* coverage capture on GitHub Actions (not PyPy), Linux may be too slow?
* collect coverage for Bio and BioSQL (although later not working)
* drop restriction on numpy (no longer an issue)
Pending - coverage upload from AppVeyor too
We want the index to use raw bytes offsets, rather
than psuedo offsets after cross platform newline
normalisation.
Note: This has left the MAF iterator able to take
either bytes or text mode handles as input.
If a program reads both a BAM file and a bgzipped compressed FASTA or VCF
file, the error message can confuse the user because it’s easy to overlook
the "e.g.", and the user might think that the BAM file is the problematic
one while it is the other.
ValueError: The truth value of an empty array is ambiguous. Use to check that an array is not empty.
Using bool(empty_array) was deprecated, and became an error in numpy 2.2.0.
With this minor change, the doctest will work on older numpy
and numpy 2.2 as well (where the array __repr__ includes
shape information by default).
This also fixed the over indentation of the PCA docstring,
and switched to the standard 'import numpy as np' idiom.
This has started to fail on 64bit Windows with:
```
CondaKeyError: 'channels': value 'defaults' not present in config
```
See #4801. We might still want to do this for 32bit Windows?
* Fixed a bug in calculating the height of clades when building a UPGMA tree
* added my name to contrib.rst alphabetically
* minor corrections
* formatting changes
* Add tests
---------
Co-authored-by: She Zhang <shz66@pitt.edu>
Co-authored-by: Fabian Egli <fabianegli@users.noreply.github.com>
Co-authored-by: Eric Talevich <etal@users.noreply.github.com>
* scaffold FOGSAA and add setter for PairwiseAligner.algorithm
* add first version of FOGSAA scoring
* add restrictions to algorithm setter and support matrix scoring in FOGSAA
* add test for running fogsaa with matrix scoring
* Remove algorithm setter in lieu of FOGSAA_Mode, scaffold PathGenerator for FOGSAA
* Add basic support for FOGSAA alignment
* Add FOGSAA alignment with matrix scoring
* Add more restrictions to FOGSAA parameters.
These restrictions come from the queue data structure used not from the
algorithm itself. Changing the priority queue implementation may ease
these restrictions at a possible loss to performance.
* Change FOGSAA priority queue implementation to a max heap
This allows for the queue sort doubles, which in turn removes the
requirement of integer scores in FOGSAA.
* Allocate memory once, fix affine gaps, remove threshold
* more fixes
* Add error checking, debugging code, and fix lower bounds
* add support for different affine gaps on edges
* remove debug printfs, warn on invalid parameters
* fix floating point comparison bugs
* only copy cells of optimal path in fogsaa align
* stop using different macros for fogsaa cell types
* fix fogsaa docstrings, iterator, and reset algorithm on set_mode
* mention fogsaa in Tutorial/chapter_pairwise.rst
* fix fogsaa documentation in Doc/Tutorial/chapter_pairwise.rst
* fix typo
- Added private alternative constructor SeqRecord._from_validated(...). This avoids type and length checks in cases when these have already been done
- Modified SeqRecord seq and letter_annotation attributes to use decorator-based formatting, and included more type annotations
- Modified sam parser to explicitly construct a new SeqRecord to remove the deepcopy bottleneck
- Modified FastaIterator, QualityIO, and SffIO parsers to use _from_validated to redundant checks and make code cleaner
- Added explicit checks in SeqRecord methods for cases when Seq is None, and specific error messages for those cases
