Merge branch 'master' of github.com:bramiozo/MedCAT

.github/workflows/main.yml

@@ -16,9 +16,9 @@ jobs:
       max-parallel: 4
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -33,7 +33,7 @@ jobs:
           flake8 medcat
       - name: Test
         run: |
-          python -m unittest discover
+          timeout 17m python -m unittest discover
 
   publish-to-test-pypi:
 
@@ -43,18 +43,19 @@ jobs:
       github.event_name == 'push' &&
       startsWith(github.ref, 'refs/tags') != true
     runs-on: ubuntu-20.04
+    timeout-minutes: 20
     concurrency: publish-to-test-pypi
     needs: [build]
 
     steps:
       - name: Checkout master
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           ref: 'master'
           fetch-depth: 0
 
       - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
 

.github/workflows/production.yml

@@ -14,13 +14,13 @@ jobs:
 
     steps:
       - name: Checkout production
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.event.release.target_commitish }}
           fetch-depth: 0
 
       - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
 

.readthedocs.yaml

@@ -7,13 +7,13 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.9"
+    python: "3.10"
 
 sphinx:
   configuration: docs/conf.py
 
 python:
   install:
+    - requirements: docs/requirements.txt
     - method: setuptools
-      path: .
-    - requirements: docs/requirements.txt
+      path: .

README.md

@@ -38,8 +38,20 @@ To download any of these models, please [follow this link](https://uts.nlm.nih.g
 - **Paper**: [What’s in a Summary? Laying the Groundwork for Advances in Hospital-Course Summarization](https://www.aclweb.org/anthology/2021.naacl-main.382.pdf)
 - ([more...](https://github.com/CogStack/MedCAT/blob/master/media/news.md))
 
+## Installation
+To install the latest version of MedCAT run the following command:
+```
+pip install medcat
+```
+Normal installations of MedCAT will install torch-gpu and all relevant dependancies (such as CUDA). This can require as much as 10 GB more disk space, which isn't required for CPU only usage.
+
+To install the latest version of MedCAT without torch GPU support run the following command:
+```
+pip install medcat --extra_index_url https://download.pytorch.org/whl/cpu/
+```
 ## Demo
 A demo application is available at [MedCAT](https://medcat.rosalind.kcl.ac.uk). This was trained on MIMIC-III and all of SNOMED-CT.
+PS: This link can take a long time to load the first time around. The machine spins up as needed and spins down when inactive.
 
 ## Tutorials
 A guide on how to use MedCAT is available at [MedCAT Tutorials](https://github.com/CogStack/MedCATtutorials). Read more about MedCAT on [Towards Data Science](https://towardsdatascience.com/medcat-introduction-analyzing-electronic-health-records-e1c420afa13a).

docs/requirements.txt

@@ -1,6 +1,104 @@
-Sphinx~=4.0
+sphinx==6.2.1
 sphinx-rtd-theme~=1.0
 myst-parser~=0.17
-sphinx-autoapi~=1.8
-setuptools>=60.0
-aiohttp==3.8.3
+sphinx-autoapi~=3.0.0
+MarkupSafe==2.1.3
+accelerate==0.23.0
+aiofiles==23.2.1
+aiohttp==3.8.5
+aiosignal==1.3.1
+asttokens==2.4.0
+async-timeout==4.0.3
+attrs==23.1.0
+backcall==0.2.0
+blis==0.7.11
+catalogue==2.0.10
+certifi==2023.7.22
+charset-normalizer==3.3.0
+click==8.1.7
+comm==0.1.4
+confection==0.1.3
+cymem==2.0.8
+datasets==2.14.5
+decorator==5.1.1
+dill==0.3.7
+exceptiongroup==1.1.3
+executing==2.0.0
+filelock==3.12.4
+flake8==4.0.1
+frozenlist==1.4.0
+fsspec==2023.6.0
+gensim==4.3.2
+huggingface-hub==0.17.3
+idna==3.4
+ipython==8.16.1
+ipywidgets==8.1.1
+jedi==0.19.1
+jinja2==3.1.2
+joblib==1.3.2
+jsonpickle==3.0.2
+jupyterlab-widgets==3.0.9
+langcodes==3.3.0
+matplotlib-inline==0.1.6
+mccabe==0.6.1
+mpmath==1.3.0
+multidict==6.0.4
+multiprocess==0.70.15
+murmurhash==1.0.10
+mypy==1.0.0
+mypy-extensions==0.4.3
+networkx==3.1
+numpy==1.25.2
+packaging==23.2
+pandas==2.1.1
+parso==0.8.3
+pathy==0.10.2
+pexpect==4.8.0
+pickleshare==0.7.5
+preshed==3.0.9
+prompt-toolkit==3.0.39
+psutil==5.9.5
+ptyprocess==0.7.0
+pure-eval==0.2.2
+pyarrow==13.0.0
+pycodestyle==2.8.0
+pydantic==1.10.13
+pyflakes==2.4.0
+pygments==2.16.1
+python-dateutil==2.8.2
+pytz==2023.3.post1
+pyyaml==6.0.1
+regex==2023.10.3
+requests==2.31.0
+safetensors==0.4.0
+scikit-learn==1.3.1
+scipy==1.9.3
+six==1.16.0
+smart-open==6.4.0
+spacy==3.4.4
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+srsly==2.4.8
+stack-data==0.6.3
+sympy==1.12
+thinc==8.1.12
+threadpoolctl==3.2.0
+tokenizers==0.14.1
+tomli==2.0.1
+torch==2.1.0
+tqdm==4.66.1
+traitlets==5.11.2
+transformers==4.34.0
+triton==2.1.0
+typer==0.7.0
+types-PyYAML==6.0.3
+types-aiofiles==0.8.3
+types-setuptools==57.4.10
+typing-extensions==4.8.0
+tzdata==2023.3
+urllib3==2.0.6
+wasabi==0.10.1
+wcwidth==0.2.8
+widgetsnbextension==4.0.9
+xxhash==3.4.1
+yarl==1.9.2