From ada16532051fe3ae637e7ea28a89e50bb263b737 Mon Sep 17 00:00:00 2001
From: bloodearnest <simon.davy@thedatalab.org>
Date: Wed, 22 Nov 2023 17:12:22 +0000
Subject: [PATCH 01/11] Add a new version of the python image.

This new version is based on 22.04 and python3.10, and has an up to date
version of all python packages.

The versioning scheme is arbitrary major version, e.g. v1, v2, etc. The
previous image is retained as v1, and the new image is v2.

This move from maintaining 1 to 2 images requires some refactoring. Each
major version has its own directory, and associated configuration files
to track dependencies. They both share the same parameterised
`Dockerfile` and `docker-compose.yaml`.

In the process, I have also improved the local development tooling:
 - move from Makefile to parameterised justfile
 - some small reording of Dockerfile steps for efficiency and reuse
 - a proper solution for user the docker images themselves to add new
   dependencies and/or upgrade existing ones. This means you a) do not
   need all the python versions installed on your machine and b) this
   can be built on macos, in theory.
---
 Dockerfile                                    |  56 +-
 Makefile                                      |  35 -
 docker-compose.yml                            |  26 +-
 justfile                                      |  40 ++
 tests/test_import.py                          |  34 +-
 .../build-dependencies.txt                    |   0
 dependencies.txt => v1/dependencies.txt       |   0
 v1/env                                        |   2 +
 requirements.in => v1/requirements.in         |   0
 requirements.txt => v1/requirements.txt       |  61 +-
 v2/build-dependencies.txt                     |  10 +
 v2/dependencies.txt                           |  15 +
 v2/env                                        |   2 +
 v2/requirements.in                            |  39 ++
 v2/requirements.txt                           | 643 ++++++++++++++++++
 15 files changed, 865 insertions(+), 98 deletions(-)
 delete mode 100644 Makefile
 create mode 100644 justfile
 rename build-dependencies.txt => v1/build-dependencies.txt (100%)
 rename dependencies.txt => v1/dependencies.txt (100%)
 create mode 100644 v1/env
 rename requirements.in => v1/requirements.in (100%)
 rename requirements.txt => v1/requirements.txt (88%)
 create mode 100644 v2/build-dependencies.txt
 create mode 100644 v2/dependencies.txt
 create mode 100644 v2/env
 create mode 100644 v2/requirements.in
 create mode 100644 v2/requirements.txt

diff --git a/Dockerfile b/Dockerfile
index 6de34b7..5ccef52 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -8,34 +8,48 @@
 # and b) we specifically always want to build on the latest base image, by
 # design.
 #
+ARG BASE
 # hadolint ignore=DL3007
-FROM ghcr.io/opensafely-core/base-action:latest as base-python
-COPY dependencies.txt /root/dependencies.txt
+FROM ghcr.io/opensafely-core/base-action:$BASE as base-python
+
+RUN mkdir /workspace
+WORKDIR /workspace
+
+ARG MAJOR_VERSION
+# ACTION_EXEC sets the default executable for the entrypoint in the base-docker image
+ENV ACTION_EXEC=python MAJOR_VERSION=${MAJOR_VERSION}
+
+COPY ${MAJOR_VERSION}/dependencies.txt /root/dependencies.txt
 # use space efficient utility from base image
 RUN /root/docker-apt-install.sh /root/dependencies.txt
 
+# now we have python, set up a venv to install packages to, for isolation from
+# system python libraries 
+# hadolint ignore=DL3059
+RUN python3 -m venv /opt/venv
+# "activate" the venv
+ENV VIRTUAL_ENV=/opt/venv/ PATH="/opt/venv/bin:$PATH"
+# We ensure up-to-date build tools (which why we ignore DL3013)
+# hadolint ignore=DL3013,DL3042
+RUN --mount=type=cache,target=/root/.cache python -m pip install -U pip setuptools wheel pip-tools
+
+
 #################################################
 #
 # Next, use the base-docker-plus-python image to create a build image
 FROM base-python as builder
+ARG MAJOR_VERSION
 
 # install build time dependencies 
-COPY build-dependencies.txt /root/build-dependencies.txt
+COPY ${MAJOR_VERSION}/build-dependencies.txt /root/build-dependencies.txt
 RUN /root/docker-apt-install.sh /root/build-dependencies.txt
 
-# install everything in venv for isolation from system python libraries
-# hadolint ignore=DL3059
-RUN python3 -m venv /opt/venv
-ENV VIRTUAL_ENV=/opt/venv/ PATH="/opt/venv/bin:$PATH" LLVM_CONFIG=/usr/bin/llvm-config-10
-
-COPY requirements.txt /root/requirements.txt
-# We ensure up-to-date build tools (which why we ignore DL3013)
+COPY ${MAJOR_VERSION}/requirements.txt /root/requirements.txt
 # Note: the mount command does two things: 1) caches across builds to speed up
 # local development and 2) ensures the pip cache does not get committed to the
 # layer (which is why we ignore DL3042).
-# hadolint ignore=DL3013,DL3042
+# hadolint ignore=DL3042
 RUN --mount=type=cache,target=/root/.cache \
-    python -m pip install -U pip setuptools wheel && \
     python -m pip install --requirement /root/requirements.txt
 
 ################################################
@@ -43,26 +57,26 @@ RUN --mount=type=cache,target=/root/.cache \
 # Finally, build the actual image from the base-python image
 FROM base-python as python
 
+
+ARG MAJOR_VERSION
 # Some static metadata for this specific image, as defined by:
 # https://github.com/opencontainers/image-spec/blob/master/annotations.md#pre-defined-annotation-keys
 # The org.opensafely.action label is used by the jobrunner to indicate this is
 # an approved action image to run.
-LABEL org.opencontainers.image.title="python" \
+LABEL org.opencontainers.image.title="python:${MAJOR_VERSION}" \
       org.opencontainers.image.description="Python action for opensafely.org" \
       org.opencontainers.image.source="https://github.com/opensafely-core/python-docker" \
-      org.opensafely.action="python"
+      org.opensafely.action="python:${MAJOR_VERSION}"
 
 # copy venv over from builder image
 COPY --from=builder /opt/venv /opt/venv
-# ACTION_EXEC sets the default executable for the entrypoint in the base-docker image
-ENV VIRTUAL_ENV=/opt/venv/ PATH="/opt/venv/bin:$PATH" ACTION_EXEC=python
-
-RUN mkdir /workspace
-WORKDIR /workspace
 
-# tag with build info as the very last step, as it will never be cached
+# tag with build info as the very last step, as it will never be cacheable
 ARG BUILD_DATE
 ARG REVISION
+ARG BUILD_NUMBER
 # RFC 3339.
 LABEL org.opencontainers.image.created=$BUILD_DATE \
-      org.opencontainers.image.revision=$REVISION
+      org.opencontainers.image.revision=$REVISION \
+      org.opencontainers.image.build=$BUILD_NUMBER \
+      org.opencontainers.image.version=$MAJOR_VERSION.$BUILD_NUMBER
diff --git a/Makefile b/Makefile
deleted file mode 100644
index 3816bc8..0000000
--- a/Makefile
+++ /dev/null
@@ -1,35 +0,0 @@
-INTERACTIVE:=$(shell [ -t 0 ] && echo 1)
-export DOCKER_BUILDKIT=1
-export BUILD_DATE=$(shell date +'%y-%m-%dT%H:%M:%S.%3NZ')
-export REVISION=$(shell git rev-parse --short HEAD)
-
-.PHONY: build
-build:
-	docker-compose build --pull python
-
-
-.PHONY: test
-test:
-	docker-compose run --rm -v $(PWD):/workspace python pytest tests -v
-
-# test basic python invocation
-functional-test:
-	docker-compose run --rm python -c ''
-	docker-compose run --rm python python -c ''
-
-
-.PHONY: lint
-lint:
-	@docker pull hadolint/hadolint:v2.8.0
-	@docker run --rm -i hadolint/hadolint:v2.8.0 < Dockerfile
-
-requirements.txt: requirements.in venv/bin/pip-compile
-	venv/bin/pip-compile requirements.in
-
-venv/bin/pip-compile: | venv
-	venv/bin/pip install pip-tools
-
-venv:
-	virtualenv -p python3 venv
-
-
diff --git a/docker-compose.yml b/docker-compose.yml
index a9751fa..e9f4f17 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,18 +1,26 @@
 services:
-  # used to build the production image
-  python:
-    image: python
+  base:
+    init: true
+    image: python:${MAJOR_VERSION}-base
     build:
       context: .
-      target: python
+      target: base-python
       cache_from:  # should speed up the build in CI, where we have a cold cache
-        - ghcr.io/opensafely-core/base-docker
-        - ghcr.io/opensafely-core/python
+        - ghcr.io/opensafely-core/base-action:${BASE}
+        - ghcr.io/opensafely-core/python:${MAJOR_VERSION}
       args:
         # this makes the image work for later cache_from: usage
         - BUILDKIT_INLINE_CACHE=1
-        # env vars supplied by make/just
+        # env vars supplied by just
+        - BUILD_NUMBER
         - BUILD_DATE
         - REVISION
-        - VERSION
-    init: true
+        - BASE
+        - MAJOR_VERSION
+
+  python:
+    extends:
+      service: base
+    image: python:${MAJOR_VERSION}
+    build:
+      target: python
diff --git a/justfile b/justfile
new file mode 100644
index 0000000..310f12e
--- /dev/null
+++ b/justfile
@@ -0,0 +1,40 @@
+export DOCKER_BUILDKIT := "1"
+export BUILD_DATE := `date +'%y-%m-%dT%H:%M:%S.%3NZ'`
+export REVISION := `git rev-parse --short HEAD`
+
+# TODO: calculate this
+export BUILD_NUMBER := "1234"
+
+build version target="python" *args="":
+    docker-compose --env-file {{ version }}/env build --pull {{ args }} {{ target }} 
+
+test version *args="tests -v":
+    docker-compose --env-file {{ version }}/env run --rm -v $PWD:/workspace python pytest {{ args }}
+
+update version *args="":
+    docker-compose --env-file {{ version }}/env run --rm -v $PWD:/workspace base pip-compile {{ args }} {{ version }}/requirements.in -o {{ version }}/requirements.txt
+
+check:
+    @docker pull hadolint/hadolint:v2.12.0
+    @docker run --rm -i hadolint/hadolint:v2.12.0 < Dockerfile
+
+publish version:
+    #!/bin/bash
+    set -euxo pipefail
+    docker tag python:{{ version }} ghcr.io/opensafely-core/python:{{ version }}
+    echo docker push ghcr.io/opensafely-core/python:{{ version }}
+
+    if test "{{ version }}" = "v1"; then
+        # jupyter is only alias for v1
+        docker tag python:{{ version }} ghcr.io/opensafely-core/jupyter:{{ version }}
+        echo docker push ghcr.io/opensafely-core/jupyter:{{ version }}
+
+        # v1 is also known as latest, at least until we transition fully
+        docker tag python:{{ version }} ghcr.io/opensafely-core/python:latest
+        docker tag python:{{ version }} ghcr.io/opensafely-core/jupyter:latest
+        echo docker push ghcr.io/opensafely-core/python:latest
+        echo docker push ghcr.io/opensafely-core/jupyter:latest
+    fi
+
+
+
diff --git a/tests/test_import.py b/tests/test_import.py
index 09d4a4a..f877650 100644
--- a/tests/test_import.py
+++ b/tests/test_import.py
@@ -1,21 +1,44 @@
+import os
 import subprocess
 from importlib import import_module
 from pathlib import Path
+import re
 
 import pytest
 from pkg_resources import Requirement, get_provider
 
 
+# packages that have no way to detect their importable name
+BAD_PACKAGES = {
+    "beautifulsoup4": "bs4",
+    "protobuf": None, # AARRRRGG
+    "qtpy": None,  # required dependency of jupyter-lab
+}
+
 def get_module_names(pkg_name):
     """Load pkg metadata to find out its importable module name(s)."""
+    # remove any extras
+    pkg_name = re.sub(r'\[.*\]', '', pkg_name)
     modules = set()
     provider = get_provider(Requirement.parse(pkg_name))
     # top level package name is typically all we need
-    if provider.has_metadata("top_level.txt"):
-        modules |= set(provider.get_metadata_lines("top_level.txt"))
+    if pkg_name in BAD_PACKAGES:
+        name = BAD_PACKAGES[pkg_name]
+        if name is None:  # unimportably package
+            return []
+        modules.add(BAD_PACKAGES[pkg_name])
+    elif provider.has_metadata("top_level.txt"):
+        first_line = list(provider.get_metadata_lines("top_level.txt"))[0]
+        modules.add(first_line)
     else:
         # badly packaged dependency, make an educated guess
-        modules.add(pkg_name.replace("-", "_"))
+        name = pkg_name
+        if pkg_name.endswith("-cffi"):
+            name = pkg_name[:-5]
+        elif pkg_name.endswith("-py"):
+            name = pkg_name[:-3]
+        
+        modules.add(name.replace("-", "_"))
 
     if provider.has_metadata("namespace_packages.txt"):
         modules |= set(provider.get_metadata_lines("namespace_packages.txt"))
@@ -24,8 +47,9 @@ def get_module_names(pkg_name):
     return [n for n in modules if n[0] != "_"]
 
 
-def generate_import_names(req_path):
+def generate_import_names(major_version):
     """Generate list of expected modules to be able to import."""
+    req_path = Path(major_version) / "requirements.txt"
     with req_path.open() as fp:
         for line in fp:
             line = line.strip()
@@ -38,7 +62,7 @@ def generate_import_names(req_path):
 
