Stabilize CICD

Jenkinsfile

@@ -13,7 +13,7 @@ pipeline {
  steps {
  sh '''
  rm -rf test-reports/TEST-*.xml
- jbsub -wait -out ccc_log.txt -queue x86_1h -mem 40g -cores "10+1" -require 'v100' ./run_all_unit_tests.sh 11.8 /dccstor/fuse_med_ml/fuse-drug/cicd/envs/
+ jbsub -wait -out ccc_log.txt -queue x86_1h -mem 40g -cores "10+1" -require 'v100' ./run_all_unit_tests.sh no /dccstor/fuse_med_ml/fuse-drug/cicd/envs/
  echo "------ printing ccc_log.txt -----"
  cat "./ccc_log.txt"
  echo "------ Done printing ccc_log.txt ------"

fusedrug/data/tokenizer/ops/pytoda_tokenizer.py

@@ -10,17 +10,13 @@
  LeftPadding,
  ToTensor,
 )
-import torch
 
 
 class Op_pytoda_SMILESTokenizer(OpBase):
  def __init__(self, SMILES_Tokenizer_kwargs: dict, **kwargs: dict):
  super().__init__(**kwargs)
  self.language = SMILESTokenizer(
  **SMILES_Tokenizer_kwargs,
- device=torch.device(
- "cpu"
- ), # this is critical for DataLoader multiprocessing to work well !!!
  )
 
  def __call__(
@@ -66,7 +62,7 @@ def __init__(
 
  if isinstance(self.protein_language, ProteinLanguage):
  # transforms += [ToTensor(device=self.device)]
- transforms += [ToTensor(torch.device("cpu"))]
+ transforms += [ToTensor()]
  else:
  # note: ProteinFeatureLanguage supported wasn't transferred here.
  raise TypeError(

fusedrug_examples/requirements.txt

@@ -1,11 +1,10 @@
-tensorflow
 dscript
 dgl
 pysmiles
 deepchem
 mol2vec @ git+https://github.com/samoturk/mol2vec
 paccmann_predictor @ git+https://[email protected]/PaccMann/paccmann_predictor#egg=paccmann-predictor
 modlamp
-torchtext==0.3.1 # old version of tokenizer - need to replace with another tokenizer and remove this
 biopython
+torchtext
 x_transformers

run_all_unit_tests.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 source ~/.bashrc
 
-export CUDA_HOME=/opt/share/cuda-11.8 #to prevent mismatch between cuda runtime and the cuda version used to compile pytorch
+export CUDA_HOME=/opt/share/cuda-12.1 #to prevent mismatch between cuda runtime and the cuda version used to compile pytorch
 
 # check if current env already exist
 find_in_conda_env(){
@@ -30,7 +30,7 @@ create_env() {
  fi
 
  # Python version
- PYTHON_VER=3.8
+ PYTHON_VER=3.11
  ENV_NAME="fuse-drug_$PYTHON_VER-CUDA-$force_cuda_version-$(echo -n $requirements | sha256sum | awk '{print $1;}')"
  echo $ENV_NAME