physverify 0.5.0__tar.gz → 0.5.1__tar.gz

{physverify-0.5.0/src/physverify.egg-info → physverify-0.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: physverify
-Version: 0.5.0
+Version: 0.5.1
 Summary: Verification checks for physics simulation code: manufactured solutions, order-of-accuracy studies and a seeded-bug benchmark.
 Author: Ram Chandra Giri
 License-Expression: MIT
@@ -45,7 +45,7 @@ Dynamic: license-file
 
 **Checks that a simulation solves the equations it claims, at the order of accuracy it claims, not just that it runs.**
 
-physverify is actively evolving (v0.5.0), welcoming contributions and test cases from the computational physics community. Scope: numerical solutions of ODEs and PDEs (time integration, convergence, conservation), plus a few Monte Carlo checks. It needs only NumPy.
+physverify is actively evolving (v0.5.1), welcoming contributions and test cases from the computational physics community. Scope: numerical solutions of ODEs and PDEs (time integration, convergence, conservation), plus a few Monte Carlo checks. It needs only NumPy.
 
 ![The check loop: your solver and an independent description of the physics go in; physverify runs the solver at several resolutions, measures the error and reports a verdict with a reason](https://raw.githubusercontent.com/rcgiri-physics/physverify/main/docs/images/check-loop.svg)
 
@@ -72,7 +72,7 @@ New to this? [Start here](https://rcgiri-physics.github.io/physverify/start-here
 A failed check fails the job, like a broken unit test ([CI guide](https://rcgiri-physics.github.io/physverify/ci/): options, pre-commit, pytest):
 
 ```yaml
-      - uses: rcgiri-physics/physverify@v0.5.0
+      - uses: rcgiri-physics/physverify@v0.5.1
         with:
           specs: tests/verify_*.py
 ```
@@ -90,3 +90,5 @@ Works best for ODEs; PDEs only in 1D so far. Your code needs a way to add a sour
 ## Contributing, citing, licence
 
 Help is welcome: a trial report on your own solver, seeded bugs written by someone other than the author, adapters, documentation. See [CONTRIBUTING.md](https://github.com/rcgiri-physics/physverify/blob/main/CONTRIBUTING.md), the [code of conduct](https://github.com/rcgiri-physics/physverify/blob/main/CODE_OF_CONDUCT.md), [SUPPORT.md](https://github.com/rcgiri-physics/physverify/blob/main/SUPPORT.md) for help, [SECURITY.md](https://github.com/rcgiri-physics/physverify/blob/main/SECURITY.md) on running untrusted code, and [AGENTS.md](https://github.com/rcgiri-physics/physverify/blob/main/AGENTS.md) for AI assistants. To cite, use [doi:10.5281/zenodo.23534512](https://doi.org/10.5281/zenodo.23534512) or [CITATION.cff](https://github.com/rcgiri-physics/physverify/blob/main/CITATION.cff). Changes: [CHANGELOG.md](https://github.com/rcgiri-physics/physverify/blob/main/CHANGELOG.md); plans: [ROADMAP.md](https://github.com/rcgiri-physics/physverify/blob/main/ROADMAP.md). MIT licence, copyright (c) 2026 Ram Chandra Giri.
+
+<!-- mcp-name: io.github.rcgiri-physics/physverify -->

{physverify-0.5.0 → physverify-0.5.1}/README.md

@@ -4,7 +4,7 @@
 
 **Checks that a simulation solves the equations it claims, at the order of accuracy it claims, not just that it runs.**
 
-physverify is actively evolving (v0.5.0), welcoming contributions and test cases from the computational physics community. Scope: numerical solutions of ODEs and PDEs (time integration, convergence, conservation), plus a few Monte Carlo checks. It needs only NumPy.
+physverify is actively evolving (v0.5.1), welcoming contributions and test cases from the computational physics community. Scope: numerical solutions of ODEs and PDEs (time integration, convergence, conservation), plus a few Monte Carlo checks. It needs only NumPy.
 
