[med-svn] [Git][med-team/fitgcp][master] 7 commits: routine-update: Packaging update
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Dec 29 10:44:47 GMT 2022
Andreas Tille pushed to branch master at Debian Med / fitgcp
Commits:
ebb4c091 by Andreas Tille at 2022-12-29T11:21:48+01:00
routine-update: Packaging update
- - - - -
06a7abb9 by Andreas Tille at 2022-12-29T11:21:48+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
9249ce0c by Andreas Tille at 2022-12-29T11:21:48+01:00
routine-update: debhelper-compat 13
- - - - -
24045f4c by Andreas Tille at 2022-12-29T11:21:59+01:00
Set upstream metadata fields: Archive.
Changes-By: lintian-brush
- - - - -
70d67bc0 by Andreas Tille at 2022-12-29T11:36:49+01:00
Fix AttributeError: module 'numpy' has no attribute 'int'
- - - - -
52922509 by Andreas Tille at 2022-12-29T11:40:45+01:00
Fix also np.float
- - - - -
e3cdc6cf by Andreas Tille at 2022-12-29T11:43:27+01:00
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/numpy_1.24.patch
- debian/patches/series
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+fitgcp (0.0.20150429-5) unstable; urgency=medium
+
+ * Standards-Version: 4.6.2 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Set upstream metadata fields: Archive.
+ * Fix AttributeError: module 'numpy' has no attribute 'int'
+ Closes: #1027199
+
+ -- Andreas Tille <tille at debian.org> Thu, 29 Dec 2022 11:41:12 +0100
+
fitgcp (0.0.20150429-4) unstable; urgency=medium
* Team upload
=====================================
debian/control
=====================================
@@ -3,11 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
dh-python,
python3,
python3-pysam
-Standards-Version: 4.5.0
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/fitgcp
Vcs-Git: https://salsa.debian.org/med-team/fitgcp.git
Homepage: http://sourceforge.net/projects/fitgcp/
=====================================
debian/patches/numpy_1.24.patch
=====================================
@@ -0,0 +1,66 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 29 Dec 2022 11:21:48 +0100
+Bug-Debian: https://bugs.debian.org/1027199
+Description: Fix AttributeError: module 'numpy' has no attribute 'int'. Did you mean: 'inf'?
+ with numpy/1.24.1
+
+--- a/fitGCP.py
++++ b/fitGCP.py
+@@ -114,7 +114,7 @@ class Zero(Distribution):
+
+ def pmf(self,x):
+ if isinstance(x,np.ndarray):
+- return (x==0).astype(np.float)
++ return (x==0).astype(float)
+ else:
+ return float(x==0)
+
+@@ -265,7 +265,7 @@ class PoissonTail(TailDistribution):
+ return 0.
+
+ xmax = int(max(np.max(x),5,stats.poisson.ppf(0.999999,self._p1)))+1
+- xs = np.arange(0,xmax, dtype=np.float)
++ xs = np.arange(0,xmax, dtype=float)
+ #backward cumulative sum
+ tx = np.cumsum((stats.poisson.pmf(xs, self._p1)/xs)[::-1])[::-1]
+ tx[0] = 0
+@@ -330,8 +330,8 @@ def init_gamma(mixture_model, dataset):
+
+ class DataSet:
+ fname = "" # path to original SAM file
+- cov = np.array([],dtype=np.int) # observed coverage values
+- count = np.array([],dtype=np.int) # number of observations for each cov
++ cov = np.array([],dtype=int) # observed coverage values
++ count = np.array([],dtype=int) # number of observations for each cov
+ rlen = 0 # average read length of mapped reads
+ rds = 0 # total number of reads
+ glen = 0 # length of the genome
+@@ -340,8 +340,8 @@ class DataSet:
+ """ read a genome coverage profile from a pickle file. """
+ data = pickle.load(open(filename,'rb'))
+
+- self.cov = np.array(data[0],dtype=np.int)
+- self.count = np.array(data[1],dtype=np.int)
++ self.cov = np.array(data[0],dtype=int)
++ self.count = np.array(data[1],dtype=int)
+ self.rlen = data[2]
+ self.rds = data[3]
+ self.glen = data[4]
+@@ -451,7 +451,7 @@ def iterative_fitting(data_set, mixture_
+ ref_pdf += dist.pmf(xs)*dist.alpha
+
+ obs_pdf = np.zeros((int(np.max(data_set.cov))+1,))
+- obs_pdf[data_set.cov.astype(np.int)] = data_set.count/float(np.sum(data_set.count))
++ obs_pdf[data_set.cov.astype(int)] = data_set.count/float(np.sum(data_set.count))
+ max_cdf_diff = np.max(np.abs(np.cumsum(ref_pdf)-np.cumsum(obs_pdf)))
+
+ yield i, max_change, max_cdf_diff
+@@ -604,7 +604,7 @@ if __name__ == "__main__":
+ DS.cov = DS.cov[np.where(DS.cov < cutoff)]
+ num_unique = len(DS.cov)
+ DS.glen = np.sum(DS.count)
+- mean_cov = np.sum(DS.cov*DS.count)/np.sum(DS.count).astype(np.float)
++ mean_cov = np.sum(DS.cov*DS.count)/np.sum(DS.count).astype(float)
+
+
+ # only view the GCP
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
2to3.patch
2to3_additions.patch
+numpy_1.24.patch
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,4 @@
+Archive: SourceForge
Reference:
- Author: >
Martin S. Lindner and Maximilian Kollock and Franziska Zickmann and
View it on GitLab: https://salsa.debian.org/med-team/fitgcp/-/compare/3a9deb1581b0afcb3e28cc34b5d354ffba593b8a...e3cdc6cf0f0fa9bbda8dcb7035ce43c178f18759
--
View it on GitLab: https://salsa.debian.org/med-team/fitgcp/-/compare/3a9deb1581b0afcb3e28cc34b5d354ffba593b8a...e3cdc6cf0f0fa9bbda8dcb7035ce43c178f18759
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