 
 @pytest.mark.parametrize(
-    "name, module", generate_import_names(Path("requirements.txt"))
+    "name, module", generate_import_names(os.environ["MAJOR_VERSION"])
 )
 @pytest.mark.filterwarnings("ignore")
 def test_import_package(name, module):
diff --git a/build-dependencies.txt b/v1/build-dependencies.txt
similarity index 100%
rename from build-dependencies.txt
rename to v1/build-dependencies.txt
diff --git a/dependencies.txt b/v1/dependencies.txt
similarity index 100%
rename from dependencies.txt
rename to v1/dependencies.txt
diff --git a/v1/env b/v1/env
new file mode 100644
index 0000000..ea122d4
--- /dev/null
+++ b/v1/env
@@ -0,0 +1,2 @@
+MAJOR_VERSION=v1
+BASE=20.04
diff --git a/requirements.in b/v1/requirements.in
similarity index 100%
rename from requirements.in
rename to v1/requirements.in
diff --git a/requirements.txt b/v1/requirements.txt
similarity index 88%
rename from requirements.txt
rename to v1/requirements.txt
index 18935e4..a00935f 100644
--- a/requirements.txt
+++ b/v1/requirements.txt
@@ -1,8 +1,8 @@
 #
-# This file is autogenerated by pip-compile with python 3.8
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.8
+# by the following command:
 #
-#    pip-compile
+#    pip-compile --output-file=v1/requirements.txt v1/requirements.in
 #
 astor==0.8.1
     # via formulaic
@@ -20,7 +20,7 @@ autograd-gamma==0.5.0
 backcall==0.1.0
     # via ipython
 bash-kernel==0.7.2
-    # via -r requirements.in
+    # via -r v1/requirements.in
 bleach==3.1.2
     # via nbconvert
 cachetools==4.0.0
@@ -28,7 +28,7 @@ cachetools==4.0.0
 cairocffi==1.4.0
     # via cairosvg
 cairosvg==2.5.2
-    # via -r requirements.in
+    # via -r v1/requirements.in
 certifi==2019.11.28
     # via requests
 cffi==1.15.1
@@ -37,6 +37,8 @@ chardet==3.0.4
     # via requests
 click==7.0
     # via
+    #   click-plugins
+    #   cligj
     #   fiona
     #   pip-tools
 click-plugins==1.1.1
@@ -120,7 +122,7 @@ ipython-genutils==0.2.0
     #   traitlets
 ipywidgets==7.5.1
     # via
-    #   -r requirements.in
+    #   -r v1/requirements.in
     #   jupyter
 jedi==0.16.0
     # via ipython
@@ -139,7 +141,7 @@ jsonschema==3.2.0
     #   jupyterlab-server
     #   nbformat
 jupyter==1.0.0
-    # via -r requirements.in
+    # via -r v1/requirements.in
 jupyter-client==5.3.4
     # via
     #   ipykernel
@@ -157,17 +159,17 @@ jupyter-core==4.6.1
     #   notebook
     #   qtconsole
 jupyterlab==1.2.6
-    # via -r requirements.in
+    # via -r v1/requirements.in
 jupyterlab-server==1.0.6
     # via jupyterlab
 jupytext==1.3.3
-    # via -r requirements.in
+    # via -r v1/requirements.in
 kaleido==0.2.1
-    # via -r requirements.in
+    # via -r v1/requirements.in
 kiwisolver==1.1.0
     # via matplotlib
 lifelines==0.26.4
-    # via -r requirements.in
+    # via -r v1/requirements.in
 llvmlite==0.34.0
     # via numba
 lz4==3.1.3
@@ -176,7 +178,7 @@ markupsafe==1.1.1
     # via jinja2
 matplotlib==3.1.3
     # via
-    #   -r requirements.in
+    #   -r v1/requirements.in
     #   descartes
     #   lifelines
     #   seaborn
@@ -200,7 +202,7 @@ nbformat==5.0.4
     #   nbval
     #   notebook
 nbval==0.9.4
-    # via -r requirements.in
+    # via -r v1/requirements.in
 notebook==6.0.3
     # via
     #   jupyter
@@ -208,10 +210,10 @@ notebook==6.0.3
     #   jupyterlab-server
     #   widgetsnbextension
 numba==0.51.2
-    # via -r requirements.in
+    # via -r v1/requirements.in
 numpy==1.18.1
     # via
-    #   -r requirements.in
+    #   -r v1/requirements.in
     #   autograd
     #   formulaic
     #   lifelines
@@ -229,12 +231,12 @@ oauthlib==3.1.0
 opensafely-cohort-extractor==1.88.0
     # via -r requirements.in
 opensafely-matching==0.2.0
-    # via -r requirements.in
+    # via -r v1/requirements.in
 packaging==20.1
     # via pytest
 pandas==1.0.1
     # via
-    #   -r requirements.in
+    #   -r v1/requirements.in
     #   ebmdatalab
     #   formulaic
     #   geopandas
@@ -247,7 +249,7 @@ pandas==1.0.1
     #   upsetplot
 pandas-gbq==0.13.0
     # via
-    #   -r requirements.in
+    #   -r v1/requirements.in
     #   ebmdatalab
 pandocfilters==1.4.2
     # via nbconvert
@@ -265,12 +267,12 @@ pickleshare==0.7.5
     # via ipython
 pillow==8.1.0
     # via
-    #   -r requirements.in
+    #   -r v1/requirements.in
     #   cairosvg
 pip-tools==6.2.0
-    # via -r requirements.in
+    # via -r v1/requirements.in
 plotly==4.5.0
-    # via -r requirements.in
+    # via -r v1/requirements.in
 pluggy==0.13.1
     # via pytest
 prometheus-client==0.7.1
@@ -283,6 +285,7 @@ protobuf==3.11.3
     # via
     #   google-api-core
     #   google-cloud-bigquery
+    #   googleapis-common-protos
 ptyprocess==0.6.0
     # via
     #   pexpect
@@ -293,7 +296,7 @@ py==1.8.1
     #   retry
 pyarrow==3.0.0
     # via
-    #   -r requirements.in
+    #   -r v1/requirements.in
     #   opensafely-cohort-extractor
 pyasn1==0.4.8
     # via
@@ -321,7 +324,7 @@ pyrsistent==0.15.7
     # via jsonschema
 pytest==5.3.5
     # via
-    #   -r requirements.in
+    #   -r v1/requirements.in
     #   nbval
 python-dateutil==2.8.1
     # via
@@ -356,10 +359,10 @@ retrying==1.3.3
 rsa==4.0
     # via google-auth
 scikit-learn==0.24.1
-    # via -r requirements.in
+    # via -r v1/requirements.in
 scipy==1.4.1
     # via
-    #   -r requirements.in
+    #   -r v1/requirements.in
     #   autograd-gamma
     #   formulaic
     #   lifelines
@@ -384,11 +387,13 @@ six==1.14.0
     #   google-cloud-bigquery
     #   google-resumable-media
     #   jsonschema
+    #   munch
     #   nbval
     #   packaging
     #   patsy
     #   plotly
     #   protobuf
+    #   pyrsistent
     #   python-dateutil
     #   retrying
     #   traitlets
@@ -420,7 +425,7 @@ tornado==6.0.3
     #   notebook
     #   terminado
 tqdm==4.42.1
-    # via -r requirements.in
+    # via -r v1/requirements.in
 traitlets==4.3.3
     # via
     #   ipykernel
@@ -433,11 +438,11 @@ traitlets==4.3.3
     #   notebook
     #   qtconsole
 upsetplot==0.6.1
-    # via -r requirements.in
+    # via -r v1/requirements.in
 urllib3==1.25.8
     # via requests
 venn==0.1.3
-    # via -r requirements.in
+    # via -r v1/requirements.in
 wcwidth==0.1.8
     # via
     #   prompt-toolkit
diff --git a/v2/build-dependencies.txt b/v2/build-dependencies.txt
new file mode 100644
index 0000000..d5c2de8
--- /dev/null
+++ b/v2/build-dependencies.txt
@@ -0,0 +1,10 @@
+# build time dependencies
+build-essential
+gcc
+python3-dev
+python3-venv
+python3-wheel
+# for numba
+#llvm-10-dev
+# for cairosvg
+libffi-dev
diff --git a/v2/dependencies.txt b/v2/dependencies.txt
new file mode 100644
index 0000000..9fb4f06
--- /dev/null
+++ b/v2/dependencies.txt
@@ -0,0 +1,15 @@
+# run time dependencies
+# ensure fully working base python3 installation
+# see: https://gist.github.com/tiran/2dec9e03c6f901814f6d1e8dad09528e
+python3
+python3-venv
+python3-pip
+python3-distutils
+tzdata
+ca-certificates
+
+# for cairosvg
+libcairo2
+
+# Some jupyter notebooks rely on using git to get current version of repo
+git
diff --git a/v2/env b/v2/env
new file mode 100644
index 0000000..7cd7324
--- /dev/null
+++ b/v2/env
@@ -0,0 +1,2 @@
+MAJOR_VERSION=v2
+BASE=22.04
diff --git a/v2/requirements.in b/v2/requirements.in
new file mode 100644
index 0000000..a89dd8b
--- /dev/null
+++ b/v2/requirements.in
@@ -0,0 +1,39 @@
+# Basic requirements for notebook infrastructure provided in base
+# docker image
+pip-tools
+jupyter
+jupyterlab
+jupytext
+bash_kernel
+nbval
+opensafely-matching
+
+# Commonly-used packages provided in base docker image
+pandas-gbq
+pandas
+numpy
+ebmdatalab
+matplotlib
+scipy
+tqdm
+numba
+opensafely-cohort-extractor
+pyarrow
+venn
+kaleido
+scikit-learn
+lifelines
+
+# Both these required for plotly+notebooks
+plotly
+ipywidgets
+
+# Add extra per-notebook packages here
+pillow
+cairosvg
+
+# Allow for projects to run tests inside the container
+pytest
+
+# For visualisation of set overlaps
+upsetplot
diff --git a/v2/requirements.txt b/v2/requirements.txt
new file mode 100644
index 0000000..aecf474
--- /dev/null
+++ b/v2/requirements.txt
@@ -0,0 +1,643 @@
+#
+# This file is autogenerated by pip-compile with Python 3.10
+# by the following command:
+#
+#    pip-compile requirements-3.10.in
+#
+anyio==4.0.0
+    # via jupyter-server
+argon2-cffi==23.1.0
+    # via jupyter-server
+argon2-cffi-bindings==21.2.0
+    # via argon2-cffi
+arrow==1.3.0
+    # via isoduration
+astor==0.8.1
+    # via formulaic
+asttokens==2.4.1
+    # via stack-data
+async-lru==2.0.4
+    # via jupyterlab
+attrs==23.1.0
+    # via
+    #   fiona
+    #   jsonschema
+    #   referencing
+autograd==1.6.2
+    # via
+    #   autograd-gamma
+    #   lifelines
+autograd-gamma==0.5.0
+    # via lifelines
+babel==2.13.1
+    # via jupyterlab-server
+bash-kernel==0.9.1
+    # via -r requirements-3.10.in
+beautifulsoup4==4.12.2
+    # via nbconvert
+bleach==6.1.0
+    # via nbconvert
+build==1.0.3
+    # via pip-tools
+cachetools==5.3.2
+    # via google-auth
+cairocffi==1.6.1
+    # via cairosvg
+cairosvg==2.7.1
+    # via -r requirements-3.10.in
+certifi==2023.11.17
+    # via
+    #   fiona
+    #   pyproj
+    #   requests
+cffi==1.16.0
+    # via
+    #   argon2-cffi-bindings
+    #   cairocffi
+charset-normalizer==3.3.2
+    # via requests
+click==8.1.7
+    # via
+    #   click-plugins
+    #   cligj
+    #   fiona
+    #   pip-tools
+click-plugins==1.1.1
+    # via fiona
+cligj==0.7.2
+    # via fiona
+comm==0.2.0
+    # via
+    #   ipykernel
+    #   ipywidgets
+contourpy==1.2.0
+    # via matplotlib
+coverage==7.3.2
+    # via nbval
+cssselect2==0.7.0
+    # via cairosvg
+cycler==0.12.1
+    # via matplotlib
+db-dtypes==1.1.1
+    # via pandas-gbq
+debugpy==1.8.0
+    # via ipykernel
+decorator==5.1.1
+    # via
+    #   ipython
+    #   retry
+defusedxml==0.7.1
+    # via
+    #   cairosvg
+    #   nbconvert
+descartes==1.1.0
+    # via ebmdatalab
+ebmdatalab==0.0.30
+    # via -r requirements-3.10.in
+exceptiongroup==1.2.0
+    # via
+    #   anyio
+    #   ipython
+    #   pytest
+executing==2.0.1
+    # via stack-data
+fastjsonschema==2.19.0
+    # via nbformat
+fiona==1.9.5
+    # via geopandas
+fonttools==4.45.0
+    # via matplotlib
+formulaic==0.6.6
+    # via lifelines
+fqdn==1.5.1
+    # via jsonschema
+future==0.18.3
+    # via autograd
+geopandas==0.14.1
+    # via ebmdatalab
+google-api-core[grpc]==2.14.0
+    # via
+    #   google-cloud-bigquery
+    #   google-cloud-bigquery-storage
+    #   google-cloud-core
+    #   pandas-gbq
+google-auth==2.23.4
+    # via
+    #   google-api-core
+    #   google-auth-oauthlib
+    #   google-cloud-core
+    #   pandas-gbq
+    #   pydata-google-auth
+google-auth-oauthlib==1.1.0
+    # via
+    #   pandas-gbq
+    #   pydata-google-auth
+google-cloud-bigquery==3.13.0
+    # via pandas-gbq
+google-cloud-bigquery-storage==2.22.0
+    # via pandas-gbq
+google-cloud-core==2.3.3
+    # via google-cloud-bigquery
+google-crc32c==1.5.0
+    # via google-resumable-media
+google-resumable-media==2.6.0
+    # via google-cloud-bigquery
+googleapis-common-protos==1.61.0
+    # via
+    #   google-api-core
+    #   grpcio-status
+grpcio==1.59.3
+    # via
+    #   google-api-core
+    #   google-cloud-bigquery
+    #   grpcio-status
+grpcio-status==1.59.3
+    # via google-api-core
+idna==3.4
+    # via
+    #   anyio
+    #   jsonschema
+    #   requests
+iniconfig==2.0.0
+    # via pytest
+interface-meta==1.3.0
+    # via formulaic
+ipykernel==6.27.0
+    # via
+    #   bash-kernel
+    #   jupyter
+    #   jupyter-console
+    #   jupyterlab
+    #   nbval
+    #   qtconsole
+ipython==8.17.2
+    # via
+    #   ipykernel
+    #   ipywidgets
+    #   jupyter-console
+ipywidgets==8.1.1
+    # via
+    #   -r requirements-3.10.in
+    #   jupyter
+isoduration==20.11.0
+    # via jsonschema
+jedi==0.19.1
+    # via ipython
+jinja2==3.1.2
+    # via
+    #   jupyter-server
+    #   jupyterlab
+    #   jupyterlab-server
+    #   nbconvert
+joblib==1.3.2
+    # via scikit-learn
+json5==0.9.14
+    # via jupyterlab-server
+jsonpointer==2.4
+    # via jsonschema
+jsonschema[format-nongpl]==4.20.0
+    # via
+    #   jupyter-events
+    #   jupyterlab-server
+    #   nbformat
+jsonschema-specifications==2023.11.1
+    # via jsonschema
+jupyter==1.0.0
+    # via -r requirements-3.10.in
+jupyter-client==8.6.0
+    # via
+    #   ipykernel
+    #   jupyter-console
+    #   jupyter-server
+    #   nbclient
+    #   nbval
+    #   qtconsole
+jupyter-console==6.6.3
+    # via jupyter
+jupyter-core==5.5.0
+    # via
+    #   ipykernel
+    #   jupyter-client
+    #   jupyter-console
+    #   jupyter-server
+    #   jupyterlab
+    #   nbclient
+    #   nbconvert
+    #   nbformat
+    #   qtconsole
+jupyter-events==0.9.0
+    # via jupyter-server
+jupyter-lsp==2.2.0
+    # via jupyterlab
+jupyter-server==2.11.0
+    # via
+    #   jupyter-lsp
+    #   jupyterlab
+    #   jupyterlab-server
+    #   notebook
+    #   notebook-shim
+jupyter-server-terminals==0.4.4
+    # via jupyter-server
+jupyterlab==4.0.9
+    # via
+    #   -r requirements-3.10.in
+    #   notebook
+jupyterlab-pygments==0.2.2
+    # via nbconvert
+jupyterlab-server==2.25.2
+    # via
+    #   jupyterlab
+    #   notebook
+jupyterlab-widgets==3.0.9
+    # via ipywidgets
+jupytext==1.15.2
+    # via -r requirements-3.10.in
+kaleido==0.2.1
+    # via -r requirements-3.10.in
+kiwisolver==1.4.5
+    # via matplotlib
+lifelines==0.27.8
+    # via -r requirements-3.10.in
+llvmlite==0.41.1
+    # via numba
+lz4==4.3.2
+    # via opensafely-cohort-extractor
+markdown-it-py==3.0.0
+    # via
+    #   jupytext
+    #   mdit-py-plugins
+markupsafe==2.1.3
+    # via
+    #   jinja2
+    #   nbconvert
+matplotlib==3.8.2
+    # via
+    #   -r requirements-3.10.in
+    #   descartes
+    #   lifelines
+    #   seaborn
+    #   upsetplot
+    #   venn
+matplotlib-inline==0.1.6
+    # via
+    #   ipykernel
+    #   ipython
+mdit-py-plugins==0.4.0
+    # via jupytext
+mdurl==0.1.2
+    # via markdown-it-py
+mistune==3.0.2
+    # via nbconvert
+nbclient==0.9.0
+    # via nbconvert
+nbconvert==7.11.0
+    # via
+    #   jupyter
+    #   jupyter-server
+nbformat==5.9.2
+    # via
+    #   jupyter-server
+    #   jupytext
+    #   nbclient
+    #   nbconvert
+    #   nbval
+nbval==0.10.0
+    # via -r requirements-3.10.in
+nest-asyncio==1.5.8
+    # via ipykernel
+notebook==7.0.6
+    # via jupyter
+notebook-shim==0.2.3
+    # via
+    #   jupyterlab
+    #   notebook
+numba==0.58.1
+    # via -r requirements-3.10.in
+numpy==1.26.2
+    # via
+    #   -r requirements-3.10.in
+    #   autograd
+    #   contourpy
+    #   db-dtypes
+    #   formulaic
+    #   lifelines
+    #   matplotlib
+    #   numba
+    #   pandas
+    #   pandas-gbq
+    #   patsy
+    #   pyarrow
+    #   scikit-learn
+    #   scipy
+    #   seaborn
+    #   shapely
+    #   statsmodels
+oauthlib==3.2.2
+    # via requests-oauthlib
+opensafely-cohort-extractor==1.90.0
+    # via -r requirements-3.10.in
+opensafely-matching==0.2.0
+    # via -r requirements-3.10.in
+overrides==7.4.0
+    # via jupyter-server
+packaging==23.2
+    # via
+    #   build
+    #   db-dtypes
+    #   geopandas
+    #   google-cloud-bigquery
+    #   ipykernel
+    #   jupyter-server
+    #   jupyterlab
+    #   jupyterlab-server
+    #   matplotlib
+    #   nbconvert
+    #   plotly
+    #   pytest
+    #   qtconsole
+    #   qtpy
+    #   statsmodels
+pandas==2.1.3
+    # via
+    #   -r requirements-3.10.in
+    #   db-dtypes
+    #   ebmdatalab
+    #   formulaic
+    #   geopandas
+    #   lifelines
+    #   opensafely-cohort-extractor
+    #   opensafely-matching
+    #   pandas-gbq
+    #   seaborn
+    #   statsmodels
+    #   upsetplot
+pandas-gbq==0.19.2
+    # via
+    #   -r requirements-3.10.in
+    #   ebmdatalab
+pandocfilters==1.5.0
+    # via nbconvert
+parso==0.8.3
+    # via jedi
+patsy==0.5.3
+    # via statsmodels
+pexpect==4.8.0
+    # via
+    #   bash-kernel
+    #   ipython
+pillow==10.1.0
+    # via
+    #   -r requirements-3.10.in
+    #   cairosvg
+    #   matplotlib
+pip-tools==7.3.0
+    # via -r requirements-3.10.in
+platformdirs==4.0.0
+    # via jupyter-core
+plotly==5.18.0
+    # via -r requirements-3.10.in
+pluggy==1.3.0
+    # via pytest
+prometheus-client==0.19.0
+    # via jupyter-server
+prompt-toolkit==3.0.41
+    # via
+    #   ipython
+    #   jupyter-console
+proto-plus==1.22.3
+    # via
+    #   google-cloud-bigquery
+    #   google-cloud-bigquery-storage
+protobuf==4.25.1
+    # via
+    #   google-api-core
+    #   google-cloud-bigquery
+    #   google-cloud-bigquery-storage
+    #   googleapis-common-protos
+    #   grpcio-status
+    #   proto-plus
+psutil==5.9.6
+    # via ipykernel
+ptyprocess==0.7.0
+    # via
+    #   pexpect
+    #   terminado
+pure-eval==0.2.2
+    # via stack-data
+py==1.11.0
+    # via retry
+pyarrow==14.0.1
+    # via
+    #   -r requirements-3.10.in
+    #   db-dtypes
+    #   opensafely-cohort-extractor
+    #   pandas-gbq
+pyasn1==0.5.1
+    # via
+    #   pyasn1-modules
+    #   rsa
+pyasn1-modules==0.3.0
+    # via google-auth
+pycparser==2.21
+    # via cffi
+pydata-google-auth==1.8.2
+    # via pandas-gbq
+pygments==2.17.1
+    # via
+    #   ipython
+    #   jupyter-console
+    #   nbconvert
+    #   qtconsole
+pyparsing==3.1.1
+    # via matplotlib
+pyproj==3.6.1
+    # via geopandas
+pyproject-hooks==1.0.0
+    # via build
+pytest==7.4.3
+    # via
+    #   -r requirements-3.10.in
+    #   nbval
+python-dateutil==2.8.2
+    # via
+    #   arrow
+    #   google-cloud-bigquery
+    #   jupyter-client
+    #   matplotlib
+    #   pandas
+python-json-logger==2.0.7
+    # via jupyter-events
+pytz==2023.3.post1
+    # via pandas
+pyyaml==6.0.1
+    # via
+    #   jupyter-events
+    #   jupytext
+    #   opensafely-cohort-extractor
+pyzmq==25.1.1
+    # via
+    #   ipykernel
+    #   jupyter-client
+    #   jupyter-console
+    #   jupyter-server
+    #   qtconsole
+qtconsole==5.5.1
+    # via jupyter
+qtpy==2.4.1
+    # via qtconsole
+referencing==0.31.0
+    # via
+    #   jsonschema
+    #   jsonschema-specifications
+    #   jupyter-events
+requests==2.31.0
+    # via
+    #   google-api-core
+    #   google-cloud-bigquery
+    #   jupyterlab-server
+    #   opensafely-cohort-extractor
+    #   requests-oauthlib
+requests-oauthlib==1.3.1
+    # via google-auth-oauthlib
+retry==0.9.2
+    # via opensafely-cohort-extractor
+rfc3339-validator==0.1.4
+    # via
+    #   jsonschema
+    #   jupyter-events
+rfc3986-validator==0.1.1
+    # via
+    #   jsonschema
+    #   jupyter-events
+rpds-py==0.13.1
+    # via
+    #   jsonschema
+    #   referencing
+rsa==4.9
+    # via google-auth
+scikit-learn==1.3.2
+    # via -r requirements-3.10.in
+scipy==1.11.4
+    # via
+    #   -r requirements-3.10.in
+    #   autograd-gamma
+    #   formulaic
+    #   lifelines
+    #   scikit-learn
+    #   statsmodels
+seaborn==0.13.0
+    # via
+    #   ebmdatalab
+    #   opensafely-cohort-extractor
+send2trash==1.8.2
+    # via jupyter-server
+shapely==2.0.2
+    # via geopandas
+six==1.16.0
+    # via
+    #   asttokens
+    #   bleach
+    #   fiona
+    #   patsy
+    #   python-dateutil
+    #   rfc3339-validator
+sniffio==1.3.0
+    # via anyio
+soupsieve==2.5
+    # via beautifulsoup4
+sqlparse==0.4.4
+    # via opensafely-cohort-extractor
+stack-data==0.6.3
+    # via ipython
+statsmodels==0.14.0
+    # via ebmdatalab
+structlog==23.2.0
+    # via opensafely-cohort-extractor
+tabulate==0.9.0
+    # via opensafely-cohort-extractor
+tenacity==8.2.3
+    # via plotly
+terminado==0.18.0
+    # via
+    #   jupyter-server
+    #   jupyter-server-terminals
+threadpoolctl==3.2.0
+    # via scikit-learn
+tinycss2==1.2.1
+    # via
+    #   cairosvg
+    #   cssselect2
+    #   nbconvert
+toml==0.10.2
+    # via jupytext
+tomli==2.0.1
+    # via
+    #   build
+    #   jupyterlab
+    #   pip-tools
+    #   pyproject-hooks
+    #   pytest
+tornado==6.3.3
+    # via
+    #   ipykernel
+    #   jupyter-client
+    #   jupyter-server
+    #   jupyterlab
+    #   notebook
+    #   terminado
+tqdm==4.66.1
+    # via -r requirements-3.10.in
+traitlets==5.13.0
+    # via
+    #   comm
+    #   ipykernel
+    #   ipython
+    #   ipywidgets
+    #   jupyter-client
+    #   jupyter-console
+    #   jupyter-core
+    #   jupyter-events
+    #   jupyter-server
+    #   jupyterlab
+    #   matplotlib-inline
+    #   nbclient
+    #   nbconvert
+    #   nbformat
+    #   qtconsole
+types-python-dateutil==2.8.19.14
+    # via arrow
+typing-extensions==4.8.0
+    # via
+    #   async-lru
+    #   formulaic
+tzdata==2023.3
+    # via pandas
+upsetplot==0.8.0
+    # via -r requirements-3.10.in
+uri-template==1.3.0
+    # via jsonschema
+urllib3==2.1.0
+    # via requests
+venn==0.1.3
+    # via -r requirements-3.10.in
+wcwidth==0.2.11
+    # via prompt-toolkit
+webcolors==1.13
+    # via jsonschema
+webencodings==0.5.1
+    # via
+    #   bleach
+    #   cssselect2
+    #   tinycss2
+websocket-client==1.6.4
+    # via jupyter-server
+wheel==0.41.3
+    # via pip-tools
+widgetsnbextension==4.0.9
+    # via ipywidgets
+wrapt==1.16.0
+    # via formulaic
+
+# The following packages are considered to be unsafe in a requirements file:
+# pip
+# setuptools

