phaseprobe 0.2.0__tar.gz → 0.2.1__tar.gz

{phaseprobe-0.2.0 → phaseprobe-0.2.1}/.github/workflows/ci.yml

@@ -50,8 +50,8 @@ jobs:
       - run: python -m ruff check .
       - run: python -m mypy src tests
       - run: python -m pytest --cov=phaseprobe --cov-report=term
-      - run: python -m phaseprobe perturb --config examples/scipy/lorenz-negative.json
-      - run: python -m phaseprobe check --config examples/scipy/predator-prey.json
+      - run: python -m phaseprobe perturb --example scipy-lorenz-negative
+      - run: python -m phaseprobe check --example scipy-predator-prey
 
   package-and-hygiene:
     runs-on: ubuntu-latest
@@ -65,14 +65,10 @@ jobs:
       - run: python -m build
       - run: python -m twine check dist/*
       - run: python scripts/audit_package.py
-      - run: python -m venv .cache/packed-smoke
-      - run: .cache/packed-smoke/bin/python -m pip install dist/*.whl
-      - run: .cache/packed-smoke/bin/python -m phaseprobe --version
-      - run: .cache/packed-smoke/bin/python -m phaseprobe scan --example logistic-negative
-      - run: .cache/packed-smoke/bin/python -c "import importlib.util; assert importlib.util.find_spec('numpy') is None; assert importlib.util.find_spec('scipy') is None"
-      - run: python -m venv .cache/scipy-smoke
-      - run: .cache/scipy-smoke/bin/python -m pip install "$(find dist -name '*.whl')[scipy]"
-      - run: .cache/scipy-smoke/bin/python -m phaseprobe check --config examples/scipy/predator-prey.json
+      - run: >-
+          python scripts/verify_artifacts.py
+          --dist-dir dist
+          --work-root "${RUNNER_TEMP}/phaseprobe artifact gate"
       - run: python scripts/check_links.py
       - run: python scripts/hygiene.py
       - uses: actions/upload-artifact@v4
@@ -80,3 +76,21 @@ jobs:
           name: phaseprobe-packages
           path: dist/*
           if-no-files-found: error
+
+  windows-artifact-install:
+    name: artifact install / windows / Python 3.12
+    runs-on: windows-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+      - run: python -m pip install --upgrade pip build twine
+      - run: python -m build
+      - run: python -m twine check dist/*
+      - run: python scripts/audit_package.py
+      - run: >-
+          python scripts/verify_artifacts.py
+          --dist-dir dist
+          --work-root "$env:RUNNER_TEMP\phaseprobe artifact gate"