 ![The check loop: your solver and an independent description of the physics go in; physverify runs the solver at several resolutions, measures the error and reports a verdict with a reason](https://raw.githubusercontent.com/rcgiri-physics/physverify/main/docs/images/check-loop.svg)
 
@@ -31,7 +31,7 @@ New to this? [Start here](https://rcgiri-physics.github.io/physverify/start-here
 A failed check fails the job, like a broken unit test ([CI guide](https://rcgiri-physics.github.io/physverify/ci/): options, pre-commit, pytest):
 
 ```yaml
-      - uses: rcgiri-physics/physverify@v0.5.0
+      - uses: rcgiri-physics/physverify@v0.5.1
         with:
           specs: tests/verify_*.py
 ```
@@ -49,3 +49,5 @@ Works best for ODEs; PDEs only in 1D so far. Your code needs a way to add a sour
 ## Contributing, citing, licence
 
 Help is welcome: a trial report on your own solver, seeded bugs written by someone other than the author, adapters, documentation. See [CONTRIBUTING.md](https://github.com/rcgiri-physics/physverify/blob/main/CONTRIBUTING.md), the [code of conduct](https://github.com/rcgiri-physics/physverify/blob/main/CODE_OF_CONDUCT.md), [SUPPORT.md](https://github.com/rcgiri-physics/physverify/blob/main/SUPPORT.md) for help, [SECURITY.md](https://github.com/rcgiri-physics/physverify/blob/main/SECURITY.md) on running untrusted code, and [AGENTS.md](https://github.com/rcgiri-physics/physverify/blob/main/AGENTS.md) for AI assistants. To cite, use [doi:10.5281/zenodo.23534512](https://doi.org/10.5281/zenodo.23534512) or [CITATION.cff](https://github.com/rcgiri-physics/physverify/blob/main/CITATION.cff). Changes: [CHANGELOG.md](https://github.com/rcgiri-physics/physverify/blob/main/CHANGELOG.md); plans: [ROADMAP.md](https://github.com/rcgiri-physics/physverify/blob/main/ROADMAP.md). MIT licence, copyright (c) 2026 Ram Chandra Giri.
+
+<!-- mcp-name: io.github.rcgiri-physics/physverify -->

{physverify-0.5.0 → physverify-0.5.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "physverify"
-version = "0.5.0"
+version = "0.5.1"
 description = "Verification checks for physics simulation code: manufactured solutions, order-of-accuracy studies and a seeded-bug benchmark."
 readme = "README.md"
 requires-python = ">=3.10"

{physverify-0.5.0 → physverify-0.5.1}/src/physverify/__init__.py

@@ -6,7 +6,7 @@ from .order import check_order, fit_order, pairwise_orders
 from .order import check_exact
 from .studies import invariant_study, ode_checks, patch_study, reference_study
 
-__version__ = "0.5.0"
+__version__ = "0.5.1"
 
 __all__ = [
     "Check",

{physverify-0.5.0 → physverify-0.5.1}/src/physverify/agent.py

@@ -55,7 +55,9 @@ def find_specs(root: Path) -> list[Path]:
         except Exception:
             config = {}
         if config.get("specs"):
-            return [(root / s).resolve() for s in config["specs"]]
+            # Entries that leave the root are dropped (GCVE-110-VULN-PYPI-2026-000391).
+            inside = root.resolve()
+            return [p for p in ((root / s).resolve() for s in config["specs"]) if p.is_relative_to(inside)]
     specs = []
     for path in sorted(root.rglob("verify_*.py")):
         parts = path.relative_to(root).parts[:-1]
@@ -111,8 +113,12 @@ def hook_main(stdin=None, stderr=None) -> int:
     edited = tool_input.get("file_path") or tool_input.get("notebook_path") or ""
     if edited and not edited.endswith(".py"):
         return 0
-    cwd = Path(event.get("cwd") or ".")
+    cwd = Path(event.get("cwd") or ".").resolve()
+    if edited and not Path(edited).resolve().is_relative_to(cwd):
+        return 0  # an edit outside the session folder must not run that folder's code (GCVE-110-VULN-PYPI-2026-000391)
     root = find_project_root(Path(edited).parent if edited else cwd)
+    if not root.is_relative_to(cwd):
+        root = cwd  # never climb above the session folder
     specs = find_specs(root)
     if not specs:
         return 0

