Remove ebmdatalab and cohortextractor packages from v2

Also, switch from generic end-user package `jupyter` package to specific
packages we need. This drops the dependency on qtconsole.

v2/packages.md

@@ -21,46 +21,27 @@ It comes pre-installed with a standard set of python packages.
 - [beautifulsoup4: 4.12.2](https://pypi.org/project/beautifulsoup4/4.12.2/)
 - [bleach: 6.1.0](https://pypi.org/project/bleach/6.1.0/)
 - [build: 1.0.3](https://pypi.org/project/build/1.0.3/)
-- [cachetools: 5.3.2](https://pypi.org/project/cachetools/5.3.2/)
 - [cairocffi: 1.6.1](https://pypi.org/project/cairocffi/1.6.1/)
 - [cairosvg: 2.7.1](https://pypi.org/project/cairosvg/2.7.1/)
 - [certifi: 2023.11.17](https://pypi.org/project/certifi/2023.11.17/)
 - [cffi: 1.16.0](https://pypi.org/project/cffi/1.16.0/)
 - [charset-normalizer: 3.3.2](https://pypi.org/project/charset-normalizer/3.3.2/)
 - [click: 8.1.7](https://pypi.org/project/click/8.1.7/)
-- [click-plugins: 1.1.1](https://pypi.org/project/click-plugins/1.1.1/)
-- [cligj: 0.7.2](https://pypi.org/project/cligj/0.7.2/)
 - [comm: 0.2.0](https://pypi.org/project/comm/0.2.0/)
 - [contourpy: 1.2.0](https://pypi.org/project/contourpy/1.2.0/)
 - [coverage: 7.3.2](https://pypi.org/project/coverage/7.3.2/)
 - [cssselect2: 0.7.0](https://pypi.org/project/cssselect2/0.7.0/)
 - [cycler: 0.12.1](https://pypi.org/project/cycler/0.12.1/)
-- [db-dtypes: 1.1.1](https://pypi.org/project/db-dtypes/1.1.1/)
 - [debugpy: 1.8.0](https://pypi.org/project/debugpy/1.8.0/)
 - [decorator: 5.1.1](https://pypi.org/project/decorator/5.1.1/)
 - [defusedxml: 0.7.1](https://pypi.org/project/defusedxml/0.7.1/)
-- [descartes: 1.1.0](https://pypi.org/project/descartes/1.1.0/)
-- [ebmdatalab: 0.0.30](https://pypi.org/project/ebmdatalab/0.0.30/)
 - [exceptiongroup: 1.2.0](https://pypi.org/project/exceptiongroup/1.2.0/)
 - [executing: 2.0.1](https://pypi.org/project/executing/2.0.1/)
 - [fastjsonschema: 2.19.0](https://pypi.org/project/fastjsonschema/2.19.0/)
-- [fiona: 1.9.5](https://pypi.org/project/fiona/1.9.5/)
 - [fonttools: 4.46.0](https://pypi.org/project/fonttools/4.46.0/)
 - [formulaic: 0.6.6](https://pypi.org/project/formulaic/0.6.6/)
 - [fqdn: 1.5.1](https://pypi.org/project/fqdn/1.5.1/)
 - [future: 0.18.3](https://pypi.org/project/future/0.18.3/)
-- [geopandas: 0.14.1](https://pypi.org/project/geopandas/0.14.1/)
-- [google-api-core[grpc]: 2.14.0](https://pypi.org/project/google-api-core/2.14.0/)
-- [google-auth: 2.24.0](https://pypi.org/project/google-auth/2.24.0/)
-- [google-auth-oauthlib: 1.1.0](https://pypi.org/project/google-auth-oauthlib/1.1.0/)
-- [google-cloud-bigquery: 3.13.0](https://pypi.org/project/google-cloud-bigquery/3.13.0/)
-- [google-cloud-bigquery-storage: 2.23.0](https://pypi.org/project/google-cloud-bigquery-storage/2.23.0/)
-- [google-cloud-core: 2.3.3](https://pypi.org/project/google-cloud-core/2.3.3/)
-- [google-crc32c: 1.5.0](https://pypi.org/project/google-crc32c/1.5.0/)
