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

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2723

           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 
http://biopython.org/DIST/docs/install/Installation.html#htoc17
I see: "3.4  mxTextTools (no longer needed)". I would propose:

3.4  mxTextTools (no longer needed since 1.49)

Similarly:
- 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)

[cut]

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
modules.


3.4  mxTextTools (no longer needed)

[cut]

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
download
---------------------------------------------------------------------^^
this.



I haven't found an answer for me yet:

test_PopGen_FDist ... skipping. Install FDist if you want to use
Bio.PopGen.FDist.
ok
test_PopGen_FDist_nodepend ... ok
test_PopGen_GenePop ... ok
test_PopGen_SimCoal ... skipping. Install SIMCOAL2 if you want to use
Bio.PopGen.SimCoal.
ok
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.
ok
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.
ok
test_seq ... ok
test_translate ... ok
test_trie ... ok
test_triefind ... ok

----------------------------------------------------------------------
Ran 96 tests in 172.215s

OK


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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