{physverify-0.5.0 → physverify-0.5.1}/src/physverify/constants.py

@@ -32,11 +32,13 @@ KNOWN = {
     "e (charge)": ((1.602176634e-19,), "C", "exact: 1.602176634e-19"),
     "m_e": ((9.1093837015e-31, 9.1093837139e-31), "kg", "CODATA 2018: 9.1093837015e-31, 2022: 9.1093837139e-31"),
     "m_p": ((1.67262192369e-27, 1.67262192595e-27), "kg", "CODATA 2018: 1.67262192369e-27, 2022: 1.67262192595e-27"),
+    "m_n": ((1.67492749804e-27, 1.67492750056e-27), "kg", "CODATA 2018: 1.67492749804e-27, 2022: 1.67492750056e-27"),
+    "atomic mass unit": ((1.66053906660e-27, 1.66053906892e-27), "kg", "CODATA 2018: 1.66053906660e-27, 2022: 1.66053906892e-27"),
     "epsilon_0": ((8.8541878128e-12,), "F/m", "8.8541878128e-12"),
     "T_c (2D Ising)": ((2 / math.log(1 + math.sqrt(2)),), "J/k_B", "2 / ln(1 + sqrt 2) = 2.269185314"),
     # exact by definition (SI 2019, IAU 2012, international units)
     "N_A": ((6.02214076e23,), "1/mol", "exact: 6.02214076e23"),
-    "R (gas constant)": ((8.314462618,), "J/(mol K)", "N_A k_B = 8.314462618..."),
+    "R (gas constant)": ((8.31446261815324,), "J/(mol K)", "exact: N_A k_B = 8.31446261815324"),
     "sigma (Stefan-Boltzmann)": ((5.670374419e-8,), "W m^-2 K^-4", "5.670374419e-8"),
     "astronomical unit": ((149597870700.0, 149597870.7, 1.495978707e13), "m, km or cm", "exact: 149597870700 m (IAU 2012)"),
     "light year": ((9460730472580800.0,), "m", "exact: 9460730472580800 m (Julian year)"),

{physverify-0.5.0 → physverify-0.5.1}/src/physverify/lint.py

@@ -129,6 +129,10 @@ def _annotation_nodes(tree) -> set[int]:
     return {id(m) for r in roots for m in ast.walk(r)}
 
 
+# a file with this many undefined names, none of them a usual module alias, is treated as getting them at run time
+_INJECTED_MIN = 6
+_COMMON_ALIASES = {"np", "plt", "pd", "sp", "scipy", "numpy", "math", "os", "sys", "re", "json", "time", "random",
+                   "torch", "jnp", "jax", "tf", "mpl", "sns", "nx", "integrate", "interpolate", "optimize", "linalg"}
 _NOQA = re.compile(r"#\s*noqa(?::[^#]*\bF821\b|\s*$|\s*#)", re.I)
 
 
@@ -155,6 +159,14 @@ def scan_names(path: Path, tree, rel: str, source: str = "") -> list[Finding]:
             continue  # annotations are not evaluated with `from __future__ import annotations` (or from Python 3.14)
         unknown.setdefault(n.id, []).append(n.lineno)
     out = []
+    if len(unknown) >= _INJECTED_MIN and not unknown.keys() & _COMMON_ALIASES:
+        # many names and none of them a forgotten import: the file most likely gets them at run time
+        # (a host program such as SpaceClaim, or a library that defines names in the caller's namespace)
+        first = min(lines[0] for lines in unknown.values())
+        shown = ", ".join(sorted(unknown)[:8]) + (", ..." if len(unknown) > 8 else "")
+        return [Finding("names", NOTE, rel, first,
+                        f"{len(unknown)} names are used but never defined or imported ({shown}); so many usually means they"
+                        " are provided at run time by a host program or a library, so they are not reported one by one")]
     for name, lines in sorted(unknown.items(), key=lambda kv: kv[1][0]):
         close = [k for k in known if k != name and len(k) > 2 and _one_edit(name, k)]
         hint = f" (did you mean {close[0]}?)" if close else ""
@@ -225,7 +237,8 @@ _SCIPY = {
                         "cumtrapz": "scipy.integrate.cumulative_trapezoid", "romb": None},
     "scipy.misc": {"*": "scipy.datasets, scipy.special or numpy (scipy.misc was removed)"},
 }
-_PY_REMOVED = {"imp": "importlib (removed in Python 3.12)", "distutils": "setuptools or sysconfig (removed in Python 3.12)",
+_SHIMMED = {"distutils"}  # still importable wherever setuptools is installed, so only a NOTE
+_PY_REMOVED = {"imp": "importlib (removed in Python 3.12)", "distutils": "setuptools or sysconfig (removed from the standard library in Python 3.12; setuptools still provides it)",
                "asynchat": "asyncio (removed in Python 3.12)", "asyncore": "asyncio (removed in Python 3.12)",
                "smtpd": "aiosmtpd (removed in Python 3.12)"}
 
