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AMPL 1.5.0 release

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@mauvais2 mauvais2 released this 01 Mar 00:43
· 735 commits to master since this release
57f2220
  • Updated AMPL to deepchem 2.7.1 and the related libraries
    -- Python 3.8.x
    -- numpy 1.21.6
    -- rdkit 2022.9.3
    -- rdkit-pypi 2022.3.5

  • Changed the environment setup from a mixture of conda and pip packages to pip exclusively
    -- Updated the related document to reflect the change
    -- Removed unused packages from the requirements list

  • Feature enhancements/code clean-up
    -- Added ability to highlight substructures and SMARTS pattern matches in molecules rendered with rdkit_easy functions mol_to_svg, mol_to_html, etc.
    -- Updated hyper_perf_plots.py to work with minimal examples
    -- Changed splitting code to allow many-to-one mapping from compound IDs to SMILES strings
    -- Change to support AD index computation for graphconv models using embeddings as features
    -- Added max_dataset_rows parameter to limit number of training set records used for AD index computation, so that AD computation is feasible for models trained on large datasets.
    -- Replaced all uses of deepchem.data.DiskDataset with NumpyDataset to boost performance and reduce creation of temporary files
    -- Added workaround for DeepChem issue #1821, which was causing predictions to fail on single-compound batches.
    -- Implemented tar archive safe extract to fix vulnerability CVE-2007-4559
    -- Turned off uncertainty for multi_class_config_delaney_fit_NN_graphconv.json
    -- Refined AMPL version/model version compatibility checking to define groups of compatible versions according to whether the associated DeepChem versions have the same format of model checkpoint files. The current compatibility groups are:
    -- Group1: '1.2', '1.3'
    -- Group2: '1.4'
    -- Group3: '1.5'

  • Bug fixes