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

[Ken Yamaguchi]

On Wed, Jan 13, 2021 at 12:04:08AM +0200, Juhani Numminen wrote:
> 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

There's a discussion of the issue at

    https://stackoverflow.com/questions/39660934/error-when-using-importlib-util-to-check-for-library/39661116

To remove the error,

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

To print an error message, perhaps the awkward-looking

-    $PYTHON_TEST -c "import imp; imp.find_module('pysam')"
-    $PYTHON_TEST -c "import imp; imp.find_module('numpy')"
+    $PYTHON_TEST -c "from importlib import util; print('pysam not found') if util.find_spec('pysam') is None else None"
+    $PYTHON_TEST -c "from importlib import util; print('numpy not found') if util.find_spec('numpy') is None else None"

Ken