@@ -281,12 +294,14 @@ def scan_api(path: Path, tree, rel: str) -> list[Finding]:
                             out.append(Finding("api", WARN, rel, n.lineno, f"{n.module}.{a.name} has been removed from SciPy"
                                                                            + (f"; use {new}" if new else "")))
             if n.module.split(".")[0] in _PY_REMOVED:
-                out.append(Finding("api", WARN, rel, n.lineno, f"{n.module}: use {_PY_REMOVED[n.module.split('.')[0]]}"))
+                top = n.module.split(".")[0]
+                out.append(Finding("api", NOTE if top in _SHIMMED else WARN, rel, n.lineno, f"{n.module}: use {_PY_REMOVED[top]}"))
         if isinstance(n, ast.Import):
             for a in n.names:
                 top = a.name.split(".")[0]
                 if top in _PY_REMOVED:
-                    out.append(Finding("api", WARN, rel, n.lineno, f"import {a.name}: use {_PY_REMOVED[top]}"))
+                    out.append(Finding("api", NOTE if top in _SHIMMED else WARN, rel, n.lineno,
+                                       f"import {a.name}: use {_PY_REMOVED[top]}"))
                 if a.name == "scipy.misc":
                     out.append(Finding("api", WARN, rel, n.lineno, "scipy.misc has been removed from SciPy"))
         if isinstance(n, ast.Attribute) and n.attr in ("simps", "cumtrapz") and isinstance(n.value, ast.Attribute) \

{physverify-0.5.0 → physverify-0.5.1}/src/physverify/scan.py

@@ -26,7 +26,7 @@ import ast
 import math
 import re
 import warnings
-from dataclasses import asdict, dataclass
+from dataclasses import asdict, dataclass, field
 from fractions import Fraction
 from pathlib import Path
 
@@ -42,6 +42,7 @@ class Finding:
     path: str
     line: int
     message: str
+    table: dict | None = field(default=None, repr=False)  # the Runge-Kutta table a "tables" finding was made from
 
     def __str__(self):
         return f"{self.level} {self.stage:9s} {self.path}:{self.line}: {self.message}"
@@ -364,7 +365,14 @@ def _check_table(lits, name, doc, stem, stated, rel, *, kind="table", stated_emb
                         msgs.append(f"embedded weights {en} have order {pe}, but order {stated_embedded} is stated")
                     else:
                         msgs.append(f"embedded weights {en} have order {pe}")
-        found.append(Finding("tables", level, rel, line, f"{where}: " + "; ".join(msgs)))
+        table = {"name": name, "kind": kind, "A": A, "b": b, "c": lits[cn][0] if cn is not None else None,
+                 "claimed": claimed if claimed is not None and claimed <= 6 else None, "claim_source": why,
+                 "stated_embedded": stated_embedded,
+                 "embedded": {en: e for en, (e, _l) in lits.items() if _BHAT_NAMES.match(en) and _vector(e, s) and en != bn},
+                 "error_weights": {en: e for en, (e, _l) in lits.items()
+                                   if (_E_NAMES.match(en) or en == "<e>") and _vector(e, s) and en != bn},
+                 "order": p}
+        found.append(Finding("tables", level, rel, line, f"{where}: " + "; ".join(msgs), table))
     return found
 
