Bio/Entrez/DTDs/modules.ent | 7 0 + 7 - 0 !
1 file changed, 7 deletions(-)

 remove non dfsg free dtd

Tests/Blast/html_msgid_29_blastx_001.html | 5 2 + 3 - 0 !
1 file changed, 2 insertions(+), 3 deletions(-)

 do not use privacy-breach-logo

Doc/cookbook/Restriction/Restriction.html | 3 0 + 3 - 0 !
1 file changed, 3 deletions(-)

 fix privacy breach with html5shiv
 Actually the script called is commented out, except when reading the page with
 Internet Explorer 9.  This patch makes sure the script is not called at all,
 even if it is very unlikely that HTML document installed in Debian will ever
 be read with this browser.

Doc/Makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix use of unversioned 'python' interpreter
 The Doc/Makefile uses python to evaluate the current version of the library in
 order to build the documentation, but the unversioned "python" interpreter is
 not available anymore, at least not in the build context.

Doc/Tutorial.tex | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 make the build reproducible
 This patch removes the last update date, which would correspond to the moment
 when the package was build, and wouldn't be too relevant in the document.
 Focusing on the version number would be a better approach here.  This patch is
 not needed upstream, as it would interfere with development releases, marked
 only with the version "dev", so would benefit of the date here.

Bio/Align/Applications/_Muscle.py | 5 5 + 0 - 0 !
1 file changed, 5 insertions(+)

 raise runtime error when trying to use wrapper on muscle 5.
 The muscle wrapper only supports muscle 3, and the biopython project is aiming
 to remove wrapper support in an upcoming version.  Port of the wrapping code
 to support both muscle versions will thus probably never happen.  The affected
 code section is due to disappear in an upcoming biopython version and it thus
 not forwarded upstream.

Bio/Align/Applications/_Muscle.py | 10 9 + 1 - 0 !
Tests/test_Muscle_tool.py | 10 8 + 2 - 0 !
2 files changed, 17 insertions(+), 3 deletions(-)

 expect muscle3 as executable instead of muscle.
 When installed concurrently, muscle3 may be a preferrable default over plain
 muscle because the latter would probably be muscle 5, which is not compatible
 with the biopython wrapper.
 .
 Forwarding is not needed since wrappers are deprecated and due to be removed
 in an upcoming biopython version.

Doc/Tutorial/chapter_align.tex | 10 5 + 5 - 0 !
1 file changed, 5 insertions(+), 5 deletions(-)

 adjust tutorial to document muscle3 usage.
 In addition to being up to date with the way of doing things for the upcoming
 Debian version, this fixes the doctest failures.

Bio/PDB/SASA.py | 2 1 + 1 - 0 !
Bio/PDB/internal_coords.py | 8 4 + 4 - 0 !
Tests/test_Cluster.py | 2 1 + 1 - 0 !
3 files changed, 6 insertions(+), 6 deletions(-)

 [patch] fixing numpy type issues - replaced `np.int` with `np.int64`
 - replaced `np.bool` with `bool`