Cu 8692wbcq5 docs builds (#359)

* CU-8692wbcq5: Pin max version of numpy

* CU-8692wbcq5: Pin max version of numpy in setup.py

* CU-8692wbcq5: Bump python version for readthedocs workflow

* CU-8692wbcq5: Pin all requirement versions in docs requirements

* CU-8692wbcq5: Move docs requirements before setuptools

* CU-8692wbcq5: Fix typo in docs requirements

* CU-8692wbcq5: Remove some less relevant stuff from docs requirements

* CU-8692wbcq5: Add back sphinx-based requirements to docs requirements

* CU-8692wbcq5: Move back to python 3.9 on docs build workflow

* CU-8692wbcq5: Bump sphinx-autoapi version

* CU-8692wbcq5: Bump sphinx version

* CU-8692wbcq5: Bump python version back to 3.10 for future-proofing

* CU-8692wbcq5: Undo pinning numpy to max version in setup.py

* CU-8692wbcq5: Remove docs-build specific dependencies in setup.py

.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: .

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==3.8.5
+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

setup.py

@@ -40,12 +40,6 @@
         'blis>=0.7.5', # allow later versions, tested with 0.7.9
         'click>=8.0.4', # allow later versions, tested with 8.1.3
         'pydantic>=1.10.0,<2.0', # for spacy compatibility; avoid 2.0 due to breaking changes
-        # the following are not direct dependencies of MedCAT but needed for docs/building
-        # hopefully will no longer need the transitive dependencies
-        'aiohttp==3.8.5', # 3.8.3 is needed for compatibility with fsspec <- datasets <- medcat
-        'blis<0.8.0,>=0.7.8', # as required by thinc <- spacy <- medcat
-        # 'smart-open==5.2.1', # 5.2.1 is needed for compatibility with pathy
-        # 'joblib~=1.2',
         ],
     classifiers=[
         "Programming Language :: Python :: 3",