[med-svn] [Git][med-team/macs][master] 4 commits: d/rules: make use of dh_numpy3 to add the numpy ABI dependency.

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / macs


Commits:
6e290ab9 by Michael R. Crusoe at 2024-02-27T16:02:24+01:00
d/rules: make use of dh_numpy3 to add the numpy ABI dependency.

- - - - -
6c410cb0 by Michael R. Crusoe at 2024-02-28T12:38:50+01:00
d/patches/spelling: fix typos.

- - - - -
9a4e39d2 by Michael R. Crusoe at 2024-02-28T12:38:50+01:00
d/lintian-overrides: update to match change in warnings.

- - - - -
96d2330a by Michael R. Crusoe at 2024-02-28T12:39:52+01:00
routine-update: Ready to upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/lintian-overrides
- debian/patches/series
- + debian/patches/spelling
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+macs (3.0.1-2) unstable; urgency=medium
+
+  * d/rules: make use of dh_numpy3 to add the numpy ABI dependency.
+  * d/patches/spelling: fix typos.
+  * d/lintian-overrides: update to match change in warnings.
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Wed, 28 Feb 2024 12:39:52 +0100
+
 macs (3.0.1-1) unstable; urgency=medium
 
   [ Andreas Tille ]


=====================================
debian/lintian-overrides
=====================================
@@ -1 +1,2 @@
-macs: manpage-has-errors-from-man usr/share/man/man1/macs3.1.gz 8: warning [p 1, 1.7i]: cannot adjust line
+macs: groff-message 8: warning [p 1, 1.7i]: cannot adjust line [usr/share/man/man1/macs3.1.gz:1]
+macs: groff-message 14: warning [p 1, 2.7i]: cannot adjust line [usr/share/man/man1/macs3.1.gz:2]


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+spelling
 invalid_escape_sequence
 adapt_to_prelease_hmmlearn.patch
 python3


=====================================
debian/patches/spelling
=====================================
@@ -0,0 +1,35 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Fix spelling typos found by lintian
+Forwarded: https://github.com/macs3-project/MACS/pull/629
+--- macs.orig/MACS3/Signal/BedGraph.pyx
++++ macs/MACS3/Signal/BedGraph.pyx
+@@ -1178,7 +1178,7 @@
+         Todos
+         -----
+ 
+-        May need to seperate this function out as a class so that we
++        May need to separate this function out as a class so that we
+         can add more ways to analyze the result. Also, we can let this
+         function return a list of dictionary or data.frame in that
+         way, instead of str object.
+--- macs.orig/MACS3/Signal/HMMR_Signal_Processing.pyx
++++ macs/MACS3/Signal/HMMR_Signal_Processing.pyx
+@@ -225,6 +225,6 @@
+                 tmp_p = tmp_e
+             # end of region, we change the mark_bin
+             mark_bin += 1
+-    # we do not merge regions in regionsbdg object so each bin will be seperated.
++    # we do not merge regions in regionsbdg object so each bin will be separated.
+     debug( f"added {n} bins" )
+     return regionsbdg
+--- macs.orig/MACS3/Signal/PileupV2.pyx
++++ macs/MACS3/Signal/PileupV2.pyx
+@@ -7,7 +7,7 @@
+ Wang. Now we allow different weights for different genomic ranges, and
+ simplify the approach.
+ 
+-For a genomic range r_i covering genomic postions from s_i to e_i to
++For a genomic range r_i covering genomic positions from s_i to e_i to
+ be piled up, we assign the start position a value w_i, and the end
+ -w_i, so we will have (s_i, w_i) and (e_i, -w_i). Then all N ranges
+ will be made into an array (2D) of position and weights as:


=====================================
debian/rules
=====================================
@@ -13,6 +13,9 @@ tagline=\- Model\-based Analysis for ChIP\-Sequencing
 %:
 	dh $@ --buildsystem=pybuild
 
+execute_before_dh_python3:
+	dh_numpy3
+
 override_dh_auto_build:
 	for pyx in $$(find MACS3/ -name "*.pyx"); do \
 		rm -f $${pyx%%.pyx}.{h,c}; touch $${pyx}; done



View it on GitLab: https://salsa.debian.org/med-team/macs/-/compare/d4e291f314735d7a0a2ad06a7379cbb8b229f2e2...96d2330abbda1fdaf8a8144907096715965b619a

-- 
View it on GitLab: https://salsa.debian.org/med-team/macs/-/compare/d4e291f314735d7a0a2ad06a7379cbb8b229f2e2...96d2330abbda1fdaf8a8144907096715965b619a
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20240228/13c7e80d/attachment-0001.htm>