CU-86973p9z4 Update tutorials to medcat 1.14 (CogStack/MedCATtutorials#28)

mart-r · web-flow · commit a921ba0af3da · 2025-01-06T10:57:28.000Z
* CU-86973p9z4: Update requirement to medcat 1.14

* CU-86973p9z4: Update installed medcat verison in notebooks to 1.14

* CU-86973p9z4: Update workflow to python 3.11

* CU-86973p9z4: Update workflow to use latest ubuntu (instead of macos-12)

* CU-86973p9z4: Update workflow to use latest macos

* CU-86973p9z4: Reverting python version to 3.9 in workflow

* CU-86973p9z4: Fix (hopefully) IPython setup

* CU-86973p9z4: Add pin for matplotlib (less than 3.8)

* Revert "CU-86973p9z4: Reverting python version to 3.9 in workflow"

This reverts commit 69ed00f48d898bfc45be8950910ab5b602600105.
diff --git a/medcat-v1-tutorials/.github/workflows/main.yml b/medcat-v1-tutorials/.github/workflows/main.yml
@@ -9,7 +9,7 @@ on:
 jobs:
   main:
 
-    runs-on: macos-12
+    runs-on: macos-latest
     strategy:
       matrix:
         part: [
@@ -27,14 +27,14 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.11"
       - name: Install dependencies
         run: |
           pip install -U pip
           pip install -r requirements-dev.txt
       - name: Install IPython kernel
         run: |
-          python -m ipykernel install --name smoketests
+          python -m ipykernel install --name smoketests --user
       - name: Smoke test tutorial
         run: |
           pytest --collect-only --nbmake ./notebooks/${{ matrix.part }}
diff --git a/medcat-v1-tutorials/notebooks/introductory/Part_1_1_OPTIONAL_Logging_With_MedCAT.html b/medcat-v1-tutorials/notebooks/introductory/Part_1_1_OPTIONAL_Logging_With_MedCAT.html
@@ -13095,7 +13095,7 @@ <h1 id="MedCAT-tutorial---logging-with-MedCAT">MedCAT tutorial - logging with Me
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Install medcat</span>
-<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.13.0
+<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.14.0
 <span class="k">try</span><span class="p">:</span>
     <span class="kn">from</span> <span class="nn">medcat.cat</span> <span class="kn">import</span> <span class="n">CAT</span>
 <span class="k">except</span><span class="p">:</span>
diff --git a/medcat-v1-tutorials/notebooks/introductory/Part_1_1_OPTIONAL_Logging_With_MedCAT.ipynb b/medcat-v1-tutorials/notebooks/introductory/Part_1_1_OPTIONAL_Logging_With_MedCAT.ipynb
@@ -19,7 +19,7 @@
    "outputs": [],
    "source": [
     "# Install medcat\n",
-    "! pip install medcat~=1.13.0\n",
+    "! pip install medcat~=1.14.0\n",
     "try:\n",
     "    from medcat.cat import CAT\n",
     "except:\n",
diff --git a/medcat-v1-tutorials/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.html b/medcat-v1-tutorials/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.html
@@ -13099,7 +13099,7 @@ <h3 id="First-we-need-to-install-MedCAT">First we need to install MedCAT<a class
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Install MedCAT</span>
-<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.13.0
+<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.14.0
 <span class="c1"># Get the scispacy model</span>
 <span class="o">!</span> python -m spacy download en_core_web_md
 <span class="k">try</span><span class="p">:</span>
diff --git a/medcat-v1-tutorials/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.ipynb b/medcat-v1-tutorials/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.ipynb
@@ -322,7 +322,7 @@
    ],
    "source": [
     "# Install MedCAT\n",
-    "! pip install medcat~=1.13.0\n",
+    "! pip install medcat~=1.14.0\n",
     "# Get the scispacy model\n",
     "! python -m spacy download en_core_web_md\n",
     "try:\n",
diff --git a/medcat-v1-tutorials/notebooks/introductory/Part_3_2_Extracting_Diseases_from_Electronic_Health_Records.html b/medcat-v1-tutorials/notebooks/introductory/Part_3_2_Extracting_Diseases_from_Electronic_Health_Records.html
@@ -13092,7 +13092,7 @@ <h1 id="Now-let's-start-extracting-concepts-from-unstructured-text!">Now let's s
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Install medcat</span>
-<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.13.0
+<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.14.0
 <span class="c1"># install seaborn</span>
 <span class="o">!</span> pip install seaborn
 <span class="k">try</span><span class="p">:</span>
@@ -14706,10 +14706,10 @@ <h2 id="Use-Multiprocessing">Use Multiprocessing<a class="anchor-link" href="#Us
 