phaseprobe-0.2.1/.github/workflows/publish-pypi.yml

@@ -0,0 +1,166 @@
+name: Publish an existing GitHub release to PyPI
+
+on:
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: Immutable release tag (for example, v0.2.1)
+        required: true
+        type: string
+      version:
+        description: Expected package version (for example, 0.2.1)
+        required: true
+        type: string
+      commit:
+        description: Expected 40-character commit for the tag
+        required: true
+        type: string
+      wheel_sha256:
+        description: Expected SHA-256 for the wheel release asset
+        required: true
+        type: string
+      sdist_sha256:
+        description: Expected SHA-256 for the source release asset
+        required: true
+        type: string
+
+permissions: {}
+
+concurrency:
+  group: pypi-${{ inputs.tag }}
+  cancel-in-progress: false
+
+jobs:
+  verify:
+    name: Verify immutable release assets
+    if: >-
+      github.repository == 'aliengineering-byte/phaseprobe' &&
+      github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    permissions: {}
+    steps:
+      - name: Download and verify the selected release
+        env:
+          TAG: ${{ inputs.tag }}
+          VERSION: ${{ inputs.version }}
+          EXPECTED_COMMIT: ${{ inputs.commit }}
+          WHEEL_SHA256: ${{ inputs.wheel_sha256 }}
+          SDIST_SHA256: ${{ inputs.sdist_sha256 }}
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          [[ "$TAG" =~ ^v[0-9]+\.[0-9]+\.[0-9]+$ ]]
+          [[ "$VERSION" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]]
+          [[ "$TAG" == "v$VERSION" ]]
+          [[ "$EXPECTED_COMMIT" =~ ^[0-9a-f]{40}$ ]]
+          [[ "$WHEEL_SHA256" =~ ^[0-9a-f]{64}$ ]]
+          [[ "$SDIST_SHA256" =~ ^[0-9a-f]{64}$ ]]
+
+          repository_url="https://github.com/${GITHUB_REPOSITORY}.git"
+          tag_refs="$(git ls-remote "$repository_url" "refs/tags/$TAG" "refs/tags/$TAG^{}")"
+          direct_commit="$(awk -v ref="refs/tags/$TAG" '$2 == ref { print $1 }' <<<"$tag_refs")"
+          peeled_commit="$(awk -v ref="refs/tags/$TAG^{}" '$2 == ref { print $1 }' <<<"$tag_refs")"
+          resolved_commit="${peeled_commit:-$direct_commit}"
+          [[ -n "$resolved_commit" ]]
+          [[ "$resolved_commit" == "$EXPECTED_COMMIT" ]]
+
+          wheel="phaseprobe-$VERSION-py3-none-any.whl"
+          sdist="phaseprobe-$VERSION.tar.gz"
+          release_url="https://github.com/${GITHUB_REPOSITORY}/releases/download/$TAG"
+          mkdir dist
+          curl --fail --location --proto '=https' --tlsv1.2 \
+            --output "dist/$wheel" "$release_url/$wheel"
+          curl --fail --location --proto '=https' --tlsv1.2 \
+            --output "dist/$sdist" "$release_url/$sdist"
+          printf '%s  %s\n%s  %s\n' \
+            "$WHEEL_SHA256" "dist/$wheel" \
+            "$SDIST_SHA256" "dist/$sdist" | sha256sum --check --strict
+
+          python3 -m venv .twine-check
+          .twine-check/bin/python -m pip install --disable-pip-version-check 'twine==7.0.0'
+          .twine-check/bin/python -m twine check "dist/$wheel" "dist/$sdist"
+
+          python3 - "$VERSION" "dist/$wheel" "dist/$sdist" <<'PY'
+          import email
+          import sys
+          import tarfile
+          import zipfile
+
+          expected_version, wheel_path, sdist_path = sys.argv[1:]
+
+          with zipfile.ZipFile(wheel_path) as archive:
+              wheel_names = set(archive.namelist())
+              metadata_names = [
+                  name for name in wheel_names if name.endswith(".dist-info/METADATA")
+              ]
+              assert len(metadata_names) == 1, metadata_names
+              wheel_metadata = email.message_from_bytes(archive.read(metadata_names[0]))
+
+          with tarfile.open(sdist_path, "r:gz") as archive:
+              sdist_names = {member.name for member in archive.getmembers()}
+              metadata_members = [
+                  member
+                  for member in archive.getmembers()
+                  if member.isfile() and member.name.count("/") == 1 and member.name.endswith("/PKG-INFO")
+              ]
+              assert len(metadata_members) == 1, [member.name for member in metadata_members]
+              extracted = archive.extractfile(metadata_members[0])
+              assert extracted is not None
+              sdist_metadata = email.message_from_bytes(extracted.read())
+
+          sdist_roots = {name.split("/", 1)[0] for name in sdist_names if "/" in name}
+          assert len(sdist_roots) == 1, sorted(sdist_roots)
+          sdist_root = next(iter(sdist_roots))
+          source_prefix = f"{sdist_root}/src/phaseprobe/"
+          runtime_files = {
+              name.removeprefix(f"{sdist_root}/src/")
+              for name in sdist_names
+              if name.startswith(source_prefix)
+              and not name.endswith(".py")
+              and "__pycache__" not in name.split("/")
+          }
+          assert "phaseprobe/py.typed" in runtime_files
+          assert not runtime_files - wheel_names, sorted(runtime_files - wheel_names)
+
+          for metadata in (wheel_metadata, sdist_metadata):
+              assert metadata["Name"] == "phaseprobe"
+              assert metadata["Version"] == expected_version
+              assert metadata["Requires-Python"] == ">=3.10"
+              assert metadata["License-Expression"] == "Apache-2.0"
+              assert "scipy" in metadata.get_all("Provides-Extra", [])
+              requirements = metadata.get_all("Requires-Dist", [])
+              assert any(req.startswith("numpy") and "extra == 'scipy'" in req for req in requirements)
+              assert any(req.startswith("scipy") and "extra == 'scipy'" in req for req in requirements)
+              project_urls = metadata.get_all("Project-URL", [])
+              assert any(url.startswith("Source, https://github.com/aliengineering-byte/phaseprobe") for url in project_urls)
+          PY
+
+      - name: Store the verified distributions
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        with:
+          name: verified-distributions-${{ inputs.tag }}
+          path: dist/*
+          if-no-files-found: error
+          retention-days: 1
+
+  publish:
+    name: Publish verified distributions
+    needs: verify
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/phaseprobe/${{ inputs.version }}/
+    permissions:
+      id-token: write
+    steps:
+      - name: Retrieve the verified distributions
+        uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4
+        with:
+          name: verified-distributions-${{ inputs.tag }}
+          path: dist
+
+      - name: Publish distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # release/v1
+        with:
+          packages-dir: dist/

