[med-svn] [Git][med-team/phyx][master] 9 commits: New upstream version 1.3.1+ds

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / phyx


Commits:
3847b64c by Étienne Mollier at 2023-08-12T22:44:42+02:00
New upstream version 1.3.1+ds
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0ac91f36 by Étienne Mollier at 2023-08-12T22:44:42+02:00
routine-update: New upstream version

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ad1eeb56 by Étienne Mollier at 2023-08-12T22:44:45+02:00
Update upstream source from tag 'upstream/1.3.1+ds'

Update to upstream version '1.3.1+ds'
with Debian dir 1f4cff6e33a73d8887cf8bcb7a2146635b512cb3
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9f3b882e by Étienne Mollier at 2023-08-12T22:44:46+02:00
routine-update: Standards-Version: 4.6.2

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d3d061a7 by Étienne Mollier at 2023-08-12T22:51:55+02:00
hardening.patch: delete: applied upstream.

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a0f04f74 by Étienne Mollier at 2023-08-12T22:52:18+02:00
build-more-programs.patch: refresh.

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203d3d14 by Étienne Mollier at 2023-08-12T23:59:58+02:00
deoptimize.patch: new: fix ftbfs with gcc-13.

This disables building phyx with -ffast-math.

Closes: #1037817

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b909cacf by Étienne Mollier at 2023-08-13T00:01:07+02:00
d/rules: remove -ffloat-store for i386.

Upstream included this change in their build routines.

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bed3ad84 by Étienne Mollier at 2023-08-13T00:11:15+02:00
ready to upload to unstable.

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30 changed files:

- .github/workflows/build-test.yml
- README.md
- debian/changelog
- debian/control
- debian/patches/build-more-programs.patch
- + debian/patches/deoptimize.patch
- − debian/patches/hardening.patch
- debian/patches/series
- debian/rules
- doc/Programs.md
- src/Makefile.in
- + src/TEST/Alignment_empty-sites
- + src/TEST/un_aln_nuc_mixed-stop.fa
- + src/TEST/un_aln_nuc_with-stop.fa
- src/aa2cdn.cpp
- src/aa2cdn.h
- src/clean_seq.cpp
- src/clean_seq.h
- src/comp_test.cpp
- src/generate_manpages.py
- src/main_aa2cdn.cpp
- src/main_bd_fit.cpp
- src/main_bd_sim.cpp
- src/main_boot.cpp
- src/main_bp.cpp
- src/main_cat.cpp
- src/main_clsq.cpp
- src/main_cltr.cpp
- src/main_colt.cpp
- src/main_comp.cpp


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/phyx/-/compare/d41126e4bfd3f6e8865151e5cad42c1f699ae6f5...bed3ad84e2fb5912f3e8979023024b0706dbe09e

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View it on GitLab: https://salsa.debian.org/med-team/phyx/-/compare/d41126e4bfd3f6e8865151e5cad42c1f699ae6f5...bed3ad84e2fb5912f3e8979023024b0706dbe09e
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