Package: python-cogent / 1.9-9

Metadata

Package Version Patches format
python-cogent 1.9-9 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
accept_newer_cdhit.patch | (download)

cogent/app/cd_hit.py | 10 8 + 2 - 0 !
1 file changed, 8 insertions(+), 2 deletions(-)

 get cogent to work with newer cd-hit that doesn't leave
 a temporary file sitting around.  This patch has only been quickly tested and
 there may be deeper issues.


fix_python_shebang_line.patch | (download)

cogent/align/dp_calculation.py | 2 1 + 1 - 0 !
cogent/data/molecular_weight.py | 2 1 + 1 - 0 !
cogent/format/text_tree.py | 2 1 + 1 - 0 !
cogent/phylo/maximum_likelihood.py | 2 1 + 1 - 0 !
cogent/recalculation/__init__.py | 2 1 + 1 - 0 !
cogent/recalculation/setting.py | 2 1 + 1 - 0 !
6 files changed, 6 insertions(+), 6 deletions(-)

 fix path to python interpreter

parsinsert_not_in_caps.patch | (download)

cogent/app/parsinsert.py | 2 1 + 1 - 0 !
tests/alltests.py | 2 1 + 1 - 0 !
tests/test_app/test_parsinsert.py | 4 2 + 2 - 0 !
3 files changed, 4 insertions(+), 4 deletions(-)

 make script compatible with spelling of debian's
 parsinsert package


fasttree_not_in_caps.patch | (download)

cogent/app/fasttree.py | 2 1 + 1 - 0 !
cogent/app/fasttree_v1.py | 2 1 + 1 - 0 !
tests/test_app/test_fasttree.py | 11 6 + 5 - 0 !
3 files changed, 8 insertions(+), 7 deletions(-)

 make script compatible with spelling of debian's
 fasttree package
 .
 One test had to be excluded.  This is reported upstream as issue #102


raxml_unsupported_version.patch | (download)

tests/test_app/test_raxml_v730.py | 3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-)

 the test is checking for an old verison of raxml
 for no good reason


cd hit test.patch | (download)

tests/test_app/test_cd_hit.py | 26 0 + 26 - 0 !
1 file changed, 26 deletions(-)

 upstream confirmed that the app controller only supports
 cd-hit 3.1.1.
 .
 See https://github.com/pycogent/pycogent/issues/101
 .
 Exclude some tests for the moment since otherwise there is no chance
 to get the new cogent version uploaded which in turn fixes lots of
 other bugs


rdp_classifier.patch | (download)

cogent/app/rdp_classifier.py | 2 1 + 1 - 0 !
tests/test_app/test_rdp_classifier.py | 2 1 + 1 - 0 !
tests/test_app/test_rdp_classifier20.py | 2 1 + 1 - 0 !
3 files changed, 3 insertions(+), 3 deletions(-)

 try to support rdp_classifier (but failed - no idea why)


skip_weak_tests.patch | (download)

tests/test_align/test_weights/test_methods.py | 42 0 + 42 - 0 !
tests/test_cluster/test_nmds.py | 53 0 + 53 - 0 !
tests/test_maths/test_optimisers.py | 7 0 + 7 - 0 !
tests/test_seqsim/test_sequence_generators.py | 39 0 + 39 - 0 !
tests/test_seqsim/test_tree.py | 15 0 + 15 - 0 !
tests/test_struct/test_asa.py | 15 0 + 15 - 0 !
6 files changed, 171 deletions(-)

 skip some tests that do not create reproducible results at package
 build time
adapt_to_ncbi data_201609.patch | (download)

tests/test_app/test_blast.py | 65 0 + 65 - 0 !
tests/test_app/test_formatdb.py | 114 0 + 114 - 0 !
2 files changed, 179 deletions(-)

 since ncbi-tools6 6.1.20160908-1 some blast relatet tests
 are failing at package Build time.  These tests are deleted here.
 .
 Without the patches in tests/test_app/test_blast.py the build hangs totally
 and needs to be interrupted by ^C.
 .
 The patches in tests/test_app/test_formatdb.py lead to regular test suite
 failures with proper output of the problem.
Bug-Debian: https://bugs.debian.org/847082
ignore_numpy_test_issue.patch | (download)

tests/test_draw/test_distribution_plots.py | 6 0 + 6 - 0 !
tests/test_util/test_array.py | 6 0 + 6 - 0 !
2 files changed, 12 deletions(-)

 skip test featuring wrong numpy usage
 Traceback (most recent call last):
   File "/<<PKGBUILDDIR>>/tests/test_util/test_array.py", line 596, in test_split_dimension
     a = split_dimension(m, 0)
   File "/<<PKGBUILDDIR>>/cogent/util/array.py", line 504, in split_dimension
     return reshape(m, new_dim)
 ...
 TypeError: 'numpy.float64' object cannot be interpreted as an index
 .
 The issue occured after upgrading from Numpy 1.11.2 to 1.12.0~b1 which
 has cause also other packages test suites failures.  Since this version
 of Cogent is in low maintenance mode it will probably not be adapted to
 any new Numpy versions so skiping two tests might be the most apropriate
 step to deal with this issue
Bug-Debian: https://bugs.debian.org/848746