From cf24b92bed6cc5e353c73e574adf82e86e41b0b7 Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Thu, 29 Aug 2024 11:01:44 -0400
Subject: [PATCH 01/25] remove scikit radon warning by adjusting radial mask
 for test image to r < .99

---
 tests/test_sinogram.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_sinogram.py b/tests/test_sinogram.py
index bbf448db97..7a1f32a0e0 100644
--- a/tests/test_sinogram.py
+++ b/tests/test_sinogram.py
@@ -113,7 +113,7 @@ def test_project_multidim(num_ang):
 
     # Generate a mask
     g = grid_2d(L, normalized=True, shifted=True)
-    mask = g["r"] < 1
+    mask = g["r"] < .99
 
     # Generate images
     imgs = Image(np.random.random((m, n, L, L))) * mask

From fd96cc0a1a2a060233ee8b979066fa62921b2beb Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Thu, 29 Aug 2024 11:36:22 -0400
Subject: [PATCH 02/25] tox

---
 tests/test_sinogram.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_sinogram.py b/tests/test_sinogram.py
index 7a1f32a0e0..dc173449b9 100644
--- a/tests/test_sinogram.py
+++ b/tests/test_sinogram.py
@@ -113,7 +113,7 @@ def test_project_multidim(num_ang):
 
     # Generate a mask
     g = grid_2d(L, normalized=True, shifted=True)
-    mask = g["r"] < .99
+    mask = g["r"] < 0.99
 
     # Generate images
     imgs = Image(np.random.random((m, n, L, L))) * mask

From 2d8b2a23dfb527d83ba80eb13d284bfc92db6506 Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Thu, 29 Aug 2024 15:11:46 -0400
Subject: [PATCH 03/25] resolve scipy cg warning by adjusting version in
 wrapper to 1.12.0

---
 src/aspire/numeric/scipy.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/aspire/numeric/scipy.py b/src/aspire/numeric/scipy.py
index 8f2e7d86d8..c913e917a3 100644
--- a/src/aspire/numeric/scipy.py
+++ b/src/aspire/numeric/scipy.py
@@ -8,10 +8,11 @@
 
 def cg(*args, **kwargs):
     """
-    Supports scipy cg before and after 1.14.0.
+    Supports scipy cg before and after 1.12.0.
     """
 
-    # older scipy cg interface uses `tol` instead of `rtol`
-    if Version(scipy.__version__) < Version("1.14.0"):
+    # older (<1.12.0) scipy cg interface uses `tol` instead of `rtol`.
+    # `tol` will be removed in scipy 1.14.0.
+    if Version(scipy.__version__) < Version("1.12.0"):
         kwargs["tol"] = kwargs.pop("rtol", None)
     return scipy.sparse.linalg.cg(*args, **kwargs)

From 7886c467c5a74fd99fea525f0372a38fc0e3fec7 Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Thu, 29 Aug 2024 15:23:30 -0400
Subject: [PATCH 04/25] Resolve Matplotlib warning by explicilty closing plots
 in testing.

---
 tests/test_simulation.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/tests/test_simulation.py b/tests/test_simulation.py
index 92a29e225e..c90caa5bdd 100644
--- a/tests/test_simulation.py
+++ b/tests/test_simulation.py
@@ -3,6 +3,7 @@
 import tempfile
 from unittest import TestCase
 
+import matplotlib.pyplot as plt
 import numpy as np
 from pytest import raises
 
@@ -38,14 +39,23 @@ def testPixelSize(self):
     def testImageShow(self):
         self.sim.images[:].show()
 
+        # Explicitly close all figures before making backend changes.
+        plt.close("all")
+
     @matplotlib_dry_run
     def testCleanImagesShow(self):
         self.sim.clean_images[:].show()
 
+        # Explicitly close all figures before making backend changes.
+        plt.close("all")
+
     @matplotlib_dry_run
     def testProjectionsShow(self):
         self.sim.projections[:].show()
 
+        # Explicitly close all figures before making backend changes.
+        plt.close("all")
+
 
 class SimVolTestCase(TestCase):
     """Test Simulation with Volume provided."""

From ba58b43f9df6c41d505bb951af0b3d5e456ff6cb Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Tue, 3 Sep 2024 10:11:49 -0400
Subject: [PATCH 05/25] explicitly close figures in matplotlib test wrapper.

---
 tests/test_utils.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/test_utils.py b/tests/test_utils.py
index ffad5bc9f6..c7617d28a8 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -399,6 +399,9 @@ def matplotlib_no_gui():
 
         yield
 
+    # Explicitly close all figures before making backend changes.
+    matplotlib.pyplot.close("all")
+
     # Restore backend
     matplotlib.use(backend)
 

From 80274fecd7c1a66d05dfa4181ec55e03a52a7adf Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Tue, 3 Sep 2024 11:10:12 -0400
Subject: [PATCH 06/25] Resolve FRC legend warning by adding default label for
 single correlation.

