[med-svn] [Git][med-team/python-pbcore][master] 7 commits: routine-update: Packaging update

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / python-pbcore


Commits:
906290ca by Andreas Tille at 2022-12-29T19:51:48+01:00
routine-update: Packaging update

- - - - -
ba75cc8c by Andreas Tille at 2022-12-29T19:51:48+01:00
routine-update: Standards-Version: 4.6.2

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d71b3ab1 by Andreas Tille at 2022-12-29T19:51:55+01:00
Add missing build dependency on python3:any | python3-all:any | python3-dev:any | python3-all-dev:any | dh-sequence-python3 for addon python3.

Changes-By: lintian-brush
Fixes: lintian: missing-build-dependency-for-dh-addon
See-also: https://lintian.debian.org/tags/missing-build-dependency-for-dh-addon.html

- - - - -
948d3025 by Andreas Tille at 2022-12-29T19:52:01+01:00
Apply multi-arch hints.
+ python-pbcore-doc: Add Multi-Arch: foreign.

Changes-By: apply-multiarch-hints

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c0595a1e by Andreas Tille at 2022-12-29T19:59:57+01:00
Revert add missing Build-Depends

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e1e1b799 by Andreas Tille at 2022-12-29T20:01:05+01:00
Fix AttributeError: module 'numpy' has no attribute 'float'.

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e82bfd09 by Andreas Tille at 2022-12-29T20:03:30+01:00
Upload to unstable

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4 changed files:

- debian/changelog
- debian/control
- + debian/patches/numpy_1.24.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+python-pbcore (2.1.2+dfsg-4) unstable; urgency=medium
+
+  * Standards-Version: 4.6.2 (routine-update)
+  * Fix AttributeError: module 'numpy' has no attribute 'float'.
+    Closes: #1027211
+
+ -- Andreas Tille <tille at debian.org>  Thu, 29 Dec 2022 20:01:16 +0100
+
 python-pbcore (2.1.2+dfsg-3) unstable; urgency=medium
 
   * enable-build-time-testing.patch: remove; cease enforcing nostests.


=====================================
debian/control
=====================================
@@ -22,7 +22,7 @@ Build-Depends: debhelper-compat (= 13),
                python3-xmlschema <!nocheck>,
                pylint,
                python3-coverage
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/python-pbcore
 Vcs-Git: https://salsa.debian.org/med-team/python-pbcore.git
 Homepage: https://github.com/PacificBiosciences/pbcore
@@ -57,6 +57,7 @@ Depends: ${misc:Depends},
          ${sphinxdoc:Depends},
          libjs-jquery,
          libjs-underscore
+Multi-Arch: foreign
 Description: Python library for processing PacBio data files (documentation)
  The pbcore package provides Python modules for processing Pacific Biosciences
  data files and building PacBio bioinformatics applications. These modules


=====================================
debian/patches/numpy_1.24.patch
=====================================
@@ -0,0 +1,31 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 29 Dec 2022 11:21:48 +0100
+Bug-Debian: https://bugs.debian.org/1027211
+Description: Fix AttributeError: module 'numpy' has no attribute 'float'.
+ with numpy/1.24.1
+
+--- a/pbcore/io/dataset/DataSetMembers.py
++++ b/pbcore/io/dataset/DataSetMembers.py
+@@ -827,7 +827,7 @@ class Filters(RecordWrapper):
+                 'mapqv': (lambda x: x.mapQV),
+                 'accuracy': (
+                     lambda x: (np.ones(len(x.nMM), dtype='f4') -
+-                               (x.nMM + x.nIns + x.nDel).astype(np.float) /
++                               (x.nMM + x.nIns + x.nDel).astype(float) /
+                                (x.nM + x.nMM + x.nIns)))
+                 }
+         base = self._pbiVecAccMap()
+@@ -869,11 +869,11 @@ class Filters(RecordWrapper):
+                 'bcq': int,
+                 'bq': int,
+                 'qs': int,
+-                'rq': np.float,
++                'rq': float,
+                 'pos': int,
+                 'tstart': int,
+                 'tend': int,
+-                'accuracy': np.float,
++                'accuracy': float,
+                 'readstart': int,
+                 'cx': PbiFlags.flagMap,
+                 'n_subreads': int,


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ doc-theme.patch
 exclude_test_missing_data.patch
 b24746790c7105212e45dc2f40115d231bd8baae.patch
 seek-curdir-for-xml.patch
+numpy_1.24.patch



View it on GitLab: https://salsa.debian.org/med-team/python-pbcore/-/compare/3eb884929402921f06ad6547dfc9b5a2b6b2ebf2...e82bfd093ecc153aa393402ef07f1247ed9af2ec

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-pbcore/-/compare/3eb884929402921f06ad6547dfc9b5a2b6b2ebf2...e82bfd093ecc153aa393402ef07f1247ed9af2ec
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