Fix `setup.py` package data so `pip install` without GitHub clone also works for `M3GNetStructure`

[kavanase]

When trying to parse Structure objects with M3GNetStructure, the following error is encountered:

Traceback (most recent call last):
  File "M3GNet_Structure_DIRECT_generation_test_Y.py", line 35, in <module>
    m3gnet_struct = M3GNetStructure()  # neither multiprocessing nor Parallel works for this
  File "/work/e05/e05/kavanase/miniconda3/envs/tf_2.14_for_DIRECT/lib/python3.10/site-packages/maml/describers/_m3gnet.py", line 35, in __init__
    self.describer_model = M3GNet.from_dir(DEFAULT_MODEL)
  File "/work/e05/e05/kavanase/miniconda3/envs/tf_2.14_for_DIRECT/lib/python3.10/site-packages/m3gnet/models/_m3gnet.py", line 336, in from_dir
    model.load_weights(model_name)
  File "/work/e05/e05/kavanase/miniconda3/envs/tf_2.14_for_DIRECT/lib/python3.10/site-packages/keras/src/utils/traceback_utils.py", line 70, in error_handler
    raise e.with_traceback(filtered_tb) from None
  File "/work/e05/e05/kavanase/miniconda3/envs/tf_2.14_for_DIRECT/lib/python3.10/site-packages/tensorflow/python/training/py_checkpoint_reader.py", line 31, in error_translator
    raise errors_impl.NotFoundError(None, None, error_message)
tensorflow.python.framework.errors_impl.NotFoundError: Unsuccessful TensorSliceReader constructor: Failed to find any matching files for /work/e05/e05/kavanase/miniconda3/envs/tf_2.14_for_DIRECT/lib/python3.10/site-packages/maml/describers/data/m3gnet_models/matbench_mp_e_form/0/m3gnet/m3gnet

which seems to be because the M3GNet model data from maml/describers/data/m3gnet_models/matbench_mp_e_form/0/m3gnet is not available in the package data – so works fine for GitHub Actions tests run in the cloned repo, but not when actually used elsewhere in scripts/notebooks. Fixing package_data in setup.py fixes this.

Also fixes a typo in setup.py for megnet_models (previously megnet_mdoels).

I would also note that this also fails with recent tensorflow versions (2.16) which uses keras v3, giving the following error:

Traceback (most recent call last):
  File "M3GNet_Structure_DIRECT_generation_test_Y.py", line 35, in <module>
    m3gnet_struct = M3GNetStructure()  # neither multiprocessing nor Parallel works for this
  File "/work/e05/e05/kavanase/miniconda3/envs/tf_2.14_for_DIRECT/lib/python3.10/site-packages/maml/describers/_m3gnet.py", line 35, in __init__
    self.describer_model = M3GNet.from_dir(DEFAULT_MODEL)
  File "/work/e05/e05/kavanase/miniconda3/envs/tf_2.14_for_DIRECT/lib/python3.10/site-packages/m3gnet/models/_m3gnet.py", line 336, in from_dir
    model.load_weights(model_name)
  File "/work/e05/e05/kavanase/miniconda3/envs/tf_2.14_for_DIRECT/lib/python3.10/site-packages/keras/src/utils/traceback_utils.py", line 122, in error_handler
    raise e.with_traceback(filtered_tb) from None
  File "/work/e05/e05/kavanase/miniconda3/envs/tf_2.14_for_DIRECT/lib/python3.10/site-packages/keras/src/saving/saving_api.py", line 262, in load_weights
    raise ValueError(
ValueError: File format not supported: filepath=/work/e05/e05/kavanase/miniconda3/envs/tf_2.14_for_DIRECT/lib/python3.10/site-packages/maml/describers/data/m3gnet_models/matbench_mp_e_form/0/m3gnet/m3gnet. Keras 3 only supports V3 `.keras` and `.weights.h5` files, or legacy V1/V2 `.h5` files.

while downgrading to tensorflow==2.15 and keras<3 fixes this issue. I'm not sure if you want to update the requirements for this, or update the code to work with recent versions.

When fixing all these issues, the code runs, but also throws many warnings:

WARNING:tensorflow:From /work/e05/e05/kavanase/miniconda3/envs/tf_2.14_for_DIRECT/lib/python3.10/site-packages/tensorflow/python/util/deprecation.py:588: calling function (from tensorflow.python.eager.polymorphic_function.polymorphic_function) with experimental_relax_shapes is deprecated and will be removed in a future version.
Instructions for updating:
experimental_relax_shapes is deprecated, use reduce_retracing instead
WARNING:tensorflow:You are casting an input of type complex64 to an incompatible dtype float32.  This will discard the imaginary part and may not be what you intended.
... (many repeats of this)
WARNING:tensorflow:You are casting an input of type complex64 to an incompatible dtype float32.  This will discard the imaginary part and may not be what you intended.
WARNING:tensorflow:You are casting an input of type complex64 to an incompatible dtype float32.  This will discard the imaginary part and may not be what you intended.
WARNING:tensorflow:You are casting an input of type complex64 to an incompatible dtype float32.  This will discard the imaginary part and may not be what you intended.
WARNING:tensorflow:Detecting that an object or model or tf.train.Checkpoint is being deleted with unrestored values. See the following logs for the specific values in question. To silence these warnings, use `status.expect_partial()`. See https://www.tensorflow.org/api_docs/python/tf/train/Checkpoint#restorefor details about the status object returned by the restore function.
WARNING:tensorflow:Value in checkpoint could not be found in the restored object: (root).final.layers.1.pipe.layers.0.kernel
WARNING:tensorflow:Value in checkpoint could not be found in the restored object: (root).final.layers.1.pipe.layers.0.bias
WARNING:tensorflow:Value in checkpoint could not be found in the restored object: (root).final.layers.1.pipe.layers.1.kernel
WARNING:tensorflow:Value in checkpoint could not be found in the restored object: (root).final.layers.1.pipe.layers.1.bias
WARNING:tensorflow:Value in checkpoint could not be found in the restored object: (root).final.layers.1.pipe.layers.2.kernel
WARNING:tensorflow:Value in checkpoint could not be found in the restored object: (root).final.layers.1.pipe.layers.2.bias

[coderabbitai[bot]]

Walkthrough

The changes in setup.py involve updating the paths for package data related to the maml package. Specifically, the paths for MegNet model files have been modified to ensure they point to the correct directories. This adjustment enhances the accuracy and functionality of the package's data management.

Changes

File	Change Summary
setup.py	Updated package data paths for maml package, changing paths for MegNet model files from "describers/data/megnet_models/*.json" to "describers/data/megnet_models/*" and from "describers/data/megnet_mdoels/*.hdf5" to "describers/data/m3gnet_models/matbench_mp_e_form/0/m3gnet/*".

---

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Commits

Files that changed from the base of the PR and between 8d124babe38fbce7895ac167bf8ff7e8b8b66644 and 5f951568530897cb1fbbfe92dae8ee42c2916862.

Files selected for processing (1)

* setup.py (1 hunks)

Additional comments not posted (1)

setup.py (1)

`125-126`: The changes to `package_data` look correct and should resolve the issue with missing model data for `M3GNetStructure`. Please ensure to verify that these files are correctly included in the built package.

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[shyuep]

Thanks