biopython/biopython — pull request #70 by semenko (2012-09-11 03:57:55+00:00)
Title: Use /dev/shm for sqlite3 testing (where possible)

The current sqlite3 tests are incredibly slow since they rely on disk. This
means that ACID compliance forces lots of fsync() calls, which are slowww.

This takes advantage of the /dev/shm ramdisk for testing. Things should fail
gracefully (back to disk if /dev/shm is inaccessible). The sqlite3 DB seems
to take only ~2 MB max, so OOM errors shouldn't be an issue.

On a blazing Ivy Bridge / RAID10 machine, this test's execution goes from:
```
real 4m3.680s
user 0m5.032s
sys 0m1.032s
```
To:
```
real 0m4.788s
user 0m4.112s
sys 0m0.648s
```
Bonus: This should fix Travis CI's intermittent timeouts, assuming /dev/shm
is accessible.

Bonus 2: PEP8 fixes.

Signed-off-by: Nick Semenkovich \