iva/tests/seed_processor_test.py | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 disable multithreaded test
 One of the tests uses Python's multiprocessing, which on some machines causes
 FTBFS due to problematic permissions on /dev/shm, resulting in:
   PermissionError: [Errno 13] Permission denied
 This patch disables this test to allow building at the minor expense of this
 missing test.

iva/ratt/embl2gff.pl | 2 1 + 1 - 0 !
iva/ratt/genbank2embl.pl | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 use debian's perl path

iva/mapping.py | 2 2 + 0 - 0 !
1 file changed, 2 insertions(+)

 fix samtools version parsing so that 1.10 > 1.2

iva/tests/assembly_test.py | 2 1 + 1 - 0 !
iva/tests/kcount_test.py | 6 3 + 3 - 0 !
2 files changed, 4 insertions(+), 4 deletions(-)

 disable tests that run kmc
 KMC needs a lot of memory (multi-gigabyte) and fails hard when that
 memory cannot be allocated, which can cause builds to fail when
 tests are crashing because of that on low-spec buildds.
 Let's disable these tests for now.

iva/external_progs.py | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 python3.12 compatibility by avoiding usage of distutils
Bug-Debian: https://bugs.debian.org/1061804

iva/external_progs.py | 20 10 + 10 - 0 !
iva/kraken.py | 6 3 + 3 - 0 !
iva/mapping.py | 4 2 + 2 - 0 !
3 files changed, 15 insertions(+), 15 deletions(-)

 raw strings for regexes.
 Starting with at least Python 3.13, bytecode compilation of iva
 scripts results in multiple syntax warnings:
 .
         Setting up iva (1.0.11+ds-5) ...
         /usr/lib/python3/dist-packages/iva/external_progs.py:33: SyntaxWarning: invalid escape sequence '\('
           'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')),
         /usr/lib/python3/dist-packages/iva/external_progs.py:34: SyntaxWarning: invalid escape sequence '\('
           'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')),
         /usr/lib/python3/dist-packages/iva/external_progs.py:37: SyntaxWarning: invalid escape sequence '\('
           'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')),
         /usr/lib/python3/dist-packages/iva/external_progs.py:38: SyntaxWarning: invalid escape sequence '\('
           'R': ('R --version', re.compile('^R version (.*) \(.*\) --')),
         /usr/lib/python3/dist-packages/iva/external_progs.py:40: SyntaxWarning: invalid escape sequence '\d'
           'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')),
         /usr/lib/python3/dist-packages/iva/kraken.py:360: SyntaxWarning: invalid escape sequence '\.'
           self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl')
         /usr/lib/python3/dist-packages/iva/kraken.py:415: SyntaxWarning: invalid escape sequence '\W'
           return re.sub('\W', '_', s).strip('_')
         /usr/lib/python3/dist-packages/iva/mapping.py:161: SyntaxWarning: invalid escape sequence '\^'
           s = re.sub('\^.', '', s)
 .
 This change goes through regexes occurrences to make them raw strings,
 in order to make them more robust to backslash usage.