physverify 0.5.0__tar.gz → 0.6.0__tar.gz

{physverify-0.5.0/src/physverify.egg-info → physverify-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: physverify
-Version: 0.5.0
+Version: 0.6.0
 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
@@ -27,6 +27,7 @@ Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy>=1.24
+Requires-Dist: tomli>=1.1; python_version < "3.11"
 Provides-Extra: symbolic
 Requires-Dist: sympy>=1.12; extra == "symbolic"
 Provides-Extra: dev
@@ -45,7 +46,7 @@ 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 (v0.6.0), 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.
 
 ![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 +73,7 @@ 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@v0.6.0
         with:
           specs: tests/verify_*.py
 ```
@@ -89,4 +90,6 @@ 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.
+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). The methods are standard and other tools do parts of this, some better (NodePy for Runge-Kutta analysis); see [related work and credits](https://rcgiri-physics.github.io/physverify/related-work/). MIT licence, copyright (c) 2026 Ram Chandra Giri.
+
+<!-- mcp-name: io.github.rcgiri-physics/physverify -->

{physverify-0.5.0 → physverify-0.6.0}/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 (v0.6.0), 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.
 
 ![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@v0.6.0
         with:
           specs: tests/verify_*.py
 ```
@@ -48,4 +48,6 @@ 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.
+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). The methods are standard and other tools do parts of this, some better (NodePy for Runge-Kutta analysis); see [related work and credits](https://rcgiri-physics.github.io/physverify/related-work/). MIT licence, copyright (c) 2026 Ram Chandra Giri.
+
+<!-- mcp-name: io.github.rcgiri-physics/physverify -->

{physverify-0.5.0 → physverify-0.6.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "physverify"
-version = "0.5.0"
+version = "0.6.0"
 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"
@@ -28,7 +28,7 @@ classifiers = [
     "Topic :: Software Development :: Testing",
     "Development Status :: 3 - Alpha",
 ]
-dependencies = ["numpy>=1.24"]
+dependencies = ["numpy>=1.24", "tomli>=1.1; python_version < '3.11'"]
 
 [project.urls]
 Homepage = "https://github.com/rcgiri-physics/physverify"

{physverify-0.5.0 → physverify-0.6.0}/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__ = "0.6.0"
 
 __all__ = [
     "Check",

{physverify-0.5.0 → physverify-0.6.0}/src/physverify/agent.py

@@ -49,13 +49,18 @@ def find_specs(root: Path) -> list[Path]:
     pyproject = root / "pyproject.toml"
     if pyproject.is_file():
         try:
-            import tomllib
+            try:
+                import tomllib
+            except ImportError:  # Python 3.10
+                import tomli as tomllib
 
             config = tomllib.loads(pyproject.read_text(encoding="utf-8")).get("tool", {}).get("physverify", {})
         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 +116,12 @@ 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-0.6.0}/src/physverify/cli.py

@@ -125,17 +125,24 @@ def _cmd_smoke(args) -> int:
 def _cmd_scan(args) -> int:
     import json
 
+    from .probes import DEFAULT_PROBES, PROBES, probe
     from .scan import STAGES, WARN, scan, to_dict
 
-    stages = args.only.split(",") if args.only else STAGES
-    unknown = set(stages) - set(STAGES)
+    known = STAGES + PROBES if args.run else STAGES
+    stages = args.only.split(",") if args.only else (STAGES + DEFAULT_PROBES if args.run else STAGES)
+    unknown = set(stages) - set(known)
     if unknown:
-        print(f"physverify: unknown stage {', '.join(sorted(unknown))}; choose from {', '.join(STAGES)}", file=sys.stderr)
+        extra = "; the probes need --run" if unknown <= set(PROBES) else ""
+        print(f"physverify: unknown stage {', '.join(sorted(unknown))}; choose from {', '.join(known)}{extra}", file=sys.stderr)
         return 2
     if not Path(args.path).exists():
         print(f"physverify: {args.path} does not exist", file=sys.stderr)
         return 2
-    findings, unparsed = scan(args.path, stages=stages)
+    findings, unparsed = scan(args.path, stages=[s for s in stages if s in STAGES])
+    probes = [s for s in stages if s in PROBES]
+    if probes:
+        print("physverify: --run calls the code; use it only on code you trust or inside the sandbox", file=sys.stderr)
+        findings += probe(args.path, probes=probes, timeout=args.timeout)
     if args.json:
         text = json.dumps(to_dict(findings, unparsed), indent=1)
         if args.json == "-":
@@ -148,8 +155,11 @@ def _cmd_scan(args) -> int:
         for u in unparsed:
             print(f"NOTE parse     {u}")
         warn = sum(f.level == WARN for f in findings)
-        print(f"{warn} warnings, {len(findings) - warn} notes, {len(unparsed)} files not parsed"
-              " (the scan reads the code and runs nothing; a clean scan means only that these patterns were not found)")
+        skip = sum(f.level == "SKIP" for f in findings)
+        ran = (f", {skip} skipped (not passed)" if probes else "")
+        how = "the probes called the code with small inputs" if probes else "the scan reads the code and runs nothing"
+        print(f"{warn} warnings, {len(findings) - warn - skip} notes{ran}, {len(unparsed)} files not parsed"
+              f" ({how}; a clean scan means only that these patterns were not found)")
     return 1 if any(f.level == WARN for f in findings) else 0
 
 
@@ -204,6 +214,10 @@ def build_parser() -> argparse.ArgumentParser:
     sc.add_argument("path", help="a Python file or a folder")
     sc.add_argument("--only", metavar="STAGES", help="comma-separated stages: constants,tables,grid,pairs,names,api,literals,units (default all)")
     sc.add_argument("--json", metavar="FILE", help="write findings as JSON to FILE, or to stdout with -")
+    sc.add_argument("--run", action="store_true",
+                    help="also run the probes smoke and branches, which CALL the code (trusted code or the sandbox only); "
+                         "the experimental probes edges,deadargs,roundtrip,siblings,known,monotone with --only")
+    sc.add_argument("--timeout", type=float, default=60.0, help="with --run: seconds per script or file of functions (default 60)")
     sc.set_defaults(func=_cmd_scan)
 
     r = sub.add_parser("references", help="list the exact reference solutions in physverify.references")

{physverify-0.5.0 → physverify-0.6.0}/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-0.6.0}/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) \