MINUTES, 2009.03.24
(or "I really should come up with a way of making notes which I could
send out without editing")
Present: Alex, Chris, Jenny, Marek, Titus
1. SeqDB review (Titus)
Work progressing but the changes already in the seqdb_review (note the -
accidental - change from original seqdb-review) on Github need to be pushed
into the master. Some of the changes will have to be merged by hand because
they conflict with metabase (the review was started long before the latter came
into being). Both things will be taken care of by Chris.
In the process of the review, Issue 76 was fixed. Jenny will verify the fix
shortly.
Next steps: PrefixUnionDict and the cache.
2. SeqDB documentation
In short: thanks to his newly-gained in-depth knowledge of SeqDB, Titus is
working on documentation. Various usage scenarios will be documented.
Organisation comment: one doc file per module!
3. Test-framework issues (Titus)
Most of the issues reported earlier have been taken care of, what remains is
mostly the matter of choice rather than objective technical issues.
The matter of path munging vs. what tests are to run: this unfortunately is, as
discussed on Python mailing lists, an endemic issue of such tests. A
recommended workaround is provide a list, or at least the number, of tests
expected to run; in practice this would of course mean multiple such lists,
depending on what suites are actually run (i.e. depending on whether MySQL is
installed). MS will discuss details with Chris and post an issue dedicated to
the matter of defining what such blocks ought to be defined.
MS will also add an issue reminding us to make error messages more helpful; it
will be an open, "post comments here" issue; right now the main (only?) one is
the "cannot import cnestedlist" error pertaining to in-place vs.
build-/install-dir testing.
Error-reporting from tests: details will be posted on the mailing list. The
general idea: add a flag to aggregate tests into one suite, run them all
together and print output together. Chris: does Istvan's verbosity flag help?
Titus: not here.
4. Metabase review
Titus: It has just begun, will continue in the next days (by Thursday evening)
- with the general idea of following Chris's examples. The first impression is
that this is a good change, as the code looks much more simple now.
Recommendation: already push this into master, after which a SeqDB-style review
will follow.
Chris+Marek: a few metabase-related issues were found in megatests, which
prevented the latter from running. Most of these required fixes to megatests
themselves in order to stop using deprecated or private interfaces which
metabase removed, the remaining few required re-adding certain methods to
metabase code. Work almost done.
5. Google Summer of Code projects
Titus: We should try submitting two projects. We need to hurry, as the timeline
for applications is very brief - applictions are due on Friday! As a reminder,
last year's ideas can be found at
http://cartwheel.idyll.org/wiki/PygrGsoc2008Projects. The initial stage is to
come up with ideas which pass initial inspection, then assign mentors.
Ideas:
- Chris: securely-signed pickles - in line with 1.0 goals, self-contained;
- MS: management interface? Titus: not defined well enough for now.
Mentor candidates: Titus, MS, Chris, maybe Jenny, maybe Istvan. Titus may find
more. Note: mentors don't have to argue for project proposals.
6. AOB
Chris: we've got too many public Git branches! Must get this under control do
that we ourselves don't get confused. In particular, we should make sure
seqdb_review and metabase are merged soon.
Titus now officially owns SeqDB code. The bottom line of the review: a lot of
work but worth it.
Chris: 0.9 branch will likely appear after 0.8-alpha; this will likely include
next-gen sequencing. Jenny: working with NGS, need illustrations/examples of
how to connect this with Pygr! Chris: let's use Jenny's case as test for seeing
how this can be integrated, what to address etc. Titus also somewhat involved,
will communicate with Jenny; also Istvan and Namshin. This will among other
things help Jenny introduce Pygr to her colleagues.
0.8 timeline: With metabase in the master, check if there are any outstanding
new-feature issues. If not, feature freeze!
--
MS
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