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Graphium 3.0#519

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Commits on Apr 13, 2024

• Added and integrated C++ graphium_cpp library, a Python module implemented in C++ for featurization and preprocessing optimizations, along with a few other optimizations, significantly reducing mem…

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Commits on Apr 17, 2024

• Small changes to support not needing label data during data loading

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• Removed FakeDataset, FakeDataModule, and SingleTaskDataset. SingleTaskDataset is still used in test_dataset.py, but won't after it's changed in a later commit.

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• Removed option to featurize using Python, (but didn't delete everything from the Python featurization yet), removed option to featurize to GraphData class instead of PyG Data class, added deprecati…

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Commits on Apr 18, 2024

• Removed newly deprecated options from yaml files

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• Added support for limiting the number of threads used by prepare_and_save_data

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• Fixed compiler warning about signed vs. unsigned comparison

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• Fixed Python syntax issues

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• Changed asymmetric inverse normalization type to be implemented using symmetric diagonalization, avoiding the need to handle complex eigenvectors and eigenvalues

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• Fixed compile errors

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Commits on Apr 19, 2024

• Some simplification in collate.py

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• Deleting most of the Python featurization code

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Commits on Apr 23, 2024

• Implemented conformer generation in get_conformer_features, trying to match behaviour from get_simple_mol_conformer Python code, but adding Hs, as recommended for conformer generation.

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• Deleted deprecated properties.py

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Commits on Apr 25, 2024

• Handle case of no label data in prepare_and_save_data. Also added concatenate_strings function, though it's not used yet.

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• Changed prepare_data to support having no label data

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Commits on Apr 26, 2024

• Removed ipu metrics, since not compatible with latest torchmetrics

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• Updated MetricWrapper to work with update and compute, compatible with torchmetrics

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• Changed requirements for torchmetrics

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• fixed the loss by adding MetricToTorchMetrics, and added a few comments on the Predictor for Todos

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Commits on May 2, 2024

• Updated license passed to setup call in setup.py

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Commits on May 3, 2024

• Major updates to predictor_summaries.py

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• Improved the predictor summaries. Added GradientNormMetric

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Commits on May 6, 2024

• Changes to get test_dataset.py and test_multitask_datamodule.py passing

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• Removed load_type option from test_training.py, because it's no longer used

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Commits on May 14, 2024

• Updated comment in setup.py about how to build graphium_cpp package

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• Rewrote test_featurizer.py. Fixed bug in mask_nans C++ function, and changed create_all_features to create all tensors even if there are nans, so that the number of atoms can still be determined fr…

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Commits on May 23, 2024

• Removed deprecation warnings and deprecated parameters from datamodule.py, keeping the notes in the function comments

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• Recommended tweaks to extract_labels in multilevel_utils.py

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• Fixed "else if"->"elif"

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Commits on May 24, 2024

• Rewrote test_pe_nodepair.py to use graphium_cpp

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• Rewrote test_pe_rw.py to use graphium_cpp. Comment update in test_pe_nodepair.py

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• Rewrote test_pe_spectral.py to use graphium_cpp

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• Removed tests/test_positional_encodings.py, because it's a duplicate of test_pe_nodepair.py, apart from a couple comments

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Commits on May 28, 2024

• Fixed handling of disconnected components vs. single component for laplacian eigenvector/eigenvalue features, especially edge case with a single atom that was being treated as having multiple compo…

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• Fixed compile warnings in one_hot.cpp

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• Rewrote test_positional_encoders.py, though it's still failing the test_laplacian_eigvec_with_encoder case

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Commits on Jun 4, 2024

• Removed commented out lines from setup.py

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• Ran linting on Python files

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Commits on Jun 5, 2024

• Hopefully explicitly installing graphium_cpp fixes the automated testing for now

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• Test fix

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• Another test fix

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• Another test fix

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• Make sure RDKit can find Boost headers

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Commits on Jun 12, 2024

• Reimplemented test_pos_transfer_funcs.py to test all supported conversions

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• Linting fixes

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• Fixed collections.abs.Callable to typing.Callable for type hint

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Commits on Jun 13, 2024

• Improved the task summaries and started to fix the training logging.

