From 1cac244259bb10a4fa149533dbae35b55e87f0d6 Mon Sep 17 00:00:00 2001
From: Richie Cahill <Richie@tmmworkshop.com>
Date: Fri, 18 Sep 2026 12:09:42 -0400
Subject: [PATCH] fix(scipy): allow rounding differences in STFT tests

Keep STFT tests enabled with precision-appropriate tolerances for
x86-64-v3 builds. Add the override under overlays/patches/scipy and
remove the commented-out test exclusions.
---
 overlays/patches/default.nix                  |  6 +++
 overlays/patches/scipy/default.nix            |  5 ++
 .../patches/scipy/stft-test-tolerances.patch  | 51 +++++++++++++++++++
 overlays/test-exclusions.nix                  | 10 ----
 4 files changed, 62 insertions(+), 10 deletions(-)
 create mode 100644 overlays/patches/scipy/default.nix
 create mode 100644 overlays/patches/scipy/stft-test-tolerances.patch

diff --git a/overlays/patches/default.nix b/overlays/patches/default.nix
index 1ffc6e6..df32fe5 100644
--- a/overlays/patches/default.nix
+++ b/overlays/patches/default.nix
@@ -1,3 +1,9 @@
 _final: prev: {
   gnutls = import ./gnutls { inherit (prev) gnutls; };
+
+  pythonPackagesExtensions = prev.pythonPackagesExtensions ++ [
+    (_pythonFinal: pythonPrev: {
+      scipy = import ./scipy { inherit (pythonPrev) scipy; };
+    })
+  ];
 }
diff --git a/overlays/patches/scipy/default.nix b/overlays/patches/scipy/default.nix
new file mode 100644
index 0000000..a6a3b5d
--- /dev/null
+++ b/overlays/patches/scipy/default.nix
@@ -0,0 +1,5 @@
+{ scipy }:
+scipy.overridePythonAttrs (old: {
+  # Keep the STFT tests enabled with tolerances for x86-64-v3 rounding.
+  patches = (old.patches or [ ]) ++ [ ./stft-test-tolerances.patch ];
+})
diff --git a/overlays/patches/scipy/stft-test-tolerances.patch b/overlays/patches/scipy/stft-test-tolerances.patch
new file mode 100644
index 0000000..016bf32
--- /dev/null
+++ b/overlays/patches/scipy/stft-test-tolerances.patch
@@ -0,0 +1,51 @@
+Subject: [PATCH] signal: allow floating-point rounding in STFT tests
+
+Keep the STFT tests enabled for x86-64-v3 builds. Allow two float32
+epsilons of relative error when comparing inverse-STFT implementations;
+float64 and the existing i686 override remain unchanged. Allow one
+float64 epsilon of absolute error in all three scaling round trips,
+which otherwise require exact zeros (observed residual: 4e-17 for a
+signal with amplitude 2).
+
+Upstream issue: https://github.com/scipy/scipy/issues/25488
+
+--- a/scipy/signal/tests/_scipy_spectral_test_shim.py
++++ b/scipy/signal/tests/_scipy_spectral_test_shim.py
+@@ -294,7 +294,7 @@
+ 
+     # Adapted tolerances to account for resolution loss:
+     atol = np.finfo(x.dtype).resolution*2  # instead of default atol = 0
+-    rtol = 1e-7  # default for np.allclose()
++    rtol = max(1e-7, 2 * np.finfo(x.dtype).eps)
+ 
+     # Relax atol on 32-Bit platforms a bit to pass CI tests.
+     #  - Not clear why there are discrepancies (in the FFT maybe?)
+--- a/scipy/signal/tests/test_spectral.py
++++ b/scipy/signal/tests/test_spectral.py
+@@ -2044,7 +2044,7 @@
+ 
+         # Test round trip:
+         x1 = istft(Zs, boundary=True, scaling='spectrum')[1]
+-        assert_allclose(x1, x)
++        assert_allclose(x1, x, atol=np.finfo(x.dtype).eps)
+ 
+         # For a Hann-windowed 256 sample length FFT, we expect a peak at
+         # frequency 64 (since it is 1/4 the length of X) with a height of 1
+@@ -2074,7 +2074,7 @@
+ 
+         # Test round trip:
+         x1 = istft(Zp, input_onesided=False, boundary=True, scaling='psd')[1]
+-        assert_allclose(x1, x)
++        assert_allclose(x1, x, atol=np.finfo(x.dtype).eps)
+ 
+         # The power of the one-sided psd-scaled STFT can be determined
+         # analogously (note that the two sides are not of equal shape):
+@@ -2094,7 +2094,7 @@
+ 
+         # Test round trip:
+         x1 = istft(Zp0, input_onesided=True, boundary=True, scaling='psd')[1]
+-        assert_allclose(x1, x)
++        assert_allclose(x1, x, atol=np.finfo(x.dtype).eps)
+ 
+ 
+ class TestSampledSpectralRepresentations:
diff --git a/overlays/test-exclusions.nix b/overlays/test-exclusions.nix
index ab8089c..48cda46 100644
--- a/overlays/test-exclusions.nix
+++ b/overlays/test-exclusions.nix
@@ -75,16 +75,6 @@ _final: prev: {
         '';
       });
 
-      # scipy = pythonPrev.scipy.overridePythonAttrs (old: {
-      #   # x86-64-v3 FFT implementations produce rounding differences outside
-      #   # these tests' strict tolerances. We accept the numerical-precision
-      #   # risk for our workloads.
-      #   disabledTests = (old.disabledTests or [ ]) ++ [
-      #     "test_roundtrip_float32"
-      #     "test_roundtrip_scaling"
-      #   ];
-      # });
-
       sentry-sdk = pythonPrev.sentry-sdk.overridePythonAttrs (old: {
         # This test globally mocks threading.current_thread while another
         # thread is running. On Python 3.14, Thread.join can race with that