---
 src/aspire/utils/resolution_estimation.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/aspire/utils/resolution_estimation.py b/src/aspire/utils/resolution_estimation.py
index 14c142bdc5..2baefe4491 100644
--- a/src/aspire/utils/resolution_estimation.py
+++ b/src/aspire/utils/resolution_estimation.py
@@ -354,7 +354,7 @@ def plot(self, cutoff=None, save_to_file=False, labels=None):
         plt.ylabel("Correlation")
         plt.ylim([0, 1.1])
         for i, line in enumerate(self.correlations):
-            _label = None
+            _label = "correlation"
             if len(self.correlations) > 1:
                 _label = f"{i}"
                 if labels is not None:

From 8011e109474f0600f2d6bb077f2e0b9a8cc14f62 Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Tue, 3 Sep 2024 11:16:35 -0400
Subject: [PATCH 07/25] resolve numpy.product warning

---
 src/aspire/sinogram/sinogram.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/aspire/sinogram/sinogram.py b/src/aspire/sinogram/sinogram.py
index 34451a396d..7c7bb43662 100644
--- a/src/aspire/sinogram/sinogram.py
+++ b/src/aspire/sinogram/sinogram.py
@@ -42,7 +42,7 @@ def __init__(self, data, dtype=None):
         self.shape = self._data.shape
         self.stack_shape = self._data.shape[:-2]
         self.stack_n_dim = self._data.ndim - 2
-        self.n = np.product(self.stack_shape)
+        self.n = np.prod(self.stack_shape)
         self.n_angles = self._data.shape[-2]
         self.n_radial_points = self._data.shape[-1]
 

From 358afa67ee5372323437baa24d28791680e4693a Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Tue, 3 Sep 2024 14:19:03 -0400
Subject: [PATCH 08/25] resolve Conversion of an array wit h ndim > 0 to a
 scalar is deprecated, by returning scalar for single value returns

---
 src/aspire/abinitio/commonline_c3_c4.py | 8 +++++++-
 src/aspire/utils/rotation.py            | 4 ++++
 tests/test_rotation.py                  | 3 +++
 3 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/aspire/abinitio/commonline_c3_c4.py b/src/aspire/abinitio/commonline_c3_c4.py
index 68469618dd..0e0ca76565 100644
--- a/src/aspire/abinitio/commonline_c3_c4.py
+++ b/src/aspire/abinitio/commonline_c3_c4.py
@@ -850,7 +850,13 @@ def cl_angles_to_ind(cl_angles, n_theta):
         thetas = np.mod(thetas, 2 * np.pi)
 
         # linear scale from [0,2*pi) to [0,n_theta).
-        return np.mod(np.round(thetas / (2 * np.pi) * n_theta), n_theta).astype(int)
+        ind = np.mod(np.round(thetas / (2 * np.pi) * n_theta), n_theta).astype(int)
+
+        # Return scalar for single value.
+        if ind.size == 1:
+            ind = ind.flat[0]
+
+        return ind
 
     @staticmethod
     def g_sync(rots, order, rots_gt):
diff --git a/src/aspire/utils/rotation.py b/src/aspire/utils/rotation.py
index 08bec4ca3d..dc713a74ad 100644
--- a/src/aspire/utils/rotation.py
+++ b/src/aspire/utils/rotation.py
@@ -408,6 +408,10 @@ def angle_dist(r1, r2, dtype=None):
         theta = (tr_r[non_zero_dist_ind] - 1) / 2
         theta = np.maximum(np.minimum(theta, 1), -1)  # Clamp theta in [-1,1]
         dist[non_zero_dist_ind] = np.arccos(theta, dtype=dtype)
+
+        # If we only have one value, return as a scalar.
+        if dist.size == 1:
+            dist = dist.flat[0]
         return dist
 
     @staticmethod
diff --git a/tests/test_rotation.py b/tests/test_rotation.py
index 9e0dba4ec6..e02e650bd5 100644
--- a/tests/test_rotation.py
+++ b/tests/test_rotation.py
@@ -173,6 +173,9 @@ def test_angle_dist(dtype):
     with pytest.raises(ValueError, match=r"r1 and r2 are not broadcastable*"):
         _ = Rotation.angle_dist(rots[:3], rots[:5])
 
+    # Test that single value returns as 0-dim.
+    assert Rotation.angle_dist(rots[0], rots[1], dtype).ndim == 0
+
 
 def test_mean_angular_distance(dtype):
     rots_z = Rotation.about_axis("z", [0, np.pi / 4, np.pi / 2], dtype=dtype).matrices

From dd65d1c0150160e5c6073e0c7d9d09120034f4f8 Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Tue, 3 Sep 2024 16:07:00 -0400
Subject: [PATCH 09/25] Resolve expected BlkDiagMatrix truncation warning.