 
@@ -745,7 +753,11 @@ def scan_code_tables(path: Path, tree, rel: str) -> list[Finding]:
                 msgs.append(f"but '{why}' suggests order {claimed} (largest residual {worst:.1e})")
             else:
                 msgs.append(f"consistent with '{why}'")
-        found.append(Finding("tables", level, rel, line, f"{fn.name}: " + "; ".join(msgs)))
+        table = {"name": fn.name, "kind": "stages written as code", "A": A, "b": b, "c": c,
+                 "claimed": claimed if claimed is not None and claimed <= 6 else None, "claim_source": why,
+                 "stated_embedded": None, "embedded": {}, "error_weights": {}, "order": p,
+                 "docstring_table": {"A": drawn[0], "b": drawn[1]} if drawn is not None and len(drawn[1]) == s else None}
+        found.append(Finding("tables", level, rel, line, f"{fn.name}: " + "; ".join(msgs), table))
     return found
 
 
@@ -850,6 +862,7 @@ def _own_grids_and_divs(scope):
     nodes = list(_own_nodes(scope))
     # a division used as the step of a slice (np.mgrid[a:b:(b-a)/n], arange-style) builds its own grid
     steps = {id(n.step) for n in nodes if isinstance(n, ast.Slice) and n.step is not None}
+    periodic = []  # linspace(a, b, M, endpoint=False): its spacing really is (b - a) / M
     for node in nodes:
         if id(node) in steps:
             continue
@@ -858,12 +871,17 @@ def _own_grids_and_divs(scope):
             if fn == "linspace" and len(node.args) >= 3:
                 if any(k.arg == "endpoint" and isinstance(k.value, ast.Constant) and k.value.value is False
                        for k in node.keywords):
+                    periodic.append(node.args[2])
                     continue
                 grids.append((node.args[0], node.args[1], node.args[2], node.lineno))
         if isinstance(node, ast.BinOp) and isinstance(node.op, ast.Div):
             den_names = _names(node.right)
             if den_names:  # x / 2 cannot be a grid spacing with a named number of points
                 divs.append((node, node.lineno, den_names))
+    if periodic:
+        # a spacing L / M next to its own periodic grid of M points is right; do not pair it with grids elsewhere
+        divs = [d for d in divs if not any(_src(d[0].right) == _src(m) or _src(d[0].right) == f"({_src(m)})"
+                                           for m in periodic)]
     return grids, divs
 
 
@@ -913,7 +931,9 @@ _PAIR = re.compile(r"^(?P<pre>.*?)(?P<x>[a-z0-9]+)(?P<sep>_to_|2)(?P<y>[a-z0-9]+
 
 
 def scan_pairs(path: Path, tree, rel: str) -> list[Finding]:
-    funcs = {n.name: n.lineno for n in all_nodes(tree) if isinstance(n, (ast.FunctionDef, ast.AsyncFunctionDef))}
+    # test_x_to_y / test_y_to_x test an inverse pair; they are not converters to run
+    funcs = {n.name: n.lineno for n in all_nodes(tree)
+             if isinstance(n, (ast.FunctionDef, ast.AsyncFunctionDef)) and not n.name.startswith("test")}
     found, seen = [], set()
     for fname, line in funcs.items():
         m = _PAIR.match(fname)
@@ -934,6 +954,11 @@ def scan_pairs(path: Path, tree, rel: str) -> list[Finding]:
 # them only when they are close; dimensional constants (6.6e-11, 3e8) rarely match by chance.
 _PURE = {"pi", "e (Euler)", "T_c (2D Ising)", "G M_sun / 4 pi^2 (au, yr)"}
 _PURE_REL = 2e-3
+# Constants with units: an old edition or a rounded value is within 0.1%, while values 2-10% away were almost all
+# other quantities in the corpus rescan (test values, the atomic mass unit next to the proton mass).
+_DIM_REL = 1e-2
+_TABLE_MIN = 8
+_MANY_CONSTANTS = 20
 # Units and constants fixed by definition: a slip or an old value sits within 0.1%, so only that close is noted.
 _DEFINED = {"N_A", "R (gas constant)", "sigma (Stefan-Boltzmann)", "astronomical unit", "light year", "parsec",
             "standard atmosphere", "torr", "nautical mile", "h (CGS)", "k_B (CGS)", "c (CGS)", "e (esu)", "m_e (g)",
@@ -946,10 +971,15 @@ def scan_constants(path: Path, tree, rel: str) -> list[Finding]:
     from . import constants
 