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Commits on Jun 17, 2024

• Removed file_opener and its test

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Commits on Jul 9, 2024

• Fixed the issue with boolean masking, introduced by F._canonical_mask in TransformerEncoder

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• Fixed the float vs double issue in laplacian pos encoding

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• Added comment

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• Fixed the ipu tests by making sure that IPUStrategy is not imported if not using IPUs

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• Update test.yml to only test python 3.10

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• Removed positional encodings from the docs

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• Merge remote-tracking branch 'origin/dom_unittest' into dom_unittest

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• Upgraded python versions in the tests

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• Removed reference to old files now in C++

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• Downgraded python version

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• Fixed other docs broken references

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• Merge pull request #1 from ndickson-nvidia/dom_unittest

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• Merge pull request #510 from ndickson-nvidia/graphium_cpp

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Commits on Jul 10, 2024

• Fixed test_metrics. Moved lots of spaces.py imports to inner functions to avoid import loops

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Commits on Jul 11, 2024

• duplicated some unit-test fixes from graphium_3.0 branch

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• Fixed the loading of a previous dummy model using older metrics by removing the metrics from the model

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• Minor documentation

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• Removed the loss from predictor_summaries

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• Removed epochs from task summaries

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• Draft implementing the update/compute logic in the predictor.

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• Fix the std metric. Still needs testing.

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• fixed all errors arising in test_finetuning.py

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Commits on Jul 12, 2024

• Fixed the test_training.py unit test

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• Standardized the test names

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• Fixed some unit-tests that were broken by previous changes

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• Added pytdc to the tests

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• Changed mamba install tdc to pip install, in the test.yml file

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• Added '--no-deps' to TDC installation in test.yml

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• Woops

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• Fixed issue with building docs

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• Removed old file from breaking docs building

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• Changed to micromamba to install pytdc

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• Added tests for the STDMetric and GradientNormMetric and fixed their outputs

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• Implemented test of MultiTaskSummaries. Only an error left for the mean and std of preds and targets

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Commits on Jul 13, 2024

• Fixed the preds and targets that were inverted in TaskSummary

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• Tried to add grad_norm to the metrics, but won't work because it's not per task

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• Moved the gradient metric directly to the Predictor

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• Removed file_opener and read_file

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• Fixed predictor grad_norm

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• Merge branch 'graphium_3.0' into torchmetrics

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Commits on Jul 15, 2024

• Fixed the progress bar logging to newest version. Fixed minor issues in the logging and imports.

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• Merge remote-tracking branch 'origin/torchmetrics' into torchmetrics

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• fixed some issue with older version of torchmetrics

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Commits on Jul 16, 2024

• Fixed reversed preds/targets. Fixed random sampling to take in the DF idx. Few other minor changes

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• fixed missing metrics computation on on_train_batch_end

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• Added toymix training to the unit-tests. Also useful to run in debug mode.

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• Adding _global/ to some metrics logging into wandb

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• Added better handling of metrics failure with logger.warn

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• Fixed metric issues on gpu by casting to the right device prior to .update

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Commits on Jul 17, 2024

• Added losses to the metrics, such that they are computed on val and test too

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• Restricting the numpy version due to issues with wandb

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• detaching preds

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• Removed cuda version restriction

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• Removed unnecessary detach, that broke the loss

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Commits on Jul 30, 2024

• Updating dep versions for bh2 install

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Commits on Jul 31, 2024

• Merge pull request #522 from datamol-io/package/bh2-install

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Commits on Aug 8, 2024

• Fix lightning backend issue; add predict_step for inference

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Commits on Aug 9, 2024

• Fixing device issue in metrics calculation

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Commits on Aug 15, 2024

• Minor gitignore

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Commits on Aug 16, 2024

• Fixed the error due to time metrics on CPU No backend type associated with device type cpu

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• Added val epoch time

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Commits on Aug 17, 2024

• Added logic to avoid crashing when resetting unused metrics

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Commits on Aug 19, 2024

• Added MetricWrapper.device

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• Disable caching model checkpoint through WandbLogger

  

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• Disabled caching model checkpoint through WandbLogger

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• Drafting unit test for node ordering

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Commits on Aug 21, 2024

• Improved the testing of the metrics reset, update, compute

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• Reverted wrong change in `train_finetune_test.py

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• Improved __len__ in MultitaskDataModule

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Commits on Aug 22, 2024

• Added a new logic to allow saving all preds and targets more efficiently for auroc and avpr

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• Fixed the concatenation to work with and without DDP. Moved to CPU for faster + less memory requirement

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• Fixed the issue with memory leaks and devices.

