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ported `cogent.util.misc.iterable` to `bipy.core.constrained_container.iterable`, as that is where it is currently being used. we should put this in a better place, if we want to keep it.
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suddenly getting this error as of 0.11.12 when i'm proxying https requests over an http proxy. am i doing things wrong? or do you have to change something?
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all_tests.py is used by Jenkins for automated pull request checks, but I think its current configuration could use some small improvements. I have encountered two things (one of which is causing #875 …
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Any translated mapping done via `map_reads_to_reference.py` should allow users to specify the genetic code that should be used for the six-frame translation step. Currently we're defaulting to the ver…
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(Slightly related to issue #1, found working on issue #63)
- The only function in that file that is [used in bipy](https://github.com/biocore/bipy/blob/master/bipy/app/util.py#L22) (`cross_comb`) exis…
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```
======================================================================
FAIL: test_format_jnlp_file_lines (__main__.TopLevelTests)
format_jnlp_file_lines: this converts files into jnlp lines
------…
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Running along with business as usual, and:
```
May 16 04:32:26 ip-10-226-3-33 kernel: [1463818.118812] rethinkdb invoked oom-killer: gfp_mask=0x201da, order=0, oom_adj=0, oom_score_adj=0
May 16 04:32…
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The required version of numpy on `setup.py` is `1.5.1`. However, I was running `1.6.1` and I got some errors (details below).I had to install `1.8.1` in order to get rid of these errors. I had no time…
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This is kind of inconvenient - would it be possible to update so values can be accessed by key (i.e., sample id) pairs?
```
In [12]: from bipy.core.distance import SymmetricDistanceMatrix
In [13]: i…