From c42b4c3db81f17bfee3b7a95dcda27399848ff9e Mon Sep 17 00:00:00 2001
From: bloodearnest <simon.davy@thedatalab.org>
Date: Wed, 22 Nov 2023 17:20:42 +0000
Subject: [PATCH 02/11] CI test and publish for versions

The github workflows have been updated to publish the v1 image as *both*
`v1` and `latest` tags for now, as well as under the jupyter alias. The
`v2` is published separately as just `v2`.
---
 .github/workflows/build_and_publish.yaml | 45 ++++++++++++------------
 .github/workflows/tests.yaml             | 31 ++++++++++------
 2 files changed, 44 insertions(+), 32 deletions(-)

diff --git a/.github/workflows/build_and_publish.yaml b/.github/workflows/build_and_publish.yaml
index 84349d8..f38c046 100644
--- a/.github/workflows/build_and_publish.yaml
+++ b/.github/workflows/build_and_publish.yaml
@@ -1,33 +1,34 @@
 name: Build and publish
 on:
+  workflow_dispatch:
   push:
     branches: [main]
-  workflow_dispatch:
-permissions:
-  packages: write
-env:
-  IMAGE_NAME: python
+
 jobs:
-  build-and-publish:
-    runs-on: ubuntu-20.04
+  publish:
+    # note: this builds/tests all versions in serial for two reasons. Firstly we
+    # want all versions to release or none of them. Secondly, we will be able
+    # publish the exact images that were built and tested.
+    runs-on: ubuntu-22.04
     steps:
-    - name: Checkout
-      uses: actions/checkout@v3
-    - name: Build image
-      run: make build
+    - uses: actions/checkout@v3
+    - uses: "opensafely-core/setup-action@v1"
+      with:
+          install-just: true
+    - name: Build images
+      run: |
+        just build v1
+        just build v2
     - name: Run tests
-      run: make test functional-test
-    - name: Run lint
-      run: make lint 
+      run: |
+        just test v1
+        just test v2
+    - name: Run linters
+      run: just check 
+
     - name: Log into GitHub Container Registry
       run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login https://ghcr.io -u ${{ github.actor }} --password-stdin
     - name: Push image to GitHub Container Registry
       run: |
-        IMAGE_ID="ghcr.io/${{ github.repository_owner }}/$IMAGE_NAME"
-        docker tag "$IMAGE_NAME" "$IMAGE_ID:latest"
-        docker push "$IMAGE_ID:latest"
-
-        JUPYTER_ID="ghcr.io/${{ github.repository_owner }}/jupyter"
-        # also publish as jupyter image for backward compatibility
-        docker tag "$IMAGE_NAME" "$JUPYTER_ID:latest"
-        docker push "$JUPYTER_ID:latest"
+        just publish v1
+        just publish v2
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index b449bd5..f5a9ed6 100644
--- a/.github/workflows/tests.yaml
+++ b/.github/workflows/tests.yaml
@@ -1,17 +1,28 @@
 name: Run tests
 on:
   pull_request:
-env:
-  IMAGE_NAME: python
 jobs:
-  tests:
-    runs-on: ubuntu-20.04
+  version-tests:
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        version: [v1, v2]
     steps:
-    - name: Checkout
-      uses: actions/checkout@master
+    - uses: actions/checkout@v3
+    - uses: "opensafely-core/setup-action@v1"
+      with:
+          install-just: true
     - name: Build image
-      run: make build
+      run: just build ${{ matrix.version }}
     - name: Run tests
-      run: make test functional-test
-    - name: Run lint
-      run: make lint 
+      run: just test ${{ matrix.version }}
+  lint:
+    runs-on: ubuntu-22.04
+    steps:
+    - uses: actions/checkout@v3
+    - uses: "opensafely-core/setup-action@v1"
+      with:
+          install-just: true
+    - name: Run linters
+      run: just check 
+

From adfa9a8a5574df5d92a56ec965a2498d9490d93f Mon Sep 17 00:00:00 2001
From: bloodearnest <simon.davy@thedatalab.org>
Date: Thu, 23 Nov 2023 16:00:16 +0000
Subject: [PATCH 03/11] Add time based build number

Used in docker image label and tag

Refactored publishing script too.
---
 .github/workflows/build_and_publish.yaml |  5 ++--
 justfile                                 | 28 ++++---------------
 scripts/publish.sh                       | 35 ++++++++++++++++++++++++
 3 files changed, 44 insertions(+), 24 deletions(-)
 create mode 100755 scripts/publish.sh

diff --git a/.github/workflows/build_and_publish.yaml b/.github/workflows/build_and_publish.yaml
index f38c046..52966bc 100644
--- a/.github/workflows/build_and_publish.yaml
+++ b/.github/workflows/build_and_publish.yaml
@@ -30,5 +30,6 @@ jobs:
       run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login https://ghcr.io -u ${{ github.actor }} --password-stdin
     - name: Push image to GitHub Container Registry
       run: |
-        just publish v1
-        just publish v2
+        # just test publish for now
+        just publish v1 false
+        just publish v2 false
diff --git a/justfile b/justfile
index 310f12e..e3844d7 100644
--- a/justfile
+++ b/justfile
@@ -1,9 +1,11 @@
 export DOCKER_BUILDKIT := "1"
+# technically, these could differ by 1 seconds, but thats unlikely and doesn't matter
+# human readable, used as label in docker image
 export BUILD_DATE := `date +'%y-%m-%dT%H:%M:%S.%3NZ'`
+# monotonic, used as label in docker image *and* in docker tag
+export BUILD_NUMBER := `date +'%y%m%d%H%M%S'`
 export REVISION := `git rev-parse --short HEAD`
 
-# TODO: calculate this
-export BUILD_NUMBER := "1234"
 
 build version target="python" *args="":
     docker-compose --env-file {{ version }}/env build --pull {{ args }} {{ target }} 
@@ -18,23 +20,5 @@ check:
     @docker pull hadolint/hadolint:v2.12.0
     @docker run --rm -i hadolint/hadolint:v2.12.0 < Dockerfile
 
-publish version:
-    #!/bin/bash
-    set -euxo pipefail
-    docker tag python:{{ version }} ghcr.io/opensafely-core/python:{{ version }}
-    echo docker push ghcr.io/opensafely-core/python:{{ version }}
-
-    if test "{{ version }}" = "v1"; then
-        # jupyter is only alias for v1
-        docker tag python:{{ version }} ghcr.io/opensafely-core/jupyter:{{ version }}
-        echo docker push ghcr.io/opensafely-core/jupyter:{{ version }}
-
-        # v1 is also known as latest, at least until we transition fully
-        docker tag python:{{ version }} ghcr.io/opensafely-core/python:latest
-        docker tag python:{{ version }} ghcr.io/opensafely-core/jupyter:latest
-        echo docker push ghcr.io/opensafely-core/python:latest
-        echo docker push ghcr.io/opensafely-core/jupyter:latest
-    fi
-
-
-
+publish version publish="false":
+    PUBLISH={{ publish }} ./scripts/publish.sh {{ version }}
diff --git a/scripts/publish.sh b/scripts/publish.sh
new file mode 100755
index 0000000..19c8027
--- /dev/null
+++ b/scripts/publish.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+set -euo pipefail
+
+version=$1
+registry=ghcr.io/opensafely-core
+
+run() {
+    echo "$@"
+    if test "${PUBLISH:-}" = "true"; then
+        # shellcheck disable=SC2068
+        $@
+    fi
+}
+
+publish() {
+    local local_tag=$1;
+    local remote_tag=$2;
+
+    run docker tag "$local_tag" "$remote_tag"
+    run docker push "$remote_tag"
+}
+
+full_version="$(docker inspect --format='{{ index .Config.Labels "org.opencontainers.image.version"}}' "python:$version")"
+
+publish "python:$version" "$registry/python:$version"
+publish "python:$version" "$registry/python:${full_version}"
+
+if test "$version" = "v1"; then
+    # jupyter is only alias for v1
+    publish "python:$version" "$registry/jupyter:$version"
+
+    # v1 is also known as latest, at least until we transition fully
+    publish "python:$version" "$registry/python:latest"
+    publish "python:$version" "$registry/jupyter:latest"
+fi

From 395ed4680142e440f1fffe9d246184338f4999a0 Mon Sep 17 00:00:00 2001
From: bloodearnest <simon.davy@thedatalab.org>
Date: Fri, 24 Nov 2023 14:08:41 +0000
Subject: [PATCH 04/11] justfile doc and tweaks

---
 justfile | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/justfile b/justfile
index e3844d7..5b4bb6a 100644
--- a/justfile
+++ b/justfile
@@ -6,19 +6,27 @@ export BUILD_DATE := `date +'%y-%m-%dT%H:%M:%S.%3NZ'`
 export BUILD_NUMBER := `date +'%y%m%d%H%M%S'`
 export REVISION := `git rev-parse --short HEAD`
 
-
+# build docker image for version
 build version target="python" *args="":
     docker-compose --env-file {{ version }}/env build --pull {{ args }} {{ target }} 
 
-test version *args="tests -v":
+
+# test docker image for version
+test version *args="tests -v": (build version)
     docker-compose --env-file {{ version }}/env run --rm -v $PWD:/workspace python pytest {{ args }}
 
-update version *args="":
+
+# run pip-compile to add new dependencies, or update existing ones with --upgrade
+update version *args="": (build version)
     docker-compose --env-file {{ version }}/env run --rm -v $PWD:/workspace base pip-compile {{ args }} {{ version }}/requirements.in -o {{ version }}/requirements.txt
 
+
+# run linters
 check:
     @docker pull hadolint/hadolint:v2.12.0
     @docker run --rm -i hadolint/hadolint:v2.12.0 < Dockerfile
 
+
+# publish version (dry run by default - pass "true" to perform publish)
 publish version publish="false":
     PUBLISH={{ publish }} ./scripts/publish.sh {{ version }}

From 71f3cb185bcc6ce48452a7f73b9c34350eb4c54c Mon Sep 17 00:00:00 2001
From: bloodearnest <simon.davy@thedatalab.org>
Date: Fri, 24 Nov 2023 15:39:57 +0000
Subject: [PATCH 05/11] Add documentation rendering of package versions

This can be enhanced as needed, but the basic versions and tooling is
there.

Jinja2 is installed in the images, so we re-use the images themselves to
render the template.
---
 Dockerfile             |   3 +-
 justfile               |   6 ++
 scripts/packages.j2.md |  12 +++
 scripts/render.py      |  24 +++++
 v1/packages.md         | 145 ++++++++++++++++++++++++++++++
 v1/requirements.txt    |   4 +-
 v2/packages.md         | 200 +++++++++++++++++++++++++++++++++++++++++
 7 files changed, 391 insertions(+), 3 deletions(-)
 create mode 100644 scripts/packages.j2.md
 create mode 100755 scripts/render.py
 create mode 100644 v1/packages.md
 create mode 100644 v2/packages.md

diff --git a/Dockerfile b/Dockerfile
index 5ccef52..7e3eec0 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -16,8 +16,9 @@ RUN mkdir /workspace
 WORKDIR /workspace
 
 ARG MAJOR_VERSION
+ARG BASE
 # ACTION_EXEC sets the default executable for the entrypoint in the base-docker image
-ENV ACTION_EXEC=python MAJOR_VERSION=${MAJOR_VERSION}
+ENV ACTION_EXEC=python MAJOR_VERSION=${MAJOR_VERSION} BASE=${BASE}
 
 COPY ${MAJOR_VERSION}/dependencies.txt /root/dependencies.txt
 # use space efficient utility from base image
diff --git a/justfile b/justfile
index 5b4bb6a..cdcf479 100644
--- a/justfile
+++ b/justfile
@@ -19,6 +19,12 @@ test version *args="tests -v": (build version)
 # run pip-compile to add new dependencies, or update existing ones with --upgrade
 update version *args="": (build version)
     docker-compose --env-file {{ version }}/env run --rm -v $PWD:/workspace base pip-compile {{ args }} {{ version }}/requirements.in -o {{ version }}/requirements.txt
+    {{ just_executable() }} render {{ version }}
+
+
+# render package version information
+render version *args:
+    docker-compose --env-file {{ version }}/env run --rm -v $PWD:/workspace python ./scripts/render.py {{ args }} > {{ version }}/packages.md
 
