add debugging info

explosion · Jul 24, 2023 · 63fb645 · 63fb645
1 parent 0d50bc9
commit 63fb645
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Showing 3 changed files with 12 additions and 5 deletions.
diff --git a/tutorials/llm_clinical_trials/falcon_requirements.txt b/tutorials/llm_clinical_trials/falcon_requirements.txt
@@ -1,4 +1,5 @@
 cupy-cuda117
-torch==1.13.1+cu117 -f https://download.pytorch.org/whl/torch_stable.html
+torch==2.0.1+cu117 -f https://download.pytorch.org/whl/torch_stable.html
 transformers
-einops
+einops
+xformers
diff --git a/tutorials/llm_clinical_trials/project.yml b/tutorials/llm_clinical_trials/project.yml
@@ -2,7 +2,7 @@ title: 'Clinical trial results extraction with LLMs'
 description: "Using an LLM in a spaCy pipeline to extract patient groups, treatments and outcomes in clinical trials."
 
 vars:
-  ner_config: "ner_dolly.cfg" # "ner_falcon.cfg"  # "ner_openai.cfg"
+  ner_config: "ner_falcon.cfg" # "ner_dolly.cfg"   # "ner_openai.cfg"
   trial_config: "trial_openai.cfg"
   pmid: 27144689
 

diff --git a/tutorials/llm_clinical_trials/scripts/visualise_entities.py b/tutorials/llm_clinical_trials/scripts/visualise_entities.py
@@ -8,8 +8,14 @@
 
 
 def visualise_entities(pmid: int, config_path: Path, verbose: bool = False):
-    msg.text(f"Processing PMID {pmid}", show=verbose)
-    msg.text(f"Loading config from {config_path}", show=verbose)
+    import logging
+    import spacy_llm
+
+    spacy_llm.logger.addHandler(logging.StreamHandler())
+    spacy_llm.logger.setLevel(logging.DEBUG)
+
+    #msg.text(f"Processing PMID {pmid}", show=verbose)
+    #msg.text(f"Loading config from {config_path}", show=verbose)
     text = read_trial(pmid, verbose=verbose)
     nlp = assemble(config_path)
     doc = nlp(text)