{phaseprobe-0.2.0 → phaseprobe-0.2.1}/.github/workflows/release.yml

@@ -20,13 +20,10 @@ jobs:
       - run: python -m build
       - run: python -m twine check dist/*
       - run: python scripts/audit_package.py
-      - run: python -m venv .cache/tag-core-smoke
-      - run: .cache/tag-core-smoke/bin/python -m pip install dist/*.whl
-      - run: .cache/tag-core-smoke/bin/python -m phaseprobe --version
-      - run: .cache/tag-core-smoke/bin/python -m phaseprobe scan --example logistic
-      - run: python -m venv .cache/tag-scipy-smoke
-      - run: .cache/tag-scipy-smoke/bin/python -m pip install "$(find dist -name '*.whl')[scipy]"
-      - run: .cache/tag-scipy-smoke/bin/python -m phaseprobe check --config examples/scipy/predator-prey.json
+      - run: >-
+          python scripts/verify_artifacts.py
+          --dist-dir dist
+          --work-root "${RUNNER_TEMP}/phaseprobe tagged artifact gate"
       - run: python scripts/hygiene.py
       - uses: actions/upload-artifact@v4
         with:

{phaseprobe-0.2.0 → phaseprobe-0.2.1}/CHANGELOG.md

@@ -2,6 +2,27 @@
 
 All notable changes are documented here. PhaseProbe follows semantic versioning.
 
+## 0.2.1 — 2026-08-31
+
+- Fixed Issue #4: all four SciPy quick-start configurations now ship inside the importable
+  package in both wheel and source distribution and load through `importlib.resources` as the
+  `scipy-lorenz`, `scipy-lorenz-negative`, `scipy-predator-prey`, and
+  `scipy-predator-prey-coarse` built-in examples.
+- Preserved the four exact former `examples/scipy/` config paths as narrow compatibility aliases
+  when no file exists at the requested path. Existing user files take precedence; matching is
+  case-sensitive and separator-portable, with no fuzzy or basename fallback.
+- Added actionable, versioned diagnostics for missing or malformed built-in resources without
+  changing arbitrary config-path or built-in-example behavior.
+- Added Linux and Windows Python 3.12 release gates that build, inspect, install, and exercise the
+  wheel and sdist outside the checkout with `PYTHONPATH` removed. The gate runs scan, replay,
+  generated pytest, SciPy Lorenz, SciPy predator–prey, `pip check`, and a dependency-free base
+  wheel check.
+- Added a source-derived runtime-resource audit and the PEP 561 `py.typed` marker.
+- Generated regression creation is now idempotent for identical evidence and rejects conflicting
+  files instead of silently overwriting them.
+- Added an analytic backward-time directional-event check while preserving all solver defaults
+  and the existing tolerance-based adaptive replay contract.
+
 ## 0.2.0 — 2026-08-02
 
 - Added the backward-compatible `TrajectoryAdapter` protocol and shared engine dispatch; all v0.1

{phaseprobe-0.2.0 → phaseprobe-0.2.1}/CITATION.cff

@@ -4,8 +4,8 @@ title: "PhaseProbe"
 type: software
 authors:
   - name: "Ali"
-version: 0.2.0
-date-released: 2026-08-02
+version: 0.2.1
+date-released: 2026-08-31
 url: "https://github.com/aliengineering-byte/phaseprobe"
 repository-code: "https://github.com/aliengineering-byte/phaseprobe"
 license: Apache-2.0

{phaseprobe-0.2.0 → phaseprobe-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: phaseprobe
-Version: 0.2.0
+Version: 0.2.1
 Summary: Find reproducible qualitative simulation transitions and turn them into regression tests.
 Project-URL: Documentation, https://github.com/aliengineering-byte/phaseprobe#readme
 Project-URL: Issues, https://github.com/aliengineering-byte/phaseprobe/issues
@@ -43,7 +43,7 @@ Description-Content-Type: text/markdown
 Maintaining a simulation is risky when a tiny parameter or initial-condition change can cross a qualitative boundary while ordinary numeric assertions still look plausible. PhaseProbe runs a bounded, deterministic search, records exactly what it tested, and emits an offline report plus an executable pytest regression.
 
 ```console
-$ python -m pip install .
+$ pip install phaseprobe pytest
 $ phaseprobe scan --example logistic
 QUALITATIVE TRANSITION FOUND
 
@@ -62,12 +62,20 @@ $ python -m pytest -q tests/generated
 
 No API key, LLM, GPU, Docker, account, telemetry, network connection, or hosted service is required at runtime. PhaseProbe's base installation has no third-party runtime dependencies; NumPy and SciPy are isolated in the optional `scipy` extra.
 
+## Installation
+
+```bash
+pip install phaseprobe
+pip install "phaseprobe[scipy]"
+pip install pytest  # needed only to execute a generated regression test
+```
+
 ## Five-minute quick start
 
 Requires Python 3.10 or newer on Windows or Linux.
 
