From 8bbf99dd8d0f4d7ddf7f9fa6270329bfedbb9f64 Mon Sep 17 00:00:00 2001 From: Katie Bickford Date: Wed, 20 May 2026 13:00:34 +0100 Subject: [PATCH 1/2] Implement dependency cooldown using `uv` - Add a global timestamp cutoff (`exclude-newer`) in pyproject.toml. For the purposes of this PR, the cut-off was set to 2026-05-18T00:00:00Z`, as this is the date that our automated dependency tools ran last and we want to try and match what we currently have in production. - Add recipes to manage the cutoff and dependency updates. - Remove version constraints from pyproject.toml where we didn't previously have a version constraint or pin. - Add an updated `uv.lock` that reflects the bumped `pyproject.toml` cutoff. Testing: - Tested the new justfile recipes: `just bump-uv-cutoff`, `just upgrade-all`, `just check-lockfile`, `just check`, and `just update-dependencies` - Ran `just prodenv`, `just devenv`, `just test`, `just run`, All succeeded locally. --- justfile | 50 ++++++- pyproject.toml | 82 +++++------ uv.lock | 371 +++++++++++++++++++++++++------------------------ 3 files changed, 277 insertions(+), 226 deletions(-) diff --git a/justfile b/justfile index 8e0c0dfd..c3d84684 100644 --- a/justfile +++ b/justfile @@ -94,13 +94,57 @@ upgrade-package package: && devenv uv lock --upgrade-package {{ package }} -# Upgrade all dev and prod dependencies to the latest versions per the pyproject.toml +# Move the cutoff date in pyproject.toml to N days ago (default: 7) at midnight UTC +bump-uv-cutoff days="7": + #!/usr/bin/env -S uvx --with tomlkit python3.13 + # Note we specify the python version here and we don't care if it's different to + # the .python-version; we need 3.11+ for the datetime code used. + + import datetime + import tomlkit + + with open("pyproject.toml", "rb") as f: + content = tomlkit.load(f) + + new_datetime = ( + datetime.datetime.now(datetime.UTC) - datetime.timedelta(days=int("{{ days }}")) + ).replace(hour=0, minute=0, second=0, microsecond=0) + new_timestamp = new_datetime.strftime("%Y-%m-%dT%H:%M:%SZ") + if existing_timestamp := content["tool"]["uv"].get("exclude-newer"): + if new_datetime < datetime.datetime.fromisoformat(existing_timestamp): + print( + f"Existing cutoff {existing_timestamp} is more recent than {new_timestamp}, not updating." + ) + exit(0) + content["tool"]["uv"]["exclude-newer"] = new_timestamp + + with open("pyproject.toml", "w") as f: + tomlkit.dump(content, f) + + +# Bump the timestamp cutoff to midnight UTC 7 days ago and upgrade all +# dev and prod dependencies to the latest version per pyproject.toml, +# then update the local venv. # This is the default input command to update-dependencies action # https://github.com/bennettoxford/update-dependencies-action -update-dependencies: && devenv +update-dependencies: bump-uv-cutoff && devenv uv lock --upgrade +# validate uv.lock +check-lockfile: + #!/usr/bin/env bash + set -euo pipefail + # Make sure dates in pyproject.toml and uv.lock are in sync + unset UV_EXCLUDE_NEWER + rc=0 + uv lock --check || rc=$? + if test "$rc" != "0" ; then + echo "Timestamp cutoffs in uv.lock must match those in pyproject.toml. See DEVELOPERS.md for details and hints." >&2 + exit $rc + fi + + # *ARGS is variadic, 0 or more. This allows us to do `just test -k match`, for example. # Run the python tests, excluding the functional tests. Run coverage. test-py *ARGS: devenv @@ -131,7 +175,7 @@ test-functional *ARGS: devenv test: assets-test test-py test-functional # lint and check formatting but don't modify anything -check *args: devenv +check *args: check-lockfile devenv $BIN/ruff format --diff --quiet . $BIN/ruff check --output-format=full . $BIN/djhtml --tabwidth 2 --check templates/ diff --git a/pyproject.toml b/pyproject.toml index 6c19603e..4b0c190f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,37 +7,37 @@ authors = [{name = "OpenSAFELY", email = "tech@opensafely.org"}] license = {file = "LICENSE"} requires-python = ">=3.12" dependencies = [ - "antlr4-python3-runtime>=4.13.2", - "beautifulsoup4>=4.14.3", - "crispy-bootstrap4>=2026.2", - "dj-database-url>=3.1.2", + "antlr4-python3-runtime", + "beautifulsoup4", + "crispy-bootstrap4", + "dj-database-url", # Pin to 5.2.x until 6.0 is released and we are happy with 6.0 compatibility - "django~=5.2.13", - "django-anymail[mailgun]>=15.0", - "django-cors-headers>=4.9.0", - "django-crispy-forms>=2.6", - "django-extensions>=4.1", - "django-structlog>=10.0.0", - "django-taggit>=6.1.0", - "django-vite>=3.1.0", - "djangorestframework>=3.17.1", - "faker>=40.15.0", - "furl>=2.1.4", - "gunicorn>=25.3.0", - "lxml>=6.1.0", - "markdown2>=2.5.5", - "nh3>=0.3.5", - "openpyxl>=3.1.5", - "opentelemetry-exporter-otlp>=1.41.1", - "opentelemetry-instrumentation-django>=0.62b1", - "opentelemetry-sdk>=1.41.1", + "django>=5.2,<6.0", + "django-anymail[mailgun]", + "django-cors-headers", + "django-crispy-forms", + "django-extensions", + "django-structlog", + "django-taggit", + "django-vite", + "djangorestframework", + "faker", + "furl", + "gunicorn", + "lxml", + "markdown2", + "nh3", + "openpyxl", + "opentelemetry-exporter-otlp", + "opentelemetry-instrumentation-django", + "opentelemetry-sdk", # pinned to mimmum version for security patch (https://github.com/opensafely-core/opencodelists/commit/99374a6aee474e6873f41f0fb2af766b9a8da61d) "requests>=2.32.4", - "sentry-sdk>=2.58.0", - "slippers>=0.7.0", - "sqlean-py>=3.50.4.5", - "structlog>=25.5.0", - "tqdm>=4.67.3", + "sentry-sdk", + "slippers", + "sqlean-py", + "structlog", + "tqdm", # Serves static files. Dependabot wasn't updating past 6.3.0 for # unclear reasons, and we want fix #612 from 6.8.0. "whitenoise[brotli]>=6.8.0", @@ -125,22 +125,26 @@ lines-after-imports = 2 "codelists/views/__init__.py" = ["F401"] "opencodelists/views/__init__.py" = ["F401"] +# Note: any `exclude-newer-package` timestamps should be removed if > 7 days old. +# See https://github.com/opensafely-core/opencodelists/blob/main/DEVELOPERS.md for details. [tool.uv] required-version = ">=0.9" +exclude-newer = "2026-05-18T00:00:00Z" +exclude-newer-package = {} [dependency-groups] dev = [ - "django-debug-toolbar>=6.3.0", - "djhtml>=3.0.11", - "hypothesis>=6.152.3", + "django-debug-toolbar", + "djhtml", + "hypothesis", # for scripts/import_codelists_from_xlsx.py - "pandas>=3.0.2", + "pandas", # For scripts/fetch_vmp_prev.py - "paramiko>=4.0.0", - "pre-commit>=4.6.0", - "pytest-cov>=7.1.0", - "pytest-django>=4.12.0", - "pytest-playwright>=0.7.2", - "responses>=0.26.0", - "ruff>=0.15.12", + "paramiko", + "pre-commit", + "pytest-cov", + "pytest-django", + "pytest-playwright", + "responses", + "ruff", ] diff --git a/uv.lock b/uv.lock index 14c94aa6..95f33c2f 100644 --- a/uv.lock +++ b/uv.lock @@ -13,6 +13,9 @@ resolution-markers = [ "python_full_version < '3.13' and sys_platform != 'emscripten' and sys_platform != 'win32'", ] +[options] +exclude-newer = "2026-05-18T00:00:00Z" + [[package]] name = "antlr4-python3-runtime" version = "4.13.2" @@ 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dependency management process and tooling, including the new `uv` workflow, cutoff usage, and troubleshooting notes. --- DEVELOPERS.md | 45 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/DEVELOPERS.md b/DEVELOPERS.md