  
  
-<div id="8d4dc075-1e4a-4520-bc59-043368d5e637"></div>
+<div id="9de888b0-4c6d-44f7-bd70-b4316f888f78"></div>
 <div class="output_subarea output_widget_view ">
 <script type="text/javascript">
-var element = $('#8d4dc075-1e4a-4520-bc59-043368d5e637');
+var element = $('#9de888b0-4c6d-44f7-bd70-b4316f888f78');
 </script>
 <script type="application/vnd.jupyter.widget-view+json">
 {"model_id": "05b18c97da9d4d05b9280df006a5fb82", "version_major": 2, "version_minor": 0}
diff --git a/medcat-v1-tutorials/notebooks/introductory/Part_3_2_Extracting_Diseases_from_Electronic_Health_Records.ipynb b/medcat-v1-tutorials/notebooks/introductory/Part_3_2_Extracting_Diseases_from_Electronic_Health_Records.ipynb
@@ -275,7 +275,7 @@
    ],
    "source": [
     "# Install medcat\n",
-    "! pip install medcat~=1.13.0\n",
+    "! pip install medcat~=1.14.0\n",
     "# install seaborn\n",
     "! pip install seaborn\n",
     "try:\n",
diff --git a/medcat-v1-tutorials/notebooks/introductory/Part_3_3_Model_technical_optimisations.html b/medcat-v1-tutorials/notebooks/introductory/Part_3_3_Model_technical_optimisations.html
@@ -13092,7 +13092,7 @@ <h1 id="Now-let's-look-at-ways-to-optimise-the-model-for-our-specific-use-case">
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Install medcat</span>
-<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.13.0
+<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.14.0
 <span class="k">try</span><span class="p">:</span>
     <span class="kn">from</span> <span class="nn">medcat.cat</span> <span class="kn">import</span> <span class="n">CAT</span>
 <span class="k">except</span><span class="p">:</span>
diff --git a/medcat-v1-tutorials/notebooks/introductory/Part_3_3_Model_technical_optimisations.ipynb b/medcat-v1-tutorials/notebooks/introductory/Part_3_3_Model_technical_optimisations.ipynb
@@ -165,7 +165,7 @@
    ],
    "source": [
     "# Install medcat\n",
-    "! pip install medcat~=1.13.0\n",
+    "! pip install medcat~=1.14.0\n",
     "try:\n",
     "    from medcat.cat import CAT\n",
     "except:\n",
diff --git a/medcat-v1-tutorials/notebooks/introductory/Part_4_1_ByteLevelBPETokenizer_and_Embeddings.html b/medcat-v1-tutorials/notebooks/introductory/Part_4_1_ByteLevelBPETokenizer_and_Embeddings.html
@@ -13093,7 +13093,7 @@ <h4><b>NOTE:</b> This tutorial is applicable for BiLSTM model not BERT as BERT m
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Install medcat</span>
-<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.13.0
+<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.14.0
 <span class="k">try</span><span class="p">:</span>
     <span class="kn">from</span> <span class="nn">medcat.cat</span> <span class="kn">import</span> <span class="n">CAT</span>
 <span class="k">except</span><span class="p">:</span>
diff --git a/medcat-v1-tutorials/notebooks/introductory/Part_4_1_ByteLevelBPETokenizer_and_Embeddings.ipynb b/medcat-v1-tutorials/notebooks/introductory/Part_4_1_ByteLevelBPETokenizer_and_Embeddings.ipynb
@@ -272,7 +272,7 @@
    ],
    "source": [
     "# Install medcat\n",
-    "! pip install medcat~=1.13.0\n",
+    "! pip install medcat~=1.14.0\n",
     "try:\n",
     "    from medcat.cat import CAT\n",
     "except:\n",
diff --git a/medcat-v1-tutorials/notebooks/introductory/Part_4_2_Supervised_Training_and_Meta_annotations.html b/medcat-v1-tutorials/notebooks/introductory/Part_4_2_Supervised_Training_and_Meta_annotations.html
@@ -13085,7 +13085,7 @@
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Install medcat</span>
-<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.13.0
+<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.14.0
 <span class="c1"># Get the spacy model</span>
 <span class="o">!</span> python -m spacy download en_core_web_md
 <span class="k">try</span><span class="p">:</span>
@@ -13968,10 +13968,10 @@ <h2 id="Fine-tuning-the-NER+L&#160;model">Fine-tuning the NER+L&#160;model<a cla
 