 
 # run linters
diff --git a/scripts/packages.j2.md b/scripts/packages.j2.md
new file mode 100644
index 0000000..e9dd3e1
--- /dev/null
+++ b/scripts/packages.j2.md
@@ -0,0 +1,12 @@
+# Package Versions for {{ MAJOR_VERSION }}
+
+This python:{{ MAJOR_VERSION }} OpenSAFELY image is based on Ubuntu {{ BASE }} with Python {{ PYTHON_VERSION }}.
+
+## Packages
+
+It comes pre-installed with a standard set of python packages.
+
+{% for pkg in PACKAGES -%}
+ - [{{ pkg | replace("==", ": ")}}](https://pypi.org/project/{{pkg.name}}/{{pkg.specs[0][1]}}/)
+{% endfor -%}
+
diff --git a/scripts/render.py b/scripts/render.py
new file mode 100755
index 0000000..f036bfe
--- /dev/null
+++ b/scripts/render.py
@@ -0,0 +1,24 @@
+#!/usr/bin/env -S python3 -W ignore
+from pathlib import Path
+import os
+import sys
+import pkg_resources
+
+from jinja2 import Environment, FileSystemLoader
+env = Environment(loader=FileSystemLoader("scripts"))
+
+version = os.environ["MAJOR_VERSION"]
+requirements = Path(version) / "requirements.txt"
+
+context = {
+    "MAJOR_VERSION": version,
+    "BASE": os.environ["BASE"],
+    "PYTHON_VERSION": "{}.{}.{}".format(*sys.version_info),
+}
+
+with requirements.open() as r:
+    context["PACKAGES"] = list(pkg_resources.parse_requirements(r))
+
+template = env.get_template("packages.j2.md")
+
+print(template.render(**context))
diff --git a/v1/packages.md b/v1/packages.md
new file mode 100644
index 0000000..58476de
--- /dev/null
+++ b/v1/packages.md
@@ -0,0 +1,145 @@
+# Package Versions for v1
+
+This python:v1 OpenSAFELY image is based on Ubuntu 20.04 with Python 3.8.10.
+
+## Packages
+
+It comes pre-installed with a standard set of python packages.
+
+- [astor: 0.8.1](https://pypi.org/project/astor/0.8.1/)
+- [attrs: 19.3.0](https://pypi.org/project/attrs/19.3.0/)
+- [autograd: 1.3](https://pypi.org/project/autograd/1.3/)
+- [autograd-gamma: 0.5.0](https://pypi.org/project/autograd-gamma/0.5.0/)
+- [backcall: 0.1.0](https://pypi.org/project/backcall/0.1.0/)
+- [bash-kernel: 0.7.2](https://pypi.org/project/bash-kernel/0.7.2/)
+- [bleach: 3.1.2](https://pypi.org/project/bleach/3.1.2/)
+- [cachetools: 4.0.0](https://pypi.org/project/cachetools/4.0.0/)
+- [cairocffi: 1.4.0](https://pypi.org/project/cairocffi/1.4.0/)
+- [cairosvg: 2.5.2](https://pypi.org/project/cairosvg/2.5.2/)
+- [certifi: 2019.11.28](https://pypi.org/project/certifi/2019.11.28/)
+- [cffi: 1.15.1](https://pypi.org/project/cffi/1.15.1/)
+- [chardet: 3.0.4](https://pypi.org/project/chardet/3.0.4/)
+- [click: 7.0](https://pypi.org/project/click/7.0/)
+- [click-plugins: 1.1.1](https://pypi.org/project/click-plugins/1.1.1/)
+- [cligj: 0.5.0](https://pypi.org/project/cligj/0.5.0/)
+- [coverage: 4.5.4](https://pypi.org/project/coverage/4.5.4/)
+- [cssselect2: 0.7.0](https://pypi.org/project/cssselect2/0.7.0/)
+- [cycler: 0.10.0](https://pypi.org/project/cycler/0.10.0/)
+- [decorator: 4.4.1](https://pypi.org/project/decorator/4.4.1/)
+- [defusedxml: 0.6.0](https://pypi.org/project/defusedxml/0.6.0/)
+- [descartes: 1.1.0](https://pypi.org/project/descartes/1.1.0/)
+- [ebmdatalab: 0.0.30](https://pypi.org/project/ebmdatalab/0.0.30/)
+- [entrypoints: 0.3](https://pypi.org/project/entrypoints/0.3/)
+- [fiona: 1.8.13](https://pypi.org/project/fiona/1.8.13/)
+- [formulaic: 0.2.4](https://pypi.org/project/formulaic/0.2.4/)
+- [future: 0.18.2](https://pypi.org/project/future/0.18.2/)
+- [geopandas: 0.6.3](https://pypi.org/project/geopandas/0.6.3/)
+- [google-api-core: 1.16.0](https://pypi.org/project/google-api-core/1.16.0/)
+- [google-auth: 1.11.0](https://pypi.org/project/google-auth/1.11.0/)
+- [google-auth-oauthlib: 0.4.1](https://pypi.org/project/google-auth-oauthlib/0.4.1/)
+- [google-cloud-bigquery: 1.24.0](https://pypi.org/project/google-cloud-bigquery/1.24.0/)
+- [google-cloud-core: 1.3.0](https://pypi.org/project/google-cloud-core/1.3.0/)
+- [google-resumable-media: 0.5.0](https://pypi.org/project/google-resumable-media/0.5.0/)
+- [googleapis-common-protos: 1.51.0](https://pypi.org/project/googleapis-common-protos/1.51.0/)
+- [idna: 2.8](https://pypi.org/project/idna/2.8/)
+- [interface-meta: 1.2.4](https://pypi.org/project/interface-meta/1.2.4/)
+- [ipykernel: 5.1.4](https://pypi.org/project/ipykernel/5.1.4/)
+- [ipython: 7.12.0](https://pypi.org/project/ipython/7.12.0/)
+- [ipython-genutils: 0.2.0](https://pypi.org/project/ipython-genutils/0.2.0/)
+- [ipywidgets: 7.5.1](https://pypi.org/project/ipywidgets/7.5.1/)
+- [jedi: 0.16.0](https://pypi.org/project/jedi/0.16.0/)
+- [jinja2: 2.11.1](https://pypi.org/project/jinja2/2.11.1/)
+- [joblib: 1.0.1](https://pypi.org/project/joblib/1.0.1/)
+- [json5: 0.9.0](https://pypi.org/project/json5/0.9.0/)
+- [jsonschema: 3.2.0](https://pypi.org/project/jsonschema/3.2.0/)
+- [jupyter: 1.0.0](https://pypi.org/project/jupyter/1.0.0/)
+- [jupyter-client: 5.3.4](https://pypi.org/project/jupyter-client/5.3.4/)
+- [jupyter-console: 6.1.0](https://pypi.org/project/jupyter-console/6.1.0/)
+- [jupyter-core: 4.6.1](https://pypi.org/project/jupyter-core/4.6.1/)
+- [jupyterlab: 1.2.6](https://pypi.org/project/jupyterlab/1.2.6/)
+- [jupyterlab-server: 1.0.6](https://pypi.org/project/jupyterlab-server/1.0.6/)
+- [jupytext: 1.3.3](https://pypi.org/project/jupytext/1.3.3/)
+- [kaleido: 0.2.1](https://pypi.org/project/kaleido/0.2.1/)
+- [kiwisolver: 1.1.0](https://pypi.org/project/kiwisolver/1.1.0/)
+- [lifelines: 0.26.4](https://pypi.org/project/lifelines/0.26.4/)
+- [llvmlite: 0.34.0](https://pypi.org/project/llvmlite/0.34.0/)
+- [lz4: 3.1.3](https://pypi.org/project/lz4/3.1.3/)
+- [markupsafe: 1.1.1](https://pypi.org/project/markupsafe/1.1.1/)
+- [matplotlib: 3.1.3](https://pypi.org/project/matplotlib/3.1.3/)
+- [mistune: 0.8.4](https://pypi.org/project/mistune/0.8.4/)
+- [more-itertools: 8.2.0](https://pypi.org/project/more-itertools/8.2.0/)
+- [munch: 2.5.0](https://pypi.org/project/munch/2.5.0/)
+- [nbconvert: 5.6.1](https://pypi.org/project/nbconvert/5.6.1/)
+- [nbformat: 5.0.4](https://pypi.org/project/nbformat/5.0.4/)
+- [nbval: 0.9.4](https://pypi.org/project/nbval/0.9.4/)
+- [notebook: 6.0.3](https://pypi.org/project/notebook/6.0.3/)
+- [numba: 0.51.2](https://pypi.org/project/numba/0.51.2/)
+- [numpy: 1.18.1](https://pypi.org/project/numpy/1.18.1/)
+- [oauthlib: 3.1.0](https://pypi.org/project/oauthlib/3.1.0/)
+- [opensafely-cohort-extractor: 1.88.0](https://pypi.org/project/opensafely-cohort-extractor/1.88.0/)
+- [opensafely-matching: 0.2.0](https://pypi.org/project/opensafely-matching/0.2.0/)
+- [packaging: 20.1](https://pypi.org/project/packaging/20.1/)
+- [pandas: 1.0.1](https://pypi.org/project/pandas/1.0.1/)
+- [pandas-gbq: 0.13.0](https://pypi.org/project/pandas-gbq/0.13.0/)
+- [pandocfilters: 1.4.2](https://pypi.org/project/pandocfilters/1.4.2/)
+- [parso: 0.6.1](https://pypi.org/project/parso/0.6.1/)
+- [patsy: 0.5.1](https://pypi.org/project/patsy/0.5.1/)
+- [pep517: 0.10.0](https://pypi.org/project/pep517/0.10.0/)
+- [pexpect: 4.8.0](https://pypi.org/project/pexpect/4.8.0/)
+- [pickleshare: 0.7.5](https://pypi.org/project/pickleshare/0.7.5/)
+- [pillow: 8.1.0](https://pypi.org/project/pillow/8.1.0/)
+- [pip-tools: 6.2.0](https://pypi.org/project/pip-tools/6.2.0/)
+- [plotly: 4.5.0](https://pypi.org/project/plotly/4.5.0/)
+- [pluggy: 0.13.1](https://pypi.org/project/pluggy/0.13.1/)
+- [prometheus-client: 0.7.1](https://pypi.org/project/prometheus-client/0.7.1/)
+- [prompt-toolkit: 3.0.3](https://pypi.org/project/prompt-toolkit/3.0.3/)
+- [protobuf: 3.11.3](https://pypi.org/project/protobuf/3.11.3/)
+- [ptyprocess: 0.6.0](https://pypi.org/project/ptyprocess/0.6.0/)
+- [py: 1.8.1](https://pypi.org/project/py/1.8.1/)
+- [pyarrow: 3.0.0](https://pypi.org/project/pyarrow/3.0.0/)
+- [pyasn1: 0.4.8](https://pypi.org/project/pyasn1/0.4.8/)
+- [pyasn1-modules: 0.2.8](https://pypi.org/project/pyasn1-modules/0.2.8/)
+- [pycparser: 2.21](https://pypi.org/project/pycparser/2.21/)
+- [pydata-google-auth: 0.3.0](https://pypi.org/project/pydata-google-auth/0.3.0/)
+- [pygments: 2.5.2](https://pypi.org/project/pygments/2.5.2/)
+- [pyparsing: 2.4.6](https://pypi.org/project/pyparsing/2.4.6/)
+- [pyproj: 2.4.2.post1](https://pypi.org/project/pyproj/2.4.2.post1/)
+- [pyrsistent: 0.15.7](https://pypi.org/project/pyrsistent/0.15.7/)
+- [pytest: 5.3.5](https://pypi.org/project/pytest/5.3.5/)
+- [python-dateutil: 2.8.1](https://pypi.org/project/python-dateutil/2.8.1/)
+- [pytz: 2019.3](https://pypi.org/project/pytz/2019.3/)
+- [pyyaml: 5.3](https://pypi.org/project/pyyaml/5.3/)
+- [pyzmq: 18.1.1](https://pypi.org/project/pyzmq/18.1.1/)
+- [qtconsole: 4.6.0](https://pypi.org/project/qtconsole/4.6.0/)
+- [requests: 2.22.0](https://pypi.org/project/requests/2.22.0/)
+- [requests-oauthlib: 1.3.0](https://pypi.org/project/requests-oauthlib/1.3.0/)
+- [retry: 0.9.2](https://pypi.org/project/retry/0.9.2/)
+- [retrying: 1.3.3](https://pypi.org/project/retrying/1.3.3/)
+- [rsa: 4.0](https://pypi.org/project/rsa/4.0/)
+- [scikit-learn: 0.24.1](https://pypi.org/project/scikit-learn/0.24.1/)
+- [scipy: 1.4.1](https://pypi.org/project/scipy/1.4.1/)
+- [seaborn: 0.10.0](https://pypi.org/project/seaborn/0.10.0/)
+- [send2trash: 1.5.0](https://pypi.org/project/send2trash/1.5.0/)
+- [shapely: 1.7.0](https://pypi.org/project/shapely/1.7.0/)
+- [six: 1.14.0](https://pypi.org/project/six/1.14.0/)
+- [sqlparse: 0.4.1](https://pypi.org/project/sqlparse/0.4.1/)
+- [statsmodels: 0.11.0](https://pypi.org/project/statsmodels/0.11.0/)
+- [structlog: 20.2.0](https://pypi.org/project/structlog/20.2.0/)
+- [tabulate: 0.8.7](https://pypi.org/project/tabulate/0.8.7/)
+- [terminado: 0.8.3](https://pypi.org/project/terminado/0.8.3/)
+- [testpath: 0.4.4](https://pypi.org/project/testpath/0.4.4/)
+- [threadpoolctl: 2.1.0](https://pypi.org/project/threadpoolctl/2.1.0/)
+- [tinycss2: 1.2.1](https://pypi.org/project/tinycss2/1.2.1/)
+- [toml: 0.10.2](https://pypi.org/project/toml/0.10.2/)
+- [tornado: 6.0.3](https://pypi.org/project/tornado/6.0.3/)
+- [tqdm: 4.42.1](https://pypi.org/project/tqdm/4.42.1/)
+- [traitlets: 4.3.3](https://pypi.org/project/traitlets/4.3.3/)
+- [upsetplot: 0.6.1](https://pypi.org/project/upsetplot/0.6.1/)
+- [urllib3: 1.25.8](https://pypi.org/project/urllib3/1.25.8/)
+- [venn: 0.1.3](https://pypi.org/project/venn/0.1.3/)
+- [wcwidth: 0.1.8](https://pypi.org/project/wcwidth/0.1.8/)
+- [webencodings: 0.5.1](https://pypi.org/project/webencodings/0.5.1/)
+- [wheel: 0.36.2](https://pypi.org/project/wheel/0.36.2/)
+- [widgetsnbextension: 3.5.1](https://pypi.org/project/widgetsnbextension/3.5.1/)
+- [wrapt: 1.13.3](https://pypi.org/project/wrapt/1.13.3/)
+
diff --git a/v1/requirements.txt b/v1/requirements.txt
index a00935f..4b4b48a 100644
--- a/v1/requirements.txt
+++ b/v1/requirements.txt
@@ -63,7 +63,7 @@ defusedxml==0.6.0
 descartes==1.1.0
     # via ebmdatalab
 ebmdatalab==0.0.30
-    # via -r requirements.in
+    # via -r v1/requirements.in
 entrypoints==0.3
     # via nbconvert
 fiona==1.8.13
@@ -229,7 +229,7 @@ numpy==1.18.1
 oauthlib==3.1.0
     # via requests-oauthlib
 opensafely-cohort-extractor==1.88.0
-    # via -r requirements.in
+    # via -r v1/requirements.in
 opensafely-matching==0.2.0
     # via -r v1/requirements.in
 packaging==20.1
diff --git a/v2/packages.md b/v2/packages.md
new file mode 100644
index 0000000..61176a1
--- /dev/null
+++ b/v2/packages.md
@@ -0,0 +1,200 @@
+# Package Versions for v2
+
+> [!NOTE]  
+> This file is auto-generated - do not edit.
+
+This python:v2 OpenSAFELY image is based on Ubuntu 22.04 with Python 3.10.12.
+
+## Packages
+
+It comes pre-installed with a standard set of python packages.
+
+- [anyio: 4.0.0](https://pypi.org/project/anyio/4.0.0/)
+- [argon2-cffi: 23.1.0](https://pypi.org/project/argon2-cffi/23.1.0/)
+- [argon2-cffi-bindings: 21.2.0](https://pypi.org/project/argon2-cffi-bindings/21.2.0/)
+- [arrow: 1.3.0](https://pypi.org/project/arrow/1.3.0/)
+- [astor: 0.8.1](https://pypi.org/project/astor/0.8.1/)
+- [asttokens: 2.4.1](https://pypi.org/project/asttokens/2.4.1/)
+- [async-lru: 2.0.4](https://pypi.org/project/async-lru/2.0.4/)
+- [attrs: 23.1.0](https://pypi.org/project/attrs/23.1.0/)
+- [autograd: 1.6.2](https://pypi.org/project/autograd/1.6.2/)
+- [autograd-gamma: 0.5.0](https://pypi.org/project/autograd-gamma/0.5.0/)
+- [babel: 2.13.1](https://pypi.org/project/babel/2.13.1/)
+- [bash-kernel: 0.9.1](https://pypi.org/project/bash-kernel/0.9.1/)
+- [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: 4.45.0](https://pypi.org/project/fonttools/4.45.0/)
+- [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: 2.23.4](https://pypi.org/project/google-auth/2.23.4/)
+- [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: 2.22.0](https://pypi.org/project/google-cloud-bigquery-storage/2.22.0/)
+- [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: 3.4](https://pypi.org/project/idna/3.4/)
+- [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/)
+- [ipykernel: 6.27.0](https://pypi.org/project/ipykernel/6.27.0/)
+- [ipython: 8.17.2](https://pypi.org/project/ipython/8.17.2/)
+- [ipywidgets: 8.1.1](https://pypi.org/project/ipywidgets/8.1.1/)
+- [isoduration: 20.11.0](https://pypi.org/project/isoduration/20.11.0/)
+- [jedi: 0.19.1](https://pypi.org/project/jedi/0.19.1/)
+- [jinja2: 3.1.2](https://pypi.org/project/jinja2/3.1.2/)
+- [joblib: 1.3.2](https://pypi.org/project/joblib/1.3.2/)
+- [json5: 0.9.14](https://pypi.org/project/json5/0.9.14/)
+- [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: 2023.11.1](https://pypi.org/project/jsonschema-specifications/2023.11.1/)
+- [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/)
+- [jupyter-events: 0.9.0](https://pypi.org/project/jupyter-events/0.9.0/)
+- [jupyter-lsp: 2.2.0](https://pypi.org/project/jupyter-lsp/2.2.0/)
+- [jupyter-server: 2.11.0](https://pypi.org/project/jupyter-server/2.11.0/)
+- [jupyter-server-terminals: 0.4.4](https://pypi.org/project/jupyter-server-terminals/0.4.4/)
+- [jupyterlab: 4.0.9](https://pypi.org/project/jupyterlab/4.0.9/)
+- [jupyterlab-pygments: 0.2.2](https://pypi.org/project/jupyterlab-pygments/0.2.2/)
+- [jupyterlab-server: 2.25.2](https://pypi.org/project/jupyterlab-server/2.25.2/)
+- [jupyterlab-widgets: 3.0.9](https://pypi.org/project/jupyterlab-widgets/3.0.9/)
+- [jupytext: 1.15.2](https://pypi.org/project/jupytext/1.15.2/)
+- [kaleido: 0.2.1](https://pypi.org/project/kaleido/0.2.1/)
+- [kiwisolver: 1.4.5](https://pypi.org/project/kiwisolver/1.4.5/)
+- [lifelines: 0.27.8](https://pypi.org/project/lifelines/0.27.8/)
+- [llvmlite: 0.41.1](https://pypi.org/project/llvmlite/0.41.1/)
+- [lz4: 4.3.2](https://pypi.org/project/lz4/4.3.2/)
+- [markdown-it-py: 3.0.0](https://pypi.org/project/markdown-it-py/3.0.0/)
+- [markupsafe: 2.1.3](https://pypi.org/project/markupsafe/2.1.3/)
+- [matplotlib: 3.8.2](https://pypi.org/project/matplotlib/3.8.2/)
+- [matplotlib-inline: 0.1.6](https://pypi.org/project/matplotlib-inline/0.1.6/)
+- [mdit-py-plugins: 0.4.0](https://pypi.org/project/mdit-py-plugins/0.4.0/)
+- [mdurl: 0.1.2](https://pypi.org/project/mdurl/0.1.2/)
+- [mistune: 3.0.2](https://pypi.org/project/mistune/3.0.2/)
+- [nbclient: 0.9.0](https://pypi.org/project/nbclient/0.9.0/)
+- [nbconvert: 7.11.0](https://pypi.org/project/nbconvert/7.11.0/)
+- [nbformat: 5.9.2](https://pypi.org/project/nbformat/5.9.2/)
+- [nbval: 0.10.0](https://pypi.org/project/nbval/0.10.0/)
+- [nest-asyncio: 1.5.8](https://pypi.org/project/nest-asyncio/1.5.8/)
+- [notebook: 7.0.6](https://pypi.org/project/notebook/7.0.6/)
+- [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: 0.5.3](https://pypi.org/project/patsy/0.5.3/)
+- [pexpect: 4.8.0](https://pypi.org/project/pexpect/4.8.0/)
+- [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/)
+- [platformdirs: 4.0.0](https://pypi.org/project/platformdirs/4.0.0/)
+- [plotly: 5.18.0](https://pypi.org/project/plotly/5.18.0/)
+- [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: 2.17.1](https://pypi.org/project/pygments/2.17.1/)
+- [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: 25.1.1](https://pypi.org/project/pyzmq/25.1.1/)
+- [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: 0.31.0](https://pypi.org/project/referencing/0.31.0/)
+- [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: 0.13.1](https://pypi.org/project/rpds-py/0.13.1/)
+- [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/)
+- [terminado: 0.18.0](https://pypi.org/project/terminado/0.18.0/)
+- [threadpoolctl: 3.2.0](https://pypi.org/project/threadpoolctl/3.2.0/)
+- [tinycss2: 1.2.1](https://pypi.org/project/tinycss2/1.2.1/)
+- [toml: 0.10.2](https://pypi.org/project/toml/0.10.2/)
+- [tomli: 2.0.1](https://pypi.org/project/tomli/2.0.1/)
+- [tornado: 6.3.3](https://pypi.org/project/tornado/6.3.3/)
+- [tqdm: 4.66.1](https://pypi.org/project/tqdm/4.66.1/)
+- [traitlets: 5.13.0](https://pypi.org/project/traitlets/5.13.0/)
+- [types-python-dateutil: 2.8.19.14](https://pypi.org/project/types-python-dateutil/2.8.19.14/)
+- [typing-extensions: 4.8.0](https://pypi.org/project/typing-extensions/4.8.0/)
+- [tzdata: 2023.3](https://pypi.org/project/tzdata/2023.3/)
+- [upsetplot: 0.8.0](https://pypi.org/project/upsetplot/0.8.0/)
+- [uri-template: 1.3.0](https://pypi.org/project/uri-template/1.3.0/)
+- [urllib3: 2.1.0](https://pypi.org/project/urllib3/2.1.0/)
+- [venn: 0.1.3](https://pypi.org/project/venn/0.1.3/)
+- [wcwidth: 0.2.11](https://pypi.org/project/wcwidth/0.2.11/)
+- [webcolors: 1.13](https://pypi.org/project/webcolors/1.13/)
+- [webencodings: 0.5.1](https://pypi.org/project/webencodings/0.5.1/)
+- [websocket-client: 1.6.4](https://pypi.org/project/websocket-client/1.6.4/)
+- [wheel: 0.41.3](https://pypi.org/project/wheel/0.41.3/)
+- [widgetsnbextension: 4.0.9](https://pypi.org/project/widgetsnbextension/4.0.9/)
+- [wrapt: 1.16.0](https://pypi.org/project/wrapt/1.16.0/)
+

From 7eff38f95f26578208660dabfeb0ef3ba8cffcfc Mon Sep 17 00:00:00 2001
From: bloodearnest <simon.davy@thedatalab.org>
Date: Mon, 27 Nov 2023 14:01:59 +0000
Subject: [PATCH 06/11] Rework documentation

