Fix ruff by sorting the class variables in _so3.py (#441)

* improve TensorNet model coverage

* Update pyproject.toml

Signed-off-by: Tsz Wai Ko <[email protected]>

* Improve the unit test for SO(3) equivarance in TensorNet class

* improve SO3Net model class coverage and simplify TensorNet implementations

* improve the coverage in MLP_norm class

* Improve the implementation of three-body interactions

* fixed black

* Optimize the speed of _compute_3body class

* type checking is added for scheduler

* update M3GNet Potential training notebook for the demonstration of obtaining and using element offsets

* Downgrade sympy to avoid crash of SO3 operations

* Smooth l1 loss function is added and united tests are improved

* merge the method predict_structure and featurize_structure into a function including both

* remove unnecessary else statement for training magmoms

* modify so3 operation implementation to make united tests pass due to the update of sympy

* skip test_load_all_models for MacOS pytest now

* Reference for CHGNet is added

* Update README.md and index.md for including CHGNet

Signed-off-by: Tsz Wai Ko <[email protected]>

* add more description for using CHGNet pretrained models in Relaxations and Simulations using the M3GNet Universal Potential.ipynb

* A command-line interface for performing ASE MD simulations is added

* added back py.typed

* ExpNormal Smearing for radial basis functions is added

* Changed deprecated torch.scalar_tensor into torch.Tensor

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Signed-off-by: Tsz Wai Ko <[email protected]>

* Converted the float number into tensor

Signed-off-by: Tsz Wai Ko <[email protected]>

* fix the united test in test_bond.py

* Bump boto3 from 1.35.38 to 1.35.39

Bumps [boto3](https://github.com/boto/boto3) from 1.35.38 to 1.35.39.
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](boto/boto3@1.35.38...1.35.39)

---
updated-dependencies:
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* fix the error from the upgrade of boto3

* Downgrade DGL to 2.2.1

* Downgrade pytorch

* fix mypy by adding self.norm_layers is not None

* Downgrade Pytorch and DGL version  (#392)

* improve TensorNet model coverage

* Update pyproject.toml

Signed-off-by: Tsz Wai Ko <[email protected]>

* Improve the unit test for SO(3) equivarance in TensorNet class

* improve SO3Net model class coverage and simplify TensorNet implementations

* improve the coverage in MLP_norm class

* Improve the implementation of three-body interactions

* fixed black

* Optimize the speed of _compute_3body class

* type checking is added for scheduler

* update M3GNet Potential training notebook for the demonstration of obtaining and using element offsets

* Downgrade sympy to avoid crash of SO3 operations

* Smooth l1 loss function is added and united tests are improved

* merge the method predict_structure and featurize_structure into a function including both

* remove unnecessary else statement for training magmoms

* modify so3 operation implementation to make united tests pass due to the update of sympy

* skip test_load_all_models for MacOS pytest now

* Reference for CHGNet is added

* Update README.md and index.md for including CHGNet

Signed-off-by: Tsz Wai Ko <[email protected]>

* add more description for using CHGNet pretrained models in Relaxations and Simulations using the M3GNet Universal Potential.ipynb

* A command-line interface for performing ASE MD simulations is added

* added back py.typed

* ExpNormal Smearing for radial basis functions is added

* Changed deprecated torch.scalar_tensor into torch.Tensor

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Signed-off-by: Tsz Wai Ko <[email protected]>

* Converted the float number into tensor

Signed-off-by: Tsz Wai Ko <[email protected]>

* fix the united test in test_bond.py

* fix the error from the upgrade of boto3

* Downgrade DGL to 2.2.1

* Downgrade pytorch

* fix mypy by adding self.norm_layers is not None

---------

Signed-off-by: Tsz Wai Ko <[email protected]>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <[email protected]>

* correct the downgrade for torch

* fix the version of torchdata

* downgrade torch to 2.2.1

* fix ruff by sorting '__all__' in _so3.py

* remove Bussi for MD now

Signed-off-by: Tsz Wai Ko <[email protected]>

* remove Bussi for now

Signed-off-by: Tsz Wai Ko <[email protected]>

* Remove trailing whitespace

---------

Signed-off-by: Tsz Wai Ko <[email protected]>
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

src/matgl/ext/ase.py

@@ -405,8 +405,8 @@ def __init__(
             stress of the atoms
             state_attr (torch.Tensor): State attr.
             stress_weight (float): conversion factor from GPa to eV/A^3
-            ensemble (str): choose from "nve", "nvt", "nvt_langevin", "nvt_andersen", "npt", "npt_berendsen",
-            "npt_nose_hoover"
+            ensemble (str): choose from "nve", "nvt", "nvt_langevin", "nvt_andersen", "nvt_bussi", "npt",
+            "npt_berendsen", "npt_nose_hoover"
             temperature (float): temperature for MD simulation, in K
             timestep (float): time step in fs
             pressure (float): pressure in eV/A^3

src/matgl/layers/_so3.py

@@ -16,10 +16,10 @@
 
 __all__ = [
     "RealSphericalHarmonics",
-    "SO3TensorProduct",
     "SO3Convolution",
     "SO3GatedNonlinearity",
     "SO3ParametricGatedNonlinearity",
+    "SO3TensorProduct",
 ]