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 <[email protected]> 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 <[email protected]> +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.
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