---
 tests/test_covar2d_denoiser.py | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/tests/test_covar2d_denoiser.py b/tests/test_covar2d_denoiser.py
index 7b4da5511e..c9b749335b 100644
--- a/tests/test_covar2d_denoiser.py
+++ b/tests/test_covar2d_denoiser.py
@@ -22,8 +22,21 @@
     pytest.param(FBBasis2D, marks=pytest.mark.expensive),
     FFBBasis2D,
     FLEBasis2D,
-    pytest.param(PSWFBasis2D, marks=pytest.mark.expensive),
-    FPSWFBasis2D,
+    pytest.param(
+        PSWFBasis2D,
+        marks=[
+            pytest.mark.expensive,
+            pytest.mark.filterwarnings(
+                "ignore:BlkDiagMatrix.from_dense truncating values*"
+            ),
+        ],
+    ),
+    pytest.param(
+        FPSWFBasis2D,
+        marks=pytest.mark.filterwarnings(
+            "ignore:BlkDiagMatrix.from_dense truncating values*"
+        ),
+    ),
 ]
 
 

From 194434c4facfa6a9d50925c16b468daa9cdf557c Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Wed, 4 Sep 2024 10:04:26 -0400
Subject: [PATCH 10/25] Resolve test_micrograph_source warnings by using zeros
 instead of empty for test images.

---
 tests/test_micrograph_source.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_micrograph_source.py b/tests/test_micrograph_source.py
index 06c5874a07..d4793cf61f 100644
--- a/tests/test_micrograph_source.py
+++ b/tests/test_micrograph_source.py
@@ -285,7 +285,7 @@ def test_rectangular_micrograph_source_files():
     """
 
     # Test inconsistent mrc files
-    imgs = [np.empty((7, 7)), np.empty((8, 8))]
+    imgs = [np.zeros((7, 7)), np.zeros((8, 8))]
     with tempfile.TemporaryDirectory() as tmp_output_dir:
         # Save the files
         for i, img in enumerate(imgs):

From 23e3a07b6e99a6a0a7f1f2a244692c13fdbd25f5 Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Mon, 9 Sep 2024 11:04:28 -0400
Subject: [PATCH 11/25] Resolve test_image.py warning. Remove Ray xfail and use
 context to check caplog.

---
 tests/test_image.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/tests/test_image.py b/tests/test_image.py
index 887e726c0d..ec7bb42e0e 100644
--- a/tests/test_image.py
+++ b/tests/test_image.py
@@ -353,14 +353,11 @@ def test_asnumpy_readonly():
         vw[0, 0, 0] = 123
 
 
-@pytest.mark.xfail(reason="Ray logging issue ray#37711", strict=False)
 def test_corrupt_mrc_load(caplog):
     """
     Test that corrupt mrc files are logged as expected.
     """
 
-    caplog.set_level(logging.WARNING)
-
     # Create a tmp dir for this test output
     with tempfile.TemporaryDirectory() as tmpdir_name:
         # tmp filename
@@ -374,13 +371,16 @@ def test_corrupt_mrc_load(caplog):
             fh.header.map = -1
 
         # Check that we get a WARNING
-        _ = Image.load(mrc_path)
+        with caplog.at_level(logging.WARNING):
+            _ = Image.load(mrc_path)
+
+            # Check the message prefix
+            assert f"Image.load of {mrc_path} reporting 1 corruptions" in caplog.text
 
-    # Check the message prefix
-    assert f"Image.load of {mrc_path} reporting 1 corruptions" in caplog.text
+            # Check the message contains the file path
+            assert mrc_path in caplog.text
 
-    # Check the message contains the file path
-    assert mrc_path in caplog.text
+            caplog.clear()
 
 
 def test_load_bad_ext():

From bb76e21311695afa6f0082d4385f8a7a6df2ddda Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Mon, 9 Sep 2024 11:42:17 -0400
Subject: [PATCH 12/25] resolve test_FLEbasis2D.py warnings.

---
 tests/test_FLEbasis2D.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_FLEbasis2D.py b/tests/test_FLEbasis2D.py
index ffb1f8f7d1..e60346f84b 100644
--- a/tests/test_FLEbasis2D.py
+++ b/tests/test_FLEbasis2D.py
@@ -232,7 +232,7 @@ def testRadialConvolution():
     # (e.g. CTF) function via FLE coefficients
 
     L = 32
-    basis = FLEBasis2D(L, match_fb=False)
+    basis = FLEBasis2D(L, match_fb=False, dtype=np.float64)
     # load test radial function
     x = np.load(os.path.join(DATA_DIR, "fle_radial_fn_32x32.npy")).reshape(1, 32, 32)
     x = x / np.max(np.abs(x.flatten()))
@@ -245,7 +245,7 @@ def testRadialConvolution():
     imgs_convolved_fle = basis.evaluate(coefs_convolved).asnumpy()
 
     # convolve using FFT
-    x = basis.evaluate(basis.evaluate_t(x)).asnumpy()
+    x = basis.evaluate(basis.evaluate_t(Image(x))).asnumpy()
     ims = basis.evaluate(coefs).asnumpy()
 
     imgs_convolved_slow = np.zeros((10, L, L))

From 1f292cc767d54b034509cf1cff926df25081a0c0 Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Mon, 9 Sep 2024 12:09:49 -0400
Subject: [PATCH 13/25] resolve numpy multiply overflow warning by using ones
 for test image instead of np.empty.