     names = constants._assigned_names(tree)
+    # numbers in long literal tables are data (measurements, reference values), not constants typed by hand
+    tabulated = {id(e) for n in all_nodes(tree) if isinstance(n, (ast.List, ast.Tuple)) and len(n.elts) >= _TABLE_MIN
+                 for e in n.elts}
     hits = {}
     for node in all_nodes(tree):
         if not (isinstance(node, ast.Constant) and isinstance(node.value, (int, float)) and not isinstance(node.value, bool)):
             continue
+        if id(node) in tabulated:
+            continue
         try:
             v = float(node.value)
         except OverflowError:
@@ -965,9 +995,16 @@ def scan_constants(path: Path, tree, rel: str) -> list[Finding]:
                 continue
         elif name in _PURE and abs(r) > _PURE_REL:
             continue
+        elif name not in _PURE and abs(r) > _DIM_REL:
+            continue  # 1.44e-19 is a test value, not a mistyped elementary charge
         if name in _DEFINED and abs(r) > (_DEFINED_REL / 10 if isinstance(node.value, int) else _DEFINED_REL):
             continue  # a definition typed wrong or taken from an old edition is close; 14666785333344 is not an au
         hits.setdefault((name, ast.unparse(node)), []).append((node.lineno, ref, r, comment))
+    if len(hits) > _MANY_CONSTANTS:
+        first = min(w[0][0] for w in hits.values())
+        return [Finding("constants", NOTE, rel, first,
+                        f"{len(hits)} different numbers in this file are close to physical constants; so many usually means"
+                        " the file holds data (fits, tables, generated code), so they are not listed one by one")]
     out = []
     for (name, literal), where in sorted(hits.items(), key=lambda kv: kv[1][0][0]):
         line, ref, r, comment = where[0]
@@ -1032,6 +1069,17 @@ def scan(path, *, stages=STAGES) -> tuple[list[Finding], list[str]]:
     return findings, unparsed
 
 
+def extract_tables(path) -> list[dict]:
+    """Every Runge-Kutta table the scan finds under `path`, as dicts with A, b, c (or None), the claimed order and
+    where the claim comes from, embedded and error weights, and the order the coefficients have. Runs nothing.
+
+    For checks the scan does not make itself, pass them on, e.g.
+    `physverify.butcher.check_tableau(t["A"], t["b"], t["c"], claimed=t["claimed"])`.
+    """
+    findings, _unparsed = scan(path, stages=("tables",))
+    return [dict(f.table, path=f.path, line=f.line, level=f.level) for f in findings if f.table is not None]
+
+
 def to_dict(findings, unparsed) -> dict:
     return {"findings": [asdict(f) for f in findings], "unparsed": unparsed,
             "warn": sum(f.level == WARN for f in findings), "note": sum(f.level == NOTE for f in findings)}

{physverify-0.5.0 → physverify-0.5.1/src/physverify.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: physverify
-Version: 0.5.0
+Version: 0.5.1
 Summary: Verification checks for physics simulation code: manufactured solutions, order-of-accuracy studies and a seeded-bug benchmark.
 Author: Ram Chandra Giri
 License-Expression: MIT
@@ -45,7 +45,7 @@ Dynamic: license-file
 
 **Checks that a simulation solves the equations it claims, at the order of accuracy it claims, not just that it runs.**
 
-physverify is actively evolving (v0.5.0), welcoming contributions and test cases from the computational physics community. Scope: numerical solutions of ODEs and PDEs (time integration, convergence, conservation), plus a few Monte Carlo checks. It needs only NumPy.
+physverify is actively evolving (v0.5.1), welcoming contributions and test cases from the computational physics community. Scope: numerical solutions of ODEs and PDEs (time integration, convergence, conservation), plus a few Monte Carlo checks. It needs only NumPy.
 
