[Biopython-dev] [Bug 2723] New: Clarify what applies to which version of biopython and other doc cleanup

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sat Jan 3 22:18:56 UTC 2009


           Summary: Clarify what applies to which version of biopython and
                    other doc cleanup
           Product: Biopython
           Version: 1.49
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Documentation
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: mmokrejs at ribosome.natur.cuni.cz

I went to look around at the docs because the built-in tests of 1.49 setup.py
spitted some messages about external programs missing. I haven't found any
hints on them in http://news.open-bio.org/news/2008/11/biopython-release-149/.

Anyway, looking at 
I see: "3.4  mxTextTools (no longer needed)". I would propose:

3.4  mxTextTools (no longer needed since 1.49)

- 3.1  Numerical Python (NumPy) (strongly recommended)
+ 3.1  Numerical Python (NumPy) (strongly recommended since 1.49)

Bad URL links are in the text:

3.3  Database Access (MySQLdb, ...) (optional)


Additionally, both MySQLdb and psycopg (a PostgreSQL database adaptor) can be
used for accessing BioSQL databases through Biopython (see ). Again if you are 
not going to use BioSQL, there shouldn’t be any need to install these

3.4  mxTextTools (no longer needed)


However, we currently recommend you install mxTextTools 2.0, as some of the API
changes made in 3.0 version were not compatible with Biopython. Goto to

I haven't found an answer for me yet:

test_PopGen_FDist ... skipping. Install FDist if you want to use
test_PopGen_FDist_nodepend ... ok
test_PopGen_GenePop ... ok
test_PopGen_SimCoal ... skipping. Install SIMCOAL2 if you want to use
test_PopGen_SimCoal_nodepend ... ok
test_ProtParam ... ok
test_Registry ... ok
test_Restriction ... ok
test_SCOP_Astral ... ok
test_SCOP_Cla ... ok
test_SCOP_Des ... ok
test_SCOP_Dom ... ok
test_SCOP_Hie ... ok
test_SCOP_Raf ... ok
test_SCOP_Residues ... ok
test_SCOP_Scop ... ok
test_SProt ... ok
test_SVDSuperimposer ... ok
test_SeqIO ... ok
test_SeqIO_online ... ok
test_SeqUtils ... ok
test_SubsMat ... ok
test_UniGene ... ok
test_Wise ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
test_align ... ok
test_docstrings ... ok
test_geo ... ok
test_interpro ... ok
test_kNN ... ok
test_lowess ... ok
test_pairwise2 ... ok
test_prodoc ... ok
test_property_manager ... ok
test_prosite ... ok
test_prosite2 ... ok
test_psw ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
test_seq ... ok
test_translate ... ok
test_trie ... ok
test_triefind ... ok

Ran 96 tests in 172.215s


Pointer to those packages would have been helpful. From the test suite as well
as from installation manual. Moreover, what database username/password would
I have to make to get the BioSQL stuff compiled and tested?  ^H^H^H^H^H^H
I see, it gets compiled anyway the tests just were not run. The installation
manual and the output from test suite should be clearer.

Thanks, Peter!

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