[Debian-med-packaging] Bug#980005: lumpy-sv: lumpyexpress fails with no args

[Juhani Numminen]

Andreas Tille kirjoitti 12.1.2021 klo 23.08:
> Hi,
> 
> I confirm I can reproduce the issue in a minimal chroot while the
> lumpyexpress command prints the help screen as expected.  This smells
> like a missing dependency but I do not have any idea which one.  It
> seems there is a similar known issue here
> 
>    https://stackoverflow.com/questions/65028261/attributeerror-module-importlib-has-no-attribute-util-ii
> 
> but there is no answer here.
> 
> Any idea how to fix this?
> 
> Kind regards
> 
>       Andreas.

It's a change made in debian/patches/lumpyexpress.config.patch.
https://salsa.debian.org/med-team/lumpy-sv/-/commit/e64a65545fbf60c5c98965bc1d00d416b2f9582c#6864ced7557ec33a7ee70c7b0c75b076f84f4fac_24_30

-    $PYTHON_TEST -c "import imp; imp.find_module('pysam')"
-    $PYTHON_TEST -c "import imp; imp.find_module('numpy')"
+    $PYTHON_TEST -c "import importlib; importlib.util.find_spec('pysam')"
+    $PYTHON_TEST -c "import importlib; importlib.util.find_spec('numpy')"

It's not entirely correct even if it worked: the original causes
a visible error message to alert if one of the required modules does
not exist. The current patch will not cause error messages or the
python check to exit non-zero.

Because it's a Debian context we could rely on dpkg dependencies i.e.
just don't perform this check and comment out the two lines.

--
Juhani