Raise the bngsim floor to 0.15.0, and make CI install what the project declares

.github/actions/setup-pybnf/action.yml

@@ -113,10 +113,17 @@ runs:
         # capability that needs a companion PyPI package (antimony>=3.1.1, pure
         # python wheel), and it is what unskips the bngsim_antimony-marked
         # tests, so install the extra rather than bare bngsim. Keep the pin in
-        # sync with pyproject.toml.
+        # sync with pyproject.toml -- and note that asking is no longer the only
+        # thing holding it there. This pin was set to 0.11.35 on 2026-07-24, when
+        # that was also pyproject's floor. pyproject then moved to 0.12.0 and to
+        # 0.12.2, on 2026-08-02 and 2026-08-04, and this line did not follow, so
+        # for three weeks CI tested against a bngsim older than PyBNF declared it
+        # needed and nothing said so. tests/test_packaging_metadata.py::
+        # test_ci_action_installs_every_dependency_pyproject_declares now reads
+        # both files and fails when they disagree.
         BNGSIM_SPEC=()
         if [ "$BNGSIM" = 'true' ]; then
-          BNGSIM_SPEC=('bngsim[antimony]>=0.11.35,<1')
+          BNGSIM_SPEC=('bngsim[antimony]>=0.15.0,<1')
         fi
         # The optional pybnf[jax] extra (jax + jaxlib + blackjax) -- the ADR-0059
         # HMC reference sampler and the jax-gated gradient-assembly tests. Heavy
@@ -145,6 +152,8 @@ runs:
         # heavy jax stack is instead gated behind the `jax` input above. Keep ALL
         # of these version bounds in sync with pyproject.toml's [tests] extra --
         # anything declared there but missing here silently reverts to a skip.
+        # tests/test_packaging_metadata.py checks that, for every requirement in
+        # this file and in pyproject.toml, both name the same version range.
         uv pip install \
           "${BNGSIM_SPEC[@]}" \
           "${JAX_SPEC[@]}" \

pybnf/_bngsim_caps.py

@@ -199,11 +199,17 @@ def _empty_capabilities():
 # So the flag resolves through three routes, first match wins, and each is
 # reported by :func:`event_sens_probe` so a refusal can say how it decided:
 #
-# 1. ``features['event_sensitivities']`` -- a dedicated key. bngsim publishes no
-#    such key today; naming it here costs nothing and means the flag starts
-#    reading the real answer, in BOTH directions, on the first build that grows
-#    one. That is #558's ask 1, and it is why this route is checked first even
-#    though it never fires yet.
+# 1. ``features['event_sensitivities']`` -- a dedicated key, and since lanl/bngsim#431
+#    a real one. It was named here before it existed, on the reasoning that doing so
+#    cost nothing and would start the flag reading the real answer, in BOTH directions,
+#    on the first build that grew one. bngsim 0.15.0 is that build, and the floor is now
+#    0.15.0, so this route fires for every install resolved from PyPI. It publishes the
+#    key on every build, so a ``False`` here is an answer rather than a silence.
+#
+#    Routes 2 and 3 are not dead. A floor binds what a resolver installs, not what a
+#    build claims, and a bngsim built from source between the version bump and the fixes
+#    declares a number it does not carry -- which is the whole of why ADR-0119 stopped
+#    reading version strings. Those routes are what such a build falls through to.
 #
 # 2. ``features['effective_ic_sensitivity']`` -- a WITNESS. This key is not the
 #    capability; it reports ``Model.effective_ic_sensitivity``, the dx(0)/dtheta

pyproject.toml

@@ -32,7 +32,7 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 dependencies = [
-    "bngsim>=0.12.2,<1",
+    "bngsim>=0.15.0,<1",
     "dask>=2024.1.0",
     "distributed>=2024.1.0",
     "libroadrunner>=1.6.0",
@@ -47,7 +47,7 @@ dependencies = [
 
 [project.optional-dependencies]
 antimony = [
-    "bngsim[antimony]>=0.12.2,<1",
+    "bngsim[antimony]>=0.15.0,<1",
 ]
 # The PEtab math translator (pybnf.petab.formula, ADR-0035): an expression
 # observableFormula is parsed/serialized through petab's sympy-backed math grammar

tests/test_gradient_sens_fallback.py

@@ -481,11 +481,12 @@ def test_a_declined_model_is_reported_identically_cold_and_warm(tmp_path,
     came back empty.
 