---
 tests/test_image.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_image.py b/tests/test_image.py
index ec7bb42e0e..89fbde4a84 100644
--- a/tests/test_image.py
+++ b/tests/test_image.py
@@ -364,7 +364,7 @@ def test_corrupt_mrc_load(caplog):
         mrc_path = os.path.join(tmpdir_name, "bad.mrc")
 
         # Create and save image
-        Image(np.empty((1, 8, 8), dtype=np.float32)).save(mrc_path)
+        Image(np.ones((1, 8, 8), dtype=np.float32)).save(mrc_path)
 
         # Open mrc file and soft corrupt it
         with mrcfile.open(mrc_path, "r+") as fh:

From 6ef824caccb654ed6b9f3447b0b84477f044e1bd Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Mon, 9 Sep 2024 15:09:38 -0400
Subject: [PATCH 14/25] resolve test_diag_matrix.py invalid cast value warning,
 by replacing empty's with ones.

---
 tests/test_diag_matrix.py | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/tests/test_diag_matrix.py b/tests/test_diag_matrix.py
index ecce899105..05805912c9 100644
--- a/tests/test_diag_matrix.py
+++ b/tests/test_diag_matrix.py
@@ -77,7 +77,7 @@ def test_repr():
     Test accessing the `repr` does not crash.
     """
 
-    d = DiagMatrix(np.empty((10, 8)))
+    d = DiagMatrix(np.ones((10, 8)))
     assert repr(d).startswith("DiagMatrix(")
 
 
@@ -86,7 +86,7 @@ def test_str():
     Test accessing the `str` does not crash.
     """
 
-    d = DiagMatrix(np.empty((10, 8)))
+    d = DiagMatrix(np.ones((10, 8)))
     assert str(d).startswith("DiagMatrix(")
 
 
@@ -104,13 +104,13 @@ def test_len():
     """
     Test the `len`.
     """
-    d = DiagMatrix(np.empty((10, 8)))
+    d = DiagMatrix(np.ones((10, 8)))
 
     assert d.size == 10
     assert d.count == 8
     assert len(d) == 10
 
-    d = DiagMatrix(np.empty((2, 5, 8)))
+    d = DiagMatrix(np.ones((2, 5, 8)))
 
     assert d.size == 10
     assert d.count == 8
@@ -121,8 +121,8 @@ def test_size_mismatch():
     """
     Test we raise operating on `DiagMatrix` having different counts.
     """
-    d1 = DiagMatrix(np.empty((10, 8)))
-    d2 = DiagMatrix(np.empty((10, 7)))
+    d1 = DiagMatrix(np.ones((10, 8)))
+    d2 = DiagMatrix(np.ones((10, 7)))
 
     with pytest.raises(RuntimeError, match=r".*not same dimension.*"):
         _ = d1 + d2
@@ -132,8 +132,8 @@ def test_dtype_mismatch():
     """
     Test we raise operating on `DiagMatrix` having different dtypes.
     """
-    d1 = DiagMatrix(np.empty((10, 8)), dtype=np.float32)
-    d2 = DiagMatrix(np.empty((10, 8)), dtype=np.float64)
+    d1 = DiagMatrix(np.ones((10, 8)), dtype=np.float32)
+    d2 = DiagMatrix(np.ones((10, 8)), dtype=np.float64)
 
     with pytest.raises(RuntimeError, match=r".*received different types.*"):
         _ = d1 + d2
@@ -144,7 +144,7 @@ def test_dtype_passthrough():
     Test that the datatype is inferred correctly.
     """
     for dtype in (int, np.float32, np.float64, np.complex64, np.complex128):
-        d_np = np.empty(42, dtype=dtype)
+        d_np = np.ones(42, dtype=dtype)
         d = DiagMatrix(d_np)
         assert d.dtype == dtype
 
@@ -154,7 +154,7 @@ def test_dtype_cast():
     Test that a datatype is cast when overridden.
     """
     for dtype in (int, np.float32, np.float64, np.complex64, np.complex128):
-        d_np = np.empty(42, dtype=np.float16)
+        d_np = np.ones(42, dtype=np.float16)
         d = DiagMatrix(d_np, dtype)
         assert d.dtype == dtype
 
@@ -444,7 +444,7 @@ def test_diag_badtype_matmul():
     """
     Test matrix multiply of `DiagMatrix` with incompatible type raises.
     """
-    d1 = DiagMatrix(np.empty(8))
+    d1 = DiagMatrix(np.ones(8))
 
