physverify 0.5.1__tar.gz → 0.6.0__tar.gz

{physverify-0.5.1/src/physverify.egg-info → physverify-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: physverify
-Version: 0.5.1
+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 (v0.5.1), 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.
+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@v0.5.1
+      - uses: rcgiri-physics/physverify@v0.6.0
         with:
           specs: tests/verify_*.py
 ```
@@ -89,6 +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-0.5.1 → 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 (v0.5.1), 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.
+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@v0.5.1
+      - uses: rcgiri-physics/physverify@v0.6.0
         with:
           specs: tests/verify_*.py
 ```
@@ -48,6 +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-0.5.1 → physverify-0.6.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "physverify"
-version = "0.5.1"
+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-0.5.1 → 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__ = "0.5.1"
+__version__ = "0.6.0"
 
 __all__ = [
     "Check",

{physverify-0.5.1 → physverify-0.6.0}/src/physverify/agent.py

@@ -49,7 +49,10 @@ 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:

{physverify-0.5.1 → 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")