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Commits on Aug 14, 2009

• fixed easy_install bug by protecting coordinator.ResourceFile in try:except block

  cjlee112

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  a3a3e68

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Commits on Aug 4, 2009

• fixed blast_test: renamed test_seq_without_db() to avoid stomping on original test_both_seq_and_db() test

  cjlee112

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  2f8c414

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• Merge commit 'remotes/ctb/minor_fixes' into minor_fixes

  cjlee112

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  6bee945

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• fix port passing in testutil.TestXMLRPCServer

  cjlee112

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  b9d603e

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• test for fix in commit 54a1ef (fixed BLASTs of sequences w/no .db attr)

  

  Titus Brown

  committed
  e605f47

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• use pair_identity_tuple() for blast_test formatting where possible

  cjlee112

  committed
  715f391

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• SixFrameInfo/KeyError should mention erroneous key, to help in debugging.

  

  Titus Brown

  committed
  7897e47

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• added BlastBase.tearDown() to close seqdbs as they should be...

  cjlee112

  committed
  f1ab4c4

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• Merge commit 'remotes/mkszuba/doc_make'

  cjlee112

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• Merge commit 'remotes/mkszuba/rpm'

  cjlee112

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Commits on Jul 31, 2009

• (At least some versions of) sphinx-build do not create the output directory, failing if they cannot find it. Added an mkdir directive to the makefile to bypass the need for creating said directory …

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  Marek Szuba

  committed
  28f1a35

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• Switch bytecode optimisation on by default for the install phase. This works around a bug in Fedora 10 and older (#236535 on bugzilla.redhat.com) which prevents the bdist_rpm target from working on…

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  Marek Szuba

  committed
  44f30c0

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• New, ReST-based HTML documentation should now be used, then again it is built independently from Pygr itself (plus we would like the docs to go into a separate RPM anyway). Therefore, doc/html has …

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  Marek Szuba

  committed
  be1e12c

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• The README file is now called README.txt, updated setup.cfg/bdist_rpm accordingly

  

  Marek Szuba

  committed
  67a5411

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• The location of gapping.fa was specified explicitly instead of using testutil.datafile. Fixed.

  

  Marek Szuba

  committed
  d18a0ca

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Commits on Jul 29, 2009

• got rid of BlastMapping.warn_about_self_matches()

  cjlee112

  committed
  842c6e1

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• changed NLMSA pairwiseMode to allow reporting of self-matches

  cjlee112

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  28dfabf

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• Merge commit 'remotes/mkszuba/debian'

  cjlee112

  committed
  8612d8c

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• retry reading port_file in TestXMLRPCServer several times before giving up

  cjlee112

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  262a2ad

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• Removed unnecessary dh_python call

  

  Marek Szuba

  committed
  9274254

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• Added instructions for building documentation, as a separate package

  

  Marek Szuba

  committed
  7d245b7

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• The README file is now called README.txt, updated debian/rules accordingly

  

  Marek Szuba

  committed
  8436e94

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• Removed trailing whitespace from the description

  

  Marek Szuba

  committed
  9565c6c

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• added comments to process_blast()

  cjlee112

  committed
  e99afa8

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• fix problem introduced in process_blast() by commit 69ba04

  cjlee112

  committed
  54a1efb

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Commits on Jul 28, 2009

• handle missing WINDIR case on Windows

  cjlee112

  committed
  026ab13

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• added SeqTranslator.__repr__()

  cjlee112

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  ae183fe

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• Merge commit 'remotes/ctb/simpleframe_formatdb_cleanup' into simpleframe

  cjlee112

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  7ebb907

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• Merge branch 'master' into simpleframe

  cjlee112

  committed
  1062ec9

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• added SeqTranslator.iter_frames() method, used in BlastxMapping.__getitem__()

  cjlee112

  committed
  4f9fa00

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• Merge commit 'remotes/ctb/simpleframe_doc_align' into simpleframe

  cjlee112

  committed
  b4d6fc1

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Commits on Jul 27, 2009

• protect 2 more tests using blast_enabled() check

  cjlee112

  committed
  4d5d181

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• fixed syntax error

  cjlee112

  committed
  3369057

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• added python 2.3 code for FilePopen to detect bad exit code, raise OSError

  cjlee112

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  0e19915

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• Merge branch 'no_edge_db'

  cjlee112

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