We (upstream) have just released Biopython 1.76 which thanks to
the Debian team's feedback from 1.75 should be less problematic
on alternative CPUs:
https://www.open-bio.org/2019/12/20/biopython-1-76-released/
https://pypi.python.org/pypi/biopython/1.76
These are the commits which I think you mig
Yes, ignore that one please.
That test has since been disabled (and replaced with a more robust one).
We eventually traced test_chapter_align_line_02819 failing on 32 bit
systems with a different overflow error:
https://github.com/biopython/biopython/pull/2297
Thanks,
Peter
On Wed, Dec 4, 2019
On Wed, Dec 04, 2019 at 01:55:26PM +, Peter Cock wrote:
> Good. If you are still missing Tests/Fasta/flowers.pro.gz that's odd,
> since it was in the official tar ball:
>
> https://files.pythonhosted.org/packages/33/55/becf2b99556588d22b542f3412990bfc79b674e198d9bc58f7bbc333439e/biopython-1.75
Good. If you are still missing Tests/Fasta/flowers.pro.gz that's odd,
since it was in the official tar ball:
https://files.pythonhosted.org/packages/33/55/becf2b99556588d22b542f3412990bfc79b674e198d9bc58f7bbc333439e/biopython-1.75.tar.gz
Peter
On Tue, Dec 3, 2019 at 9:13 PM Andreas Tille wrote:
Hi Peter,
On Mon, Dec 02, 2019 at 03:42:21PM +, Peter Cock wrote:
> 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?
Arghhh, sorry fo
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 (
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 no
On Wed, Nov 20, 2019 at 11:40:27AM +, Peter Cock wrote:
> It seems we have some invalid doctests in the C code (which might
> reveal a bug or two, but are mostly likely harmless oversights).
> There is some key difference in your build setup and our continuous
> integration which is not looking
It seems we have some invalid doctests in the C code (which might
reveal a bug or two, but are mostly likely harmless oversights).
There is some key difference in your build setup and our continuous
integration which is not looking at the C code's docstests:
https://github.com/biopython/biopython/
On Tue, Nov 19, 2019 at 10:03:25AM +, Peter Cock wrote:
>
> Do you have a list of things still depending on Biopython & Python 2.7
> handy? We're discussing when exactly to drop Python 2.7 support -
> with a final compatible release in December 2019 or January 2020
> looking most likely.
Spea
Hi Peter,
On Tue, Nov 19, 2019 at 10:03:25AM +, Peter Cock wrote:
> > I'd like to give you credit as the fastest upstream answering a
> > question. ;-) Thanks a lot for it!
>
> Lucky timing.
Anyway: Thanks a lot.
> > On Tue, Nov 19, 2019 at 09:17:17AM +, Peter Cock wrote:
> > > Curio
On Tue, Nov 19, 2019 at 10:03 AM Peter Cock wrote:
>
> I mean I would not worry about this particular test failing - and would
> consider whitelisting this test acceptable.
>
> Without yet being able to reproduce this and test it, does this work?:
>
> https://github.com/peterjc/biopython/commit/5a
On Tue, Nov 19, 2019 at 9:43 AM Andreas Tille wrote:
>
> Hi Peter,
>
> I'd like to give you credit as the fastest upstream answering a
> question. ;-) Thanks a lot for it!
Lucky timing.
> On Tue, Nov 19, 2019 at 09:17:17AM +, Peter Cock wrote:
> > Curious - do you have the Python 2.7 versio
Hi Peter,
I'd like to give you credit as the fastest upstream answering a
question. ;-) Thanks a lot for it!
On Tue, Nov 19, 2019 at 09:17:17AM +, Peter Cock wrote:
> Curious - do you have the Python 2.7 version and build details?
I've attached the full build log.
> Missing docstrings are
Curious - do you have the Python 2.7 version and build details?
Missing docstrings are unfortunate (and in this case they are in C
code which is a bit different), but ultimately this is harmless. What
puzzles me is what has triggered this, that we fail to see it on our
own testing.
As an aside, f
Hi,
it seems that BioPython 1.75 has solved all issues with Python 3.8.
However, when trying to build the Debian package I get the following
issues in the Build-Time test suite:
...
==
ERROR: Bio.KDTree._CKDTree
-
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