[med-svn] [Git][med-team/macs][master] 2 commits: d/patches/adapt_to_prelease_hmmlearn.patch: patch from the upstream author to...

[Michael R. Crusoe (@crusoe)]

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 <crusoe at 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.liu at 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 <crusoe at 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
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