- Completely new user-facing README.md content
- DEVELOPERS.md with playbook style info
- Issue template for requesting packages
---
 .github/ISSUE_TEMPLATE/new-package.md | 29 +++++++++++
 DEVELOPERS.md                         | 71 +++++++++++++++++++++++++++
 README.md                             | 60 +++++++++++++++++++---
 justfile                              |  2 +-
 4 files changed, 155 insertions(+), 7 deletions(-)
 create mode 100644 .github/ISSUE_TEMPLATE/new-package.md
 create mode 100644 DEVELOPERS.md

diff --git a/.github/ISSUE_TEMPLATE/new-package.md b/.github/ISSUE_TEMPLATE/new-package.md
new file mode 100644
index 0000000..6ed3097
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/new-package.md
@@ -0,0 +1,29 @@
+---
+name: New Package
+about: Request a new python package and/or system library be installed
+title: "Request a New Package"
+labels: 'new-package'
+
+---
+
+Please fill in the fields below to request new packages for the OpenSAFELY python image.
+
+
+### Python package(s) you wish to add to the image
+
+<!-- please add packages, including links to pypi.org page if possible -->
+
+
+### System Libraries
+
+<! --Any system libraries that this package may require. Leave blank if unsure -->
+
+
+### Requesting Project
+
+<!-- Link to the OpenSAFELY Project that will use these packages -->
+
+
+### Rationale
+
+<!-- Rationale for use in OpenSAFELY -->
diff --git a/DEVELOPERS.md b/DEVELOPERS.md
new file mode 100644
index 0000000..1c9deea
--- /dev/null
+++ b/DEVELOPERS.md
@@ -0,0 +1,71 @@
+# Basics
+
+Each major version has its configuration in a subdirectory named after the
+version, e.g. ./v1/ has all the configuration for the `v1` image.
+
+Inside each version's directory there are 4 main files:
+
+- `env`: environment variables used to parameterise the Docker/docker-compose
+  files:
+    - `BASE`: the base Ubuntu version to build from, e.g. `22.04`
+    - `MAJOR_VERSION`: this shoud match the directory name.
+- `dependencies.txt`: the Ubuntu packages that need to be installed
+- `build-dependencies.txt`: the Ubuntu package needed to *build* any
+  dependencies (these will *not* be included in the final image).
+- `requirements.in`: the list of packages to install (*without* version
+  specfiers, unless needed for some reason).
+
+There will also be two autogenerated files:
+
+- `requirements.txt`: the fully pinned set of python dependences generated with
+  `pip-compile`.
+- `packages.md`: generated user facing documentation of package versions
+
+
+Use just to build and test image versions:
+
+```
+just build v2
+just test v2
+```
+
+
+## Add a new package to existing version
+
+* Add the new package without version specifier to all relevant version's
+  `requirement.in` files
+* For each version, do the following:
+    * Run `just update $VERSION`. This will update pacakges, then build and
+      test the new image.
+    * If the build fails, depending on the error message:
+        - you may need to add a new system package to `dependencies.txt`
+        - you may need to add a new build dependency package to
+          `build-dependencies.txt`
+        - you may need to finesse the tests for poorly packaged libraries: see
+          [`BAD_PACKAGES`](./tests/test_import.py)
+    * Inspect the changes to requirements.txt
+        - ensure no pre-existing package has been updated by this change.
+
+
+## Create a new version
+
+TODO, but basically, `cp -a v$N v${N+1}` and edit.
+
+
+## Publishing
+
+> ![WARNING]
+> By default, these images are published via CI, so only do this if you know
+> you need to, e.g. testing publishing a new version
+
+To publish a version locally, you will need to be logged in to ghcr.io with the
+right permissions (`docker login ghcr.io`)
+
+By default, this command is a dry run, and will show you the commands it *will* run:
+
+`just publish $version`
+
+To run for real, pass `true`:
+
+`just publish $version true`
+
diff --git a/README.md b/README.md
index ba68d92..19fe6f9 100644
--- a/README.md
+++ b/README.md
@@ -1,9 +1,57 @@
-# OpenSAFELY Python image
+# OpenSAFELY Python Runtime Image
 
-This is a dockerfile for running python in an OpenSAFELY
-environment.
+This repo manages the Docker image for the OpenSAFELY Python runtime. These
+images are based on a base Ubuntu LTS version, and come pre-installed with
+a set of standard scientific python packages.
 
-To make a new release, use conventional commits to bump version
-(i.e. subject lines starting `feat:` or `fix:`)
+The current latest version is `v2`, and you should use that unless you have
+a specific reason. You can use it in your `project.yaml` like so:
 
-See `requirements.txt` for current available packages and versions
+```
+actions:
+  my_action:
+    run: python:v2 my_script.py ...
+```
+
+## Version List
+
+Current available versions, in reverse chronological order:
+
+ - v2: Ubuntu 22.04 and Python 3.10 - [full package list](v2/packages.md)
+ - v1: Ubuntu 20.04 and Python 3.8 - [full package list](v1/packages.md)
+
+### Legacy version: `latest`
+
+Initially, OpenSAFELY only had one version of the python image. This is the
+`v1` image, but was originally published under the `:latest` tag. You can use
+either `v1` or `latest` - they are the same version.  In future, we may
+deprecate the `latest` tag and require users to update their `project.yaml` to
+use `v1` instead of `latest`.
+
+
+## Update Policy
+
+### Python Package Versions
+
+For each version of the python image, we do *not* upgade the python packages
+from their initially installed version. This is done in order to backwards
+compatiblity and thus ensure reproduciblity. We do [add new packages on user
+request](https://github.com/opensafely-core/python-dockerissues/new?template=new-package.md),
+as such a change will not break backwards incompatibilty.
+
+Occasionally, we will create a new major version of the image with all packages
+updated to their latest version. We may also possibly remove old and uneeded
+pacakges at this point.  A new major version is chance to make backwards
+incompatible changes, which is occasionally needed.
+
+Once this new version of the image is intially released, its set of package
+versions will be frozen and no longer updatable.
+
+### Operating System Packages
+
+We *do* update the underlying operating system packages on a regular basis, in
+order to apply security updates to the base system. It is very unlikely that
+this will break backwards compatibility, as these are a small set very
+conservative set of updates to address security issues.
+
+We also add additional operating system libraries on user request.
diff --git a/justfile b/justfile
index cdcf479..996271b 100644
--- a/justfile
+++ b/justfile
@@ -20,7 +20,7 @@ test version *args="tests -v": (build version)
 update version *args="": (build version)
     docker-compose --env-file {{ version }}/env run --rm -v $PWD:/workspace base pip-compile {{ args }} {{ version }}/requirements.in -o {{ version }}/requirements.txt
     {{ just_executable() }} render {{ version }}
-
+    {{ just_executable() }} test {{ version }}
 
 # render package version information
 render version *args:

From 45ab7ddeb29c4014fb086d0f80c273a7b77b9ee8 Mon Sep 17 00:00:00 2001
From: bloodearnest <simon.davy@thedatalab.org>
Date: Tue, 5 Dec 2023 14:53:29 +0000
Subject: [PATCH 07/11] Include package metadata in image for local
 interrogation

Seems like a useful thing to bundle documentation.
---
 Dockerfile | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 7e3eec0..8bdf3af 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -20,9 +20,9 @@ ARG BASE
 # ACTION_EXEC sets the default executable for the entrypoint in the base-docker image
 ENV ACTION_EXEC=python MAJOR_VERSION=${MAJOR_VERSION} BASE=${BASE}
 
-COPY ${MAJOR_VERSION}/dependencies.txt /root/dependencies.txt
+COPY ${MAJOR_VERSION}/dependencies.txt /opt/dependencies.txt
 # use space efficient utility from base image
-RUN /root/docker-apt-install.sh /root/dependencies.txt
+RUN /root/docker-apt-install.sh /opt/dependencies.txt
 
 # now we have python, set up a venv to install packages to, for isolation from
 # system python libraries 
@@ -42,16 +42,17 @@ FROM base-python as builder
 ARG MAJOR_VERSION
 
 # install build time dependencies 
-COPY ${MAJOR_VERSION}/build-dependencies.txt /root/build-dependencies.txt
-RUN /root/docker-apt-install.sh /root/build-dependencies.txt
+COPY ${MAJOR_VERSION}/build-dependencies.txt /opt/build-dependencies.txt
+RUN /root/docker-apt-install.sh /opt/build-dependencies.txt
 
-COPY ${MAJOR_VERSION}/requirements.txt /root/requirements.txt
+COPY ${MAJOR_VERSION}/requirements.txt /opt/requirements.txt
+COPY ${MAJOR_VERSION}/packages.md /opt/packages.md
 # Note: the mount command does two things: 1) caches across builds to speed up
 # local development and 2) ensures the pip cache does not get committed to the
 # layer (which is why we ignore DL3042).
 # hadolint ignore=DL3042
 RUN --mount=type=cache,target=/root/.cache \
-    python -m pip install --requirement /root/requirements.txt
+    python -m pip install --requirement /opt/requirements.txt
 
 ################################################
 #
@@ -70,7 +71,7 @@ LABEL org.opencontainers.image.title="python:${MAJOR_VERSION}" \
       org.opensafely.action="python:${MAJOR_VERSION}"
 
 # copy venv over from builder image
-COPY --from=builder /opt/venv /opt/venv
+COPY --from=builder /opt/ /opt/
 
 # tag with build info as the very last step, as it will never be cacheable
 ARG BUILD_DATE

From b9032c4ff2faf3de523e1c034a51f6a8f897446f Mon Sep 17 00:00:00 2001
From: bloodearnest <simon.davy@thedatalab.org>
Date: Tue, 5 Dec 2023 14:57:49 +0000
Subject: [PATCH 08/11] Use compose v2

Also, updated missed rendering of v1/packages.md
---
 justfile       |   8 +-
 v1/packages.md | 290 ++++++++++++++++++++++++-------------------------
 2 files changed, 149 insertions(+), 149 deletions(-)

diff --git a/justfile b/justfile
index 996271b..582c373 100644
--- a/justfile
+++ b/justfile
@@ -8,23 +8,23 @@ export REVISION := `git rev-parse --short HEAD`
 
 # build docker image for version
 build version target="python" *args="":
-    docker-compose --env-file {{ version }}/env build --pull {{ args }} {{ target }} 
+    docker compose --env-file {{ version }}/env build --pull {{ args }} {{ target }} 
 
 
 # test docker image for version
 test version *args="tests -v": (build version)
-    docker-compose --env-file {{ version }}/env run --rm -v $PWD:/workspace python pytest {{ args }}
+    docker compose --env-file {{ version }}/env run --rm -v $PWD:/workspace python pytest {{ args }}
 
 
 # run pip-compile to add new dependencies, or update existing ones with --upgrade
 update version *args="": (build version)
-    docker-compose --env-file {{ version }}/env run --rm -v $PWD:/workspace base pip-compile {{ args }} {{ version }}/requirements.in -o {{ version }}/requirements.txt
+    docker compose --env-file {{ version }}/env run --rm -v $PWD:/workspace base pip-compile {{ args }} {{ version }}/requirements.in -o {{ version }}/requirements.txt
     {{ just_executable() }} render {{ version }}
     {{ just_executable() }} test {{ version }}
 
 # render package version information
 render version *args:
-    docker-compose --env-file {{ version }}/env run --rm -v $PWD:/workspace python ./scripts/render.py {{ args }} > {{ version }}/packages.md
+    docker compose --env-file {{ version }}/env run --rm -v $PWD:/workspace python ./scripts/render.py {{ args }} > {{ version }}/packages.md
 