-- [google-resumable-media: 2.6.0](https://pypi.org/project/google-resumable-media/2.6.0/)
-- [googleapis-common-protos: 1.61.0](https://pypi.org/project/googleapis-common-protos/1.61.0/)
-- [grpcio: 1.59.3](https://pypi.org/project/grpcio/1.59.3/)
-- [grpcio-status: 1.59.3](https://pypi.org/project/grpcio-status/1.59.3/)
 - [idna: 3.6](https://pypi.org/project/idna/3.6/)
 - [iniconfig: 2.0.0](https://pypi.org/project/iniconfig/2.0.0/)
 - [interface-meta: 1.3.0](https://pypi.org/project/interface-meta/1.3.0/)
@@ -75,7 +56,6 @@ It comes pre-installed with a standard set of python packages.
 - [jsonpointer: 2.4](https://pypi.org/project/jsonpointer/2.4/)
 - [jsonschema[format-nongpl]: 4.20.0](https://pypi.org/project/jsonschema/4.20.0/)
 - [jsonschema-specifications: 2023.11.2](https://pypi.org/project/jsonschema-specifications/2023.11.2/)
-- [jupyter: 1.0.0](https://pypi.org/project/jupyter/1.0.0/)
 - [jupyter-client: 8.6.0](https://pypi.org/project/jupyter-client/8.6.0/)
 - [jupyter-console: 6.6.3](https://pypi.org/project/jupyter-console/6.6.3/)
 - [jupyter-core: 5.5.0](https://pypi.org/project/jupyter-core/5.5.0/)
@@ -109,16 +89,13 @@ It comes pre-installed with a standard set of python packages.
 - [notebook-shim: 0.2.3](https://pypi.org/project/notebook-shim/0.2.3/)
 - [numba: 0.58.1](https://pypi.org/project/numba/0.58.1/)
 - [numpy: 1.26.2](https://pypi.org/project/numpy/1.26.2/)
-- [oauthlib: 3.2.2](https://pypi.org/project/oauthlib/3.2.2/)
 - [opensafely-cohort-extractor: 1.90.0](https://pypi.org/project/opensafely-cohort-extractor/1.90.0/)
 - [opensafely-matching: 0.2.0](https://pypi.org/project/opensafely-matching/0.2.0/)
 - [overrides: 7.4.0](https://pypi.org/project/overrides/7.4.0/)
 - [packaging: 23.2](https://pypi.org/project/packaging/23.2/)
 - [pandas: 2.1.3](https://pypi.org/project/pandas/2.1.3/)
-- [pandas-gbq: 0.19.2](https://pypi.org/project/pandas-gbq/0.19.2/)
 - [pandocfilters: 1.5.0](https://pypi.org/project/pandocfilters/1.5.0/)
 - [parso: 0.8.3](https://pypi.org/project/parso/0.8.3/)
-- [patsy: 0.5.4](https://pypi.org/project/patsy/0.5.4/)
 - [pexpect: 4.9.0](https://pypi.org/project/pexpect/4.9.0/)
 - [pillow: 10.1.0](https://pypi.org/project/pillow/10.1.0/)
 - [pip-tools: 7.3.0](https://pypi.org/project/pip-tools/7.3.0/)
@@ -127,48 +104,36 @@ It comes pre-installed with a standard set of python packages.
 - [pluggy: 1.3.0](https://pypi.org/project/pluggy/1.3.0/)
 - [prometheus-client: 0.19.0](https://pypi.org/project/prometheus-client/0.19.0/)
 - [prompt-toolkit: 3.0.41](https://pypi.org/project/prompt-toolkit/3.0.41/)
-- [proto-plus: 1.22.3](https://pypi.org/project/proto-plus/1.22.3/)
-- [protobuf: 4.25.1](https://pypi.org/project/protobuf/4.25.1/)
 - [psutil: 5.9.6](https://pypi.org/project/psutil/5.9.6/)
 - [ptyprocess: 0.7.0](https://pypi.org/project/ptyprocess/0.7.0/)
 - [pure-eval: 0.2.2](https://pypi.org/project/pure-eval/0.2.2/)
 - [py: 1.11.0](https://pypi.org/project/py/1.11.0/)