     # matmul
     with pytest.raises(RuntimeError, match=r".*not implemented for.*"):
@@ -576,7 +576,7 @@ def test_bad_as_blk_diag(matrix_size, blk_diag):
     """
     with pytest.raises(RuntimeError, match=r".*only implemented for singletons.*"):
         # Construct via Numpy.
-        d_np = np.empty((2, matrix_size), dtype=blk_diag.dtype)
+        d_np = np.ones((2, matrix_size), dtype=blk_diag.dtype)
 
         # Create DiagMatrix then convert to BlkDiagMatrix
         d = DiagMatrix(d_np)
@@ -654,7 +654,7 @@ def test_diag_blk_mul():
     """
     Test mixing `BlkDiagMatrix` with `DiagMatrix` element-wise multiplication raises.
     """
-    d = DiagMatrix(np.empty(8))
+    d = DiagMatrix(np.ones(8))
 
     partition = [(4, 4), (4, 4)]
     b = BlkDiagMatrix.ones(partition, dtype=d.dtype)
@@ -672,7 +672,7 @@ def test_non_square_as_blk_diag():
     """
     Test non square partition blocks raise an error in as_blk_diag.
     """
-    d = DiagMatrix(np.empty(8))
+    d = DiagMatrix(np.ones(8))
 
     partition = [(4, 5), (4, 3)]
     with pytest.raises(RuntimeError, match=r".*not square.*"):
@@ -683,8 +683,8 @@ def test_bad_broadcast():
     """
     Test incompatible stack shapes raise appropriate error.
     """
-    d1 = DiagMatrix(np.empty((2, 3, 8)))
-    d2 = DiagMatrix(np.empty((2, 2, 8)))
+    d1 = DiagMatrix(np.ones((2, 3, 8)))
+    d2 = DiagMatrix(np.ones((2, 2, 8)))
 
     with pytest.raises(ValueError, match=r".*incompatible shapes.*"):
         _ = d1 + d2

From a641921daa3732f3417af79f691da46df2371b54 Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Tue, 10 Sep 2024 09:21:06 -0400
Subject: [PATCH 15/25] catch np.exp overflow warnings

---
 src/aspire/abinitio/commonline_sync3n.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/aspire/abinitio/commonline_sync3n.py b/src/aspire/abinitio/commonline_sync3n.py
index 3c40eb3ac5..6efb429818 100644
--- a/src/aspire/abinitio/commonline_sync3n.py
+++ b/src/aspire/abinitio/commonline_sync3n.py
@@ -1,5 +1,6 @@
 import logging
 import os.path
+import warnings
 
 import numpy as np
 from numpy.linalg import norm
@@ -727,7 +728,13 @@ def fun(x, B, P, b, x0, A=A, a=a):
 
         # Calculate probabilities
         ln_f_ind, ln_f_arb = self._pairs_probabilities(Rijs, P**2, A, a, B, b, x0)
-        Pij = 1 / (1 + (1 - P) / P * np.exp(ln_f_arb - ln_f_ind))
+
+        with warnings.catch_warnings():
+            # For large values of (ln_f_arb - ln_f_ind), numpy exponential will overflow. We still
+            # get the intended result of Pij = 0, so we capture and ignore the overflow warning.
+            warnings.filterwarnings("ignore", r".*overflow encountered in exp.*")
+
+            Pij = 1 / (1 + (1 - P) / P * np.exp(ln_f_arb - ln_f_ind))
 
         # Fix singular output
         num_nan = np.sum(np.isnan(Pij))

From 0f9e9b50f34b2ee2e05fae3e9dfd6c3014591c6e Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Tue, 10 Sep 2024 10:21:43 -0400
Subject: [PATCH 16/25] Add comments explaining changes.

---
 src/aspire/utils/resolution_estimation.py | 1 +
 src/aspire/utils/rotation.py              | 2 +-
 tests/test_FLEbasis2D.py                  | 5 +++--
 tests/test_covar2d_denoiser.py            | 3 +++
 4 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/aspire/utils/resolution_estimation.py b/src/aspire/utils/resolution_estimation.py
index 2baefe4491..af5a46f8a9 100644
--- a/src/aspire/utils/resolution_estimation.py
+++ b/src/aspire/utils/resolution_estimation.py
@@ -354,6 +354,7 @@ def plot(self, cutoff=None, save_to_file=False, labels=None):
         plt.ylabel("Correlation")
         plt.ylim([0, 1.1])
         for i, line in enumerate(self.correlations):
+            # Set default label for single correlation (required by plt.legend() below).
             _label = "correlation"
             if len(self.correlations) > 1:
                 _label = f"{i}"
diff --git a/src/aspire/utils/rotation.py b/src/aspire/utils/rotation.py
index dc713a74ad..07a31df9df 100644
--- a/src/aspire/utils/rotation.py
+++ b/src/aspire/utils/rotation.py
@@ -409,7 +409,7 @@ def angle_dist(r1, r2, dtype=None):
         theta = np.maximum(np.minimum(theta, 1), -1)  # Clamp theta in [-1,1]
         dist[non_zero_dist_ind] = np.arccos(theta, dtype=dtype)
 
