - All public docstrings use ``r"""`` raw-string prefix, LaTeX math for tensor shapes, double backticks for inline code, and Examples sections. - ``Notes`` block in ``branches.py`` documents the ``num_unet_layers`` 8x memory/compute penalty (Peter NVIDIA#49). Theme 6 — Tests (Peter NVIDIA#60, NVIDIA#61, NVIDIA#62, NVIDIA#63, Charlelie NVIDIA#29): - ``_FIXTURE_REGISTRY`` drives all non-regression tests across 9 scenarios: u_deeponet 2D/3D, fourier_deeponet, mionet, temporal_projection, multi-channel packed 2D, xfno trunkless 3D (with and without time-axis-extend), and core 2D MLP-branch. - New 3D gradient-flow test and 3D ``torch.compile`` test. - ``fullgraph=True`` probe tests for 2D and 3D marked ``@pytest.mark.xfail(strict=False)`` to empirically answer Peter NVIDIA#63. - ``_load_golden`` uses ``pytest.skip`` for missing fixtures so CI passes pending cluster-side golden regeneration. - Test class structure mirrors MOD-008a/b/c: ``TestDeepONetConstructor``, ``TestDeepONetNonRegression``, ``TestDeepONetCheckpoint``, ``TestDeepONetGradientFlow``, ``TestDeepONetCompile``, ``TestDeepONetTimeAxisExtend``. CHANGELOG bullet rewritten to describe the actual shipped API (was stale, still described the old config-driven 8-variant model).
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Adding OSS licenses