 ![The check loop: your solver and an independent description of the physics go in; physverify runs the solver at several resolutions, measures the error and reports a verdict with a reason](https://raw.githubusercontent.com/rcgiri-physics/physverify/main/docs/images/check-loop.svg)
 
@@ -72,7 +72,7 @@ New to this? [Start here](https://rcgiri-physics.github.io/physverify/start-here
 A failed check fails the job, like a broken unit test ([CI guide](https://rcgiri-physics.github.io/physverify/ci/): options, pre-commit, pytest):
 
 ```yaml
-      - uses: rcgiri-physics/physverify@v0.5.0
+      - uses: rcgiri-physics/physverify@v0.5.1
         with:
           specs: tests/verify_*.py
 ```
@@ -90,3 +90,5 @@ Works best for ODEs; PDEs only in 1D so far. Your code needs a way to add a sour
 ## Contributing, citing, licence
 
 Help is welcome: a trial report on your own solver, seeded bugs written by someone other than the author, adapters, documentation. See [CONTRIBUTING.md](https://github.com/rcgiri-physics/physverify/blob/main/CONTRIBUTING.md), the [code of conduct](https://github.com/rcgiri-physics/physverify/blob/main/CODE_OF_CONDUCT.md), [SUPPORT.md](https://github.com/rcgiri-physics/physverify/blob/main/SUPPORT.md) for help, [SECURITY.md](https://github.com/rcgiri-physics/physverify/blob/main/SECURITY.md) on running untrusted code, and [AGENTS.md](https://github.com/rcgiri-physics/physverify/blob/main/AGENTS.md) for AI assistants. To cite, use [doi:10.5281/zenodo.23534512](https://doi.org/10.5281/zenodo.23534512) or [CITATION.cff](https://github.com/rcgiri-physics/physverify/blob/main/CITATION.cff). Changes: [CHANGELOG.md](https://github.com/rcgiri-physics/physverify/blob/main/CHANGELOG.md); plans: [ROADMAP.md](https://github.com/rcgiri-physics/physverify/blob/main/ROADMAP.md). MIT licence, copyright (c) 2026 Ram Chandra Giri.
+
+<!-- mcp-name: io.github.rcgiri-physics/physverify -->

{physverify-0.5.0 → physverify-0.5.1}/tests/test_agent.py

@@ -68,6 +68,22 @@ def test_hook_ignores_non_python_edits_and_bad_input(project):
     assert hook_main(io.StringIO("not json"), io.StringIO()) == 0
 
 
+def test_hook_does_not_run_code_outside_the_session_folder(project, tmp_path_factory):
+    session = tmp_path_factory.mktemp("session")
+    seed_bug(project)
+    edit = io.StringIO(json.dumps({"cwd": str(session),
+                                   "tool_input": {"file_path": str(project / "damped_oscillator.py")}}))
+    assert hook_main(edit, io.StringIO()) == 0
+
+
+def test_pyproject_specs_outside_the_root_are_dropped(project, tmp_path_factory):
+    outside = tmp_path_factory.mktemp("outside") / "verify_evil.py"
+    outside.write_text("raise SystemExit('must not be imported')\n")
+    (project / "pyproject.toml").write_text(
+        f"[tool.physverify]\nspecs = ['verify_damped_oscillator.py', {str(outside)!r}, '../verify_up.py']\n")
+    assert find_specs(project) == [(project / "verify_damped_oscillator.py").resolve()]
+
+
 def test_mcp_lists_and_runs_the_tool(project):
     init = handle({"jsonrpc": "2.0", "id": 1, "method": "initialize", "params": {"protocolVersion": "2025-06-18"}})
     assert init["result"]["serverInfo"]["name"] == "physverify"

