[med-svn] [python-skbio] branch upstream updated (9f57339 -> 76aae4f)
Kevin Murray
daube-guest at moszumanska.debian.org
Thu Feb 18 00:53:56 UTC 2016
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a change to branch upstream
in repository python-skbio.
from 9f57339 Imported Upstream version 0.4.1
new 76aae4f Imported Upstream version 0.4.2
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
CHANGELOG.md | 33 +-
RELEASE.md | 4 +-
ci/pip_requirements.txt | 2 +-
doc/source/_static/style.css | 4 +
doc/source/conf.py | 7 +-
skbio/__init__.py | 2 +-
skbio/alignment/_pairwise.py | 26 +-
skbio/alignment/_tabular_msa.py | 45 +-
skbio/alignment/tests/test_pairwise.py | 18 +-
skbio/alignment/tests/test_tabular_msa.py | 36 +-
skbio/diversity/alpha/_lladser.py | 2 +-
skbio/io/__init__.py | 9 +-
skbio/io/_exception.py | 5 +
skbio/io/format/_base.py | 2 +-
skbio/io/format/clustal.py | 12 +-
skbio/io/format/fasta.py | 9 +-
skbio/io/format/fastq.py | 9 +-
skbio/io/format/genbank.py | 8 +-
skbio/io/format/phylip.py | 8 +-
skbio/io/format/stockholm.py | 710 +++++++++++++++++++++
.../io/format/tests/data/stockholm_all_data_types | 15 +
skbio/io/format/tests/data/stockholm_blank_lines | 6 +
skbio/io/format/tests/data/stockholm_data_only | 5 +
.../tests/data/stockholm_differing_gc_data_length | 4 +
.../tests/data/stockholm_differing_gr_data_length | 4 +
.../tests/data/stockholm_differing_seq_lengths | 4 +
skbio/io/format/tests/data/stockholm_duplicate_gc | 7 +
skbio/io/format/tests/data/stockholm_duplicate_gr | 8 +
.../tests/data/stockholm_duplicate_sequence_names | 6 +
.../format/tests/data/stockholm_duplicate_tree_ids | 6 +
skbio/io/format/tests/data/stockholm_extensive | 15 +
.../io/format/tests/data/stockholm_extensive_mixed | 15 +
.../format/tests/data/stockholm_invalid_data_type | 4 +
.../tests/data/stockholm_invalid_nonexistent_gr | 7 +
.../tests/data/stockholm_invalid_nonexistent_gs | 5 +
.../tests/data/stockholm_malformed_data_line | 3 +
.../format/tests/data/stockholm_malformed_gc_line | 4 +
.../format/tests/data/stockholm_malformed_gf_line | 3 +
.../format/tests/data/stockholm_malformed_gr_line | 4 +
.../format/tests/data/stockholm_malformed_gs_line | 4 +
skbio/io/format/tests/data/stockholm_metadata_only | 4 +
skbio/io/format/tests/data/stockholm_minimal | 3 +
.../io/format/tests/data/stockholm_missing_footer | 4 +
.../io/format/tests/data/stockholm_missing_header | 4 +
skbio/io/format/tests/data/stockholm_multiple_msa | 18 +
.../io/format/tests/data/stockholm_multiple_trees | 8 +
skbio/io/format/tests/data/stockholm_no_data | 2 +
.../format/tests/data/stockholm_nonstring_labels | 7 +
skbio/io/format/tests/data/stockholm_rna | 9 +
skbio/io/format/tests/data/stockholm_runon_gf | 5 +
skbio/io/format/tests/data/stockholm_runon_gs | 5 +
.../tests/data/stockholm_single_tree_with_id | 4 +
.../tests/data/stockholm_single_tree_without_id | 3 +
.../tests/data/stockholm_two_of_each_metadata | 11 +
.../tests/data/stockholm_whitespace_only_lines | 5 +
skbio/io/format/tests/test_base.py | 4 +-
skbio/io/format/tests/test_clustal.py | 15 +-
skbio/io/format/tests/test_fasta.py | 17 +-
skbio/io/format/tests/test_fastq.py | 17 +-
skbio/io/format/tests/test_genbank.py | 15 +-
skbio/io/format/tests/test_stockholm.py | 701 ++++++++++++++++++++
skbio/io/registry.py | 28 +-
skbio/io/tests/test_registry.py | 36 +-
skbio/io/tests/test_util.py | 36 +-
skbio/sequence/__init__.py | 13 +-
skbio/sequence/_dna.py | 33 +-
.../{_iupac_sequence.py => _grammared_sequence.py} | 189 +++++-
skbio/sequence/_nucleotide_mixin.py | 2 +-
skbio/sequence/_protein.py | 39 +-
skbio/sequence/_rna.py | 33 +-
skbio/sequence/_sequence.py | 90 ++-
skbio/sequence/distance.py | 115 ++++
skbio/sequence/tests/test_distance.py | 130 ++++
skbio/sequence/tests/test_dna.py | 6 +
skbio/sequence/tests/test_grammared_sequence.py | 613 ++++++++++++++++++
