Bump pipeline version and add custom warning formatting

DEVELOPERS.md

@@ -15,6 +15,12 @@ The tool makes the process relatively painless. There are a few
 workarounds (crude string subsitutions) we need to apply which are all
 configured in [pyproject.toml](./pyproject.toml).
 
+To update vendored dependecies, run:
+
+```
+./scripts/update.sh
+```
+
 ## opensafely run
 
 Historically, this repo consumed [`job-runner`](https://github.com/opensafely-core/job-runner)

opensafely/__init__.py

@@ -3,6 +3,7 @@
 import os
 import sys
 import tempfile
+import warnings
 from datetime import datetime, timedelta
 from pathlib import Path
 
@@ -32,6 +33,26 @@
 VERSION_FILE = Path(tempfile.gettempdir()) / "opensafely-version-check"
 
 
+_original_formatwarning = warnings.formatwarning
+
+
+# format ProjectWarnings (warnings about project.yamls from the pipeline library)
+# to print only the message on the console
+def warning_message_only(
+    message,
+    category,
+    filename,
+    lineno,
+    line=None,
+):
+    if str(message).startswith("ProjectWarning"):
+        return f"{message}\n"
+    return _original_formatwarning(message, category, filename, lineno, line)
+
+
+warnings.formatwarning = warning_message_only
+
+
 def should_version_check():
     if not VERSION_FILE.exists():
         return True

opensafely/_vendor/pipeline/__init__.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from .constants import RUN_ALL_COMMAND
 from .exceptions import ProjectValidationError, YAMLError
 from .main import load_pipeline

opensafely/_vendor/pipeline/features.py

@@ -9,6 +9,8 @@
     "UNIQUE_OUTPUT_PATH": (2, None),
     "EXPECTATIONS_POPULATION": (3, 3),
     "REMOVE_SUPPORT_FOR_COHORT_EXTRACTOR": (4, None),
+    "REMOVE_SUPPORT_FOR_RUN_ALL_ACTION": (5, None),
+    "REMOVE_SUPPORT_FOR_LATEST_TAG": (5, None),
 }
 
 LATEST_VERSION = max([v[0] for v in FEATURE_FLAGS_BY_VERSION.values()])

opensafely/_vendor/pipeline/models.py

@@ -3,6 +3,7 @@
 import pathlib
 import re
 import shlex
+import warnings
 from collections import defaultdict
 from dataclasses import dataclass
 from typing import Any
@@ -17,6 +18,8 @@
     validate_glob_pattern,
     validate_no_kwargs,
     validate_not_cohort_extractor_action,
+    validate_not_latest_tag,
+    validate_not_run_all_action,
     validate_type,
 )
 
@@ -270,12 +273,20 @@ def build(
             raise ValidationError(
                 f"`version` must be a number between 1 and {LATEST_VERSION}"
             )
+        else:
+            if version != LATEST_VERSION:
+                warnings.warn(
+                    f"ProjectWarning: Your project file is using an old version ({version}); consider updating to version {LATEST_VERSION}",
+                    stacklevel=2,
+                )
+
         feat = get_feature_flags_for_version(version)
 
         validate_type(actions, dict, "Project `actions` section")
 
         _actions = dict()
         for action_id, action_config in actions.items():
+            validate_not_run_all_action(action_id, feat)
             validate_action_config(action_id, action_config)
             _actions[action_id] = Action.build(action_id, **action_config)
         actions = _actions
@@ -284,6 +295,10 @@ def build(
             for config in actions.values():
                 validate_not_cohort_extractor_action(config)
 
+        if feat.REMOVE_SUPPORT_FOR_LATEST_TAG:
+            for config in actions.values():
+                validate_not_latest_tag(config)
+
         seen: dict[Command, list[str]] = defaultdict(list)
         for name, config in actions.items():
             run = config.run
@@ -339,9 +354,10 @@ def all_actions(self) -> list[str]:
         """
         Get all actions for this Pipeline instance
 
-        We ignore any manually defined run_all action (in later project
-        versions this will be an error). We use a list comprehension rather
-        than set operators as previously so we preserve the original order.
+        Versions < 5 ignore any manually defined run_all action and raise a
+        warning (later project versions the raise an error).
+        We use a list comprehension rather than set operators as previously so we preserve
+        the original order.
         """
         return [action for action in self.actions.keys() if action != RUN_ALL_COMMAND]
 