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• Fixed the CPU syncing of MetricToConcatenatedTorchMetrics and GPU for other metrics

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• Fixed the training metrics, and grouped all epoch-time and tput metrics

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• Fixing unit tests

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• Fixed epoch_time tracking (because train ends after val)

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Commits on Aug 23, 2024

• Using the torchmetrics.Metric.sync instead of torch_distributed

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Commits on Aug 29, 2024

• Fixed issue that NaNs are always removed with mean-per-label

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• Changed the name of logging variables

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• Removed some IPU logic

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• Fixed the syncing of MetricToConcatenatedTorchMetrics

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• Fixed classification metric calculation when multitask_handling=flatten

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Commits on Sep 5, 2024

• Partial fix of node label ordering

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Commits on Sep 7, 2024

• Fixed all unit-test, except those for IPU

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• First pass at removing IPU

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• More removal of ipu

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• More removal of ipus

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• More removal of ipus

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• Remove packing

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• Fixing most unit-tests

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• Updated env file

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• Fixed the dummy model, toymix run, and most unit-tests

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• Minor

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• Fixed all remaining unit-tests - mostly the attention layers

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• minor changes to env

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• Added comments to env file

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Commits on Sep 10, 2024

• Merge branch 'graphium_3.0' into torchmetrics

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• Merge pull request #517 from datamol-io/torchmetrics

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Commits on Sep 11, 2024

• Merge branch 'torchmetrics' into remove_ipu

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• Forcing gcc_linux_64 in the env file

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Commits on Sep 16, 2024

• Update test.yml

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• Update test.yml

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• Update test.yml

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Commits on Sep 19, 2024

• Changed persistent_workers=True to False

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Commits on Sep 23, 2024

• Reorder atoms in node-level and nodepair-level label data, when the same molecule appears in multiple tasks with different atom orders, to be consistent with the first task's atom order

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• Merging of equivalent molecules is now optional, but still defaults to true.

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• Fixed bug with recent change in smiles_to_brief_data

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• Fix graphium_cpp.prepare_and_save_data call in test_dataset.py to include merge_equivalent_mols parameter

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• In MultitaskFromSmilesDataModule.get_data_hash, include options used during pre-processing

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• Linter fixes in python files already modified in this branch

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• Split prepare_and_save_data into get_task_data, get_indices_and_strings, compute_mol_keys, compute_stats, save_non_label_data, and save_label_data, to make the code more manageable.

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• Added support for reordering edge label data if there are multiple tasks with the same molecule and one of them has edge-level label data. This should order bonds consistent with the first copy of …

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• Changed parse_mol in graphium_cpp.cpp to order based only on explicit atom classes in the SMILES strings, and only if they represent a complete atom order, to fix the accidental removal of support …

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• The datasets use 0-based indexing for explicit ordering via atom classes in SMILES strings, not 1-based

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• Started adding doxygen comments to the C++ code. Also changed compute_laplacian_eigendecomp to accept const int32_t* instead of const std::vector<int32_t>*

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• Adding unit test for node ordering

  

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• Added doxygen comments for functions and enums related to one-hot feature encoding

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• Added more doxygen comments

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• Added and updated more comments

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• Added comments to each function in features.cpp

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• Investigating failing unit tests

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• Added more comments to labels.cpp

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• Merge branch 'atom_order' of ssh://github.com/ndickson-nvidia/graphium into atom_order

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• Build fix in features.cpp

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• Skipping test_training.py for now

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• Merge pull request #521 from ndickson-nvidia/atom_order

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Commits on Sep 27, 2024

• Updated documentation

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• Updated documentation

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Commits on Oct 31, 2024

• Wrapping up finetuning updates

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• Update readme

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• Fixed finetuning unit test

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• Fixing docs

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Commits on Nov 4, 2024

• Merge pull request #530 from datamol-io/remove_ipu

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• Reducing size of example finetuning dataset

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• Cleaning up configs and naming conventions

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• Minor changes and documentation

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• Minor change

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• Merge pull request #529 from datamol-io/upgrade-finetuning

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• Added C++ file description comments

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• Merge pull request #532 from ndickson-nvidia/cpp_file_descriptions

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