     The verdict is the half ADR-0121 pins, and it must not depend on the cache. The
-    reason is prose, and the pin ``bngsim>=0.12.2,<1`` admits builds on both sides of a
-    recent upstream change: a build from before it generates no source on a warm cache
-    and so replays no reason, while a build that carries the note beside the cached
-    artifact replays the reason a cold build gave, in the same words. Both are fine
-    here, and a replayed reason is strictly more useful than silence.
+    reason is prose, and it used to be allowed to go missing: the pin ``bngsim>=0.12.2,<1``
+    admitted builds on both sides of the upstream change that writes the reason into a note
+    beside the cached artifact, so a warm cache could legitimately say nothing. The floor is
+    now ``bngsim>=0.15.0,<1``, which is the release that carries the note, so silence is no
+    longer one of the answers and the warm reason is asserted word for word against the cold
+    one.
     """
     cold = _sbml_model(tmp_path, _DECLINED_LAW, 'declined').analytic_sens_rhs_status()
     assert cold.analytic is False
@@ -502,8 +503,9 @@ def test_a_declined_model_is_reported_identically_cold_and_warm(tmp_path,
     bngsim_sbml_model._ENGINE_TEMPLATE_WARM_ATTEMPTED.clear()
     warm = _sbml_model(tmp_path, _DECLINED_LAW, 'declined2').analytic_sens_rhs_status()
     assert warm.analytic is False, 'the verdict must not depend on the codegen cache'
-    assert warm.reasons in ([], cold.reasons), (
-        'a warm cache either says nothing or replays the cold reason word for word')
+    assert warm.reasons == cold.reasons, (
+        'the floor guarantees the note beside the cached artifact, so a warm cache must '
+        'replay the cold reason word for word rather than fall silent')
 
 
 # --- the config surface ------------------------------------------------------- #

tests/test_packaging_metadata.py

@@ -1,24 +1,187 @@
 import fnmatch
 import os
+import re
 import subprocess
 import sys
 import textwrap
 import tomllib
 from pathlib import Path
 
 
+REPO_ROOT = Path(__file__).resolve().parents[1]
+CI_ACTION = REPO_ROOT / '.github' / 'actions' / 'setup-pybnf' / 'action.yml'
+
+
 def test_project_metadata_declares_python_floor_and_bngsim_dependency():
-    pyproject_path = Path(__file__).resolve().parents[1] / 'pyproject.toml'
+    pyproject_path = REPO_ROOT / 'pyproject.toml'
     metadata = tomllib.loads(pyproject_path.read_text())
     project = metadata['project']
 