@@ -355,7 +371,7 @@ def action_images(self) -> set[str]:
         images = set()
         for action in self.actions.values():
             # for hysterical raisins, :latest is actually mapped to v1, not v2 or later.
-            # We hope to fix this at some point
+            # version 5 removes use of :latest
             version = "v1" if action.run.version == "latest" else action.run.version
             images.add(f"{action.run.name}:{version}")
 

opensafely/_vendor/pipeline/validation.py

@@ -2,7 +2,9 @@
 
 import fnmatch
 import posixpath
+import warnings
 from pathlib import Path, PurePath, PurePosixPath, PureWindowsPath
+from types import SimpleNamespace
 from typing import TYPE_CHECKING, Any
 
 from .constants import LEVEL4_FILE_TYPES
@@ -97,6 +99,28 @@ def validate_not_cohort_extractor_action(action: Action) -> None:
         )
 
 
+def validate_not_run_all_action(action_id: str, feat: SimpleNamespace) -> None:
+    if action_id != "run_all":
+        return
+    if feat.REMOVE_SUPPORT_FOR_RUN_ALL_ACTION:
+        raise ValidationError(
+            "`run_all` is a reserved action name and is not allowed for user-defined actions."
+        )
+    else:
+        warnings.warn(
+            "ProjectWarning: `run_all` is a reserved action name; user-defined actions with this name "
+            "are ignored and will raise an error in later versions.",
+            stacklevel=3,
+        )
+
+
+def validate_not_latest_tag(action: Action) -> None:
+    if action.run.parts[0].endswith(":latest"):
+        raise ValidationError(
+            f"Action {action.action_id} uses `{action.run.parts[0]}`, which is not supported. Provide a version e.g. `:v2` instead"
+        )
+
+
 def validate_cohortextractor_outputs(action_id: str, action: Action) -> None:
     """
     Check cohortextractor's output config is valid for this command

pyproject.toml

@@ -158,3 +158,10 @@ target-version = "py38"
 [tool.ruff.isort]
 lines-after-imports = 2
 known-third-party = ["opensafely._vendor"]
+
+[tool.pytest.ini_options]
+markers = ["functional: mark as a functional test."]
+filterwarnings = [
+    "ignore:ProjectWarning:UserWarning:opensafely._vendor.pipeline.*:",
+    "ignore:ProjectWarning:UserWarning:tests.*:",
+]

requirements.prod.in

@@ -1,4 +1,4 @@
-opensafely-pipeline@https://github.com/opensafely-core/pipeline/archive/refs/tags/v2026.01.26.163426.zip
+opensafely-pipeline@https://github.com/opensafely-core/pipeline/archive/refs/tags/v2026.03.12.140752.zip
 ruyaml
 requests
 opentelemetry-api==1.33.1

requirements.prod.txt

@@ -16,7 +16,7 @@ idna==3.10
     # via requests
 importlib-metadata==8.5.0
     # via opentelemetry-api
-opensafely-pipeline @ https://github.com/opensafely-core/pipeline/archive/refs/tags/v2026.01.26.163426.zip
+opensafely-pipeline @ https://github.com/opensafely-core/pipeline/archive/refs/tags/v2026.03.12.140752.zip
     # via -r requirements.prod.in
 opentelemetry-api==1.33.1
     # via -r requirements.prod.in

tests/test_init.py

@@ -1,6 +1,9 @@
 import os
+import warnings
 from datetime import datetime, timedelta
 
+import pytest
+
 import opensafely
 from tests.test_pull import expect_local_images
 
@@ -52,3 +55,29 @@ def test_warn_if_updates_needed_images_outdated(capsys, monkeypatch, tmp_path, r
         "    opensafely pull",
         "",
     ]
+
+
+def test_warnings_format():
+    with pytest.warns(UserWarning) as raised_warnings:
+        warnings.warn("Warning: foo", UserWarning)
+        warnings.warn("ProjectWarning: foo", UserWarning)
+
+    assert len(raised_warnings.list) == 2
+    standard_warning, project_warning = raised_warnings.list
+
+    # standard warning includes the warning category (and other standard warning formatting)
+    assert "UserWarning: Warning: foo" in warnings.formatwarning(
+        standard_warning.message,
+        standard_warning.category,
+        standard_warning.filename,
+        standard_warning.lineno,
+        standard_warning.line,
+    )
+    # project warning contains just the warning message
+    assert "ProjectWarning: foo\n" == warnings.formatwarning(
+        project_warning.message,
+        project_warning.category,
+        project_warning.filename,
+        project_warning.lineno,
+        project_warning.line,
+    )