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Fix a few warnings and ensure polysomy is built in the CI tests #2307

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merged 4 commits into from
Oct 31, 2024

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Fix a couple of warnings that appeared when using ./configure --enable-libgsl or with optimisation -Og. Also tidies up the CI builds a bit as compiler flags weren't being applied consistently, and updates the MacOS build to Sonoma.

These triggered a "variable is set but not used" warning when
building with --enable-libgsl
These are probably false positives, but with low optimisation
the compiler isn't able to work out that the variables are always
set before use.  Fix by always assigning them.
Add packages needed for these options and enable them
on configure builds.  The perl IO::Pty package is also added
for Debian and Ubuntu so the usage tests work.

Also adjust how flags are set in the CI builds to ensure they
are applied consistently.
This is the only image currently supported by Cirrus-CI, which
was automatically switching from the one requested.
@pd3 pd3 merged commit 5d57c7b into samtools:develop Oct 31, 2024
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