  
  
-<div id="ceec6296-b746-4c96-8788-05db7293ee48"></div>
+<div id="02d1928a-9e76-4203-8150-39600f768606"></div>
 <div class="output_subarea output_widget_view ">
 <script type="text/javascript">
-var element = $('#ceec6296-b746-4c96-8788-05db7293ee48');
+var element = $('#02d1928a-9e76-4203-8150-39600f768606');
 </script>
 <script type="application/vnd.jupyter.widget-view+json">
 {"model_id": "6fd10f1692234019836a7b40e83b56dd", "version_major": 2, "version_minor": 0}
@@ -13990,10 +13990,10 @@ <h2 id="Fine-tuning-the-NER+L&#160;model">Fine-tuning the NER+L&#160;model<a cla
 
  
  
-<div id="9c6977b2-1990-4658-ba7e-bdb30e192142"></div>
+<div id="668a03f9-0945-44b2-a586-e04d9712fb71"></div>
 <div class="output_subarea output_widget_view ">
 <script type="text/javascript">
-var element = $('#9c6977b2-1990-4658-ba7e-bdb30e192142');
+var element = $('#668a03f9-0945-44b2-a586-e04d9712fb71');
 </script>
 <script type="application/vnd.jupyter.widget-view+json">
 {"model_id": "9a5ab9cfecc242b7aaf0f140e87bdde6", "version_major": 2, "version_minor": 0}
@@ -14072,10 +14072,10 @@ <h2 id="Fine-tuning-the-NER+L&#160;model">Fine-tuning the NER+L&#160;model<a cla
 
  
  
-<div id="ba6953ec-49d6-42c4-bdd5-4f6917e60e23"></div>
+<div id="8572cdcc-32eb-4e5b-a949-5daf8d13babd"></div>
 <div class="output_subarea output_widget_view ">
 <script type="text/javascript">
-var element = $('#ba6953ec-49d6-42c4-bdd5-4f6917e60e23');
+var element = $('#8572cdcc-32eb-4e5b-a949-5daf8d13babd');
 </script>
 <script type="application/vnd.jupyter.widget-view+json">
 {"model_id": "434496e448984f55925d22fad0349ada", "version_major": 2, "version_minor": 0}
@@ -14094,10 +14094,10 @@ <h2 id="Fine-tuning-the-NER+L&#160;model">Fine-tuning the NER+L&#160;model<a cla
 
  
  
-<div id="7bd224d3-94ac-4ce9-b7e3-c76c30f51853"></div>
+<div id="fd91c526-e2a4-4fc0-866f-a728dad07fb1"></div>
 <div class="output_subarea output_widget_view ">
 <script type="text/javascript">
-var element = $('#7bd224d3-94ac-4ce9-b7e3-c76c30f51853');
+var element = $('#fd91c526-e2a4-4fc0-866f-a728dad07fb1');
 </script>
 <script type="application/vnd.jupyter.widget-view+json">
 {"model_id": "f7d1803b3c6c4197b6612c5fdf189746", "version_major": 2, "version_minor": 0}
@@ -14116,10 +14116,10 @@ <h2 id="Fine-tuning-the-NER+L&#160;model">Fine-tuning the NER+L&#160;model<a cla
 
  
  