 ```bash
-python -m pip install .
+pip install phaseprobe pytest
 phaseprobe scan --example logistic
 phaseprobe replay .phaseprobe/runs/<run-id>/replay.json
 phaseprobe generate-test .phaseprobe/runs/<run-id>/replay.json
@@ -90,22 +98,41 @@ Five-minute path:
 [![SciPy demo: solve_ivp evidence, tolerance replay, and generated pytest](assets/scipy-demo-static.png)](assets/scipy-demo.gif)
 
 The verified command transcript is [assets/scipy-demo-session.txt](assets/scipy-demo-session.txt),
-with a self-contained [HTML example report](examples/scipy/report.html).
+with a self-contained [HTML example report](examples/scipy/report.html). The following path starts
+from a clean environment and does not require a source checkout:
 
 ```bash
-python -m pip install "phaseprobe[scipy]"
-phaseprobe perturb --config examples/scipy/lorenz.json
-phaseprobe check --config examples/scipy/predator-prey.json
+python -m venv .venv
+# Linux: source .venv/bin/activate
+# Windows PowerShell: .venv\Scripts\Activate.ps1
+python -m pip install "phaseprobe[scipy]" "pytest==8.4.1"
+phaseprobe perturb --example scipy-lorenz
+phaseprobe check --example scipy-predator-prey
 phaseprobe replay .phaseprobe/runs/<run-id>/replay.json
 phaseprobe generate-test .phaseprobe/runs/<run-id>/replay.json
 python -m pytest -q tests/generated
 ```
 
+PhaseProbe 0.2.1 also recognizes the former Issue #4 command
+`phaseprobe perturb --config examples/scipy/lorenz.json` when that relative file is absent and
+loads the corresponding packaged example. This compatibility is limited to the four former
+`examples/scipy/` paths: an existing file always takes precedence, matching is case-sensitive,
+both slash styles are accepted, and unrelated missing paths remain errors. New documentation and
+automation should use the installed-safe `--example scipy-*` names.
+
 The Lorenz command searches a declared initial-`x` perturbation and reports only finite-time
-divergence evidence. `examples/scipy/lorenz-negative.json` is its short-window negative control.
-The predator–prey command checks the declared first integral with tightly resolved DOP853 settings;
-`examples/scipy/predator-prey-coarse.json` deliberately fails the same policy with loose RK23
-settings.
+divergence evidence and prints `FINITE-TIME TRAJECTORY DIVERGENCE FOUND`. Its installed
+short-window control is `--example scipy-lorenz-negative`. The predator–prey command checks the
+declared first integral with tightly resolved DOP853 settings and prints `CHECK POLICY PASSED`;
+`--example scipy-predator-prey-coarse` deliberately fails the same policy with loose RK23 settings.
+Each successful command writes a replay fixture and offline report below
+`.phaseprobe/runs/<run-id>/`.
+
+Run `phaseprobe perturb --help` or `phaseprobe check --help` to list installed example names. A
+missing packaged resource reports the PhaseProbe version and resource name. Adaptive SciPy replay
+compares the declared state, observable, invariant, endpoint, event, and retained-grid
+tolerances—it does not promise bitwise trajectory equality across platforms or dependency
+versions.
 
 For a direct Python API:
 
@@ -144,7 +171,7 @@ does not import it. See [the audited contract](docs/SCIPY_SOLVE_IVP_AUDIT.md),
 | `perturb` | Baseline/perturbed twin runs over bounded initial-state changes | Finding or no finding, exit `0` |
 | `check` | Execute a declared configuration policy for CI | Exit `1` only when policy fails |
 | `replay` | Validate fixture integrity and re-execute model, parameters, seed, initial state, tolerances, and retention | Declared `exact` or `tolerance` comparison passes |
-| `generate-test` | Validate and copy a fixture into a non-extensible pytest template | Executable test under `tests/generated/` |
+| `generate-test` | Validate and copy a fixture into a non-extensible pytest template without conflicting overwrites | Executable test under `tests/generated/` |
 | `report` | Regenerate terminal, versioned JSON, and self-contained offline HTML evidence | Local report files |
 