 
 # run linters
diff --git a/v1/packages.md b/v1/packages.md
index 58476de..e578dc2 100644
--- a/v1/packages.md
+++ b/v1/packages.md
@@ -1,145 +1,145 @@
-# Package Versions for v1
-
-This python:v1 OpenSAFELY image is based on Ubuntu 20.04 with Python 3.8.10.
-
-## Packages
-
-It comes pre-installed with a standard set of python packages.
-
-- [astor: 0.8.1](https://pypi.org/project/astor/0.8.1/)
-- [attrs: 19.3.0](https://pypi.org/project/attrs/19.3.0/)
-- [autograd: 1.3](https://pypi.org/project/autograd/1.3/)
-- [autograd-gamma: 0.5.0](https://pypi.org/project/autograd-gamma/0.5.0/)
-- [backcall: 0.1.0](https://pypi.org/project/backcall/0.1.0/)
-- [bash-kernel: 0.7.2](https://pypi.org/project/bash-kernel/0.7.2/)
-- [bleach: 3.1.2](https://pypi.org/project/bleach/3.1.2/)
-- [cachetools: 4.0.0](https://pypi.org/project/cachetools/4.0.0/)
-- [cairocffi: 1.4.0](https://pypi.org/project/cairocffi/1.4.0/)
-- [cairosvg: 2.5.2](https://pypi.org/project/cairosvg/2.5.2/)
-- [certifi: 2019.11.28](https://pypi.org/project/certifi/2019.11.28/)
-- [cffi: 1.15.1](https://pypi.org/project/cffi/1.15.1/)
-- [chardet: 3.0.4](https://pypi.org/project/chardet/3.0.4/)
-- [click: 7.0](https://pypi.org/project/click/7.0/)
-- [click-plugins: 1.1.1](https://pypi.org/project/click-plugins/1.1.1/)
-- [cligj: 0.5.0](https://pypi.org/project/cligj/0.5.0/)
-- [coverage: 4.5.4](https://pypi.org/project/coverage/4.5.4/)
-- [cssselect2: 0.7.0](https://pypi.org/project/cssselect2/0.7.0/)
-- [cycler: 0.10.0](https://pypi.org/project/cycler/0.10.0/)
-- [decorator: 4.4.1](https://pypi.org/project/decorator/4.4.1/)
-- [defusedxml: 0.6.0](https://pypi.org/project/defusedxml/0.6.0/)
-- [descartes: 1.1.0](https://pypi.org/project/descartes/1.1.0/)
-- [ebmdatalab: 0.0.30](https://pypi.org/project/ebmdatalab/0.0.30/)
-- [entrypoints: 0.3](https://pypi.org/project/entrypoints/0.3/)
-- [fiona: 1.8.13](https://pypi.org/project/fiona/1.8.13/)
-- [formulaic: 0.2.4](https://pypi.org/project/formulaic/0.2.4/)
-- [future: 0.18.2](https://pypi.org/project/future/0.18.2/)
-- [geopandas: 0.6.3](https://pypi.org/project/geopandas/0.6.3/)
-- [google-api-core: 1.16.0](https://pypi.org/project/google-api-core/1.16.0/)
-- [google-auth: 1.11.0](https://pypi.org/project/google-auth/1.11.0/)
-- [google-auth-oauthlib: 0.4.1](https://pypi.org/project/google-auth-oauthlib/0.4.1/)
-- [google-cloud-bigquery: 1.24.0](https://pypi.org/project/google-cloud-bigquery/1.24.0/)
-- [google-cloud-core: 1.3.0](https://pypi.org/project/google-cloud-core/1.3.0/)
-- [google-resumable-media: 0.5.0](https://pypi.org/project/google-resumable-media/0.5.0/)
-- [googleapis-common-protos: 1.51.0](https://pypi.org/project/googleapis-common-protos/1.51.0/)
-- [idna: 2.8](https://pypi.org/project/idna/2.8/)
-- [interface-meta: 1.2.4](https://pypi.org/project/interface-meta/1.2.4/)
-- [ipykernel: 5.1.4](https://pypi.org/project/ipykernel/5.1.4/)
-- [ipython: 7.12.0](https://pypi.org/project/ipython/7.12.0/)
-- [ipython-genutils: 0.2.0](https://pypi.org/project/ipython-genutils/0.2.0/)
-- [ipywidgets: 7.5.1](https://pypi.org/project/ipywidgets/7.5.1/)
-- [jedi: 0.16.0](https://pypi.org/project/jedi/0.16.0/)
-- [jinja2: 2.11.1](https://pypi.org/project/jinja2/2.11.1/)
-- [joblib: 1.0.1](https://pypi.org/project/joblib/1.0.1/)
-- [json5: 0.9.0](https://pypi.org/project/json5/0.9.0/)
-- [jsonschema: 3.2.0](https://pypi.org/project/jsonschema/3.2.0/)
-- [jupyter: 1.0.0](https://pypi.org/project/jupyter/1.0.0/)
-- [jupyter-client: 5.3.4](https://pypi.org/project/jupyter-client/5.3.4/)
-- [jupyter-console: 6.1.0](https://pypi.org/project/jupyter-console/6.1.0/)
-- [jupyter-core: 4.6.1](https://pypi.org/project/jupyter-core/4.6.1/)
-- [jupyterlab: 1.2.6](https://pypi.org/project/jupyterlab/1.2.6/)
-- [jupyterlab-server: 1.0.6](https://pypi.org/project/jupyterlab-server/1.0.6/)
-- [jupytext: 1.3.3](https://pypi.org/project/jupytext/1.3.3/)
-- [kaleido: 0.2.1](https://pypi.org/project/kaleido/0.2.1/)
-- [kiwisolver: 1.1.0](https://pypi.org/project/kiwisolver/1.1.0/)
-- [lifelines: 0.26.4](https://pypi.org/project/lifelines/0.26.4/)
-- [llvmlite: 0.34.0](https://pypi.org/project/llvmlite/0.34.0/)
-- [lz4: 3.1.3](https://pypi.org/project/lz4/3.1.3/)
-- [markupsafe: 1.1.1](https://pypi.org/project/markupsafe/1.1.1/)
-- [matplotlib: 3.1.3](https://pypi.org/project/matplotlib/3.1.3/)
-- [mistune: 0.8.4](https://pypi.org/project/mistune/0.8.4/)
-- [more-itertools: 8.2.0](https://pypi.org/project/more-itertools/8.2.0/)
-- [munch: 2.5.0](https://pypi.org/project/munch/2.5.0/)
-- [nbconvert: 5.6.1](https://pypi.org/project/nbconvert/5.6.1/)
-- [nbformat: 5.0.4](https://pypi.org/project/nbformat/5.0.4/)
-- [nbval: 0.9.4](https://pypi.org/project/nbval/0.9.4/)
-- [notebook: 6.0.3](https://pypi.org/project/notebook/6.0.3/)
-- [numba: 0.51.2](https://pypi.org/project/numba/0.51.2/)
-- [numpy: 1.18.1](https://pypi.org/project/numpy/1.18.1/)
-- [oauthlib: 3.1.0](https://pypi.org/project/oauthlib/3.1.0/)
-- [opensafely-cohort-extractor: 1.88.0](https://pypi.org/project/opensafely-cohort-extractor/1.88.0/)
-- [opensafely-matching: 0.2.0](https://pypi.org/project/opensafely-matching/0.2.0/)
-- [packaging: 20.1](https://pypi.org/project/packaging/20.1/)
-- [pandas: 1.0.1](https://pypi.org/project/pandas/1.0.1/)
-- [pandas-gbq: 0.13.0](https://pypi.org/project/pandas-gbq/0.13.0/)
-- [pandocfilters: 1.4.2](https://pypi.org/project/pandocfilters/1.4.2/)
-- [parso: 0.6.1](https://pypi.org/project/parso/0.6.1/)
-- [patsy: 0.5.1](https://pypi.org/project/patsy/0.5.1/)
-- [pep517: 0.10.0](https://pypi.org/project/pep517/0.10.0/)
-- [pexpect: 4.8.0](https://pypi.org/project/pexpect/4.8.0/)
-- [pickleshare: 0.7.5](https://pypi.org/project/pickleshare/0.7.5/)
-- [pillow: 8.1.0](https://pypi.org/project/pillow/8.1.0/)
-- [pip-tools: 6.2.0](https://pypi.org/project/pip-tools/6.2.0/)
-- [plotly: 4.5.0](https://pypi.org/project/plotly/4.5.0/)
-- [pluggy: 0.13.1](https://pypi.org/project/pluggy/0.13.1/)
-- [prometheus-client: 0.7.1](https://pypi.org/project/prometheus-client/0.7.1/)
-- [prompt-toolkit: 3.0.3](https://pypi.org/project/prompt-toolkit/3.0.3/)
-- [protobuf: 3.11.3](https://pypi.org/project/protobuf/3.11.3/)
-- [ptyprocess: 0.6.0](https://pypi.org/project/ptyprocess/0.6.0/)
-- [py: 1.8.1](https://pypi.org/project/py/1.8.1/)
-- [pyarrow: 3.0.0](https://pypi.org/project/pyarrow/3.0.0/)
-- [pyasn1: 0.4.8](https://pypi.org/project/pyasn1/0.4.8/)
-- [pyasn1-modules: 0.2.8](https://pypi.org/project/pyasn1-modules/0.2.8/)
-- [pycparser: 2.21](https://pypi.org/project/pycparser/2.21/)
-- [pydata-google-auth: 0.3.0](https://pypi.org/project/pydata-google-auth/0.3.0/)
-- [pygments: 2.5.2](https://pypi.org/project/pygments/2.5.2/)
-- [pyparsing: 2.4.6](https://pypi.org/project/pyparsing/2.4.6/)
-- [pyproj: 2.4.2.post1](https://pypi.org/project/pyproj/2.4.2.post1/)
-- [pyrsistent: 0.15.7](https://pypi.org/project/pyrsistent/0.15.7/)
-- [pytest: 5.3.5](https://pypi.org/project/pytest/5.3.5/)
-- [python-dateutil: 2.8.1](https://pypi.org/project/python-dateutil/2.8.1/)
-- [pytz: 2019.3](https://pypi.org/project/pytz/2019.3/)
-- [pyyaml: 5.3](https://pypi.org/project/pyyaml/5.3/)
-- [pyzmq: 18.1.1](https://pypi.org/project/pyzmq/18.1.1/)
-- [qtconsole: 4.6.0](https://pypi.org/project/qtconsole/4.6.0/)
-- [requests: 2.22.0](https://pypi.org/project/requests/2.22.0/)
-- [requests-oauthlib: 1.3.0](https://pypi.org/project/requests-oauthlib/1.3.0/)
-- [retry: 0.9.2](https://pypi.org/project/retry/0.9.2/)
-- [retrying: 1.3.3](https://pypi.org/project/retrying/1.3.3/)
-- [rsa: 4.0](https://pypi.org/project/rsa/4.0/)
-- [scikit-learn: 0.24.1](https://pypi.org/project/scikit-learn/0.24.1/)
-- [scipy: 1.4.1](https://pypi.org/project/scipy/1.4.1/)
-- [seaborn: 0.10.0](https://pypi.org/project/seaborn/0.10.0/)
-- [send2trash: 1.5.0](https://pypi.org/project/send2trash/1.5.0/)
-- [shapely: 1.7.0](https://pypi.org/project/shapely/1.7.0/)
-- [six: 1.14.0](https://pypi.org/project/six/1.14.0/)
-- [sqlparse: 0.4.1](https://pypi.org/project/sqlparse/0.4.1/)
-- [statsmodels: 0.11.0](https://pypi.org/project/statsmodels/0.11.0/)
-- [structlog: 20.2.0](https://pypi.org/project/structlog/20.2.0/)
-- [tabulate: 0.8.7](https://pypi.org/project/tabulate/0.8.7/)
-- [terminado: 0.8.3](https://pypi.org/project/terminado/0.8.3/)
-- [testpath: 0.4.4](https://pypi.org/project/testpath/0.4.4/)
-- [threadpoolctl: 2.1.0](https://pypi.org/project/threadpoolctl/2.1.0/)
-- [tinycss2: 1.2.1](https://pypi.org/project/tinycss2/1.2.1/)
-- [toml: 0.10.2](https://pypi.org/project/toml/0.10.2/)
-- [tornado: 6.0.3](https://pypi.org/project/tornado/6.0.3/)
-- [tqdm: 4.42.1](https://pypi.org/project/tqdm/4.42.1/)
-- [traitlets: 4.3.3](https://pypi.org/project/traitlets/4.3.3/)
-- [upsetplot: 0.6.1](https://pypi.org/project/upsetplot/0.6.1/)
-- [urllib3: 1.25.8](https://pypi.org/project/urllib3/1.25.8/)
-- [venn: 0.1.3](https://pypi.org/project/venn/0.1.3/)
-- [wcwidth: 0.1.8](https://pypi.org/project/wcwidth/0.1.8/)
-- [webencodings: 0.5.1](https://pypi.org/project/webencodings/0.5.1/)
-- [wheel: 0.36.2](https://pypi.org/project/wheel/0.36.2/)
-- [widgetsnbextension: 3.5.1](https://pypi.org/project/widgetsnbextension/3.5.1/)
-- [wrapt: 1.13.3](https://pypi.org/project/wrapt/1.13.3/)
-
+# Package Versions for v1
+
+This python:v1 OpenSAFELY image is based on Ubuntu 20.04 with Python 3.8.10.
+
+## Packages
+
+It comes pre-installed with a standard set of python packages.
+
+- [astor: 0.8.1](https://pypi.org/project/astor/0.8.1/)
+- [attrs: 19.3.0](https://pypi.org/project/attrs/19.3.0/)
+- [autograd: 1.3](https://pypi.org/project/autograd/1.3/)
+- [autograd-gamma: 0.5.0](https://pypi.org/project/autograd-gamma/0.5.0/)
+- [backcall: 0.1.0](https://pypi.org/project/backcall/0.1.0/)
+- [bash-kernel: 0.7.2](https://pypi.org/project/bash-kernel/0.7.2/)
+- [bleach: 3.1.2](https://pypi.org/project/bleach/3.1.2/)
+- [cachetools: 4.0.0](https://pypi.org/project/cachetools/4.0.0/)
+- [cairocffi: 1.4.0](https://pypi.org/project/cairocffi/1.4.0/)
+- [cairosvg: 2.5.2](https://pypi.org/project/cairosvg/2.5.2/)
+- [certifi: 2019.11.28](https://pypi.org/project/certifi/2019.11.28/)
+- [cffi: 1.15.1](https://pypi.org/project/cffi/1.15.1/)
+- [chardet: 3.0.4](https://pypi.org/project/chardet/3.0.4/)
+- [click: 7.0](https://pypi.org/project/click/7.0/)
+- [click-plugins: 1.1.1](https://pypi.org/project/click-plugins/1.1.1/)
+- [cligj: 0.5.0](https://pypi.org/project/cligj/0.5.0/)
+- [coverage: 4.5.4](https://pypi.org/project/coverage/4.5.4/)
+- [cssselect2: 0.7.0](https://pypi.org/project/cssselect2/0.7.0/)
+- [cycler: 0.10.0](https://pypi.org/project/cycler/0.10.0/)
+- [decorator: 4.4.1](https://pypi.org/project/decorator/4.4.1/)
+- [defusedxml: 0.6.0](https://pypi.org/project/defusedxml/0.6.0/)
+- [descartes: 1.1.0](https://pypi.org/project/descartes/1.1.0/)
+- [ebmdatalab: 0.0.30](https://pypi.org/project/ebmdatalab/0.0.30/)
+- [entrypoints: 0.3](https://pypi.org/project/entrypoints/0.3/)
+- [fiona: 1.8.13](https://pypi.org/project/fiona/1.8.13/)
+- [formulaic: 0.2.4](https://pypi.org/project/formulaic/0.2.4/)
+- [future: 0.18.2](https://pypi.org/project/future/0.18.2/)
+- [geopandas: 0.6.3](https://pypi.org/project/geopandas/0.6.3/)
+- [google-api-core: 1.16.0](https://pypi.org/project/google-api-core/1.16.0/)
+- [google-auth: 1.11.0](https://pypi.org/project/google-auth/1.11.0/)
+- [google-auth-oauthlib: 0.4.1](https://pypi.org/project/google-auth-oauthlib/0.4.1/)
+- [google-cloud-bigquery: 1.24.0](https://pypi.org/project/google-cloud-bigquery/1.24.0/)
+- [google-cloud-core: 1.3.0](https://pypi.org/project/google-cloud-core/1.3.0/)
+- [google-resumable-media: 0.5.0](https://pypi.org/project/google-resumable-media/0.5.0/)
+- [googleapis-common-protos: 1.51.0](https://pypi.org/project/googleapis-common-protos/1.51.0/)
+- [idna: 2.8](https://pypi.org/project/idna/2.8/)
+- [interface-meta: 1.2.4](https://pypi.org/project/interface-meta/1.2.4/)
+- [ipykernel: 5.1.4](https://pypi.org/project/ipykernel/5.1.4/)
+- [ipython: 7.12.0](https://pypi.org/project/ipython/7.12.0/)
+- [ipython-genutils: 0.2.0](https://pypi.org/project/ipython-genutils/0.2.0/)
+- [ipywidgets: 7.5.1](https://pypi.org/project/ipywidgets/7.5.1/)
+- [jedi: 0.16.0](https://pypi.org/project/jedi/0.16.0/)
+- [jinja2: 2.11.1](https://pypi.org/project/jinja2/2.11.1/)
+- [joblib: 1.0.1](https://pypi.org/project/joblib/1.0.1/)
+- [json5: 0.9.0](https://pypi.org/project/json5/0.9.0/)
+- [jsonschema: 3.2.0](https://pypi.org/project/jsonschema/3.2.0/)
+- [jupyter: 1.0.0](https://pypi.org/project/jupyter/1.0.0/)
+- [jupyter-client: 5.3.4](https://pypi.org/project/jupyter-client/5.3.4/)
+- [jupyter-console: 6.1.0](https://pypi.org/project/jupyter-console/6.1.0/)
+- [jupyter-core: 4.6.1](https://pypi.org/project/jupyter-core/4.6.1/)
+- [jupyterlab: 1.2.6](https://pypi.org/project/jupyterlab/1.2.6/)
+- [jupyterlab-server: 1.0.6](https://pypi.org/project/jupyterlab-server/1.0.6/)
+- [jupytext: 1.3.3](https://pypi.org/project/jupytext/1.3.3/)
+- [kaleido: 0.2.1](https://pypi.org/project/kaleido/0.2.1/)
+- [kiwisolver: 1.1.0](https://pypi.org/project/kiwisolver/1.1.0/)
+- [lifelines: 0.26.4](https://pypi.org/project/lifelines/0.26.4/)
+- [llvmlite: 0.34.0](https://pypi.org/project/llvmlite/0.34.0/)
+- [lz4: 3.1.3](https://pypi.org/project/lz4/3.1.3/)
+- [markupsafe: 1.1.1](https://pypi.org/project/markupsafe/1.1.1/)
+- [matplotlib: 3.1.3](https://pypi.org/project/matplotlib/3.1.3/)
+- [mistune: 0.8.4](https://pypi.org/project/mistune/0.8.4/)
+- [more-itertools: 8.2.0](https://pypi.org/project/more-itertools/8.2.0/)
+- [munch: 2.5.0](https://pypi.org/project/munch/2.5.0/)
+- [nbconvert: 5.6.1](https://pypi.org/project/nbconvert/5.6.1/)
+- [nbformat: 5.0.4](https://pypi.org/project/nbformat/5.0.4/)
+- [nbval: 0.9.4](https://pypi.org/project/nbval/0.9.4/)
+- [notebook: 6.0.3](https://pypi.org/project/notebook/6.0.3/)
+- [numba: 0.51.2](https://pypi.org/project/numba/0.51.2/)
+- [numpy: 1.18.1](https://pypi.org/project/numpy/1.18.1/)
+- [oauthlib: 3.1.0](https://pypi.org/project/oauthlib/3.1.0/)
+- [opensafely-cohort-extractor: 1.88.0](https://pypi.org/project/opensafely-cohort-extractor/1.88.0/)
+- [opensafely-matching: 0.2.0](https://pypi.org/project/opensafely-matching/0.2.0/)
+- [packaging: 20.1](https://pypi.org/project/packaging/20.1/)
+- [pandas: 1.0.1](https://pypi.org/project/pandas/1.0.1/)
+- [pandas-gbq: 0.13.0](https://pypi.org/project/pandas-gbq/0.13.0/)
+- [pandocfilters: 1.4.2](https://pypi.org/project/pandocfilters/1.4.2/)
+- [parso: 0.6.1](https://pypi.org/project/parso/0.6.1/)
+- [patsy: 0.5.1](https://pypi.org/project/patsy/0.5.1/)
+- [pep517: 0.10.0](https://pypi.org/project/pep517/0.10.0/)
+- [pexpect: 4.8.0](https://pypi.org/project/pexpect/4.8.0/)
+- [pickleshare: 0.7.5](https://pypi.org/project/pickleshare/0.7.5/)
+- [pillow: 8.1.0](https://pypi.org/project/pillow/8.1.0/)
+- [pip-tools: 6.2.0](https://pypi.org/project/pip-tools/6.2.0/)
+- [plotly: 4.5.0](https://pypi.org/project/plotly/4.5.0/)
+- [pluggy: 0.13.1](https://pypi.org/project/pluggy/0.13.1/)
+- [prometheus-client: 0.7.1](https://pypi.org/project/prometheus-client/0.7.1/)
+- [prompt-toolkit: 3.0.3](https://pypi.org/project/prompt-toolkit/3.0.3/)
+- [protobuf: 3.11.3](https://pypi.org/project/protobuf/3.11.3/)
+- [ptyprocess: 0.6.0](https://pypi.org/project/ptyprocess/0.6.0/)
+- [py: 1.8.1](https://pypi.org/project/py/1.8.1/)
+- [pyarrow: 3.0.0](https://pypi.org/project/pyarrow/3.0.0/)
+- [pyasn1: 0.4.8](https://pypi.org/project/pyasn1/0.4.8/)
+- [pyasn1-modules: 0.2.8](https://pypi.org/project/pyasn1-modules/0.2.8/)
+- [pycparser: 2.21](https://pypi.org/project/pycparser/2.21/)
+- [pydata-google-auth: 0.3.0](https://pypi.org/project/pydata-google-auth/0.3.0/)
+- [pygments: 2.5.2](https://pypi.org/project/pygments/2.5.2/)
+- [pyparsing: 2.4.6](https://pypi.org/project/pyparsing/2.4.6/)
+- [pyproj: 2.4.2.post1](https://pypi.org/project/pyproj/2.4.2.post1/)
+- [pyrsistent: 0.15.7](https://pypi.org/project/pyrsistent/0.15.7/)
+- [pytest: 5.3.5](https://pypi.org/project/pytest/5.3.5/)
+- [python-dateutil: 2.8.1](https://pypi.org/project/python-dateutil/2.8.1/)
+- [pytz: 2019.3](https://pypi.org/project/pytz/2019.3/)
+- [pyyaml: 5.3](https://pypi.org/project/pyyaml/5.3/)
+- [pyzmq: 18.1.1](https://pypi.org/project/pyzmq/18.1.1/)
+- [qtconsole: 4.6.0](https://pypi.org/project/qtconsole/4.6.0/)
+- [requests: 2.22.0](https://pypi.org/project/requests/2.22.0/)
+- [requests-oauthlib: 1.3.0](https://pypi.org/project/requests-oauthlib/1.3.0/)
+- [retry: 0.9.2](https://pypi.org/project/retry/0.9.2/)
+- [retrying: 1.3.3](https://pypi.org/project/retrying/1.3.3/)
+- [rsa: 4.0](https://pypi.org/project/rsa/4.0/)
+- [scikit-learn: 0.24.1](https://pypi.org/project/scikit-learn/0.24.1/)
+- [scipy: 1.4.1](https://pypi.org/project/scipy/1.4.1/)
+- [seaborn: 0.10.0](https://pypi.org/project/seaborn/0.10.0/)
+- [send2trash: 1.5.0](https://pypi.org/project/send2trash/1.5.0/)
+- [shapely: 1.7.0](https://pypi.org/project/shapely/1.7.0/)
+- [six: 1.14.0](https://pypi.org/project/six/1.14.0/)
+- [sqlparse: 0.4.1](https://pypi.org/project/sqlparse/0.4.1/)
+- [statsmodels: 0.11.0](https://pypi.org/project/statsmodels/0.11.0/)
+- [structlog: 20.2.0](https://pypi.org/project/structlog/20.2.0/)
+- [tabulate: 0.8.7](https://pypi.org/project/tabulate/0.8.7/)
+- [terminado: 0.8.3](https://pypi.org/project/terminado/0.8.3/)
+- [testpath: 0.4.4](https://pypi.org/project/testpath/0.4.4/)
+- [threadpoolctl: 2.1.0](https://pypi.org/project/threadpoolctl/2.1.0/)
+- [tinycss2: 1.2.1](https://pypi.org/project/tinycss2/1.2.1/)
+- [toml: 0.10.2](https://pypi.org/project/toml/0.10.2/)
+- [tornado: 6.0.3](https://pypi.org/project/tornado/6.0.3/)
+- [tqdm: 4.42.1](https://pypi.org/project/tqdm/4.42.1/)
+- [traitlets: 4.3.3](https://pypi.org/project/traitlets/4.3.3/)
+- [upsetplot: 0.6.1](https://pypi.org/project/upsetplot/0.6.1/)
+- [urllib3: 1.25.8](https://pypi.org/project/urllib3/1.25.8/)
+- [venn: 0.1.3](https://pypi.org/project/venn/0.1.3/)
+- [wcwidth: 0.1.8](https://pypi.org/project/wcwidth/0.1.8/)
+- [webencodings: 0.5.1](https://pypi.org/project/webencodings/0.5.1/)
+- [wheel: 0.36.2](https://pypi.org/project/wheel/0.36.2/)
+- [widgetsnbextension: 3.5.1](https://pypi.org/project/widgetsnbextension/3.5.1/)
+- [wrapt: 1.13.3](https://pypi.org/project/wrapt/1.13.3/)
+

From 1bb8b105829a7ab9b576342554c83155b2b4cc51 Mon Sep 17 00:00:00 2001
From: bloodearnest <simon.davy@thedatalab.org>
Date: Tue, 5 Dec 2023 15:47:25 +0000
Subject: [PATCH 09/11] Update to latest packages

---
 justfile            |   2 +-
 v2/packages.md      | 397 ++++++++++++++++++++++----------------------
 v2/requirements.txt | 109 ++++++------
 3 files changed, 253 insertions(+), 255 deletions(-)

diff --git a/justfile b/justfile
index 582c373..2b05e3f 100644
--- a/justfile
+++ b/justfile
@@ -17,7 +17,7 @@ test version *args="tests -v": (build version)
 
