From 5ae3ed7b92e2330c450da695cf659f7d3daa5d82 Mon Sep 17 00:00:00 2001 From: mart-r Date: Wed, 18 Sep 2024 13:51:01 +0100 Subject: [PATCH 1/2] CU-8695vnd6h: Update requirement to medcat 1.13 --- requirements-dev.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements-dev.txt b/requirements-dev.txt index c03b137..0ee8594 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -1,4 +1,4 @@ -medcat~=1.12.0 +medcat~=1.13.0 pandas<2.0.0 seaborn~=0.11.2 pytest-xdist~=2.5.0 From 2a038545e43dca9511611fde4690b5f89e6f20a8 Mon Sep 17 00:00:00 2001 From: mart-r Date: Wed, 18 Sep 2024 13:54:33 +0100 Subject: [PATCH 2/2] CU-8695vnd6h: Update installs in notebooks to medcat 1.13 --- ...Part_1_1_OPTIONAL_Logging_With_MedCAT.html | 2 +- ...art_1_1_OPTIONAL_Logging_With_MedCAT.ipynb | 2 +- ...ing_a_Concept_Database_and_Vocabulary.html | 2 +- ...ng_a_Concept_Database_and_Vocabulary.ipynb | 2 +- ...seases_from_Electronic_Health_Records.html | 6 +- ...eases_from_Electronic_Health_Records.ipynb | 2 +- ...art_3_3_Model_technical_optimisations.html | 2 +- ...rt_3_3_Model_technical_optimisations.ipynb | 2 +- ..._ByteLevelBPETokenizer_and_Embeddings.html | 26137 +++++++-------- ...ByteLevelBPETokenizer_and_Embeddings.ipynb | 2 +- ...ervised_Training_and_Meta_annotations.html | 27222 ++++++++-------- ...rvised_Training_and_Meta_annotations.ipynb | 2 +- ..._MedCAT_pipeline_with_MetaAnnotations.html | 2 +- ...MedCAT_pipeline_with_MetaAnnotations.ipynb | 2 +- ...lence_of_Physical_and_Mental_Diseases.html | 2 +- ...ence_of_Physical_and_Mental_Diseases.ipynb | 2 +- ...Comparing_Models_with_RegressionSuite.html | 2 +- ...omparing_Models_with_RegressionSuite.ipynb | 2 +- 18 files changed, 25054 insertions(+), 28341 deletions(-) diff --git a/notebooks/introductory/Part_1_1_OPTIONAL_Logging_With_MedCAT.html b/notebooks/introductory/Part_1_1_OPTIONAL_Logging_With_MedCAT.html index 68c3753..2ab6ae0 100644 --- a/notebooks/introductory/Part_1_1_OPTIONAL_Logging_With_MedCAT.html +++ b/notebooks/introductory/Part_1_1_OPTIONAL_Logging_With_MedCAT.html @@ -13095,7 +13095,7 @@

MedCAT tutorial - logging with Me 
# Install medcat
-! pip install medcat~=1.12.0
+! pip install medcat~=1.13.0
 try:
     from medcat.cat import CAT
 except:
diff --git a/notebooks/introductory/Part_1_1_OPTIONAL_Logging_With_MedCAT.ipynb b/notebooks/introductory/Part_1_1_OPTIONAL_Logging_With_MedCAT.ipynb
index 4c5b0ef..d1ee6bd 100644
--- a/notebooks/introductory/Part_1_1_OPTIONAL_Logging_With_MedCAT.ipynb
+++ b/notebooks/introductory/Part_1_1_OPTIONAL_Logging_With_MedCAT.ipynb
@@ -19,7 +19,7 @@
    "outputs": [],
    "source": [
     "# Install medcat\n",
-    "! pip install medcat~=1.12.0\n",
+    "! pip install medcat~=1.13.0\n",
     "try:\n",
     "    from medcat.cat import CAT\n",
     "except:\n",
diff --git a/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.html b/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.html
index 0b33cac..467b5d4 100644
--- a/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.html
+++ b/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.html
@@ -13099,7 +13099,7 @@ 
First we need to install MedCAT
     

 
# Install MedCAT
-! pip install medcat~=1.12.0
+! pip install medcat~=1.13.0
 # Get the scispacy model
 ! python -m spacy download en_core_web_md
 try:
diff --git a/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.ipynb b/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.ipynb
index 7a3bd23..1d3e25c 100644
--- a/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.ipynb
+++ b/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.ipynb
@@ -322,7 +322,7 @@
    ],
    "source": [
     "# Install MedCAT\n",
-    "! pip install medcat~=1.12.0\n",
+    "! pip install medcat~=1.13.0\n",
     "# Get the scispacy model\n",
     "! python -m spacy download en_core_web_md\n",
     "try:\n",
diff --git a/notebooks/introductory/Part_3_2_Extracting_Diseases_from_Electronic_Health_Records.html b/notebooks/introductory/Part_3_2_Extracting_Diseases_from_Electronic_Health_Records.html
index 201d63f..eb5f3df 100644
--- a/notebooks/introductory/Part_3_2_Extracting_Diseases_from_Electronic_Health_Records.html
+++ b/notebooks/introductory/Part_3_2_Extracting_Diseases_from_Electronic_Health_Records.html
@@ -13092,7 +13092,7 @@ 
Now let's s
 

     

 
# Install medcat
-! pip install medcat~=1.12.0
+! pip install medcat~=1.13.0
 # install seaborn
 ! pip install seaborn
 try:
@@ -14706,10 +14706,10 @@ 
Use Multiprocessing

+

 

 
 
+Part_4_1_ByteLevelBPETokenizer_and_Embeddings
 
+
+
 
 
 
 
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+
 
-.jp-OutputArea-output.jp-OutputArea-executeResult {
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-/* Hiding the collapser by default */
-.jp-Collapser {
-  display: none;
+
 
+
+
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+
 
-    
+    
     
     
     
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+  

+    

 
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