Issues

• SpecifiedSplitter crashes with IndexError when valid_indices or test_indices is omitted or empty

  deepchem/deepchem#5264 · Filter by author muskan-creates352 opened on Nov 6, 2026

• SingletaskStratifiedSplitter drops leftover samples and crashes on NumpyDataset

  deepchem/deepchem#5261 · Filter by author robinbishtt opened on Nov 3, 2026
  1

• Cell_Counting_Tutorial fails on current Colab: pip resolves deepchem to 2.6.0.dev, torch_models.CNN missing

  deepchem/deepchem#5257 · Filter by author jiyac-code opened on Nov 1, 2026
  3

• SingletaskStratifiedSplitter returns float indices (crashes on NumpyDataset) and TaskSplitter.k_fold_split can return an empty fold

  deepchem/deepchem#5253 · Filter by author Aditya365x opened on Oct 30, 2026

• KFACOptimizer crashes on step() because torch.symeig was removed, and optimizers.KFAC cannot be used with TorchModel

  deepchem/deepchem#5251 · Filter by author Aditya365x opened on Oct 30, 2026

• PINNModel fails on MPS/CUDA: loss accumulators and boundary data stay on CPU

  deepchem/deepchem#5240 · Filter by author anirudh12032008 opened on Oct 21, 2026

• unzip_file and untargz_file mishandle dest_dir=None and name

  deepchem/deepchem#5237 · Filter by author AmoghPalasamudram opened on Oct 21, 2026
  2

• PFMFeaturizer ignores the charset argument

  deepchem/deepchem#5236 · Filter by author AmoghPalasamudram opened on Oct 21, 2026

• load_molecule() drops all but the first record from multi-molecule SDF files

  deepchem/deepchem#5234 · Filter by author TheegalaYeseswini opened on Oct 21, 2026

• DiskDataset.reshard() can hang with a zero or negative shard size

  deepchem/deepchem#5231 · Filter by author Programmer-Develops opened on Oct 20, 2026

• voxelize rejects documented multi-channel feature vectors

  deepchem/deepchem#5226 · Filter by author SiyuanChenToDo opened on Oct 19, 2026

• OneHotFeaturizer accepts invalid multi character charset entries

  deepchem/deepchem#5217 · Filter by author Galax1513 opened on Oct 14, 2026

• Misleading "requires PyTorch" ImportError when a non-torch dependency (tqdm) is missing

  deepchem/deepchem#5214 · Filter by author AmoghPalasamudram opened on Oct 14, 2026

• angle_between returns pi (antiparallel) for nearly parallel float32 vectors

  deepchem/deepchem#5211 · Filter by author ChenziqiAdam opened on Oct 11, 2026
  1

• DiskDataset: make_pytorch_dataset duplicates samples with num_workers > 1

  deepchem/deepchem#5198 · Filter by author HESleagacy opened on Oct 6, 2026

• ElectronSampler.log_prob_gaussian returns a wrong log-density unless sigma has one entry per electron

  deepchem/deepchem#5195 · Filter by author ChenziqiAdam opened on Oct 6, 2026

• compute_hydrogen_bonds misses hydrogen bonds depending on fragment order / hydrogen order, and ignores the angle cutoff

  deepchem/deepchem#5194 · Filter by author ChenziqiAdam opened on Oct 6, 2026

• Metric(bedroc_score) returns wrong values (0.51 for a perfect ranking)

  deepchem/deepchem#5191 · Filter by author Zhuoxi2000 opened on Oct 1, 2026
  1

• sequence_utils hhsearch/hhblits never reject an unsupported file type, and the '-M first' branch is dead code

  deepchem/deepchem#5186 · Filter by author aniruddhaadak80 opened on Sep 29, 2026

• FingerprintSplitter raises ZeroDivisionError when int(frac_train * len(dataset)) floors to zero

  deepchem/deepchem#5171 · Filter by author aniruddhaadak80 opened on Sep 28, 2026
  1

• CircularFingerprint.__eq__/__hash__ ignore is_counts_based, so counts and bit-vector featurizers compare equal and collapse in a set

  deepchem/deepchem#5169 · Filter by author aniruddhaadak80 opened on Sep 28, 2026

• load_csv_files() leaves a NaN label with weight 1 when shard_size is None, so shard_size silently changes the training set

  deepchem/deepchem#5167 · Filter by author aniruddhaadak80 opened on Sep 28, 2026
  1

• create_char_to_idx() returns a different char->index mapping in every process (set iteration order leaks into the vocabulary)

  deepchem/deepchem#5165 · Filter by author aniruddhaadak80 opened on Sep 28, 2026

• Placement for a reproducible Tox21 PyTorch example with optional Nebius Jobs instructions

  deepchem/deepchem#5164 · Filter by author SalikovAlex opened on Sep 28, 2026
  1

• RandomSplitter accepts negative split fractions and produces invalid splits

  deepchem/deepchem#5159 · Filter by author MateehUllah opened on Sep 26, 2026
  2