Michael R. Crusoe pushed to branch master at Debian Med / macs
Commits: 26895c55 by Michael R. Crusoe at 2024-02-24T12:08:35+01:00 d/patches/adapt_to_prelease_hmmlearn.patch: patch from the upstream author to match the prelease version of hmmlearn in the archive. - - - - - 70cffbb1 by Michael R. Crusoe at 2024-02-24T12:29:40+01:00 d/patches/invalid_escape_sequence: fix a SyntaxWarning. - - - - - 4 changed files: - debian/changelog - + debian/patches/adapt_to_prelease_hmmlearn.patch - + debian/patches/invalid_escape_sequence - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -29,6 +29,9 @@ macs (3.0.1-1) UNRELEASED; urgency=medium * d/patch/no_install_depends_cython.patch removed, applied upstream. * add patch to force the use of Python3. * d/control: add build-dep on bc for the tests. + * d/patches/adapt_to_prelease_hmmlearn.patch: patch from the upstream + author to match the prelease version of hmmlearn in the archive. + * d/patches/invalid_escape_sequence: fix a SyntaxWarning. -- Michael R. Crusoe <cru...@debian.org> Fri, 23 Feb 2024 14:26:24 +0100 ===================================== debian/patches/adapt_to_prelease_hmmlearn.patch ===================================== @@ -0,0 +1,26 @@ +Author: Tao Liu <vladimir....@gmail.com> +Description: Adapt to Debian's pre-release version of hmmlearn +Forwarded: not-needed + +https://github.com/macs3-project/MACS/issues/615#issuecomment-1961928064 + +--- macs.orig/MACS3/Signal/HMMR_HMM.pyx ++++ macs/MACS3/Signal/HMMR_HMM.pyx +@@ -90,7 +90,7 @@ + # according to base documentation, if init_prob not stated, it is set to be equally likely for any state (1/ # of components) + # if we have other known parameters, we should set these (ie: means_weights, covariance_type etc.) + rs = np.random.RandomState(np.random.MT19937(np.random.SeedSequence(random_seed))) +- hmm_model = GaussianHMM_modified( n_components= n_states, covariance_type = covar, random_state = rs, verbose = False ) ++ hmm_model = hmm.GaussianHMM( n_components= n_states, covariance_type = covar, random_state = rs, verbose = False ) + hmm_model = hmm_model.fit( training_data, training_data_lengths ) + assert hmm_model.n_features == 4 + return hmm_model +@@ -121,7 +121,7 @@ + cpdef list hmm_model_init( str model_file ): + with open( model_file ) as f: + m = json.load( f ) +- hmm_model = GaussianHMM_modified( n_components=3, covariance_type=m["covariance_type"] ) ++ hmm_model = hmm.GaussianHMM( n_components=3, covariance_type=m["covariance_type"] ) + hmm_model.startprob_ = np.array(m["startprob"]) + hmm_model.transmat_ = np.array(m["transmat"]) + hmm_model.means_ = np.array(m["means"]) ===================================== debian/patches/invalid_escape_sequence ===================================== @@ -0,0 +1,16 @@ +From: Michael R. Crusoe <cru...@debian.org> +Subject: fix SyntaxWarning by marking a regex as such +Forwarded: https://github.com/macs3-project/MACS/pull/624 + +Fixes: <string>:78: SyntaxWarning: invalid escape sequence '\s' +--- macs.orig/setup.py ++++ macs/setup.py +@@ -75,7 +75,7 @@ + clang = True + else: + gcc_version_check = gcc_version_check.split('\n')[0] # get the first line +- m = re.search( "\s+(\d+\.\d+)\.\d+", gcc_version_check ) ++ m = re.search(r"\s+(\d+\.\d+)\.\d+", gcc_version_check ) + if m: + gcc_version = float( m[1] ) + if gcc_version > 4.8: ===================================== debian/patches/series ===================================== @@ -1,3 +1,5 @@ +invalid_escape_sequence +adapt_to_prelease_hmmlearn.patch python3 keep_debug simde.patch View it on GitLab: https://salsa.debian.org/med-team/macs/-/compare/1ee064daf6a894783b157c69644703a491a3d5d1...70cffbb1f61c1d97f118a531dc39c72a0c21b063 -- View it on GitLab: https://salsa.debian.org/med-team/macs/-/compare/1ee064daf6a894783b157c69644703a491a3d5d1...70cffbb1f61c1d97f118a531dc39c72a0c21b063 You're receiving this email because of your account on salsa.debian.org.
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