     assert project['requires-python'] == '>=3.11'
-    # bngsim >= 0.12.0: parameter_scan/bifurcate carry the equilibration's dx/dθ into the scan
-    # (lanl/bngsim#81) and resolve an on_point hook's own ∂x(0)/∂θ (lanl/bngsim#111), which make
-    # a scored PRE-EQUILIBRATED dose-response scan differentiable (#532). (0.11.35 added the
-    # steady-state SteadyStateResult.output_sensitivities of lanl/bngsim#12 for #478; 0.11.34 the
-    # native carried-state parameter_scan/bifurcate + named saved states of lanl/bngsim#11 for #474.)
-    assert 'bngsim>=0.12.2,<1' in project['dependencies']
+    # bngsim >= 0.15.0 is bought by a CONTRACT, not by a feature PyBNF wants. lanl/bngsim#431
+    # publishes `event_sensitivities` as a real capabilities() feature key. Until it existed
+    # PyBNF read `effective_ic_sensitivity` as a WITNESS for the same thing (ADR-0119), which
+    # was sound only because lanl/bngsim#155 happened to land a few commits after the event
+    # fixes -- a fact about commit ordering that stops being evidence the moment the two are
+    # decoupled, silently. Guessing wrong here is not symmetric: a build without those fixes
+    # does not refuse, it returns a finite gradient with a term missing, so the fit converges
+    # and reports a plausible number. 0.15.0 is the first release where PyBNF asks the real
+    # question. It also carries the codegen-cache decline reason PyBNF reads (#647), and, on
+    # the refusal side, a RuleMonkey re-vendor that declines a TotalRate rule where RuleMonkey
+    # and NFsim genuinely disagree rather than picking a reading.
+    # (0.12.2/0.12.0 bought the carried-state parameter_scan/bifurcate sensitivities of
+    # lanl/bngsim#81 and #111 for #532; 0.11.35 the steady-state
+    # SteadyStateResult.output_sensitivities of lanl/bngsim#12 for #478; 0.11.34 the native
+    # carried-state parameter_scan + named saved states of lanl/bngsim#11 for #474.)
+    assert 'bngsim>=0.15.0,<1' in project['dependencies']
+
+
+def _canonical_name(name):
+    """PEP 503 normalization, so `pytest-xdist` and `pytest_xdist` are one name."""
+    return re.sub(r'[-_.]+', '-', name).lower()
+
+
+_REQUIREMENT = re.compile(
+    r'^([A-Za-z][A-Za-z0-9._-]*)'   # distribution name
+    r'(?:\[[^\]]*\])?'             # extras, which the two files are allowed to differ on
+    r'\s*(.*)$'                     # the version specifier, or nothing at all
+)
+
+
+def _split_requirement(text):
+    """``'bngsim[antimony]>=0.15.0,<1'`` -> ``('bngsim', '>=0.15.0,<1')``.
+
+    Extras are dropped on purpose: the CI action installs ``bngsim[antimony]`` where
+    pyproject's runtime list declares bare ``bngsim``, and that difference is deliberate
+    (the extra is what unskips the bngsim_antimony-marked tests). The version range is
+    the part that has to agree. Returns None for a string that is not a requirement.
+    """
+    match = _REQUIREMENT.match(text.strip())
+    if match is None:
+        return None
+    name, specifier = match.groups()
+    return _canonical_name(name), specifier.replace(' ', '')
+
+
+def _requirements_quoted_in(text):
+    """Every single-quoted requirement in a YAML file, keyed by distribution name.
+
+    The CI action is a shell script embedded in YAML, so its requirements are ordinary
+    single-quoted shell words -- in the `uv pip install` argument list, in the BNGSIM_SPEC
+    and JAX_SPEC arrays, and in the `petab-spec` input's default. Quotes are matched
+    within a single line and comment lines are dropped, because the surrounding YAML prose
+    is full of apostrophes ("pyproject.toml's", "the action's") that otherwise pair up with
+    each other and swallow the real strings.
+    """
+    found = {}
+    for line in text.splitlines():
+        if line.lstrip().startswith('#'):
+            continue
+        for quoted in re.findall(r"'([^'\n]*)'", line):
+            parsed = _split_requirement(quoted)
+            if parsed is not None:
+                found.setdefault(parsed[0], parsed[1])
+    return found
+
+
+def test_ci_action_installs_every_dependency_pyproject_declares():
+    """The CI action and pyproject.toml must name the same version range for every package.
+
+    The action does not install PyBNF's dependencies by resolving pyproject.toml. It
+    installs a hand-written list that mirrors it, because a `bngsim: false` leg has to be
+    able to leave bngsim out and a re-resolve would pull it back in. Two hand-maintained
+    copies of one list drift, and this one did: the action pinned `bngsim>=0.11.35` while
+    pyproject declared `bngsim>=0.12.2`. The two were set to the same number on 2026-07-24;
+    pyproject moved twice over the following fortnight and the action never followed, so for
+    three weeks continuous integration tested against a bngsim older than the project said
+    it required. Nothing caught it. Both files carried a comment asking a human to keep them
+    in sync, which is what a comment can do.
+
+    The failure is quiet in both directions. Too low a floor means CI passes on a build the
+    published wheel will not accept. A package declared in pyproject's [tests] extra but
+    absent from the action does not fail a job either -- the suite that needs it