 Common options:
@@ -152,6 +179,7 @@ Common options:
 ```console
 phaseprobe scan --config examples/configs/logistic-scan.json
 phaseprobe perturb --example lorenz --json
+phaseprobe perturb --example scipy-lorenz --json
 phaseprobe check --example predator-prey
 phaseprobe scan --example logistic --fail-on-finding
 ```
@@ -166,6 +194,8 @@ Exit codes are stable: `0` completed, `1` declared policy or explicit `--fail-on
 | Lorenz system | `phaseprobe perturb --example lorenz` | Small initial separation exceeds the declared finite-time trajectory-distance threshold | Short window plus unreachable threshold reports no finding | [Lorenz, 1963](https://journals.ametsoc.org/view/journals/atsc/20/2/1520-0469_1963_020_0130_dnf_2_0_co_2.xml) |
 | Predator–prey | `phaseprobe check --example predator-prey` | Refined RK4 step preserves the analytic first integral within tolerance | Coarse step fails the invariant-drift policy | [Lotka, 1920](https://doi.org/10.1073/pnas.6.7.410) |
 | Genetic toggle | `phaseprobe perturb --example toggle` | Bounded initial-state perturbation reaches the opposite dominant state | Smaller declared range stays in the baseline basin | [Gardner, Cantor & Collins, 2000](https://www.nature.com/articles/35002131) |
+| SciPy Lorenz | `phaseprobe perturb --example scipy-lorenz` | DOP853 twin trajectories cross the declared finite-time distance threshold | `--example scipy-lorenz-negative` shortens the window | [Lorenz, 1963](https://journals.ametsoc.org/view/journals/atsc/20/2/1520-0469_1963_020_0130_dnf_2_0_co_2.xml) |
+| SciPy predator–prey | `phaseprobe check --example scipy-predator-prey` | Tight DOP853 settings preserve the declared first integral tolerance | `--example scipy-predator-prey-coarse` deliberately fails | [Lotka, 1920](https://doi.org/10.1073/pnas.6.7.410) |
 
 Each configuration records the seed, fixed integration/iteration settings, tolerances, burn-in, observation window, classification rule, refinement rule, invalid-state policy, and trace cap. See [examples/README.md](examples/README.md) for equations and interpretation.
 

{phaseprobe-0.2.0 → phaseprobe-0.2.1}/README.md

@@ -5,7 +5,7 @@
 Maintaining a simulation is risky when a tiny parameter or initial-condition change can cross a qualitative boundary while ordinary numeric assertions still look plausible. PhaseProbe runs a bounded, deterministic search, records exactly what it tested, and emits an offline report plus an executable pytest regression.
 
 ```console
-$ python -m pip install .
+$ pip install phaseprobe pytest
 $ phaseprobe scan --example logistic
 QUALITATIVE TRANSITION FOUND
 
@@ -24,12 +24,20 @@ $ python -m pytest -q tests/generated
 
 No API key, LLM, GPU, Docker, account, telemetry, network connection, or hosted service is required at runtime. PhaseProbe's base installation has no third-party runtime dependencies; NumPy and SciPy are isolated in the optional `scipy` extra.
 
+## Installation
+
+```bash
+pip install phaseprobe
+pip install "phaseprobe[scipy]"
+pip install pytest  # needed only to execute a generated regression test
+```
+
 ## Five-minute quick start
 
 Requires Python 3.10 or newer on Windows or Linux.
 
 ```bash
-python -m pip install .
+pip install phaseprobe pytest
 phaseprobe scan --example logistic
 phaseprobe replay .phaseprobe/runs/<run-id>/replay.json
 phaseprobe generate-test .phaseprobe/runs/<run-id>/replay.json
@@ -52,22 +60,41 @@ Five-minute path:
 [![SciPy demo: solve_ivp evidence, tolerance replay, and generated pytest](assets/scipy-demo-static.png)](assets/scipy-demo.gif)
 
 The verified command transcript is [assets/scipy-demo-session.txt](assets/scipy-demo-session.txt),
-with a self-contained [HTML example report](examples/scipy/report.html).
+with a self-contained [HTML example report](examples/scipy/report.html). The following path starts
+from a clean environment and does not require a source checkout:
 
 ```bash
-python -m pip install "phaseprobe[scipy]"
-phaseprobe perturb --config examples/scipy/lorenz.json
-phaseprobe check --config examples/scipy/predator-prey.json
+python -m venv .venv
+# Linux: source .venv/bin/activate
+# Windows PowerShell: .venv\Scripts\Activate.ps1
+python -m pip install "phaseprobe[scipy]" "pytest==8.4.1"
+phaseprobe perturb --example scipy-lorenz
+phaseprobe check --example scipy-predator-prey
 phaseprobe replay .phaseprobe/runs/<run-id>/replay.json
 phaseprobe generate-test .phaseprobe/runs/<run-id>/replay.json
 python -m pytest -q tests/generated
 ```
 