skbio/sequence/tests/test_iupac_sequence.py | 506 ---------------
skbio/sequence/tests/test_nucleotide_sequences.py | 27 +-
skbio/sequence/tests/test_protein.py | 6 +
skbio/sequence/tests/test_rna.py | 5 +
skbio/sequence/tests/test_sequence.py | 216 +++++--
skbio/stats/composition.py | 28 +-
skbio/stats/distance/_base.py | 4 +-
skbio/stats/distance/tests/test_base.py | 53 +-
.../ordination/tests/test_redundancy_analysis.py | 2 +
skbio/stats/power.py | 14 +-
skbio/stats/tests/test_composition.py | 20 +-
skbio/stats/tests/test_gradient.py | 42 +-
skbio/tree/_tree.py | 67 +-
skbio/tree/tests/test_tree.py | 13 +
skbio/util/__init__.py | 15 +-
skbio/util/_decorator.py | 3 +-
skbio/util/_misc.py | 22 +-
skbio/util/_testing.py | 27 +-
skbio/util/_warning.py | 14 +-
skbio/util/tests/test_decorator.py | 9 +-
skbio/util/tests/test_misc.py | 2 +-
96 files changed, 3529 insertions(+), 870 deletions(-)
create mode 100644 skbio/io/format/stockholm.py
create mode 100644 skbio/io/format/tests/data/stockholm_all_data_types
create mode 100644 skbio/io/format/tests/data/stockholm_blank_lines
create mode 100644 skbio/io/format/tests/data/stockholm_data_only
create mode 100644 skbio/io/format/tests/data/stockholm_differing_gc_data_length
create mode 100644 skbio/io/format/tests/data/stockholm_differing_gr_data_length
create mode 100644 skbio/io/format/tests/data/stockholm_differing_seq_lengths
create mode 100644 skbio/io/format/tests/data/stockholm_duplicate_gc
create mode 100644 skbio/io/format/tests/data/stockholm_duplicate_gr
create mode 100644 skbio/io/format/tests/data/stockholm_duplicate_sequence_names
create mode 100644 skbio/io/format/tests/data/stockholm_duplicate_tree_ids
create mode 100644 skbio/io/format/tests/data/stockholm_extensive
create mode 100644 skbio/io/format/tests/data/stockholm_extensive_mixed
create mode 100644 skbio/io/format/tests/data/stockholm_invalid_data_type
create mode 100644 skbio/io/format/tests/data/stockholm_invalid_nonexistent_gr
create mode 100644 skbio/io/format/tests/data/stockholm_invalid_nonexistent_gs
create mode 100644 skbio/io/format/tests/data/stockholm_malformed_data_line
create mode 100644 skbio/io/format/tests/data/stockholm_malformed_gc_line
create mode 100644 skbio/io/format/tests/data/stockholm_malformed_gf_line
create mode 100644 skbio/io/format/tests/data/stockholm_malformed_gr_line
create mode 100644 skbio/io/format/tests/data/stockholm_malformed_gs_line
create mode 100644 skbio/io/format/tests/data/stockholm_metadata_only
create mode 100644 skbio/io/format/tests/data/stockholm_minimal
create mode 100644 skbio/io/format/tests/data/stockholm_missing_footer
create mode 100644 skbio/io/format/tests/data/stockholm_missing_header
create mode 100644 skbio/io/format/tests/data/stockholm_multiple_msa
create mode 100644 skbio/io/format/tests/data/stockholm_multiple_trees
create mode 100644 skbio/io/format/tests/data/stockholm_no_data
create mode 100644 skbio/io/format/tests/data/stockholm_nonstring_labels
create mode 100644 skbio/io/format/tests/data/stockholm_rna
create mode 100644 skbio/io/format/tests/data/stockholm_runon_gf
create mode 100644 skbio/io/format/tests/data/stockholm_runon_gs
create mode 100644 skbio/io/format/tests/data/stockholm_single_tree_with_id
create mode 100644 skbio/io/format/tests/data/stockholm_single_tree_without_id
create mode 100644 skbio/io/format/tests/data/stockholm_two_of_each_metadata
create mode 100644 skbio/io/format/tests/data/stockholm_whitespace_only_lines
create mode 100644 skbio/io/format/tests/test_stockholm.py
rename skbio/sequence/{_iupac_sequence.py => _grammared_sequence.py} (71%)
create mode 100644 skbio/sequence/distance.py
create mode 100644 skbio/sequence/tests/test_distance.py
create mode 100644 skbio/sequence/tests/test_grammared_sequence.py
delete mode 100644 skbio/sequence/tests/test_iupac_sequence.py
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