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IntelLabs / matsciml

Open MatSci ML Toolkit is a framework for prototyping and scaling out deep learning models for materials discovery supporting widely used materials science datasets, and built on top of PyTorch Lightning, the Deep Graph Library, and PyTorch Geometric.
MIT License
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[Bug]: pytorch_geometric import when not installed in datasets.transformation.frame_averaging #91

Closed JonathanSchmidt1 closed 10 months ago

JonathanSchmidt1 commented 10 months ago

Expected behavior

schnet_dgl.py example should run in environment without torch_geometric

Actual behavior

Running the schnet_dgl example in an environment without pytorch geometric it crashes with 

  File "/home/sjonathan/Downloads/matsciml_alexandria/examples/model_demos/schnet_dgl.py", line 6, in <module>
    from matsciml.datasets.transforms import DistancesTransform
  File "/home/sjonathan/Downloads/matsciml_alexandria/matsciml/datasets/transforms/__init__.py", line 5, in <module>
    from matsciml.datasets.transforms.frame_averaging import FrameAveraging
  File "/home/sjonathan/Downloads/matsciml_alexandria/matsciml/datasets/transforms/frame_averaging.py", line 13, in <module>
    import torch_geometric
ModuleNotFoundError: No module named 'torch_geometric'

because in frame_averaging.py there are two import statements of torch_geomtric before the registry check

import torch_geometric
from torch_geometric.transforms import LinearTransformation