-        # If we only have one value, return as a scalar.
+        # Return scalar for single value.
         if dist.size == 1:
             dist = dist.flat[0]
         return dist
diff --git a/tests/test_FLEbasis2D.py b/tests/test_FLEbasis2D.py
index e60346f84b..0873d61bab 100644
--- a/tests/test_FLEbasis2D.py
+++ b/tests/test_FLEbasis2D.py
@@ -230,16 +230,17 @@ def testLowPass():
 def testRadialConvolution():
     # test ability to accurately convolve with a radial
     # (e.g. CTF) function via FLE coefficients
-
     L = 32
-    basis = FLEBasis2D(L, match_fb=False, dtype=np.float64)
+
     # load test radial function
     x = np.load(os.path.join(DATA_DIR, "fle_radial_fn_32x32.npy")).reshape(1, 32, 32)
     x = x / np.max(np.abs(x.flatten()))
 
     # get sample images
     ims = create_images(L, 10)
+
     # convolve using coefficients
+    basis = FLEBasis2D(L, match_fb=False, dtype=ims.dtype)
     coefs = basis.evaluate_t(ims)
     coefs_convolved = basis.radial_convolve(coefs, x)
     imgs_convolved_fle = basis.evaluate(coefs_convolved).asnumpy()
diff --git a/tests/test_covar2d_denoiser.py b/tests/test_covar2d_denoiser.py
index c9b749335b..ea5410fb34 100644
--- a/tests/test_covar2d_denoiser.py
+++ b/tests/test_covar2d_denoiser.py
@@ -18,6 +18,9 @@
     RadialCTFFilter(5, 200, defocus=d, Cs=2.0, alpha=0.1)
     for d in np.linspace(1.5e4, 2.5e4, 7)
 ]
+
+# For (F)PSWFBasis2D we get off-block entries which are truncated
+# when converting to block-diagonal. We filter these warnings.
 BASIS = [
     pytest.param(FBBasis2D, marks=pytest.mark.expensive),
     FFBBasis2D,

From 6ed06437afc50b5ce9e30872a344e25e1bb14adc Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Tue, 10 Sep 2024 13:55:48 -0400
Subject: [PATCH 17/25] Add pytest --strict-warnings to CI workflows.

---
 .github/workflows/long_workflow.yml | 2 +-
 .github/workflows/workflow.yml      | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/long_workflow.yml b/.github/workflows/long_workflow.yml
index ec5714a29e..d483ac5912 100644
--- a/.github/workflows/long_workflow.yml
+++ b/.github/workflows/long_workflow.yml
@@ -36,6 +36,6 @@ jobs:
         export OMP_NUM_THREADS=1
         ASPIREDIR=${{ env.WORK_DIR }} python -c \
         "import aspire; print(aspire.config['ray']['temp_dir'])"
-        ASPIREDIR=${{ env.WORK_DIR }} python -m pytest -n8 -m "expensive" --durations=0
+        ASPIREDIR=${{ env.WORK_DIR }} python -m pytest -n8 -m "expensive" --durations=0 --strict-warnings
     - name: Cleanup
       run: rm -rf ${{ env.WORK_DIR }}
diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index b2263a460b..ead21b923f 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -99,7 +99,7 @@ jobs:
       run: |
         export OMP_NUM_THREADS=2
         # -n runs test in parallel using pytest-xdist
-        pytest -n2 --durations=50 -s
+        pytest -n2 --durations=50 -s --strict-warnings
 
   # Build and Deploy production (main) docs.
   docs_deploy:
@@ -157,7 +157,7 @@ jobs:
       run: |
         ASPIREDIR=${{ env.WORK_DIR }} python -c \
         "import aspire; print(aspire.config['ray']['temp_dir'])"
-        ASPIREDIR=${{ env.WORK_DIR }} python -m pytest --durations=50
+        ASPIREDIR=${{ env.WORK_DIR }} python -m pytest --durations=50 --strict-warnings
     - name: Cache Data
       run: |
         ASPIREDIR=${{ env.WORK_DIR }} python -c \
@@ -247,4 +247,4 @@ jobs:
         pip install -e ".[dev]"  # install aspire
         pip freeze
     - name: Test
-      run: python -m pytest -n3 --durations=50
+      run: python -m pytest -n3 --durations=50 --strict-warnings

From 0366a10ce54543f815de1f4069a2acfd57c24b4e Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Tue, 10 Sep 2024 14:15:10 -0400
Subject: [PATCH 18/25] Use PYTHONWARNINGS=error when python runs pytest.

