MINUTES, 2009.07.21
Present: Chris, Istvan, Jenny, Marek, Namshin, Titus
1. 0.8 release
The following schedule has been agreed on:
a. WITHIN A WEEK, wrap up and merge all recent minor changes;
b. Release 0.8.0-beta1, accompanied by an announcement/appeal to
users on pygr-dev (and the Pygr Web site?);
c. Work on the four tutorials Titus mentioned in his "tutorials for
0.8" e-mail to pygr-dev. Ideally they should all be ready for review BY
THE 21ST OF AUGUST (SciPy) and done by the end of August. The following
assignments have been made during the meeting:
- alignment tutorial - pretty much completed (Titus), will be
reviewed by Chris;
- XML-RPC tutorial - Namshin, with assistance (in the "novice" role)
from MS;
- gene-build loading tutorial - Chris and Jenny;
- storage type (scalability) tutorial - Titus;
Side note from Titus: use doctests wherever possible and make sure
your code in tutorials has the form of working Python scripts.
d. Release Pygr-0.8.0 ON THE 1ST OF SEPTEMBER regardless of the status
of tutorials.
Work on tutorials is expected to be driven by user feedback.
Moreover, after 0.8.0 has been released we would like to switch to a
more frequent release cycle. Basing on our commit frequency so far,
point releases are to be published every 1-2 months. Note that these
will be strictly maintenance/fix-type releases - all major
modifications, API changes, new features etc. will be dedicated to 0.9
and go to a SEPARATE branch.
2. Megatests
In light of recently-discovered version incompatibility, we'd better
have megatests run automatically, even if only sporadically, on
different Python versions. According to Titus the buildbot system can't
handle this yet (ongoing reliability issues, inexperienced students,
resource limitations) so MS will set something up on the new MBI
megatest machine.
Current incompatibility between 2.4 and 2.5: Namshin will file
appropriate issues in the tracker, as well as work on isolating the
errors as minimal test cases, not requiring running the whole suite and
producing the relevant errors quickly.
Excessive memory consumption with full data sets: again, Namshin will
develop a minimal test case and post an issue. Not clear when this
crept in since megatests have never tracked memory usage - we'd better
begin doing so! Istvan has mentioned Heapy (part of the Guppy package),
a Python memory-usage profiler which would do the job here.
3. PyEnsembl updates
Jenny hasn't been able to address this yet, moreover this is a
two-sided issue:
- PyEnsembl vs. Pygr-0.8; and
- PyEnsembl vs. the Ensembl database after updates.
We have decided to postpone work on this subject till September, i.e.
until after Pygr-0.8.0 has been released.
--
MS
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