Steps to reproduce the problem

run schnet_dgl.py in environment without torch_geometric

Specifications

absl-py==1.4.0 aiohttp==3.8.5 aioitertools==0.11.0 aiosignal==1.3.1 alabaster==0.7.13 annotated-types==0.5.0 anyio==3.7.0 argon2-cffi @ file:///opt/conda/conda-bld/argon2-cffi_1645000214183/work argon2-cffi-bindings @ file:///tmp/build/80754af9/argon2-cffi-bindings_1644553347904/work arrow==1.2.3 ase==3.22.1 asttokens==2.2.1 astunparse==1.6.3 async-timeout==4.0.3 atomate==1.0.3 atomate2 @ file:///home/sjonathan/Downloads/atomate2_other_forcefields attrs==23.1.0 Babel @ file:///croot/babel_1671781930836/work backcall @ file:///home/ktietz/src/ci/backcall_1611930011877/work bandit==1.7.6 bcrypt==4.0.1 beautifulsoup4==4.12.2 biopython==1.81 black==23.12.1 bleach==6.0.0 boto3==1.28.4 botocore==1.31.4 bracex==2.3.post1 brotlipy==0.7.0 cachelib==0.9.0 cachetools==5.3.0 castepxbin==0.2.0 cclib==1.8 CellConstructor==1.3.2 certifi @ file:///croot/certifi_1671487769961/work/certifi cffi @ file:///croot/cffi_1670423208954/work cfgv==3.4.0 chardet==5.2.0 charset-normalizer==3.3.2 chemview==0.6 chgnet==0.2.0 click==8.1.7 cloudpickle==3.0.0 colorama==0.4.6 colormath==3.0.0 comm==0.1.3 contextlib2==21.6.0 contourpy==1.0.7 cryptography @ file:///croot/cryptography_1677533068310/work crystal-toolkit==2023.6.1 crystaltoolkit-extension==0.6.0 custodian==2023.7.22 cycler==0.11.0 Cython==3.0.2 dash==2.10.2 dash-core-components==2.0.0 dash-html-components==2.0.0 dash-mp-components==0.4.34 dash-table==5.0.0 debugpy==1.6.7 decorator @ file:///opt/conda/conda-bld/decorator_1643638310831/work defusedxml @ file:///tmp/build/80754af9/defusedxml_1615228127516/work dgl==0.9.1 dgllife==0.3.2 distlib==0.3.8 dnspython==2.3.0 docstring-parser==0.15 docutils==0.20.1 dpdata==0.2.15 dscribe==2.1.0 e3nn==0.5.1 einops==0.7.0 email-validator==2.1.0.post1 emmet-core==0.64.0 entrypoints @ file:///tmp/build/80754af9/entrypoints_1649908313000/work exceptiongroup==1.1.1 executing==1.2.0 f90wrap==0.2.13 fabric==3.1.0 fastapi==0.100.0 fastcore==1.5.29 fasteners==0.18 fastjsonschema==2.17.1 fforces==0.1 filelock==3.12.2 FireWorks==2.0.3 flake8==7.0.0 flake8-bandit==4.1.1 flake8-black==0.3.6 Flake8-pyproject==1.2.3 Flask==2.2.5 Flask-Caching==2.0.2 flask-paginate==2022.1.8 flatbuffers==23.3.3 flit_core @ file:///opt/conda/conda-bld/flit-core_1644941570762/work/source/flit_core fonttools==4.39.0 fqdn==1.5.1 frozenlist==1.4.0 fsspec==2023.9.2 future==0.18.3 gast==0.4.0 gdown==4.7.1 geometric-algebra-attention==0.5.1 gitdb==4.0.11 GitPython==3.1.41 google-auth==2.17.1 google-auth-oauthlib==1.0.0 google-pasta==0.2.0 greenlet==3.0.3 GridDataFormats==1.0.1 grpcio==1.53.0 gunicorn==20.1.0 h11==0.14.0 h5py==3.8.0 hiphive==1.1 httpcore==1.0.2 httpx==0.26.0 hyperopt==0.2.7 identify==2.5.33 idna @ file:///croot/idna_1666125576474/work imageio==2.31.0 imagesize==1.4.1 importlib-metadata==6.8.0 importlib-resources==6.1.1 inflect==6.0.4 iniconfig==2.0.0 invoke==2.1.3 ipykernel==6.23.2 ipython==8.14.0 ipython-genutils @ file:///tmp/build/80754af9/ipython_genutils_1606773439826/work ipywidgets==7.7.5 isoduration==20.11.0 itsdangerous==2.1.2 jax==0.4.8 jedi==0.18.2 Jinja2 @ file:///croot/jinja2_1666908132255/work