v0.2.13.1

Minor update to increment version number in the code.

v0.2.13

This release fixes a deprecated matplotlib call, and deprecated pandas calls.

v0.2.12

This release fixes Issue #177: input filenames that contain an open or a closed parenthesis produce the message: 'WARNING: At least one BLAST run failed. ANIb may fail.'

v0.2.11

This release fixes issues due to pandas API changes.

• exceptions used in pyani are now found in pandas.errors not pandas.io.common
• changes to the testing API (will not affect most users)

v0.2.10

This release fixes the bug reported in issue #178 that affected graphical output if all input filenames could be interpreted as floating point numbers.

v0.2.9

This release fixes issue #132 (TETRA analysis failing when one or more 4-mers are missing from input sequences).

Thanks to @ghbio for the bug report!

v0.2.8

This release implements several changes:

• fixed warnings about deprecated usage of pandas and other syntax
• ANIb now respects the --workers argument (PR #127 from Özcan Esen)
• distance matrices are converted from square to condensed form for linkage analysis
• matplotlib calls use new API ('false', 'off' -> False; 'true', 'on' -> True)
• deprecate legacy BLAST testing: ANIblastall commands are no longer supported
• update concordance tests (issue #105)
• extend test suites (issue #104)
• modify ANIm concordance test to accommodate new command structure
• add delta-filter wrapper for compatibility with SGE/OGE schedulers

v0.2.7

This release fixes issue #97 in which numeric arguments to the GenBank download script were not recognised.

v0.2.5: Fix for installation problem

This release fixes a PyPI installation problem, resulting from a badly-built .whl wheel.

v0.2.4: Bugfixes and other improvements

• ANIm now uses delta-filter to remove alignments of repeat regions (issue #91)
• added --filter_exe option to specify location of delta-filter utility (issue #91)
• fixed --format option so that GenBank downloads work again (issue #89)
• add --SGEargs option to average_nucleotide_identity.py for custom qsub settings
• README.md badges now clickable
• --version switch added to average_nucleotide_identity.py
• FTP timeouts are now caught differently in genbank_get_genomes_by_taxon.py
• Additional characters in NCBI FTP URIs now escaped in genbank_get_genomes_by_taxon.py - should be fewer failed downloads
• Modified error messaging when NUCmer alignment fails
• average_nucleotide_identity.py argument documentation improvements
• Script now fails immediately if label or class files missing (issue #78)
• Changes to --noclobber log behaviour (issue #79)
• fixed --rerender code (issue #85)