 - [pyarrow: 14.0.1](https://pypi.org/project/pyarrow/14.0.1/)
-- [pyasn1: 0.5.1](https://pypi.org/project/pyasn1/0.5.1/)
-- [pyasn1-modules: 0.3.0](https://pypi.org/project/pyasn1-modules/0.3.0/)
 - [pycparser: 2.21](https://pypi.org/project/pycparser/2.21/)
-- [pydata-google-auth: 1.8.2](https://pypi.org/project/pydata-google-auth/1.8.2/)
 - [pygments: 2.17.2](https://pypi.org/project/pygments/2.17.2/)
 - [pyparsing: 3.1.1](https://pypi.org/project/pyparsing/3.1.1/)
-- [pyproj: 3.6.1](https://pypi.org/project/pyproj/3.6.1/)
 - [pyproject-hooks: 1.0.0](https://pypi.org/project/pyproject-hooks/1.0.0/)
 - [pytest: 7.4.3](https://pypi.org/project/pytest/7.4.3/)
 - [python-dateutil: 2.8.2](https://pypi.org/project/python-dateutil/2.8.2/)
 - [python-json-logger: 2.0.7](https://pypi.org/project/python-json-logger/2.0.7/)
 - [pytz: 2023.3.post1](https://pypi.org/project/pytz/2023.3.post1/)
 - [pyyaml: 6.0.1](https://pypi.org/project/pyyaml/6.0.1/)
 - [pyzmq: 25.1.2](https://pypi.org/project/pyzmq/25.1.2/)
-- [qtconsole: 5.5.1](https://pypi.org/project/qtconsole/5.5.1/)
-- [qtpy: 2.4.1](https://pypi.org/project/qtpy/2.4.1/)
 - [referencing: 0.31.1](https://pypi.org/project/referencing/0.31.1/)
 - [requests: 2.31.0](https://pypi.org/project/requests/2.31.0/)
-- [requests-oauthlib: 1.3.1](https://pypi.org/project/requests-oauthlib/1.3.1/)
 - [retry: 0.9.2](https://pypi.org/project/retry/0.9.2/)
 - [rfc3339-validator: 0.1.4](https://pypi.org/project/rfc3339-validator/0.1.4/)
 - [rfc3986-validator: 0.1.1](https://pypi.org/project/rfc3986-validator/0.1.1/)
 - [rpds-py: 0.13.2](https://pypi.org/project/rpds-py/0.13.2/)
-- [rsa: 4.9](https://pypi.org/project/rsa/4.9/)
 - [scikit-learn: 1.3.2](https://pypi.org/project/scikit-learn/1.3.2/)
 - [scipy: 1.11.4](https://pypi.org/project/scipy/1.11.4/)
 - [seaborn: 0.13.0](https://pypi.org/project/seaborn/0.13.0/)
 - [send2trash: 1.8.2](https://pypi.org/project/send2trash/1.8.2/)
-- [shapely: 2.0.2](https://pypi.org/project/shapely/2.0.2/)
 - [six: 1.16.0](https://pypi.org/project/six/1.16.0/)
 - [sniffio: 1.3.0](https://pypi.org/project/sniffio/1.3.0/)
 - [soupsieve: 2.5](https://pypi.org/project/soupsieve/2.5/)
 - [sqlparse: 0.4.4](https://pypi.org/project/sqlparse/0.4.4/)
 - [stack-data: 0.6.3](https://pypi.org/project/stack-data/0.6.3/)
-- [statsmodels: 0.14.0](https://pypi.org/project/statsmodels/0.14.0/)
 - [structlog: 23.2.0](https://pypi.org/project/structlog/23.2.0/)
 - [tabulate: 0.9.0](https://pypi.org/project/tabulate/0.9.0/)
 - [tenacity: 8.2.3](https://pypi.org/project/tenacity/8.2.3/)

v2/requirements.in

@@ -1,18 +1,17 @@
 # Basic requirements for notebook infrastructure provided in base
 # docker image
 pip-tools
-jupyter
+notebook
+jupyter-console
 jupyterlab
 jupytext
 bash_kernel
 nbval
 opensafely-matching
 
 # Commonly-used packages provided in base docker image
-pandas-gbq
 pandas
 numpy
-ebmdatalab
 matplotlib
 scipy
 tqdm