jmespath==1.0.1 jobflow==0.1.13 joblib==1.2.0 json5 @ file:///tmp/build/80754af9/json5_1624432770122/work jsonargparse==4.27.1 jsonpointer==2.3 jsonschema @ file:///croot/jsonschema_1676558650973/work julia==0.6.1 jupyter @ file:///tmp/abs_33h4eoipez/croots/recipe/jupyter_1659349046347/work jupyter-console==6.6.3 jupyter-events==0.6.3 jupyter_client==8.2.0 jupyter_core==5.3.1 jupyter_server==2.6.0 jupyter_server_terminals==0.4.4 jupyterlab @ file:///croot/jupyterlab_1675354114448/work jupyterlab-pygments==0.2.2 jupyterlab-widgets==1.1.4 jupyterlab_server @ file:///croot/jupyterlab_server_1677143054853/work kaleido==0.2.1 keras==2.12.0 kiwisolver==1.4.4 lark==1.1.8 latexcodec==2.0.1 lazy_loader==0.2 libclang==16.0.0 lightning-utilities==0.9.0 llvmlite==0.39.1 lmdb==1.3.0 lobsterpy==0.3.0 lovely-numpy==0.2.8 lxml @ file:///opt/conda/conda-bld/lxml_1657545139709/work mace @ file:///home/sjonathan/Downloads/mace maggma==0.56.0 Markdown==3.4.3 markdown-it-py==3.0.0 MarkupSafe==2.1.3 matgl==0.8.5 matminer==0.8.0 matplotlib==3.7.1 matplotlib-inline @ file:///opt/conda/conda-bld/matplotlib-inline_1662014470464/work -e git+https://github.com/JonathanSchmidt1/matsciml_alexandria.git@9568e18f0d3546cbd565a87655a88bff9bf45d42#egg=matsciml matscipy==0.8.0 mccabe==0.7.0 MDAnalysis==2.6.0 mdtraj==1.9.7 mdurl==0.1.2 mendeleev==0.14.0 mistune==2.0.5 ml-dtypes==0.0.4 mmtf-python==1.1.3 mongogrant==0.3.3 mongomock==4.1.2 monty==2023.9.5 mp-api==0.33.3 mpi4py==3.1.4 mpmath==1.3.0 mrcfile==1.4.3 msgpack==1.0.5 multidict==6.0.4 munch==2.5.0 mypy-extensions==1.0.0 nbclassic==1.0.0 nbclient==0.8.0 nbconvert==7.5.0 nbformat==5.9.0 nequip @ file:///home/sjonathan/fusessh/dgx3/nequip2/nequip3/nequip nest-asyncio @ file:///croot/nest-asyncio_1672387112409/work networkx==3.0 nglview==3.0.5 nodeenv==1.8.0 notebook==6.5.4 notebook_shim==0.2.3 numba==0.56.4 numpy==1.23.5 nvidia-cublas-cu12==12.1.3.1 nvidia-cuda-cupti-cu12==12.1.105 nvidia-cuda-nvrtc-cu12==12.1.105 nvidia-cuda-runtime-cu12==12.1.105 nvidia-cudnn-cu12==8.9.2.26 nvidia-cufft-cu12==11.0.2.54 nvidia-curand-cu12==10.3.2.106 nvidia-cusolver-cu12==11.4.5.107 nvidia-cusparse-cu12==12.1.0.106 nvidia-ml-py3==7.352.0 nvidia-nccl-cu12==2.18.1 nvidia-nvjitlink-cu12==12.3.101 nvidia-nvtx-cu12==12.1.105 oauthlib==3.2.2 openai==0.28.1 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optimade==1.0.1 orjson==3.9.2 overrides==7.3.1 packaging==23.1 palettable==3.3.0 pandas==1.5.3 pandocfilters @ file:///opt/conda/conda-bld/pandocfilters_1643405455980/work paramiko==3.2.0 parso @ file:///opt/conda/conda-bld/parso_1641458642106/work pathspec==0.12.1 pbr==6.0.0 pdyna @ file:///home/sjonathan/Downloads/PDynA periodictable==1.6.1 pexpect @ file:///tmp/build/80754af9/pexpect_1605563209008/work phonopy==2.20.0 pickleshare @ file:///tmp/build/80754af9/pickleshare_1606932040724/work Pillow==9.4.0 platformdirs==4.1.0 plotly==5.13.1 pluggy==1.0.0 ply==3.11 pooch==1.7.0 pre-commit==3.6.0 prettytable==3.7.0 prometheus-client==0.17.0 prompt-toolkit==3.0.38 protobuf==4.22.1 psutil==5.9.5 ptyprocess @ file:///tmp/build/80754af9/ptyprocess_1609355006118/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl PubChemPy==1.0.4 pure-eval @ file:///opt/conda/conda-bld/pure_eval_1646925070566/work py4j==0.10.9.7 py4vasp==0.7.3 pyasn1==0.4.8 pyasn1-modules==0.2.8 pybind11==2.11.1 pybtex==0.24.0 pycodestyle==2.11.1 pycparser @ file:///tmp/build/80754af9/pycparser_1636541352034/work pydantic==1.10.12 pydantic-settings==2.0.3 pydantic_core==2.14.6 pydash==7.0.5 pyfiglet==0.8.post1 pyflakes==3.2.0 Pygments==2.15.1 pymatgen==2023.7.20 pymatgen-analysis-defects==2023.8.22 pymatgen-analysis-diffusion==2022.7.21 pymatgen-db==2023.2.23 pymongo==4.3.3 PyNaCl==1.5.0 pynndescent==0.5.8 pyOpenSSL @ file:///croot/pyopenssl_1677607685877/work pyparsing==3.0.9 PyProcar==6.0.0 PyQt5-sip==12.11.0 pyrsistent==0.19.3 PySocks @ file:///home/builder/ci_310/pysocks_1640793678128/work pysr==0.12.0 pytest==7.3.2 python-dateutil @ file:///tmp/build/80754af9/python-dateutil_1626374649649/work python-dotenv==1.0.0 python-json-logger==2.0.7 python-sscha==1.3.2.1 pytorch-lightning==1.8.6 pytz==2022.7.1 pyvista==0.40.1 PyWavelets==1.4.1 PyYAML==6.0.1 pyzmq==24.0.1 qtconsole==5.4.3 QtPy==2.3.1 quippy-ase==0.9.14 rdkit==2023.3.1 requests==2.28.2 requests-oauthlib==1.3.1 rfc3339-validator==0.1.4 rfc3986-validator==0.1.1 rich==13.7.0 robocrys==0.2.8 rowan==1.3.0.post1 rsa==4.9 ruamel.yaml==0.17.21 ruamel.yaml.clib==0.2.7 s3transfer==0.6.1 schema==0.7.5 scikit-image==0.21.0 scikit-learn==1.0 scipy==1.10.1 scooby==0.7.2 seaborn==0.12.2 seekpath==2.1.0 Send2Trash==1.8.2 sentinels==1.0.0 sentry-sdk==1.26.0 shakenbreak==3.0.0 shapely==2.0.1 sip @ file:///tmp/abs_44cd77b_pu/croots/recipe/sip_1659012365470/work six @ file:///tmp/build/80754af9/six_1644875935023/work smmap==5.0.1 sniffio==1.3.0 snowballstemmer==2.2.0 soupsieve==2.4.1 sparse==0.14.0 spglib==2.0.2 Sphinx==7.2.6 sphinx-argparse==0.4.0 sphinx-pdj-theme==0.2.1 sphinxcontrib-applehelp==1.0.7 sphinxcontrib-devhelp==1.0.5 sphinxcontrib-htmlhelp==2.0.4 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.6 sphinxcontrib-serializinghtml==1.1.9 SQLAlchemy==2.0.25 sshtunnel==0.4.0 stack-data==0.6.2 starlette==0.27.0 stevedore==5.1.0 sumo==2.3.5 sympy==1.11.1 tabulate==0.9.0 tdscha==1.0.1 tenacity==8.2.2 tensorboard==2.12.1 tensorboard-data-server==0.7.0 tensorboard-plugin-wit==1.8.1 tensorboardX==2.6.2.2 tensorflow==2.12.0 tensorflow-estimator==2.12.0 tensorflow-io-gcs-filesystem==0.32.0 termcolor==2.2.0 terminado @ file:///croot/terminado_1671751832461/work threadpoolctl==3.1.0 tifffile==2023.4.12 tinycss2 @ file:///croot/tinycss2_1668168815555/work toml @ file:///tmp/build/80754af9/toml_1616166611790/work tomli @ file:///opt/conda/conda-bld/tomli_1657175507142/work torch==2.1.2 torch-cluster==1.6.3 torch-ema==0.3 torch-runstats==0.2.0 torch-scatter==2.1.2 torch-sparse==0.6.18 torchmetrics==1.2.0 tornado==6.3.2 tqdm==4.65.0 trainstation==1.0 traitlets==5.9.0 trimesh==3.22.3 triton==2.1.0 typeshed-client==2.4.0 typing==3.7.4.3 typing_extensions==4.8.0 umap-learn==0.5.3 uncertainties==3.1.7 uri-template==1.2.0 urllib3==2.1.0 uvicorn==0.23.2 Vapory==0.1.2 virtualenv==20.25.0 vtk==9.2.6 wcmatch==8.4.1 wcwidth==0.2.6 webcolors==1.13 webencodings==0.5.1 websocket-client==1.5.3 Werkzeug==2.2.3 widgetsnbextension==3.6.4 wrapt==1.14.1 yarl==1.9.2 zipp==3.16.2

laserkelvin commented 10 months ago

Addressed in #93