index 34dd0a15..a918c127 100644 --- a/DEVELOPERS.md +++ b/DEVELOPERS.md @@ -150,6 +150,51 @@ require them or build codelists. Refer to the team manual [OpenCodelists playbook](https://bennett.wiki/tech-group/playbooks/opencodelists/) for how to do those tasks on our infrastructure. +## Dependency management +We use [Dependabot](https://github.com/opensafely-core/opencodelists/blob/main/.github/dependabot.yml) and an [automated update workflow](https://github.com/opensafely-core/opencodelists/blob/main/.github/workflows/update-python-dependencies.yml) to keep our dependencies up to date. + +Dependencies are managed with `uv`. + +### Overview + +See the [uv documentation](https://docs.astral.sh/uv/concepts/projects/dependencies) for details on usage. +Commands for adding, removing or modifying constraints of dependencies will automatically respect the +global timestamp cutoff specified in the `pyproject.toml`: +```toml +[tool.uv] +exclude-newer = "YYYY-MM-DDTHH:MM:SSZ" +``` +Changes to dependencies should be made via `uv` commands, or by modifying `pyproject.toml` directly, followed by +[locking and syncing](https://docs.astral.sh/uv/concepts/projects/sync/) via `uv` or `just` commands like +`just devenv` or `just update-dependencies`. You should not modify `uv.lock` manually. + +Note that `uv.lock` must be reproducible from `pyproject.toml`. Otherwise, `just check` and `just check-lockfile` will fail. +If either of these recipes fails with an error saying that the timestamps must match, you might have modified one file but not the other: + - If you modified `pyproject.toml`, you must update `uv.lock` via `uv lock` / `just update-dependencies` or similar. + - If you did not modify `pyproject.toml` but have changes in the `uv.lock` file, you should revert the changes to `uv.lock`, modify `pyproject.toml` as you require, then run `uv lock` to update the `uv.lock` file. + +The timestamp cutoff should usually be set to midnight UTC of a past date. +In general, the date is expected to be between 7 and 14 days ago as a result of automated weekly dependency updates. + +If you require a package version that is newer than the cutoff allows, you can either manually bump the global cutoff date or add a package-specific timestamp cutoff. Both options are described below. + +### Manually bumping the cutoff date +The cutoff timestamp can be modified to a more recent date either manually in the `pyproject.toml` or with `just bump-uv-cutoff `. +For example, to set the cutoff to today's date and upgrade all dependencies, run: +``` +just bump-uv-cutoff 0 +just update-dependencies +``` + +### Adding a package-specific timestamp cutoff +It is possible to specify a package-specific timestamp cutoff in addition to the global cutoff. +This should be done in the `pyproject.toml` to ensure reproducible installs; see the [uv documentation](https://docs.astral.sh/uv/reference/settings/#exclude-newer-package) for details. +If set, the package-specific cutoff will take precedence over the global cutoff regardless of which one is more recent. + +You should not set a package-specific cutoff that is older than the global cutoff - use a version constraint instead. +If there is good reason to set a package-specific cutoff that is more recent than the global cutoff, **care should be taken to ensure that the package-specific cutoff is manually removed once it is over 7 days old**, as otherwise future automated updates of that package will be indefinitely blocked. +Currently no automated tooling is in place to enforce removal of stale package-specific cutoffs. + ## Local development ### Prerequisites: