nullcal 0.3.0__tar.gz → 0.3.1__tar.gz

{nullcal-0.3.0 → nullcal-0.3.1}/.github/workflows/codeql.yml

@@ -22,13 +22,13 @@ jobs:
               uses: actions/checkout@d23441a48e516b6c34aea4fa41551a30e30af803 # v6
 
             - name: Initialize CodeQL
-              uses: github/codeql-action/init@2892aa5e19bbd11bc0cff5427e3b750a04d9e3c2 # v4
+              uses: github/codeql-action/init@24c54180a607b1449ed407dd24f251e4e9147c8d # v4
               with:
                   languages: python
                   queries: security-and-quality
 
             - name: Autobuild
-              uses: github/codeql-action/autobuild@2892aa5e19bbd11bc0cff5427e3b750a04d9e3c2 # v4
+              uses: github/codeql-action/autobuild@24c54180a607b1449ed407dd24f251e4e9147c8d # v4
 
             - name: Perform CodeQL Analysis
-              uses: github/codeql-action/analyze@2892aa5e19bbd11bc0cff5427e3b750a04d9e3c2 # v4
+              uses: github/codeql-action/analyze@24c54180a607b1449ed407dd24f251e4e9147c8d # v4

{nullcal-0.3.0 → nullcal-0.3.1}/.github/workflows/scheduled_release.yml

@@ -31,7 +31,7 @@ jobs:
 
             - name: Check for new commits
               id: check_commits
-              uses: isaac-cf-wong/detect-git-changes-action@051225b2ef2faf2a02d61f16d1a027cdf941498d # v0.0.21
+              uses: isaac-cf-wong/detect-git-changes-action@9863c3c0ba155ed10b54072f711ae8807aedbc87 # v0.0.22
               with:
                   use-latest-tag: true
 

{nullcal-0.3.0 → nullcal-0.3.1}/.github/workflows/support_floor_update.yml

@@ -22,7 +22,7 @@ jobs:
 
             - name: Apply support policy (spec0, from pyproject tool table)
               id: policy
-              uses: isaac-cf-wong/dependency-support-policy-action@af9e20cfdcb7d14a4c08614e981e8c2339d3da0f # v0.2.11
+              uses: isaac-cf-wong/dependency-support-policy-action@f83b1c576c82b2a7dde5d3c38c222d68b76bb9cf # v0.2.12
               with:
                   mode: update
 

{nullcal-0.3.0 → nullcal-0.3.1}/.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
           - id: check-json
 
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.16.10
+      rev: v0.17.0
       hooks:
           - id: ruff
             args: [--fix, --config=pyproject.toml]
@@ -29,13 +29,13 @@ repos:
           - id: taplo-format
 
     - repo: https://github.com/crate-ci/typos
-      rev: v1.50.3
+      rev: v1.51.1
       hooks:
           - id: typos
             args: []
 
     - repo: https://github.com/rbubley/mirrors-prettier
-      rev: v3.9.9
+      rev: v3.9.10
       hooks:
           - id: prettier
             exclude: ^tests/e2e/diagnostics/likelihood_agreement\.json$
@@ -54,7 +54,7 @@ repos:
           - id: actionlint
 
     - repo: https://github.com/astral-sh/uv-pre-commit
-      rev: 0.12.23
+      rev: 0.13.0
       hooks:
           # Update the uv lockfile
           - id: uv-lock

{nullcal-0.3.0 → nullcal-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: nullcal
-Version: 0.3.0
+Version: 0.3.1
 Summary: A package to constrain calibration errors of a closed-geometry network of gravitational-wave detectors.
 Project-URL: Source, https://github.com/Leuven-Gravity-Institute/nullcal
 Project-URL: Tracker, https://github.com/Leuven-Gravity-Institute/nullcal/issues

{nullcal-0.3.0 → nullcal-0.3.1}/pyproject.toml

@@ -53,15 +53,15 @@ Tracker = "https://github.com/Leuven-Gravity-Institute/nullcal/issues"
 
 [dependency-groups]
 dev = [
-  "ruff>=0.16.10",
-  "prek>=0.5.4",
+  "ruff>=0.17.0",
+  "prek>=0.5.5",
   "pytest-github-actions-annotate-failures>=0.4.2",
   "pytest-cov>=7.1.0",
   "pytest-mock>=3.16.0",
   "pytest>=9.1.1",
 ]
 
-docs = ["zensical>=0.0.67", "mkdocstrings-python>=2.0.9"]
+docs = ["zensical>=0.0.69", "mkdocstrings-python>=2.0.9"]
 build = ["hatch>=1.18.1"]
 release = ["git-cliff>=2.14.2"]
 

{nullcal-0.3.0 → nullcal-0.3.1}/scripts/lwa_leakage_study.py

@@ -146,7 +146,7 @@ def write_readme(path: Path, results: list[dict[str, float | int]], commit: str,
             else "; no failure occurs on the tested grid"
         )
         recommendation = (
-            f"Use **20-{validity_maximum:.0f} Hz** as the conservative M3 LWA validity band on this grid{bracket}. "
+            f"Use **20-{validity_maximum:.0f} Hz** as the conservative LWA validity band on this grid{bracket}. "
             "This is a pre-check recommendation, not a measured continuous-frequency boundary."
         )
     maximum_failure_count = max(int(row["map_failure_count"]) for row in results)
@@ -168,7 +168,7 @@ The complete numerical table is `bias_vs_frequency.csv`; it also reports p99 and
 signal-minus-null statistic shift, the noise-only false-alarm fraction, ET-D PSD, and MAP convergence.
 No frequency has more than {maximum_failure_count} failed MAP fits.
 
-## Validity-band recommendation for M3
+## Validity-band recommendation
 
 {recommendation}
 
@@ -216,9 +216,10 @@ signal-present versus signal-absent pair is retained for the leakage significanc
 - The sky-factor distribution, leakage SNRs, MAP biases, and recommended band are new computational
   results produced by this run. No external numerical replication was found; they remain **unanchored
   to an independent numerical reference**. Agreement between code paths is not presented as accuracy.
-- This pre-check is not the M4 D2 result: it uses monochromatic bins, fixed SNR, independent equal ET-D
-  noise, a MAP rather than a posterior, and calibration parameters free at each frequency. M4 must use
-  a broadband source, the 19-knot calibration curve, posterior coverage, more noise realizations, and
+- This pre-check is not the full leakage-to-calibration-bias measurement: it uses monochromatic
+  bins, fixed SNR, independent equal ET-D noise, a MAP rather than a posterior, and calibration
+  parameters free at each frequency. That measurement must use a broadband source, the 19-knot
+  calibration curve, posterior coverage, more noise realizations, and
   frequency-dependent null mitigation. The ET-D curve affects physical strain/noise scaling, while the
   fixed-SNR whitened statistics deliberately isolate the geometric frequency dependence.
 

{nullcal-0.3.0 → nullcal-0.3.1}/scripts/run_reference_blackjax.py

@@ -1,4 +1,4 @@
-"""Run the fixed BlackJAX acceptance posterior against immutable R1 inputs."""
+"""Run the fixed BlackJAX acceptance posterior against the immutable end-to-end reference inputs."""
 
 from __future__ import annotations
 

{nullcal-0.3.0 → nullcal-0.3.1}/tests/e2e/generate_reference.py

@@ -30,6 +30,20 @@ MANIFEST_PATH = REFERENCE_DIR / "manifest.json"
 
 TRACKED_PACKAGES = ("nullcal", "bilby", "numpy", "scipy", "lalsuite")
 
+#: Written verbatim into the manifest's ``fixed_defects``. Kept here as the single source so the
+#: stored manifest can be checked against it; edit the text here and regenerate, never the JSON alone.
+FIXED_DEFECTS = {
+    "noise_log_likelihood": (
+        "Fixed. Before the fix, RecalibrationLikelihood.noise_log_likelihood() raised "
+        "IndexError, because compute_uncalibrated_time_frequency_domain_null_stream applied "
+        "the 2-D time-frequency filter to the 2-D frequency-domain array it had already "
+        "consumed and returned the time-frequency array unfiltered. The fix filters the "
+        "array it returns, matching the calibrated path. noise_log_likelihood and "
+        "uncalibrated_time_frequency_domain_null_stream are frozen artifacts from this "
+        "revision onward; earlier manifests record them as absent under known_defects."
+    )
+}
+
 
 def _digest(array: np.ndarray) -> str:
     """Content digest of an array, independent of how numpy chooses to lay it out."""
@@ -40,10 +54,11 @@ def _digest(array: np.ndarray) -> str:
 def _git_is_dirty() -> bool:
     """Whether tracked sources differ from HEAD, ignoring the reference artifacts being written.
 
-    Recorded because ``git_revision`` alone can lie. The R17 artifacts were first generated from a
-    working tree carrying an uncommitted fix, so the manifest named a revision that raises
-    ``IndexError`` and cannot produce them — provenance pointing at the opposite implementation
-    from the one that ran. A reviewer caught it; this makes it self-reporting.
+    Recorded because ``git_revision`` alone can lie. The artifacts frozen with the
+    ``noise_log_likelihood`` fix were first generated from a working tree carrying that fix
+    uncommitted, so the manifest named a revision that raises ``IndexError`` and cannot produce
+    them — provenance pointing at the opposite implementation from the one that ran. A reviewer
+    caught it; this makes it self-reporting.
     """
     try:
         output = subprocess.check_output(
@@ -113,17 +128,7 @@ def main() -> int:
             }
             for key, value in artifacts.items()
         },
-        "fixed_defects": {
-            "noise_log_likelihood": (
-                "Fixed in R17. Before that, RecalibrationLikelihood.noise_log_likelihood() raised "
-                "IndexError, because compute_uncalibrated_time_frequency_domain_null_stream applied "
-                "the 2-D time-frequency filter to the 2-D frequency-domain array it had already "
-                "consumed and returned the time-frequency array unfiltered. The fix filters the "
-                "array it returns, matching the calibrated path. noise_log_likelihood and "
-                "uncalibrated_time_frequency_domain_null_stream are frozen artifacts from this "
-                "revision onward; earlier manifests record them as absent under known_defects."
-            )
-        },
+        "fixed_defects": FIXED_DEFECTS,
     }
     MANIFEST_PATH.write_text(json.dumps(manifest, indent=2, sort_keys=True) + "\n")
 

{nullcal-0.3.0 → nullcal-0.3.1}/tests/e2e/reference/manifest.json

@@ -95,7 +95,7 @@
         }
     },
     "fixed_defects": {
-        "noise_log_likelihood": "Fixed in R17. Before that, RecalibrationLikelihood.noise_log_likelihood() raised IndexError, because compute_uncalibrated_time_frequency_domain_null_stream applied the 2-D time-frequency filter to the 2-D frequency-domain array it had already consumed and returned the time-frequency array unfiltered. The fix filters the array it returns, matching the calibrated path. noise_log_likelihood and uncalibrated_time_frequency_domain_null_stream are frozen artifacts from this revision onward; earlier manifests record them as absent under known_defects."
+        "noise_log_likelihood": "Fixed. Before the fix, RecalibrationLikelihood.noise_log_likelihood() raised IndexError, because compute_uncalibrated_time_frequency_domain_null_stream applied the 2-D time-frequency filter to the 2-D frequency-domain array it had already consumed and returned the time-frequency array unfiltered. The fix filters the array it returns, matching the calibrated path. noise_log_likelihood and uncalibrated_time_frequency_domain_null_stream are frozen artifacts from this revision onward; earlier manifests record them as absent under known_defects."
     },
     "git_dirty": false,
     "git_revision": "549a50ad86a3935d7c37abf24445ba78beb639e5",

{nullcal-0.3.0 → nullcal-0.3.1}/tests/e2e/reference/posterior_manifest.json

@@ -150,6 +150,6 @@
     },
     "smoke": false,
     "unavailable_at_this_revision": {
-        "log_noise_evidence": "NaN by construction: noise_log_likelihood() raises IndexError on this revision (the R1 defect, fixed in R17), and bilby calls it unconditionally after sampling. log_bayes_factor is NaN for the same reason. Neither is part of the anchor."
+        "log_noise_evidence": "NaN by construction: noise_log_likelihood() raises IndexError on this revision (a defect fixed in a later revision; see fixed_defects in manifest.json), and bilby calls it unconditionally after sampling. log_bayes_factor is NaN for the same reason. Neither is part of the anchor."
     }
 }

{nullcal-0.3.0 → nullcal-0.3.1}/tests/e2e/test_reference_artifacts.py

@@ -16,13 +16,14 @@ from pathlib import Path
 import numpy as np
 import pytest
 
-from . import generate_reference_inputs, pipeline
+from . import generate_reference, generate_reference_inputs, pipeline
 
 REFERENCE_DIR = Path(__file__).parent / "reference"
 ARTIFACT_PATH = REFERENCE_DIR / "artifacts.npz"
 MANIFEST_PATH = REFERENCE_DIR / "manifest.json"
 INPUT_ARTIFACT_PATH = REFERENCE_DIR / "inputs.npz"
 INPUT_MANIFEST_PATH = REFERENCE_DIR / "inputs_manifest.json"
+POSTERIOR_MANIFEST_PATH = REFERENCE_DIR / "posterior_manifest.json"
 
 pytestmark = [pytest.mark.e2e, pytest.mark.slow]
 
@@ -279,11 +280,50 @@ def test_manifest_configuration_matches_the_live_config(manifest):
         assert recorded[key] == value, f"manifest configuration[{key!r}] = {recorded[key]!r}, config.py says {value!r}"
 
 
+def test_manifest_fixed_defects_match_the_generator(manifest):
+    """The stored defect notes must be exactly what the generator writes.
+
+    The same prose lives in two places: ``generate_reference.FIXED_DEFECTS`` and the committed
+    ``manifest.json``. Nothing else reads it, so an edit to one copy alone would leave the manifest
+    describing a fix the generator no longer states, with every other test still green. Compare the
+    UTF-8 bytes per key, not just the parsed dicts, so the failure names the entry that drifted.
+    """
+    stored = manifest.get("fixed_defects")
+    assert isinstance(stored, dict), "manifest has no fixed_defects mapping"
+    expected = generate_reference.FIXED_DEFECTS
+    assert set(stored) == set(expected), (
+        f"manifest fixed_defects keys {sorted(stored)} differ from the generator's {sorted(expected)}"
+    )
+    for key, text in expected.items():
+        assert stored[key].encode("utf-8") == text.encode("utf-8"), (
+            f"fixed_defects[{key!r}] in manifest.json differs from generate_reference.FIXED_DEFECTS; "
+            "edit the generator and regenerate rather than editing either copy alone"
+        )
+
+
+def test_posterior_manifest_defect_note_points_at_a_recorded_fix(manifest):
+    """The posterior manifest explains its NaN noise evidence by pointing at ``fixed_defects``.
+
+    That note has no generator in this repository, so it cannot be compared against one. What can
+    be checked is that the pointer resolves: the defect it names must have an entry in the
+    artifact manifest, or the explanation sends the reader to a record that does not exist.
+    """
+    if not POSTERIOR_MANIFEST_PATH.exists():
+        pytest.fail(f"reference posterior manifest absent: {POSTERIOR_MANIFEST_PATH}")
+    note = json.loads(POSTERIOR_MANIFEST_PATH.read_text())["unavailable_at_this_revision"]["log_noise_evidence"]
+    assert "noise_log_likelihood()" in note, "log_noise_evidence note no longer names the defective method"
+    assert "fixed_defects in manifest.json" in note, "log_noise_evidence note no longer points at fixed_defects"
+    assert "noise_log_likelihood" in manifest.get("fixed_defects", {}), (
+        "posterior manifest points at fixed_defects for noise_log_likelihood, but manifest.json has no such entry"
+    )
+
+
 def test_manifest_provenance_is_not_from_a_dirty_tree(manifest):
     """A recorded revision that cannot reproduce the artifacts is worse than none.
 
-    R17's artifacts were first generated from a working tree carrying an uncommitted fix, so the
-    manifest named ``main``, whose code raises ``IndexError`` and cannot produce two of the keys
+    The artifacts frozen with the ``noise_log_likelihood`` fix were first generated from a working
+    tree carrying that fix uncommitted, so the manifest named ``main``, whose code raises
+    ``IndexError`` and cannot produce two of the keys
     the manifest describes. Nothing detected it — the digests were self-consistent and every test
     passed. This asserts the generator was run on a clean tree, which is what makes
     ``git_revision`` a reproduction instruction rather than a decoration.