+PhaseProbe 0.2.1 also recognizes the former Issue #4 command
+`phaseprobe perturb --config examples/scipy/lorenz.json` when that relative file is absent and
+loads the corresponding packaged example. This compatibility is limited to the four former
+`examples/scipy/` paths: an existing file always takes precedence, matching is case-sensitive,
+both slash styles are accepted, and unrelated missing paths remain errors. New documentation and
+automation should use the installed-safe `--example scipy-*` names.
+
 The Lorenz command searches a declared initial-`x` perturbation and reports only finite-time
-divergence evidence. `examples/scipy/lorenz-negative.json` is its short-window negative control.
-The predator–prey command checks the declared first integral with tightly resolved DOP853 settings;
-`examples/scipy/predator-prey-coarse.json` deliberately fails the same policy with loose RK23
-settings.
+divergence evidence and prints `FINITE-TIME TRAJECTORY DIVERGENCE FOUND`. Its installed
+short-window control is `--example scipy-lorenz-negative`. The predator–prey command checks the
+declared first integral with tightly resolved DOP853 settings and prints `CHECK POLICY PASSED`;
+`--example scipy-predator-prey-coarse` deliberately fails the same policy with loose RK23 settings.
+Each successful command writes a replay fixture and offline report below
+`.phaseprobe/runs/<run-id>/`.
+
+Run `phaseprobe perturb --help` or `phaseprobe check --help` to list installed example names. A
+missing packaged resource reports the PhaseProbe version and resource name. Adaptive SciPy replay
+compares the declared state, observable, invariant, endpoint, event, and retained-grid
+tolerances—it does not promise bitwise trajectory equality across platforms or dependency
+versions.
 
 For a direct Python API:
 
@@ -106,7 +133,7 @@ does not import it. See [the audited contract](docs/SCIPY_SOLVE_IVP_AUDIT.md),
 | `perturb` | Baseline/perturbed twin runs over bounded initial-state changes | Finding or no finding, exit `0` |
 | `check` | Execute a declared configuration policy for CI | Exit `1` only when policy fails |
 | `replay` | Validate fixture integrity and re-execute model, parameters, seed, initial state, tolerances, and retention | Declared `exact` or `tolerance` comparison passes |
-| `generate-test` | Validate and copy a fixture into a non-extensible pytest template | Executable test under `tests/generated/` |
+| `generate-test` | Validate and copy a fixture into a non-extensible pytest template without conflicting overwrites | Executable test under `tests/generated/` |
 | `report` | Regenerate terminal, versioned JSON, and self-contained offline HTML evidence | Local report files |
 
 Common options:
@@ -114,6 +141,7 @@ Common options:
 ```console
 phaseprobe scan --config examples/configs/logistic-scan.json
 phaseprobe perturb --example lorenz --json
+phaseprobe perturb --example scipy-lorenz --json
 phaseprobe check --example predator-prey
 phaseprobe scan --example logistic --fail-on-finding
 ```
@@ -128,6 +156,8 @@ Exit codes are stable: `0` completed, `1` declared policy or explicit `--fail-on
 | Lorenz system | `phaseprobe perturb --example lorenz` | Small initial separation exceeds the declared finite-time trajectory-distance threshold | Short window plus unreachable threshold reports no finding | [Lorenz, 1963](https://journals.ametsoc.org/view/journals/atsc/20/2/1520-0469_1963_020_0130_dnf_2_0_co_2.xml) |
 | Predator–prey | `phaseprobe check --example predator-prey` | Refined RK4 step preserves the analytic first integral within tolerance | Coarse step fails the invariant-drift policy | [Lotka, 1920](https://doi.org/10.1073/pnas.6.7.410) |
 | Genetic toggle | `phaseprobe perturb --example toggle` | Bounded initial-state perturbation reaches the opposite dominant state | Smaller declared range stays in the baseline basin | [Gardner, Cantor & Collins, 2000](https://www.nature.com/articles/35002131) |
+| SciPy Lorenz | `phaseprobe perturb --example scipy-lorenz` | DOP853 twin trajectories cross the declared finite-time distance threshold | `--example scipy-lorenz-negative` shortens the window | [Lorenz, 1963](https://journals.ametsoc.org/view/journals/atsc/20/2/1520-0469_1963_020_0130_dnf_2_0_co_2.xml) |
+| SciPy predator–prey | `phaseprobe check --example scipy-predator-prey` | Tight DOP853 settings preserve the declared first integral tolerance | `--example scipy-predator-prey-coarse` deliberately fails | [Lotka, 1920](https://doi.org/10.1073/pnas.6.7.410) |
 