 
 # run pip-compile to add new dependencies, or update existing ones with --upgrade
-update version *args="": (build version)
+update version *args="":
     docker compose --env-file {{ version }}/env run --rm -v $PWD:/workspace base pip-compile {{ args }} {{ version }}/requirements.in -o {{ version }}/requirements.txt
     {{ just_executable() }} render {{ version }}
     {{ just_executable() }} test {{ version }}
diff --git a/v2/packages.md b/v2/packages.md
index 61176a1..4320c60 100644
--- a/v2/packages.md
+++ b/v2/packages.md
@@ -1,200 +1,197 @@
-# Package Versions for v2
-
-> [!NOTE]  
-> This file is auto-generated - do not edit.
-
-This python:v2 OpenSAFELY image is based on Ubuntu 22.04 with Python 3.10.12.
-
-## Packages
-
-It comes pre-installed with a standard set of python packages.
-
-- [anyio: 4.0.0](https://pypi.org/project/anyio/4.0.0/)
-- [argon2-cffi: 23.1.0](https://pypi.org/project/argon2-cffi/23.1.0/)
-- [argon2-cffi-bindings: 21.2.0](https://pypi.org/project/argon2-cffi-bindings/21.2.0/)
-- [arrow: 1.3.0](https://pypi.org/project/arrow/1.3.0/)
-- [astor: 0.8.1](https://pypi.org/project/astor/0.8.1/)
-- [asttokens: 2.4.1](https://pypi.org/project/asttokens/2.4.1/)
-- [async-lru: 2.0.4](https://pypi.org/project/async-lru/2.0.4/)
-- [attrs: 23.1.0](https://pypi.org/project/attrs/23.1.0/)
-- [autograd: 1.6.2](https://pypi.org/project/autograd/1.6.2/)
-- [autograd-gamma: 0.5.0](https://pypi.org/project/autograd-gamma/0.5.0/)
-- [babel: 2.13.1](https://pypi.org/project/babel/2.13.1/)
-- [bash-kernel: 0.9.1](https://pypi.org/project/bash-kernel/0.9.1/)
-- [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: 4.45.0](https://pypi.org/project/fonttools/4.45.0/)
-- [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: 2.23.4](https://pypi.org/project/google-auth/2.23.4/)
-- [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: 2.22.0](https://pypi.org/project/google-cloud-bigquery-storage/2.22.0/)
-- [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: 3.4](https://pypi.org/project/idna/3.4/)
-- [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/)
-- [ipykernel: 6.27.0](https://pypi.org/project/ipykernel/6.27.0/)
-- [ipython: 8.17.2](https://pypi.org/project/ipython/8.17.2/)
-- [ipywidgets: 8.1.1](https://pypi.org/project/ipywidgets/8.1.1/)
-- [isoduration: 20.11.0](https://pypi.org/project/isoduration/20.11.0/)
-- [jedi: 0.19.1](https://pypi.org/project/jedi/0.19.1/)
-- [jinja2: 3.1.2](https://pypi.org/project/jinja2/3.1.2/)
-- [joblib: 1.3.2](https://pypi.org/project/joblib/1.3.2/)
-- [json5: 0.9.14](https://pypi.org/project/json5/0.9.14/)
-- [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: 2023.11.1](https://pypi.org/project/jsonschema-specifications/2023.11.1/)
-- [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/)
-- [jupyter-events: 0.9.0](https://pypi.org/project/jupyter-events/0.9.0/)
-- [jupyter-lsp: 2.2.0](https://pypi.org/project/jupyter-lsp/2.2.0/)
-- [jupyter-server: 2.11.0](https://pypi.org/project/jupyter-server/2.11.0/)
-- [jupyter-server-terminals: 0.4.4](https://pypi.org/project/jupyter-server-terminals/0.4.4/)
-- [jupyterlab: 4.0.9](https://pypi.org/project/jupyterlab/4.0.9/)
-- [jupyterlab-pygments: 0.2.2](https://pypi.org/project/jupyterlab-pygments/0.2.2/)
-- [jupyterlab-server: 2.25.2](https://pypi.org/project/jupyterlab-server/2.25.2/)
-- [jupyterlab-widgets: 3.0.9](https://pypi.org/project/jupyterlab-widgets/3.0.9/)
-- [jupytext: 1.15.2](https://pypi.org/project/jupytext/1.15.2/)
-- [kaleido: 0.2.1](https://pypi.org/project/kaleido/0.2.1/)
-- [kiwisolver: 1.4.5](https://pypi.org/project/kiwisolver/1.4.5/)
-- [lifelines: 0.27.8](https://pypi.org/project/lifelines/0.27.8/)
-- [llvmlite: 0.41.1](https://pypi.org/project/llvmlite/0.41.1/)
-- [lz4: 4.3.2](https://pypi.org/project/lz4/4.3.2/)
-- [markdown-it-py: 3.0.0](https://pypi.org/project/markdown-it-py/3.0.0/)
-- [markupsafe: 2.1.3](https://pypi.org/project/markupsafe/2.1.3/)
-- [matplotlib: 3.8.2](https://pypi.org/project/matplotlib/3.8.2/)
-- [matplotlib-inline: 0.1.6](https://pypi.org/project/matplotlib-inline/0.1.6/)
-- [mdit-py-plugins: 0.4.0](https://pypi.org/project/mdit-py-plugins/0.4.0/)
-- [mdurl: 0.1.2](https://pypi.org/project/mdurl/0.1.2/)
-- [mistune: 3.0.2](https://pypi.org/project/mistune/3.0.2/)
-- [nbclient: 0.9.0](https://pypi.org/project/nbclient/0.9.0/)
-- [nbconvert: 7.11.0](https://pypi.org/project/nbconvert/7.11.0/)
-- [nbformat: 5.9.2](https://pypi.org/project/nbformat/5.9.2/)
-- [nbval: 0.10.0](https://pypi.org/project/nbval/0.10.0/)
-- [nest-asyncio: 1.5.8](https://pypi.org/project/nest-asyncio/1.5.8/)
-- [notebook: 7.0.6](https://pypi.org/project/notebook/7.0.6/)
-- [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: 0.5.3](https://pypi.org/project/patsy/0.5.3/)
-- [pexpect: 4.8.0](https://pypi.org/project/pexpect/4.8.0/)
-- [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/)
-- [platformdirs: 4.0.0](https://pypi.org/project/platformdirs/4.0.0/)
-- [plotly: 5.18.0](https://pypi.org/project/plotly/5.18.0/)
-- [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: 2.17.1](https://pypi.org/project/pygments/2.17.1/)
-- [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: 25.1.1](https://pypi.org/project/pyzmq/25.1.1/)
-- [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: 0.31.0](https://pypi.org/project/referencing/0.31.0/)
-- [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: 0.13.1](https://pypi.org/project/rpds-py/0.13.1/)
-- [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/)
-- [terminado: 0.18.0](https://pypi.org/project/terminado/0.18.0/)
-- [threadpoolctl: 3.2.0](https://pypi.org/project/threadpoolctl/3.2.0/)
-- [tinycss2: 1.2.1](https://pypi.org/project/tinycss2/1.2.1/)
-- [toml: 0.10.2](https://pypi.org/project/toml/0.10.2/)
-- [tomli: 2.0.1](https://pypi.org/project/tomli/2.0.1/)
-- [tornado: 6.3.3](https://pypi.org/project/tornado/6.3.3/)
-- [tqdm: 4.66.1](https://pypi.org/project/tqdm/4.66.1/)
-- [traitlets: 5.13.0](https://pypi.org/project/traitlets/5.13.0/)
-- [types-python-dateutil: 2.8.19.14](https://pypi.org/project/types-python-dateutil/2.8.19.14/)
-- [typing-extensions: 4.8.0](https://pypi.org/project/typing-extensions/4.8.0/)
-- [tzdata: 2023.3](https://pypi.org/project/tzdata/2023.3/)
-- [upsetplot: 0.8.0](https://pypi.org/project/upsetplot/0.8.0/)
-- [uri-template: 1.3.0](https://pypi.org/project/uri-template/1.3.0/)
-- [urllib3: 2.1.0](https://pypi.org/project/urllib3/2.1.0/)
-- [venn: 0.1.3](https://pypi.org/project/venn/0.1.3/)
-- [wcwidth: 0.2.11](https://pypi.org/project/wcwidth/0.2.11/)
-- [webcolors: 1.13](https://pypi.org/project/webcolors/1.13/)
-- [webencodings: 0.5.1](https://pypi.org/project/webencodings/0.5.1/)
-- [websocket-client: 1.6.4](https://pypi.org/project/websocket-client/1.6.4/)
-- [wheel: 0.41.3](https://pypi.org/project/wheel/0.41.3/)
-- [widgetsnbextension: 4.0.9](https://pypi.org/project/widgetsnbextension/4.0.9/)
-- [wrapt: 1.16.0](https://pypi.org/project/wrapt/1.16.0/)
-
+# Package Versions for v2
+
+This python:v2 OpenSAFELY image is based on Ubuntu 22.04 with Python 3.10.12.
+
+## Packages
+
+It comes pre-installed with a standard set of python packages.
+
+- [anyio: 4.1.0](https://pypi.org/project/anyio/4.1.0/)
+- [argon2-cffi: 23.1.0](https://pypi.org/project/argon2-cffi/23.1.0/)
+- [argon2-cffi-bindings: 21.2.0](https://pypi.org/project/argon2-cffi-bindings/21.2.0/)
+- [arrow: 1.3.0](https://pypi.org/project/arrow/1.3.0/)
+- [astor: 0.8.1](https://pypi.org/project/astor/0.8.1/)
+- [asttokens: 2.4.1](https://pypi.org/project/asttokens/2.4.1/)
+- [async-lru: 2.0.4](https://pypi.org/project/async-lru/2.0.4/)
+- [attrs: 23.1.0](https://pypi.org/project/attrs/23.1.0/)
+- [autograd: 1.6.2](https://pypi.org/project/autograd/1.6.2/)
+- [autograd-gamma: 0.5.0](https://pypi.org/project/autograd-gamma/0.5.0/)
+- [babel: 2.13.1](https://pypi.org/project/babel/2.13.1/)
+- [bash-kernel: 0.9.3](https://pypi.org/project/bash-kernel/0.9.3/)
+- [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/)
+- [ipykernel: 6.27.1](https://pypi.org/project/ipykernel/6.27.1/)
+- [ipython: 8.18.1](https://pypi.org/project/ipython/8.18.1/)
+- [ipywidgets: 8.1.1](https://pypi.org/project/ipywidgets/8.1.1/)
+- [isoduration: 20.11.0](https://pypi.org/project/isoduration/20.11.0/)
+- [jedi: 0.19.1](https://pypi.org/project/jedi/0.19.1/)
+- [jinja2: 3.1.2](https://pypi.org/project/jinja2/3.1.2/)
+- [joblib: 1.3.2](https://pypi.org/project/joblib/1.3.2/)
+- [json5: 0.9.14](https://pypi.org/project/json5/0.9.14/)
+- [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/)
+- [jupyter-events: 0.9.0](https://pypi.org/project/jupyter-events/0.9.0/)
+- [jupyter-lsp: 2.2.1](https://pypi.org/project/jupyter-lsp/2.2.1/)
+- [jupyter-server: 2.11.2](https://pypi.org/project/jupyter-server/2.11.2/)
+- [jupyter-server-terminals: 0.4.4](https://pypi.org/project/jupyter-server-terminals/0.4.4/)
+- [jupyterlab: 4.0.9](https://pypi.org/project/jupyterlab/4.0.9/)
+- [jupyterlab-pygments: 0.3.0](https://pypi.org/project/jupyterlab-pygments/0.3.0/)
+- [jupyterlab-server: 2.25.2](https://pypi.org/project/jupyterlab-server/2.25.2/)
+- [jupyterlab-widgets: 3.0.9](https://pypi.org/project/jupyterlab-widgets/3.0.9/)
+- [jupytext: 1.16.0](https://pypi.org/project/jupytext/1.16.0/)
+- [kaleido: 0.2.1](https://pypi.org/project/kaleido/0.2.1/)
+- [kiwisolver: 1.4.5](https://pypi.org/project/kiwisolver/1.4.5/)
+- [lifelines: 0.27.8](https://pypi.org/project/lifelines/0.27.8/)
+- [llvmlite: 0.41.1](https://pypi.org/project/llvmlite/0.41.1/)
+- [lz4: 4.3.2](https://pypi.org/project/lz4/4.3.2/)
+- [markdown-it-py: 3.0.0](https://pypi.org/project/markdown-it-py/3.0.0/)
+- [markupsafe: 2.1.3](https://pypi.org/project/markupsafe/2.1.3/)
+- [matplotlib: 3.8.2](https://pypi.org/project/matplotlib/3.8.2/)
+- [matplotlib-inline: 0.1.6](https://pypi.org/project/matplotlib-inline/0.1.6/)
+- [mdit-py-plugins: 0.4.0](https://pypi.org/project/mdit-py-plugins/0.4.0/)
+- [mdurl: 0.1.2](https://pypi.org/project/mdurl/0.1.2/)
+- [mistune: 3.0.2](https://pypi.org/project/mistune/3.0.2/)
+- [nbclient: 0.9.0](https://pypi.org/project/nbclient/0.9.0/)
+- [nbconvert: 7.12.0](https://pypi.org/project/nbconvert/7.12.0/)
+- [nbformat: 5.9.2](https://pypi.org/project/nbformat/5.9.2/)
+- [nbval: 0.10.0](https://pypi.org/project/nbval/0.10.0/)
+- [nest-asyncio: 1.5.8](https://pypi.org/project/nest-asyncio/1.5.8/)
+- [notebook: 7.0.6](https://pypi.org/project/notebook/7.0.6/)
+- [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/)
+- [platformdirs: 4.1.0](https://pypi.org/project/platformdirs/4.1.0/)
+- [plotly: 5.18.0](https://pypi.org/project/plotly/5.18.0/)
+- [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/)
+- [terminado: 0.18.0](https://pypi.org/project/terminado/0.18.0/)
+- [threadpoolctl: 3.2.0](https://pypi.org/project/threadpoolctl/3.2.0/)
+- [tinycss2: 1.2.1](https://pypi.org/project/tinycss2/1.2.1/)
+- [toml: 0.10.2](https://pypi.org/project/toml/0.10.2/)
+- [tomli: 2.0.1](https://pypi.org/project/tomli/2.0.1/)
+- [tornado: 6.4](https://pypi.org/project/tornado/6.4/)
+- [tqdm: 4.66.1](https://pypi.org/project/tqdm/4.66.1/)
+- [traitlets: 5.14.0](https://pypi.org/project/traitlets/5.14.0/)
+- [types-python-dateutil: 2.8.19.14](https://pypi.org/project/types-python-dateutil/2.8.19.14/)
+- [typing-extensions: 4.8.0](https://pypi.org/project/typing-extensions/4.8.0/)
+- [tzdata: 2023.3](https://pypi.org/project/tzdata/2023.3/)
+- [upsetplot: 0.8.0](https://pypi.org/project/upsetplot/0.8.0/)
+- [uri-template: 1.3.0](https://pypi.org/project/uri-template/1.3.0/)
+- [urllib3: 2.1.0](https://pypi.org/project/urllib3/2.1.0/)
+- [venn: 0.1.3](https://pypi.org/project/venn/0.1.3/)
+- [wcwidth: 0.2.12](https://pypi.org/project/wcwidth/0.2.12/)
+- [webcolors: 1.13](https://pypi.org/project/webcolors/1.13/)
+- [webencodings: 0.5.1](https://pypi.org/project/webencodings/0.5.1/)
+- [websocket-client: 1.7.0](https://pypi.org/project/websocket-client/1.7.0/)
+- [wheel: 0.42.0](https://pypi.org/project/wheel/0.42.0/)
+- [widgetsnbextension: 4.0.9](https://pypi.org/project/widgetsnbextension/4.0.9/)
+- [wrapt: 1.16.0](https://pypi.org/project/wrapt/1.16.0/)
+
diff --git a/v2/requirements.txt b/v2/requirements.txt
index aecf474..25c762f 100644
--- a/v2/requirements.txt
+++ b/v2/requirements.txt
@@ -2,9 +2,9 @@
 # This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
-#    pip-compile requirements-3.10.in
+#    pip-compile --output-file=v2/requirements.txt v2/requirements.in
 #
-anyio==4.0.0
+anyio==4.1.0
     # via jupyter-server
 argon2-cffi==23.1.0
     # via jupyter-server
@@ -31,8 +31,8 @@ autograd-gamma==0.5.0
     # via lifelines
 babel==2.13.1
     # via jupyterlab-server
-bash-kernel==0.9.1
-    # via -r requirements-3.10.in
+bash-kernel==0.9.3
+    # via -r v2/requirements.in
 beautifulsoup4==4.12.2
     # via nbconvert
 bleach==6.1.0
@@ -44,7 +44,7 @@ cachetools==5.3.2
 cairocffi==1.6.1
     # via cairosvg
 cairosvg==2.7.1
-    # via -r requirements-3.10.in
+    # via -r v2/requirements.in
 certifi==2023.11.17
     # via
     #   fiona
@@ -93,7 +93,7 @@ defusedxml==0.7.1
 descartes==1.1.0
     # via ebmdatalab
 ebmdatalab==0.0.30
-    # via -r requirements-3.10.in
+    # via -r v2/requirements.in
 exceptiongroup==1.2.0
     # via
     #   anyio
@@ -105,7 +105,7 @@ fastjsonschema==2.19.0
     # via nbformat
 fiona==1.9.5
     # via geopandas
-fonttools==4.45.0
+fonttools==4.46.0
     # via matplotlib
 formulaic==0.6.6
     # via lifelines
@@ -121,7 +121,7 @@ google-api-core[grpc]==2.14.0
     #   google-cloud-bigquery-storage
     #   google-cloud-core
     #   pandas-gbq
-google-auth==2.23.4
+google-auth==2.24.0
     # via
     #   google-api-core
     #   google-auth-oauthlib
@@ -134,7 +134,7 @@ google-auth-oauthlib==1.1.0
     #   pydata-google-auth
 google-cloud-bigquery==3.13.0
     # via pandas-gbq
-google-cloud-bigquery-storage==2.22.0
+google-cloud-bigquery-storage==2.23.0
     # via pandas-gbq
 google-cloud-core==2.3.3
     # via google-cloud-bigquery
@@ -153,7 +153,7 @@ grpcio==1.59.3
     #   grpcio-status
 grpcio-status==1.59.3
     # via google-api-core
-idna==3.4
+idna==3.6
     # via
     #   anyio
     #   jsonschema
@@ -162,7 +162,7 @@ iniconfig==2.0.0
     # via pytest
 interface-meta==1.3.0
     # via formulaic
-ipykernel==6.27.0
+ipykernel==6.27.1
     # via
     #   bash-kernel
     #   jupyter
@@ -170,14 +170,14 @@ ipykernel==6.27.0
     #   jupyterlab
     #   nbval
     #   qtconsole
-ipython==8.17.2
+ipython==8.18.1
     # via
     #   ipykernel
     #   ipywidgets
     #   jupyter-console
 ipywidgets==8.1.1
     # via
-    #   -r requirements-3.10.in
+    #   -r v2/requirements.in
     #   jupyter
 isoduration==20.11.0
     # via jsonschema
@@ -200,10 +200,10 @@ jsonschema[format-nongpl]==4.20.0
     #   jupyter-events
     #   jupyterlab-server
     #   nbformat
-jsonschema-specifications==2023.11.1
+jsonschema-specifications==2023.11.2
     # via jsonschema
 jupyter==1.0.0
-    # via -r requirements-3.10.in
+    # via -r v2/requirements.in
 jupyter-client==8.6.0
     # via
     #   ipykernel
@@ -227,9 +227,9 @@ jupyter-core==5.5.0
     #   qtconsole
 jupyter-events==0.9.0
     # via jupyter-server
-jupyter-lsp==2.2.0
+jupyter-lsp==2.2.1
     # via jupyterlab
-jupyter-server==2.11.0
+jupyter-server==2.11.2
     # via
     #   jupyter-lsp
     #   jupyterlab
@@ -240,9 +240,9 @@ jupyter-server-terminals==0.4.4
     # via jupyter-server
 jupyterlab==4.0.9
     # via
-    #   -r requirements-3.10.in
+    #   -r v2/requirements.in
     #   notebook
-jupyterlab-pygments==0.2.2
+jupyterlab-pygments==0.3.0
     # via nbconvert
 jupyterlab-server==2.25.2
     # via
@@ -250,14 +250,14 @@ jupyterlab-server==2.25.2
     #   notebook
 jupyterlab-widgets==3.0.9
     # via ipywidgets
-jupytext==1.15.2
-    # via -r requirements-3.10.in
+jupytext==1.16.0
+    # via -r v2/requirements.in
 kaleido==0.2.1
-    # via -r requirements-3.10.in
+    # via -r v2/requirements.in
 kiwisolver==1.4.5
     # via matplotlib
 lifelines==0.27.8
-    # via -r requirements-3.10.in
+    # via -r v2/requirements.in
 llvmlite==0.41.1
     # via numba
 lz4==4.3.2
@@ -272,7 +272,7 @@ markupsafe==2.1.3
     #   nbconvert
 matplotlib==3.8.2
     # via
-    #   -r requirements-3.10.in
+    #   -r v2/requirements.in
     #   descartes
     #   lifelines
     #   seaborn
@@ -290,7 +290,7 @@ mistune==3.0.2
     # via nbconvert
 nbclient==0.9.0
     # via nbconvert
-nbconvert==7.11.0
+nbconvert==7.12.0
     # via
     #   jupyter
     #   jupyter-server
@@ -302,7 +302,7 @@ nbformat==5.9.2
     #   nbconvert
     #   nbval
 nbval==0.10.0
-    # via -r requirements-3.10.in
+    # via -r v2/requirements.in
 nest-asyncio==1.5.8
     # via ipykernel
 notebook==7.0.6
@@ -312,10 +312,10 @@ notebook-shim==0.2.3
     #   jupyterlab
     #   notebook
 numba==0.58.1
-    # via -r requirements-3.10.in
+    # via -r v2/requirements.in
 numpy==1.26.2
     # via
-    #   -r requirements-3.10.in
+    #   -r v2/requirements.in
     #   autograd
     #   contourpy
     #   db-dtypes
@@ -335,9 +335,9 @@ numpy==1.26.2
 oauthlib==3.2.2
     # via requests-oauthlib
 opensafely-cohort-extractor==1.90.0
-    # via -r requirements-3.10.in
+    # via -r v2/requirements.in
 opensafely-matching==0.2.0
-    # via -r requirements-3.10.in
+    # via -r v2/requirements.in
 overrides==7.4.0
     # via jupyter-server
 packaging==23.2
@@ -350,6 +350,7 @@ packaging==23.2
     #   jupyter-server
     #   jupyterlab
     #   jupyterlab-server
+    #   jupytext
     #   matplotlib
     #   nbconvert
     #   plotly
@@ -359,7 +360,7 @@ packaging==23.2
     #   statsmodels
 pandas==2.1.3
     # via
-    #   -r requirements-3.10.in
+    #   -r v2/requirements.in
     #   db-dtypes
     #   ebmdatalab
     #   formulaic
@@ -373,29 +374,29 @@ pandas==2.1.3
     #   upsetplot
 pandas-gbq==0.19.2
     # via
-    #   -r requirements-3.10.in
+    #   -r v2/requirements.in
     #   ebmdatalab
 pandocfilters==1.5.0
     # via nbconvert
 parso==0.8.3
     # via jedi
-patsy==0.5.3
+patsy==0.5.4
     # via statsmodels
-pexpect==4.8.0
+pexpect==4.9.0
     # via
     #   bash-kernel
     #   ipython
 pillow==10.1.0
     # via
-    #   -r requirements-3.10.in
+    #   -r v2/requirements.in
     #   cairosvg
     #   matplotlib
 pip-tools==7.3.0
-    # via -r requirements-3.10.in
-platformdirs==4.0.0
+    # via -r v2/requirements.in
+platformdirs==4.1.0
     # via jupyter-core
 plotly==5.18.0
-    # via -r requirements-3.10.in
+    # via -r v2/requirements.in
 pluggy==1.3.0
     # via pytest
 prometheus-client==0.19.0
@@ -428,7 +429,7 @@ py==1.11.0
     # via retry
 pyarrow==14.0.1
     # via
-    #   -r requirements-3.10.in
+    #   -r v2/requirements.in
     #   db-dtypes
     #   opensafely-cohort-extractor
     #   pandas-gbq
@@ -442,7 +443,7 @@ pycparser==2.21
     # via cffi
 pydata-google-auth==1.8.2
     # via pandas-gbq
-pygments==2.17.1
+pygments==2.17.2
     # via
     #   ipython
     #   jupyter-console
@@ -456,7 +457,7 @@ pyproject-hooks==1.0.0
     # via build
 pytest==7.4.3
     # via
-    #   -r requirements-3.10.in
+    #   -r v2/requirements.in
     #   nbval
 python-dateutil==2.8.2
     # via
@@ -474,7 +475,7 @@ pyyaml==6.0.1
     #   jupyter-events
     #   jupytext
     #   opensafely-cohort-extractor
-pyzmq==25.1.1
+pyzmq==25.1.2
     # via
     #   ipykernel
     #   jupyter-client
@@ -485,7 +486,7 @@ qtconsole==5.5.1
     # via jupyter
 qtpy==2.4.1
     # via qtconsole
-referencing==0.31.0
+referencing==0.31.1
     # via
     #   jsonschema
     #   jsonschema-specifications
@@ -509,17 +510,17 @@ rfc3986-validator==0.1.1
     # via
     #   jsonschema
     #   jupyter-events
-rpds-py==0.13.1
+rpds-py==0.13.2
     # via
     #   jsonschema
     #   referencing
 rsa==4.9
     # via google-auth
 scikit-learn==1.3.2
-    # via -r requirements-3.10.in
+    # via -r v2/requirements.in
 scipy==1.11.4
     # via
-    #   -r requirements-3.10.in
+    #   -r v2/requirements.in
     #   autograd-gamma
     #   formulaic
     #   lifelines
@@ -577,7 +578,7 @@ tomli==2.0.1
     #   pip-tools
     #   pyproject-hooks
     #   pytest
-tornado==6.3.3
+tornado==6.4
     # via
     #   ipykernel
     #   jupyter-client
@@ -586,8 +587,8 @@ tornado==6.3.3
     #   notebook
     #   terminado
 tqdm==4.66.1
-    # via -r requirements-3.10.in
-traitlets==5.13.0
+    # via -r v2/requirements.in
+traitlets==5.14.0
     # via
     #   comm
     #   ipykernel
@@ -613,14 +614,14 @@ typing-extensions==4.8.0
 tzdata==2023.3
     # via pandas
 upsetplot==0.8.0
-    # via -r requirements-3.10.in
+    # via -r v2/requirements.in
 uri-template==1.3.0
     # via jsonschema
 urllib3==2.1.0
     # via requests
 venn==0.1.3
-    # via -r requirements-3.10.in
-wcwidth==0.2.11
+    # via -r v2/requirements.in
+wcwidth==0.2.12
     # via prompt-toolkit
 webcolors==1.13
     # via jsonschema
@@ -629,9 +630,9 @@ webencodings==0.5.1
     #   bleach
     #   cssselect2
     #   tinycss2
-websocket-client==1.6.4
+websocket-client==1.7.0
     # via jupyter-server
-wheel==0.41.3
+wheel==0.42.0
     # via pip-tools
 widgetsnbextension==4.0.9
     # via ipywidgets