{physverify-0.5.0 → physverify-0.5.1}/tests/test_scan.py

@@ -532,3 +532,74 @@ def test_environment_names_and_nan_tests_are_quiet(tmp_path):
     _write(tmp_path / "tests", "test_nan.py", "import math\nassert not (1.0 == math.nan)\n")
     f = scan(tmp_path)[0]
     assert not _by_stage(f, "names") and not _by_stage(f, "literals")
+
+
+def test_extract_tables_returns_the_coefficients(tmp_path):
+    from physverify.butcher import check_tableau
+    from physverify.scan import extract_tables
+
+    _write(tmp_path, "rk.py", _RK4_CODE)
+    _write(tmp_path, "tab.py", '''
+        def ssprk3():
+            """order 3"""
+            A = [[0, 0, 0], [1, 0, 0], [0.25, 0.25, 0]]
+            b = [1/6, 1/6, 2/3]
+            c = [0, 1, 0.5]
+            return A, b, c
+        ''')
+    tables = {t["name"]: t for t in extract_tables(tmp_path)}
+    assert set(tables) == {"rk4", "ssprk3"}
+    assert tables["rk4"]["kind"] == "stages written as code" and tables["rk4"]["claimed"] == 4
+    t = tables["ssprk3"]
+    assert check_tableau(t["A"], t["b"], t["c"], claimed=t["claimed"]).status == "PASS"
+
+
+def test_spacing_of_its_own_periodic_grid_is_not_paired_elsewhere(tmp_path):
+    _write(tmp_path, "spectral.py", """
+        import numpy as np
+        def evolve(x_min, x_max, n_points):
+            x = np.linspace(x_min, x_max, n_points, endpoint=False)
+            dx = (x_max - x_min) / n_points
+            return x, dx
+        """)
+    _write(tmp_path, "fd.py", """
+        import numpy as np
+        def states(x_min, x_max, n_points):
+            x = np.linspace(x_min, x_max, n_points)
+            return x, x[1] - x[0]
+        """)
+    assert not _by_stage(scan(tmp_path)[0], "grid")
+
+
+def test_many_injected_names_become_one_note(tmp_path):
+    _write(tmp_path, "host.py", """
+        sel = NamedSelection.Create(FaceSelection.Create(GetRootPart().Faces), Selection.Empty())
+        opts = FixMissingFacesOptions()
+        DocumentSave.Execute(GetRootPart().Document.Path)
+        CloseWindow()
+        """)
+    _write(tmp_path, "forgot.py", "x = np.sin(1)\ny = plt.plot(x)\nz = sparse.eye(3)\nw = linalg.inv(z)\nv = a + b + c\n")
+    f = _by_stage(scan(tmp_path)[0], "names")
+    host = [x for x in f if x.path == "host.py"]
+    assert len(host) == 1 and host[0].level == NOTE and "run time" in host[0].message
+    assert len([x for x in f if x.path == "forgot.py" and x.level == WARN]) >= 5
+
+
+def test_constants_in_data_files_and_tables_are_summarised(tmp_path):
+    _write(tmp_path, "rates.py", "\n".join(f"r{i} = rate({2.7175 + 1e-5 * i:.6f}, {3.1405 + 1e-5 * i:.6f})"
+                                            for i in range(30)) + "\n")
+    _write(tmp_path, "table.py", "y = [3.1, 3.12, 3.13, 3.14, 3.15, 2.27, 2.71, 2.72]\n")
+    _write(tmp_path, "masses.py", "amu = 1.66053906660e-27\nm_n = 1.67492749804e-27\ncharge = 1.44e-19\n")
+    f = _by_stage(scan(tmp_path)[0], "constants")
+    assert [(x.path, "close to physical constants" in x.message) for x in f] == [("rates.py", True)]
+
+
+def test_test_functions_are_not_inverse_pairs(tmp_path):
+    _write(tmp_path, "t.py", """
+        def test_xyz_to_lab(): pass
+        def test_lab_to_xyz(): pass
+        def c2k(t): return t
+        def k2c(t): return t
+        """)
+    f = _by_stage(scan(tmp_path)[0], "pairs")
+    assert len(f) == 1 and "c2k" in f[0].message