 Each configuration records the seed, fixed integration/iteration settings, tolerances, burn-in, observation window, classification rule, refinement rule, invalid-state policy, and trace cap. See [examples/README.md](examples/README.md) for equations and interpretation.
 

{phaseprobe-0.2.0 → phaseprobe-0.2.1}/SCIENTIFIC_METHODS.md

@@ -19,6 +19,9 @@ Tolerance replay compares retained times/states, named numeric observables, clas
 invariant results and stored thresholds, endpoint/event evidence, and expected solver success.
 Environment and solver evidence are retained for interpretation. Artifact hashes still detect
 fixture tampering, but an adaptive trace hash is not required to match across supported platforms.
+The adapter validation suite checks an exponential system with an analytic terminal crossing in
+both forward and backward integration directions; this validates event plumbing, not exhaustive
+root detection between adaptive internal steps.
 See [the complete SciPy audit](docs/SCIPY_SOLVE_IVP_AUDIT.md).
 
 PhaseProbe 0.1.0 produces bounded computational evidence. It does not perform formal verification, model validation against observations, or computer-assisted proof.

{phaseprobe-0.2.0 → phaseprobe-0.2.1}/assets/scipy-demo-session.txt

@@ -1,4 +1,4 @@
-$ phaseprobe perturb --config examples/scipy/lorenz.json
+$ phaseprobe perturb --example scipy-lorenz
 FINITE-TIME TRAJECTORY DIVERGENCE FOUND
 
 Model: lorenz-scipy
@@ -10,12 +10,12 @@ Baseline regime: bounded-finite-window
 Changed regime: bounded-finite-window
 Invariant violations: 0
 Repeatable: true
-Replay: <repository>/.cache/phaseprobe-scipy-demo-uqyijm6y/runs/lorenz/20260802T175927Z-786e1809/replay.json
+Replay: <repository>/.cache/phaseprobe-scipy-demo-4sai_vv1/runs/lorenz/20260831T174342Z-7fcc5f8d/replay.json
 
 Scope: Smallest reproducible perturbation found within the declared finite search; not a proof of global minimality.
-HTML report: <repository>/.cache/phaseprobe-scipy-demo-uqyijm6y/runs/lorenz/20260802T175927Z-786e1809/report.html
+HTML report: <repository>/.cache/phaseprobe-scipy-demo-4sai_vv1/runs/lorenz/20260831T174342Z-7fcc5f8d/report.html
 
-$ phaseprobe check --config examples/scipy/predator-prey.json
+$ phaseprobe check --example scipy-predator-prey
 CHECK POLICY PASSED
 
 Model: predator-prey-scipy
@@ -23,8 +23,8 @@ Baseline regime: positive-oscillation
 Changed regime: n/a
 Invariant violations: 0
 Repeatable: true
-Replay: <repository>/.cache/phaseprobe-scipy-demo-uqyijm6y/runs/predator-prey/20260802T175928Z-073e812d/replay.json
-HTML report: <repository>/.cache/phaseprobe-scipy-demo-uqyijm6y/runs/predator-prey/20260802T175928Z-073e812d/report.html
+Replay: <repository>/.cache/phaseprobe-scipy-demo-4sai_vv1/runs/predator-prey/20260831T174343Z-38b5e8de/replay.json
+HTML report: <repository>/.cache/phaseprobe-scipy-demo-4sai_vv1/runs/predator-prey/20260831T174343Z-38b5e8de/report.html
 
 $ phaseprobe replay .phaseprobe/runs/<run-id>/replay.json
 REPLAY VERIFIED
@@ -36,11 +36,11 @@ baseline: declared tolerances=True
 $ phaseprobe generate-test .phaseprobe/runs/<run-id>/replay.json
 PYTEST REGRESSION GENERATED
 
-Test: <repository>/.cache/phaseprobe-scipy-demo-uqyijm6y/generated/test_predator_prey_scipy_transition.py
-Replay fixture: <repository>/.cache/phaseprobe-scipy-demo-uqyijm6y/generated/fixtures/predator_prey_scipy-replay.json
+Test: <repository>/.cache/phaseprobe-scipy-demo-4sai_vv1/generated/test_predator_prey_scipy_transition.py
+Replay fixture: <repository>/.cache/phaseprobe-scipy-demo-4sai_vv1/generated/fixtures/predator_prey_scipy-replay.json
 
 $ python -m pytest -q tests/generated
 .                                                                        [100%]
-1 passed in 1.04s
+1 passed in 1.08s
 
-Measured demo run: lorenz=5.916s, predator-prey=1.397s, replay=1.343s, generate=1.300s, pytest=1.759s.
+Measured demo run: lorenz=6.285s, predator-prey=1.409s, replay=1.336s, generate=1.340s, pytest=1.814s.