---
 .github/workflows/long_workflow.yml | 2 +-
 .github/workflows/workflow.yml      | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/long_workflow.yml b/.github/workflows/long_workflow.yml
index d483ac5912..a2f2938c8f 100644
--- a/.github/workflows/long_workflow.yml
+++ b/.github/workflows/long_workflow.yml
@@ -36,6 +36,6 @@ jobs:
         export OMP_NUM_THREADS=1
         ASPIREDIR=${{ env.WORK_DIR }} python -c \
         "import aspire; print(aspire.config['ray']['temp_dir'])"
-        ASPIREDIR=${{ env.WORK_DIR }} python -m pytest -n8 -m "expensive" --durations=0 --strict-warnings
+        ASPIREDIR=${{ env.WORK_DIR }} PYTHONWARNINGS=error python -m pytest -n8 -m "expensive" --durations=0
     - name: Cleanup
       run: rm -rf ${{ env.WORK_DIR }}
diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index ead21b923f..253876f83c 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -157,7 +157,7 @@ jobs:
       run: |
         ASPIREDIR=${{ env.WORK_DIR }} python -c \
         "import aspire; print(aspire.config['ray']['temp_dir'])"
-        ASPIREDIR=${{ env.WORK_DIR }} python -m pytest --durations=50 --strict-warnings
+        ASPIREDIR=${{ env.WORK_DIR }} PYTHONWARNINGS=error python -m pytest --durations=50
     - name: Cache Data
       run: |
         ASPIREDIR=${{ env.WORK_DIR }} python -c \
@@ -247,4 +247,4 @@ jobs:
         pip install -e ".[dev]"  # install aspire
         pip freeze
     - name: Test
-      run: python -m pytest -n3 --durations=50 --strict-warnings
+      run: PYTHONWARNINGS=error python -m pytest -n3 --durations=50

From 41e8c57d452e6143a6f26202f0417dfd86a60406 Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Tue, 10 Sep 2024 15:24:35 -0400
Subject: [PATCH 19/25] enforce C order on signal for cufinufft transform.

---
 src/aspire/nufft/cufinufft.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/aspire/nufft/cufinufft.py b/src/aspire/nufft/cufinufft.py
index 218fbd5fb7..fd869aacfd 100644
--- a/src/aspire/nufft/cufinufft.py
+++ b/src/aspire/nufft/cufinufft.py
@@ -107,7 +107,8 @@ def transform(self, signal):
                 " In the future this will be an error."
             )
 
-        signal = cp.asarray(signal, dtype=self.complex_dtype)
+        # Note, if not C order, cuFINUFFT will copy-cast anyway.
+        signal = cp.asarray(signal, order="C", dtype=self.complex_dtype)
 
         sig_shape = signal.shape
         res_shape = self.num_pts

From 3fc856bc99571ffbddbac676c8562e61c6f90ce5 Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Wed, 11 Sep 2024 08:27:53 -0400
Subject: [PATCH 20/25] Skip jobs on CI that will error on cached warnings.
 ampere, osx, long_running.

---
 tests/test_volume.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/tests/test_volume.py b/tests/test_volume.py
index ac86c4096b..b6e4f74a89 100644
--- a/tests/test_volume.py
+++ b/tests/test_volume.py
@@ -813,6 +813,12 @@ def test_transformation_symmetry_warnings(symmetric_vols):
     assert str(vol_c3.symmetry_group) == "C3"
 
 
+@pytest.mark.skipif(
+    (os.getenv("GITHUB_JOB") == "ampere_gpu")
+    or (os.getenv("GITHUB_JOB") == "osx_arm")
+    or (os.getenv("GITHUB_JOB") == "expensive_tests"),
+    reason="Cached warnings will error for these jobs.",
+)
 def test_aglebraic_ops_symmetry_warnings(symmetric_vols):
     """
     A warning should be emitted for  add, sub, mult, and div.

From b350ea0d9c8bb2e41b137d39649b8f95547af461 Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Wed, 11 Sep 2024 10:28:05 -0400
Subject: [PATCH 21/25] Only check warnings on ampere_gpu job.

---
 .github/workflows/long_workflow.yml | 2 +-
 .github/workflows/workflow.yml      | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/long_workflow.yml b/.github/workflows/long_workflow.yml
index a2f2938c8f..ec5714a29e 100644
--- a/.github/workflows/long_workflow.yml
+++ b/.github/workflows/long_workflow.yml
@@ -36,6 +36,6 @@ jobs:
         export OMP_NUM_THREADS=1
         ASPIREDIR=${{ env.WORK_DIR }} python -c \
         "import aspire; print(aspire.config['ray']['temp_dir'])"
-        ASPIREDIR=${{ env.WORK_DIR }} PYTHONWARNINGS=error python -m pytest -n8 -m "expensive" --durations=0
+        ASPIREDIR=${{ env.WORK_DIR }} python -m pytest -n8 -m "expensive" --durations=0
     - name: Cleanup
       run: rm -rf ${{ env.WORK_DIR }}
diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index 253876f83c..69156dc0e0 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -99,7 +99,7 @@ jobs:
       run: |
         export OMP_NUM_THREADS=2
         # -n runs test in parallel using pytest-xdist
-        pytest -n2 --durations=50 -s --strict-warnings
+        pytest -n2 --durations=50 -s
 
