fix an error using cytotrace2_py

[Starlitnightly]

We noticed that when using concurrent.futures.ProcessPoolExecutor, the program may raise an error during runtime, so we replaced it with concurrent.futures.ThreadPoolExecutor.

BrokenProcessPool Traceback (most recent call last)
Cell In[16], line 1
----> 1 results = cytotrace2(adata_control,
2 use_model_dir="../ov/cymodels/5_models_weights",
3 species="human")

File ~/software/rsc/lib/python3.10/site-packages/omicverse/single/_cytotrace2.py:188, in cytotrace2(adata, use_model_dir, species, batch_size, smooth_batch_size, disable_parallelization, max_cores, max_pcs, seed, output_dir)
183 results.append(executor.submit(process_subset, idx,
184 chunked_expression, smooth_batch_size,
185 smooth_cores_to_use, species,
186 use_model_dir, output_dir, max_pcs, seed))
187 for f in concurrent.futures.as_completed(results):
--> 188 smooth_by_knn_df = f.result()
189 predictions.append(smooth_by_knn_df)
191 for idx in range(chunk_number):

File ~/software/rsc/lib/python3.10/concurrent/futures/_base.py:451, in Future.result(self, timeout)
449 raise CancelledError()
450 elif self._state == FINISHED:
--> 451 return self.__get_result()
453 self._condition.wait(timeout)
455 if self._state in [CANCELLED, CANCELLED_AND_NOTIFIED]:

File ~/software/rsc/lib/python3.10/concurrent/futures/_base.py:403, in Future.__get_result(self)
401 if self._exception:
402 try:
--> 403 raise self._exception
404 finally:
405 # Break a reference cycle with the exception in self._exception
406 self = None

BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending

We added smooth_data_kNN.py to instead the smooth_data_kNN.R in cytotrace2_py.

    if chunked_expression.shape[0] < 100:
        print('cytotrace2: Fewer than 100 cells in dataset. Skipping KNN smoothing step.')
        smooth_by_knn_df = binned_score_pred_df.copy()
    else:
        #run_script = pkg_resources.resource_filename("cytotrace2_py","resources/smoothDatakNN.R")
        #knn_path = output_dir+'/smoothbykNNresult'+suffix+'.txt'
        #out = subprocess.run(['Rscript', run_script, '--output-dir', output_dir,
                               #'--suffix', suffix, '--max-pcs', str(max_pcs), '--seed', str(seed)], check=True)
        from .common.smoothDatakNN import smooth_data_kNN
        smooth_data_kNN(output_dir=output_dir, suffix=suffix, max_pcs=max_pcs, seed=seed)
        knn_path = os.path.join(output_dir, f'smoothbykNNresult{suffix}.txt')
        smooth_by_knn_df = pd.read_csv(knn_path, index_col=0, sep='\t')