{phaseprobe-0.2.0 → phaseprobe-0.2.1}/docs/upstream/SCIPY_INTEGRATION_PROPOSAL.md

@@ -44,8 +44,8 @@ plus solver configuration metadata; it does not hash or serialize callable sourc
 
 ```bash
 python -m pip install "phaseprobe[scipy]"
-phaseprobe perturb --config examples/scipy/lorenz.json
-phaseprobe check --config examples/scipy/predator-prey.json
+phaseprobe perturb --example scipy-lorenz
+phaseprobe check --example scipy-predator-prey
 phaseprobe replay .phaseprobe/runs/<run-id>/replay.json
 phaseprobe generate-test .phaseprobe/runs/<run-id>/replay.json
 ```
@@ -95,15 +95,51 @@ propose this external qualitative regression/replay layer.
 Project quick start and terminal assets:
 https://github.com/aliengineering-byte/phaseprobe#use-with-scipy
 
-## Suggested discussion title
+## Discussion title and body
 
-`PhaseProbe: tolerance-aware qualitative regression fixtures for SciPy solve_ivp models`
+`PhaseProbe: reproducible transition detection and regression generation for solve_ivp models`
 
-## Human-editable outreach message
+Hi SciPy community,
 
-> I built an optional, dependency-isolated PhaseProbe adapter for public `solve_ivp` models. It
-> keeps SciPy responsible for integration and adds bounded qualitative searches, explicit
-> tolerance replay, and generated pytest regressions. The examples include finite-time Lorenz
-> divergence with a negative control and a Lotka–Volterra invariant refinement check. I reviewed
-> related tolerance, event, work-bound, and callback discussions and do not propose a SciPy API
-> change. Would this workflow be useful to users maintaining scientific simulation regressions?
+I built PhaseProbe, an open-source downstream testing tool for dynamical-system simulations. It
+uses `scipy.integrate.solve_ivp` through a trajectory-level adapter to search bounded parameter or
+initial-condition regions for reproducible qualitative transitions, preserve replay evidence, and
+generate pytest regression tests from the findings.
+
+The motivation is a practical testing problem: a numerical model can continue integrating
+successfully while a small parameter or initial-condition change moves it into a different
+qualitative regime. PhaseProbe records the search configuration, solver method and tolerances,
+environment evidence, trajectory hashes, observables, classifications, and transition bracket so
+that the result can be independently replayed.
+
+The current release includes examples for Lorenz finite-time divergence and predator–prey
+invariant drift. For adaptive SciPy integrations, replay is tolerance-based rather than claimed to
+be bit-exact. The results are explicitly bounded, finite-time numerical evidence—not proofs of
+chaos, exact bifurcation locations, Lyapunov estimates, or globally minimal perturbations.
+
+Repository:
+https://github.com/aliengineering-byte/phaseprobe
+
+Release:
+https://github.com/aliengineering-byte/phaseprobe/releases/tag/v0.2.0
+
+PyPI:
+https://pypi.org/project/phaseprobe/
+
+Technical proposal and limitations:
+https://github.com/aliengineering-byte/phaseprobe/blob/v0.2.0/docs/upstream/SCIPY_INTEGRATION_PROPOSAL.md
+
+The release links above preserve the original 0.2.0 integration record. The installed-safe
+`--example scipy-*` commands shown here are included in the planned 0.2.1 packaging fix.
+
+I am not proposing to add PhaseProbe to SciPy core. I would value feedback on three points:
+
+1. Whether the tolerance-based replay evidence for adaptive `solve_ivp` trajectories is
+   scientifically and practically appropriate.
+2. Whether the trajectory-level adapter and recorded solver/environment metadata omit evidence
+   that SciPy users would expect.
+3. Whether a downstream example or ecosystem/documentation reference could be appropriate if the
+   tool proves useful to users.
+
+Feedback on the design, terminology, numerical claims, and useful real-world test cases would be
+very welcome.