+    `importorskip`s and reports as skipped.
+    """
+    metadata = tomllib.loads((REPO_ROOT / 'pyproject.toml').read_text())
+    declared = {}
+    for requirement in (
+        metadata['project']['dependencies']
+        + metadata['project']['optional-dependencies']['tests']
+    ):
+        name, specifier = _split_requirement(requirement)
+        declared[name] = specifier
+
+    installed = _requirements_quoted_in(CI_ACTION.read_text())
+
+    missing = sorted(name for name in declared if name not in installed)
+    assert not missing, (
+        'pyproject.toml declares these but %s never installs them, so the tests that '
+        'need them skip in CI instead of failing: %s' % (CI_ACTION.name, ', '.join(missing))
+    )
+
+    drifted = {
+        name: (declared[name], installed[name])
+        for name in declared
+        if declared[name] != installed[name]
+    }
+    assert not drifted, (
+        'the CI action and pyproject.toml disagree about a version range '
+        '(name: pyproject wants, action installs): %s' % drifted
+    )
+
+
+def test_the_version_is_the_same_everywhere_it_is_written_down():
+    """One release version, written by hand into four files, must agree in all of them.
+
+    pyproject.toml does not carry the number: it declares `dynamic = ["version"]` and reads
+    `pybnf.__version__`, which makes `pybnf/__init__.py` the source of truth and the built
+    wheel correct by construction. The other three are separate copies that a release has to
+    remember to bump, and nothing has been checking them. A stale `CITATION.cff` tells anyone
+    citing PyBNF the wrong version, and a stale `docs/conf.py` labels the published
+    documentation with the previous release.
+
+    The changelog is checked in the same breath because it is the same ritual and the same
+    mistake. `[Unreleased]` is promoted to a dated heading at release time, so the newest
+    versioned heading is the released version at every commit -- both before a release, when
+    the promotion has not happened and neither has the bump, and after it, when both have.
+    Bumping one without the other is what this catches.
+    """
+    init_text = (REPO_ROOT / 'pybnf' / '__init__.py').read_text()
+    match = re.search(r'^__version__ = [\'"]([^\'"]+)[\'"]', init_text, re.MULTILINE)
+    assert match is not None, 'pybnf/__init__.py does not define __version__'
+    version = match.group(1)
+
+    # The mechanism that makes __init__.py authoritative. If this ever changes, the rest of
+    # this test is checking copies against something that is no longer the original.
+    metadata = tomllib.loads((REPO_ROOT / 'pyproject.toml').read_text())
+    assert 'version' in metadata['project']['dynamic']
+    assert metadata['tool']['setuptools']['dynamic']['version'] == {
+        'attr': 'pybnf.__version__'
+    }
+
+    citation = (REPO_ROOT / 'CITATION.cff').read_text()
+    assert re.search(r'^version: %s$' % re.escape(version), citation, re.MULTILINE), (
+        "CITATION.cff does not say version %s -- anyone citing PyBNF gets the wrong "
+        'release' % version
+    )
+
+    conf = (REPO_ROOT / 'docs' / 'conf.py').read_text()
+    assert re.search(r"^version = '%s'$" % re.escape(version), conf, re.MULTILINE), (
+        "docs/conf.py's `version` is not %s" % version
+    )
+    # `release` carries a leading v; `version` does not. Both are bumped by hand.
+    assert re.search(r"^release = 'v%s'$" % re.escape(version), conf, re.MULTILINE), (
+        "docs/conf.py's `release` is not v%s" % version
+    )
+
+    changelog = (REPO_ROOT / 'CHANGELOG.md').read_text()
+    headings = re.findall(r'^## \[v?([^\]]+)\]', changelog, re.MULTILINE)
+    released = [h for h in headings if h != 'Unreleased']
+    assert released, 'CHANGELOG.md has no released version heading'
+    assert released[0] == version, (
+        "CHANGELOG.md's newest released heading is %s but __version__ is %s -- one of the "
+        'two was bumped without the other' % (released[0], version)
+    )
 
 
 def test_every_pybnf_subpackage_is_shipped():

tests/test_sbml_solver_tolerances.py

@@ -925,8 +925,12 @@ def test_the_backend_default_atol_is_what_corrupted_those_sensitivities(tmp_path
     simply less catastrophic than it was.
 
     So each threshold now sits a decade under the *worse* of the two measurements -- the
-    rule the two-scale test above states -- and both hold across the declared
-    ``bngsim>=0.12.2,<1`` range rather than on the one release that drew them.
+    rule the two-scale test above states -- rather than on the one release that drew them.
+    The declared range is now ``bngsim>=0.15.0,<1``, which puts both of those measurements
+    below the floor. That leaves the guard conservative rather than stale: raising the floor
+    removed the worse end of the pair, and a threshold set a decade under the worse end is
+    still under the better one. It has not been re-derived on 0.15.0, and it does not need
+    to be until a release moves the numbers back up.
     """
     model = _piecewise_model(tmp_path, atol=_BNGSIM_DEFAULT_ATOL)
     model.enable_output_sensitivities(params=['k0', 'k1', 'k2'])