-<div id="565c3c46-42bc-476b-80d3-63c43230dc7c"></div>
+<div id="bab4d1c5-252c-4d7e-afe3-3e3b4a1f97b4"></div>
 <div class="output_subarea output_widget_view ">
 <script type="text/javascript">
-var element = $('#565c3c46-42bc-476b-80d3-63c43230dc7c');
+var element = $('#bab4d1c5-252c-4d7e-afe3-3e3b4a1f97b4');
 </script>
 <script type="application/vnd.jupyter.widget-view+json">
 {"model_id": "c8d633f579de438a916d9ef3de9d8fe0", "version_major": 2, "version_minor": 0}
@@ -14138,10 +14138,10 @@ <h2 id="Fine-tuning-the-NER+L&#160;model">Fine-tuning the NER+L&#160;model<a cla
 
  
  
-<div id="e6eccfb7-05da-41e0-9ad2-a24706c7a258"></div>
+<div id="bc225930-70cb-43aa-b2b6-017ab3597788"></div>
 <div class="output_subarea output_widget_view ">
 <script type="text/javascript">
-var element = $('#e6eccfb7-05da-41e0-9ad2-a24706c7a258');
+var element = $('#bc225930-70cb-43aa-b2b6-017ab3597788');
 </script>
 <script type="application/vnd.jupyter.widget-view+json">
 {"model_id": "de6c01c6983041e2b972f6008caefaea", "version_major": 2, "version_minor": 0}
@@ -14160,10 +14160,10 @@ <h2 id="Fine-tuning-the-NER+L&#160;model">Fine-tuning the NER+L&#160;model<a cla
 
  
  
-<div id="bf3cdb22-2e50-4fae-a443-ed3fcf31a3b9"></div>
+<div id="4abb72a2-705e-4dc8-9229-75b84d24d4ab"></div>
 <div class="output_subarea output_widget_view ">
 <script type="text/javascript">
-var element = $('#bf3cdb22-2e50-4fae-a443-ed3fcf31a3b9');
+var element = $('#4abb72a2-705e-4dc8-9229-75b84d24d4ab');
 </script>
 <script type="application/vnd.jupyter.widget-view+json">
 {"model_id": "05132c907a874fe2a2eb9cb6c81da3b3", "version_major": 2, "version_minor": 0}
@@ -17611,10 +17611,10 @@ <h2 id="Fine-tuning-the-NER+L&#160;model">Fine-tuning the NER+L&#160;model<a cla
 
  
  
-<div id="8c028480-4f6a-4f3b-a177-7fbb6346d4a6"></div>
+<div id="3914899e-a762-49a2-b57a-6caa51f70938"></div>
 <div class="output_subarea output_widget_view ">
 <script type="text/javascript">
-var element = $('#8c028480-4f6a-4f3b-a177-7fbb6346d4a6');
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 <script type="application/vnd.jupyter.widget-view+json">
 {"model_id": "00325922360c45009329d82ed6420f16", "version_major": 2, "version_minor": 0}
@@ -17633,10 +17633,10 @@ <h2 id="Fine-tuning-the-NER+L&#160;model">Fine-tuning the NER+L&#160;model<a cla
 
  
  
-<div id="4c3b3bbc-25e5-4940-b962-47d5ee3da5e4"></div>
+<div id="4f7ef80d-855e-4107-a803-d4ffe94ce9eb"></div>
 <div class="output_subarea output_widget_view ">
 <script type="text/javascript">
-var element = $('#4c3b3bbc-25e5-4940-b962-47d5ee3da5e4');
+var element = $('#4f7ef80d-855e-4107-a803-d4ffe94ce9eb');
 </script>
 <script type="application/vnd.jupyter.widget-view+json">
 {"model_id": "d48e2f4d6dd3467fb3f17e0244b0e361", "version_major": 2, "version_minor": 0}
diff --git a/medcat-v1-tutorials/notebooks/introductory/Part_4_2_Supervised_Training_and_Meta_annotations.ipynb b/medcat-v1-tutorials/notebooks/introductory/Part_4_2_Supervised_Training_and_Meta_annotations.ipynb
@@ -331,7 +331,7 @@
    ],
    "source": [
     "# Install medcat\n",
-    "! pip install medcat~=1.13.0\n",
+    "! pip install medcat~=1.14.0\n",
     "# Get the spacy model\n",
     "! python -m spacy download en_core_web_md\n",
     "try:\n",
diff --git a/medcat-v1-tutorials/notebooks/introductory/Part_4_3_Annotating_documents_with_the_full_MedCAT_pipeline_with_MetaAnnotations.html b/medcat-v1-tutorials/notebooks/introductory/Part_4_3_Annotating_documents_with_the_full_MedCAT_pipeline_with_MetaAnnotations.html
@@ -13085,7 +13085,7 @@
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Install medcat</span>
-<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.13.0
+<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.14.0
 <span class="c1"># install seaborn</span>
 <span class="o">!</span> pip install seaborn
 <span class="k">try</span><span class="p">:</span>
diff --git a/medcat-v1-tutorials/notebooks/introductory/Part_4_3_Annotating_documents_with_the_full_MedCAT_pipeline_with_MetaAnnotations.ipynb b/medcat-v1-tutorials/notebooks/introductory/Part_4_3_Annotating_documents_with_the_full_MedCAT_pipeline_with_MetaAnnotations.ipynb
@@ -265,7 +265,7 @@
    ],
    "source": [
     "# Install medcat\n",
-    "! pip install medcat~=1.13.0\n",
+    "! pip install medcat~=1.14.0\n",
     "# install seaborn\n",
     "! pip install seaborn\n",
     "try:\n",
diff --git a/medcat-v1-tutorials/notebooks/introductory/Part_5_Prevalence_of_Physical_and_Mental_Diseases.html b/medcat-v1-tutorials/notebooks/introductory/Part_5_Prevalence_of_Physical_and_Mental_Diseases.html
@@ -13085,7 +13085,7 @@
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Install medcat</span>
-<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.13.0
+<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.14.0
 <span class="c1"># install seaborn</span>
 <span class="o">!</span> pip install seaborn
 <span class="k">try</span><span class="p">:</span>
diff --git a/medcat-v1-tutorials/notebooks/introductory/Part_5_Prevalence_of_Physical_and_Mental_Diseases.ipynb b/medcat-v1-tutorials/notebooks/introductory/Part_5_Prevalence_of_Physical_and_Mental_Diseases.ipynb
@@ -265,7 +265,7 @@
    ],
    "source": [
     "# Install medcat\n",
-    "! pip install medcat~=1.13.0\n",
+    "! pip install medcat~=1.14.0\n",
     "# install seaborn\n",
     "! pip install seaborn\n",
     "try:\n",
diff --git a/medcat-v1-tutorials/notebooks/specialised/Comparing_Models_with_RegressionSuite.html b/medcat-v1-tutorials/notebooks/specialised/Comparing_Models_with_RegressionSuite.html
@@ -13115,7 +13115,7 @@ <h1 id="Comparing-models-using-regression-test-tooling">Comparing models using r
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Install medcat</span>
-<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.13.0 # regression suite fully available starting version <span class="m">1</span>.7.0
+<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.14.0 # regression suite fully available starting version <span class="m">1</span>.7.0
 <span class="k">try</span><span class="p">:</span>
     <span class="kn">from</span> <span class="nn">medcat.cat</span> <span class="kn">import</span> <span class="n">CAT</span>
 <span class="k">except</span><span class="p">:</span>
diff --git a/medcat-v1-tutorials/notebooks/specialised/Comparing_Models_with_RegressionSuite.ipynb b/medcat-v1-tutorials/notebooks/specialised/Comparing_Models_with_RegressionSuite.ipynb
@@ -176,7 +176,7 @@
    ],
    "source": [
     "# Install medcat\n",
-    "! pip install medcat~=1.13.0 # regression suite fully available starting version 1.7.0\n",
+    "! pip install medcat~=1.14.0 # regression suite fully available starting version 1.7.0\n",
     "try:\n",
     "    from medcat.cat import CAT\n",
     "except:\n",
diff --git a/medcat-v1-tutorials/requirements-dev.txt b/medcat-v1-tutorials/requirements-dev.txt
@@ -1,8 +1,9 @@
-medcat~=1.13.0
+medcat~=1.14.0
 pandas<2.0.0
 seaborn~=0.11.2
 pytest-xdist~=2.5.0
 nbmake<1.4
 nbconvert<6
 jinja2<=3.0
+matplotlib>=3.4.0,<3.8.0
 seaborn
