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 <[email protected]> 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 <[email protected]> +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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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