[med-svn] [Git][med-team/nitime][master] 2 commits: Adapt to numpy 1.24
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Jan 20 19:40:57 GMT 2023
Andreas Tille pushed to branch master at Debian Med / nitime
Commits:
88b90af1 by Andreas Tille at 2023-01-20T19:54:57+01:00
Adapt to numpy 1.24
- - - - -
039897c4 by Andreas Tille at 2023-01-20T20:40:33+01:00
Fix numpydoc 1.24 issues
- - - - -
4 changed files:
- debian/changelog
- + debian/patches/numpy_1.24.patch
- + debian/patches/numpydoc_1.24.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+nitime (0.9-5) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Adapt to numpy 1.24
+ Closes: #1029245
+ * Fix numpydoc 1.24 issues
+
+ -- Andreas Tille <tille at debian.org> Fri, 20 Jan 2023 19:21:34 +0100
+
nitime (0.9-4) unstable; urgency=medium
* Add patch to fix test_psd_matlab (Closes: #1027550)
=====================================
debian/patches/numpy_1.24.patch
=====================================
@@ -0,0 +1,71 @@
+Description: Adapt to numpy 1.24
+Bug-Debian: https://bugs.debian.org/1029245
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 20 Jan 2023 19:21:34 +0100
+
+--- a/nitime/algorithms/cohere.py
++++ b/nitime/algorithms/cohere.py
+@@ -1005,7 +1005,7 @@ def cache_fft(time_series, ij, lb=0, ub=
+ FFT_conj_slices = {}
+
+ for i_channel in all_channels:
+- Slices = np.zeros((n_slices, n_freqs), dtype=np.complex)
++ Slices = np.zeros((n_slices, n_freqs), dtype=complex)
+ for iSlice in range(n_slices):
+ thisSlice = time_series[i_channel,
+ i_times[iSlice]:i_times[iSlice] + NFFT]
+@@ -1161,7 +1161,7 @@ def cache_to_relative_phase(cache, ij):
+ channels_i = max(1, max(ij_array[:, 0]) + 1)
+ channels_j = max(1, max(ij_array[:, 1]) + 1)
+ # Pre-allocate for speed:
+- Phi_xy = np.zeros((channels_i, channels_j, freqs), dtype=np.complex)
++ Phi_xy = np.zeros((channels_i, channels_j, freqs), dtype=complex)
+
+ # These checks take time, so do them up front, not in every iteration:
+ if list(FFT_slices.items())[0][1].shape[0] > 1:
+@@ -1221,7 +1221,7 @@ def cache_to_coherency(cache, ij):
+
+ channels_i = max(1, max(ij_array[:, 0]) + 1)
+ channels_j = max(1, max(ij_array[:, 1]) + 1)
+- Cxy = np.zeros((channels_i, channels_j, freqs), dtype=np.complex)
++ Cxy = np.zeros((channels_i, channels_j, freqs), dtype=complex)
+
+ #These checks take time, so do them up front, not in every iteration:
+ if list(FFT_slices.items())[0][1].shape[0] > 1:
+--- a/nitime/analysis/coherence.py
++++ b/nitime/analysis/coherence.py
+@@ -653,10 +653,10 @@ class SeedCoherenceAnalyzer(object):
+ if len(self.seed.shape) > 1:
+ Cxy = np.empty((self.seed.data.shape[0],
+ self.target.data.shape[0],
+- self.frequencies.shape[0]), dtype=np.complex)
++ self.frequencies.shape[0]), dtype=complex)
+ else:
+ Cxy = np.empty((self.target.data.shape[0],
+- self.frequencies.shape[0]), dtype=np.complex)
++ self.frequencies.shape[0]), dtype=complex)
+
+ #Get the fft window cache for the target time-series:
+ cache = self.target_cache
+--- a/nitime/tests/test_algorithms.py
++++ b/nitime/tests/test_algorithms.py
+@@ -145,7 +145,7 @@ def test_psd_matlab():
+ ts = np.loadtxt(os.path.join(test_dir_path, 'tseries12.txt'))
+
+ #Complex signal!
+- ts0 = ts[1] + ts[0] * np.complex(0, 1)
++ ts0 = ts[1] + ts[0] * complex(0, 1)
+
+ NFFT = 256
+ Fs = 1.0
+--- a/nitime/analysis/correlation.py
++++ b/nitime/analysis/correlation.py
+@@ -147,7 +147,7 @@ class SeedCorrelationAnalyzer(object):
+
+ # Preallocate results
+ Cxy = np.empty((self.seed.data.shape[0],
+- self.target.data.shape[0]), dtype=np.float)
++ self.target.data.shape[0]), dtype=float)
+
+ for seed_idx, this_seed in enumerate(self.seed.data):
+
=====================================
debian/patches/numpydoc_1.24.patch
=====================================
@@ -0,0 +1,18 @@
+Description: Adapt to numpydoc 1.24
+Bug-Debian: https://bugs.debian.org/1029245
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 20 Jan 2023 19:21:34 +0100
+
+--- a/doc/sphinxext/docscrape.py
++++ b/doc/sphinxext/docscrape.py
+@@ -428,8 +428,8 @@ class FunctionDoc(NumpyDocString):
+ func, func_name = self.get_func()
+ try:
+ # try to read signature
+- argspec = inspect.getargspec(func)
+- argspec = inspect.formatargspec(*argspec)
++ argspec = inspect.getfullargspec(func)
++ # FIXME: No idea what to do here - just commenting it out# argspec = inspect.formatargspec(*argspec)
+ argspec = argspec.replace('*','\*')
+ signature = '%s%s' % (func_name, argspec)
+ except TypeError as e:
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,5 @@ python3
sphinx_ignore_github.patch
do-not-set-lowerbound-zero-in-iir.patch
fix-psd-test.patch
+numpy_1.24.patch
+numpydoc_1.24.patch
View it on GitLab: https://salsa.debian.org/med-team/nitime/-/compare/e863169b4b32411a5aebd8f55aa0b471c62460ca...039897c46ec436a513463fcfa997d02dcbea1417
--
View it on GitLab: https://salsa.debian.org/med-team/nitime/-/compare/e863169b4b32411a5aebd8f55aa0b471c62460ca...039897c46ec436a513463fcfa997d02dcbea1417
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