From ddeb4285af58c869e9478f9c38b74c79f6eab61f Mon Sep 17 00:00:00 2001
From: bloodearnest <simon.davy@thedatalab.org>
Date: Mon, 11 Dec 2023 11:58:02 +0000
Subject: [PATCH 10/11] 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      |  35 ----------
 v2/requirements.in  |   5 +-
 v2/requirements.txt | 159 ++------------------------------------------
 3 files changed, 9 insertions(+), 190 deletions(-)

diff --git a/v2/packages.md b/v2/packages.md
index 4320c60..b9d3e05 100644
--- a/v2/packages.md
+++ b/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/)
@@ -127,20 +104,14 @@ 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/)
@@ -148,27 +119,21 @@ It comes pre-installed with a standard set of python packages.
 - [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/)
diff --git a/v2/requirements.in b/v2/requirements.in
index a89dd8b..82a8776 100644
--- a/v2/requirements.in
+++ b/v2/requirements.in
@@ -1,7 +1,8 @@
 # Basic requirements for notebook infrastructure provided in base
 # docker image
 pip-tools
-jupyter
+notebook
+jupyter-console
 jupyterlab
 jupytext
 bash_kernel
@@ -9,10 +10,8 @@ nbval
 opensafely-matching
 
 # Commonly-used packages provided in base docker image
-pandas-gbq
 pandas
 numpy
-ebmdatalab
 matplotlib
 scipy
 tqdm
diff --git a/v2/requirements.txt b/v2/requirements.txt
index 25c762f..cf29f44 100644
--- a/v2/requirements.txt
+++ b/v2/requirements.txt
@@ -20,7 +20,6 @@ async-lru==2.0.4
     # via jupyterlab
 attrs==23.1.0
     # via
-    #   fiona
     #   jsonschema
     #   referencing
 autograd==1.6.2
@@ -39,17 +38,12 @@ bleach==6.1.0
     # via nbconvert
 build==1.0.3
     # via pip-tools
-cachetools==5.3.2
-    # via google-auth
 cairocffi==1.6.1
     # via cairosvg
 cairosvg==2.7.1
     # via -r v2/requirements.in
 certifi==2023.11.17
-    # via
-    #   fiona
-    #   pyproj
-    #   requests
+    # via requests
 cffi==1.16.0
     # via
     #   argon2-cffi-bindings
@@ -57,15 +51,7 @@ cffi==1.16.0
 charset-normalizer==3.3.2
     # via requests
 click==8.1.7
-    # via
-    #   click-plugins
-    #   cligj
-    #   fiona
-    #   pip-tools
-click-plugins==1.1.1
-    # via fiona
-cligj==0.7.2
-    # via fiona
+    # via pip-tools
 comm==0.2.0
     # via
     #   ipykernel
@@ -78,8 +64,6 @@ cssselect2==0.7.0
     # via cairosvg
 cycler==0.12.1
     # via matplotlib
-db-dtypes==1.1.1
-    # via pandas-gbq
 debugpy==1.8.0
     # via ipykernel
 decorator==5.1.1
@@ -90,10 +74,6 @@ defusedxml==0.7.1
     # via
     #   cairosvg
     #   nbconvert
-descartes==1.1.0
-    # via ebmdatalab
-ebmdatalab==0.0.30
-    # via -r v2/requirements.in
 exceptiongroup==1.2.0
     # via
     #   anyio
@@ -103,8 +83,6 @@ executing==2.0.1
     # via stack-data
 fastjsonschema==2.19.0
     # via nbformat
-fiona==1.9.5
-    # via geopandas
 fonttools==4.46.0
     # via matplotlib
 formulaic==0.6.6
@@ -113,46 +91,6 @@ fqdn==1.5.1
     # via jsonschema
 future==0.18.3
     # via autograd
-geopandas==0.14.1
-    # via ebmdatalab
-google-api-core[grpc]==2.14.0
-    # via
-    #   google-cloud-bigquery
-    #   google-cloud-bigquery-storage
-    #   google-cloud-core
-    #   pandas-gbq
-google-auth==2.24.0
-    # via
-    #   google-api-core
-    #   google-auth-oauthlib
-    #   google-cloud-core
-    #   pandas-gbq
-    #   pydata-google-auth
-google-auth-oauthlib==1.1.0
-    # via
-    #   pandas-gbq
-    #   pydata-google-auth
-google-cloud-bigquery==3.13.0
-    # via pandas-gbq
-google-cloud-bigquery-storage==2.23.0
-    # via pandas-gbq
-google-cloud-core==2.3.3
-    # via google-cloud-bigquery
-google-crc32c==1.5.0
-    # via google-resumable-media
-google-resumable-media==2.6.0
-    # via google-cloud-bigquery
-googleapis-common-protos==1.61.0
-    # via
-    #   google-api-core
-    #   grpcio-status
-grpcio==1.59.3
-    # via
-    #   google-api-core
-    #   google-cloud-bigquery
-    #   grpcio-status
-grpcio-status==1.59.3
-    # via google-api-core
 idna==3.6
     # via
     #   anyio
@@ -165,20 +103,16 @@ interface-meta==1.3.0
 ipykernel==6.27.1
     # via
     #   bash-kernel
-    #   jupyter
     #   jupyter-console
     #   jupyterlab
     #   nbval
-    #   qtconsole
 ipython==8.18.1
     # via
     #   ipykernel
     #   ipywidgets
     #   jupyter-console
 ipywidgets==8.1.1
-    # via
-    #   -r v2/requirements.in
-    #   jupyter
+    # via -r v2/requirements.in
 isoduration==20.11.0
     # via jsonschema
 jedi==0.19.1
@@ -202,8 +136,6 @@ jsonschema[format-nongpl]==4.20.0
     #   nbformat
 jsonschema-specifications==2023.11.2
     # via jsonschema
-jupyter==1.0.0
-    # via -r v2/requirements.in
 jupyter-client==8.6.0
     # via
     #   ipykernel
@@ -211,9 +143,8 @@ jupyter-client==8.6.0
     #   jupyter-server
     #   nbclient
     #   nbval
-    #   qtconsole
 jupyter-console==6.6.3
-    # via jupyter
+    # via -r v2/requirements.in
 jupyter-core==5.5.0
     # via
     #   ipykernel
@@ -224,7 +155,6 @@ jupyter-core==5.5.0
     #   nbclient
     #   nbconvert
     #   nbformat
-    #   qtconsole
 jupyter-events==0.9.0
     # via jupyter-server
 jupyter-lsp==2.2.1
@@ -273,7 +203,6 @@ markupsafe==2.1.3
 matplotlib==3.8.2
     # via
     #   -r v2/requirements.in
-    #   descartes
     #   lifelines
     #   seaborn
     #   upsetplot
@@ -291,9 +220,7 @@ mistune==3.0.2
 nbclient==0.9.0
     # via nbconvert
 nbconvert==7.12.0
-    # via
-    #   jupyter
-    #   jupyter-server
+    # via jupyter-server
 nbformat==5.9.2
     # via
     #   jupyter-server
@@ -306,7 +233,7 @@ nbval==0.10.0
 nest-asyncio==1.5.8
     # via ipykernel
 notebook==7.0.6
-    # via jupyter
+    # via -r v2/requirements.in
 notebook-shim==0.2.3
     # via
     #   jupyterlab
@@ -318,22 +245,15 @@ numpy==1.26.2
     #   -r v2/requirements.in
     #   autograd
     #   contourpy
-    #   db-dtypes
     #   formulaic
     #   lifelines
     #   matplotlib
     #   numba
     #   pandas
-    #   pandas-gbq
-    #   patsy
     #   pyarrow
     #   scikit-learn
     #   scipy
     #   seaborn
-    #   shapely
-    #   statsmodels
-oauthlib==3.2.2
-    # via requests-oauthlib
 opensafely-cohort-extractor==1.90.0
     # via -r v2/requirements.in
 opensafely-matching==0.2.0
@@ -343,9 +263,6 @@ overrides==7.4.0
 packaging==23.2
     # via
     #   build
-    #   db-dtypes
-    #   geopandas
-    #   google-cloud-bigquery
     #   ipykernel
     #   jupyter-server
     #   jupyterlab
@@ -355,33 +272,19 @@ packaging==23.2
     #   nbconvert
     #   plotly
     #   pytest
-    #   qtconsole
-    #   qtpy
-    #   statsmodels
 pandas==2.1.3
     # via
     #   -r v2/requirements.in
-    #   db-dtypes
-    #   ebmdatalab
     #   formulaic
-    #   geopandas
     #   lifelines
     #   opensafely-cohort-extractor
     #   opensafely-matching
-    #   pandas-gbq
     #   seaborn
-    #   statsmodels
     #   upsetplot
-pandas-gbq==0.19.2
-    # via
-    #   -r v2/requirements.in
-    #   ebmdatalab
 pandocfilters==1.5.0
     # via nbconvert
 parso==0.8.3
     # via jedi
-patsy==0.5.4
-    # via statsmodels
 pexpect==4.9.0
     # via
     #   bash-kernel
@@ -405,18 +308,6 @@ prompt-toolkit==3.0.41
     # via
     #   ipython
     #   jupyter-console
-proto-plus==1.22.3
-    # via
-    #   google-cloud-bigquery
-    #   google-cloud-bigquery-storage
-protobuf==4.25.1
-    # via
-    #   google-api-core
-    #   google-cloud-bigquery
-    #   google-cloud-bigquery-storage
-    #   googleapis-common-protos
-    #   grpcio-status
-    #   proto-plus
 psutil==5.9.6
     # via ipykernel
 ptyprocess==0.7.0
@@ -430,29 +321,16 @@ py==1.11.0
 pyarrow==14.0.1
     # via
     #   -r v2/requirements.in
-    #   db-dtypes
     #   opensafely-cohort-extractor
-    #   pandas-gbq
-pyasn1==0.5.1
-    # via
-    #   pyasn1-modules
-    #   rsa
-pyasn1-modules==0.3.0
-    # via google-auth
 pycparser==2.21
     # via cffi
-pydata-google-auth==1.8.2
-    # via pandas-gbq
 pygments==2.17.2
     # via
     #   ipython
     #   jupyter-console
     #   nbconvert
-    #   qtconsole
 pyparsing==3.1.1
     # via matplotlib
-pyproj==3.6.1
-    # via geopandas
 pyproject-hooks==1.0.0
     # via build
 pytest==7.4.3
@@ -462,7 +340,6 @@ pytest==7.4.3
 python-dateutil==2.8.2
     # via
     #   arrow
-    #   google-cloud-bigquery
     #   jupyter-client
     #   matplotlib
     #   pandas
@@ -481,11 +358,6 @@ pyzmq==25.1.2
     #   jupyter-client
     #   jupyter-console
     #   jupyter-server
-    #   qtconsole
-qtconsole==5.5.1
-    # via jupyter
-qtpy==2.4.1
-    # via qtconsole
 referencing==0.31.1
     # via
     #   jsonschema
@@ -493,13 +365,8 @@ referencing==0.31.1
     #   jupyter-events
 requests==2.31.0
     # via
-    #   google-api-core
-    #   google-cloud-bigquery
     #   jupyterlab-server
     #   opensafely-cohort-extractor
-    #   requests-oauthlib
-requests-oauthlib==1.3.1
-    # via google-auth-oauthlib
 retry==0.9.2
     # via opensafely-cohort-extractor
 rfc3339-validator==0.1.4
@@ -514,8 +381,6 @@ rpds-py==0.13.2
     # via
     #   jsonschema
     #   referencing
-rsa==4.9
-    # via google-auth
 scikit-learn==1.3.2
     # via -r v2/requirements.in
 scipy==1.11.4
@@ -525,21 +390,14 @@ scipy==1.11.4
     #   formulaic
     #   lifelines
     #   scikit-learn
-    #   statsmodels
 seaborn==0.13.0
-    # via
-    #   ebmdatalab
-    #   opensafely-cohort-extractor
+    # via opensafely-cohort-extractor
 send2trash==1.8.2
     # via jupyter-server
-shapely==2.0.2
-    # via geopandas
 six==1.16.0
     # via
     #   asttokens
     #   bleach
-    #   fiona
-    #   patsy
     #   python-dateutil
     #   rfc3339-validator
 sniffio==1.3.0
@@ -550,8 +408,6 @@ sqlparse==0.4.4
     # via opensafely-cohort-extractor
 stack-data==0.6.3
     # via ipython
-statsmodels==0.14.0
-    # via ebmdatalab
 structlog==23.2.0
     # via opensafely-cohort-extractor
 tabulate==0.9.0
@@ -604,7 +460,6 @@ traitlets==5.14.0
     #   nbclient
     #   nbconvert
     #   nbformat
-    #   qtconsole
 types-python-dateutil==2.8.19.14
     # via arrow
 typing-extensions==4.8.0

From 39e93f98c74cf59be4be1177fbc83e5fa5d082a6 Mon Sep 17 00:00:00 2001
From: bloodearnest <simon.davy@thedatalab.org>
Date: Mon, 11 Dec 2023 12:05:50 +0000
Subject: [PATCH 11/11] enable publishing

---
 .github/workflows/build_and_publish.yaml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build_and_publish.yaml b/.github/workflows/build_and_publish.yaml
index 52966bc..ad4161e 100644
--- a/.github/workflows/build_and_publish.yaml
+++ b/.github/workflows/build_and_publish.yaml
@@ -30,6 +30,5 @@ jobs:
       run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login https://ghcr.io -u ${{ github.actor }} --password-stdin
     - name: Push image to GitHub Container Registry
       run: |
-        # just test publish for now
-        just publish v1 false
-        just publish v2 false
+        just publish v1 true
+        just publish v2 true