There are indeed a LOT of errors in there (and a sprinkling of
harmless warnings which ought really to be silenced within the test
framework).
Picking on the very last one as a simple case, you got:
```
======================================================================
FAIL: test_ColumnUnit (test_psw.TestPSW)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/tmp/python-biopython-test.HGclMQ/Tests/test_psw.py", line 75,
in test_ColumnUnit
"ColumnUnit(unit=0, column=33, SEQUENCE)")
AssertionError: "ColumnUnit(unit=0, column=33, kind='SEQUENCE')" !=
'ColumnUnit(unit=0, column=33, SEQUENCE)'
- ColumnUnit(unit=0, column=33, kind='SEQUENCE')
? ------ -
+ ColumnUnit(unit=0, column=33, SEQUENCE)
```
This change relates to adding __repr__ to some of the PSW objects,
https://github.com/biopython/biopython/commit/37f235066616c950a6b4b5544785a5c4a88f1ea1
This was included in Biopython 1.74 and 1.75, yet your copy of Tests/test_psw.py
would seem to date from Biopython 1.73 or older.
I suspect an old cached copy of the test folder is largely to blame?
Peter
On Mon, Dec 2, 2019 at 3:28 PM Andreas Tille <andr...@an3as.eu> wrote:
>
> Hi Peter,
>
> On Wed, Nov 20, 2019 at 01:36:50PM +0100, Andreas Tille wrote:
> > >
> > > https://github.com/biopython/biopython/issues/2350
>
> Since I urgently need Biopython >= 1.74 to fix some other bugs I decided
> to try to ignore those issues we discussed here and made sure that build
> time tests will not fail. However the Debian package is also running a
> Continuous Integration test (autopkgtest in Debian terminology). The
> test for biopython is basically copying the test files to a temporary dir
> and execute the tests[1].
>
> In the attached log I injected a `set -x` and was running:
>
> sh run-unit-test 2>&1 | tee > tes_suite_errors.out
>
> Unfortunately there are more errors than I expected. Do you have any
> idea why?
>
> Kind regards
>
> Andreas.
>
>
> [1]
> https://salsa.debian.org/med-team/python-biopython/blob/master/debian/tests/run-unit-test
>
> --
> http://fam-tille.de