   # Build and Deploy production (main) docs.
   docs_deploy:
@@ -247,4 +247,4 @@ jobs:
         pip install -e ".[dev]"  # install aspire
         pip freeze
     - name: Test
-      run: PYTHONWARNINGS=error python -m pytest -n3 --durations=50
+      run: python -m pytest -n3 --durations=50

From 00a02c4021bad3bf226963aef84a377dc4cee39c Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Wed, 11 Sep 2024 10:31:53 -0400
Subject: [PATCH 22/25] remove symmetry warning pytest skips.

---
 tests/test_volume.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/tests/test_volume.py b/tests/test_volume.py
index b6e4f74a89..162904a63c 100644
--- a/tests/test_volume.py
+++ b/tests/test_volume.py
@@ -814,10 +814,8 @@ def test_transformation_symmetry_warnings(symmetric_vols):
 
 
 @pytest.mark.skipif(
-    (os.getenv("GITHUB_JOB") == "ampere_gpu")
-    or (os.getenv("GITHUB_JOB") == "osx_arm")
-    or (os.getenv("GITHUB_JOB") == "expensive_tests"),
-    reason="Cached warnings will error for these jobs.",
+    (os.getenv("GITHUB_JOB") == "ampere_gpu"),
+    reason="Cached warnings will error for this job.",
 )
 def test_aglebraic_ops_symmetry_warnings(symmetric_vols):
     """

From a36dfa46b90d5096d36ee31cbd0ae02f9fddec99 Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Wed, 11 Sep 2024 14:28:03 -0400
Subject: [PATCH 23/25] remove unnecesary plt.close()

---
 tests/test_simulation.py | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/tests/test_simulation.py b/tests/test_simulation.py
index c90caa5bdd..7892a4e8de 100644
--- a/tests/test_simulation.py
+++ b/tests/test_simulation.py
@@ -39,23 +39,14 @@ def testPixelSize(self):
     def testImageShow(self):
         self.sim.images[:].show()
 
-        # Explicitly close all figures before making backend changes.
-        plt.close("all")
-
     @matplotlib_dry_run
     def testCleanImagesShow(self):
         self.sim.clean_images[:].show()
 
-        # Explicitly close all figures before making backend changes.
-        plt.close("all")
-
     @matplotlib_dry_run
     def testProjectionsShow(self):
         self.sim.projections[:].show()
 
-        # Explicitly close all figures before making backend changes.
-        plt.close("all")
-
 
 class SimVolTestCase(TestCase):
     """Test Simulation with Volume provided."""

From 673323a96d362a091dc3bb1caa1de33ceb5d9c7b Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Wed, 11 Sep 2024 14:29:58 -0400
Subject: [PATCH 24/25] unused import

---
 tests/test_simulation.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/test_simulation.py b/tests/test_simulation.py
index 7892a4e8de..92a29e225e 100644
--- a/tests/test_simulation.py
+++ b/tests/test_simulation.py
@@ -3,7 +3,6 @@
 import tempfile
 from unittest import TestCase
 
-import matplotlib.pyplot as plt
 import numpy as np
 from pytest import raises
 

From 9a0afa95ee86f9a18bc965002c2ea96568c12793 Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Wed, 11 Sep 2024 14:35:56 -0400
Subject: [PATCH 25/25] Remove useless test case.

---
 tests/test_volume.py | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/tests/test_volume.py b/tests/test_volume.py
index 162904a63c..1f55645e10 100644
--- a/tests/test_volume.py
+++ b/tests/test_volume.py
@@ -813,10 +813,6 @@ def test_transformation_symmetry_warnings(symmetric_vols):
     assert str(vol_c3.symmetry_group) == "C3"
 
 
-@pytest.mark.skipif(
-    (os.getenv("GITHUB_JOB") == "ampere_gpu"),
-    reason="Cached warnings will error for this job.",
-)
 def test_aglebraic_ops_symmetry_warnings(symmetric_vols):
     """
     A warning should be emitted for  add, sub, mult, and div.
@@ -850,12 +846,6 @@ def test_aglebraic_ops_symmetry_warnings(symmetric_vols):
     # Should have 4 warnings on record.
     assert len(record) == 4
 
-    # Check that warning occurs only once per line.
-    with warnings.catch_warnings(record=True) as record:
-        for _ in range(5):
-            vol_c3 + vol_c4
-    assert len(record) == 1
-
 
 def test_volume_load_with_symmetry():
     # Check we can load a Volume with symmetry_group.