-
Martin Larralde authoredMartin Larralde authored
To find the state of this project's repository at the time of any of these versions, check out the tags.
- Changelog
- Unreleased
- v0.5.1 - 2024-02-20
- Added
- Fixed
- v0.5.0 - 2023-07-22
- Changed
- Fixed
- v0.4.1 - 2022-08-20
- Changed
- v0.4.0 - 2022-08-04
- Added
- Fixed
- v0.3.1 - 2022-07-22
- Added
- v0.3.0 - 2022-07-17
- Added
- Changed
- Fixed
- v0.2.1 - 2021-06-20
- Fixed
- v0.2.0 - 2021-06-20
- Added
- Changed
- Fixed
- v0.1.2 - 2021-06-15
- Changed
- v0.1.1 - 2021-06-13
- Fixed
- v0.1.0 - 2021-06-13
CHANGELOG.md 3.94 KiB
Changelog
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
Unreleased
v0.5.1 - 2024-02-20
Added
- Pre-compiled wheels for Python 3.12 and PyPy 3.10.
Fixed
- Use NEON and SSE2 unconditionally on platforms where they are available by default.
v0.5.0 - 2023-07-22
Changed
- Bump Cython dependency to
v3.0
.
Fixed
- Add missing signature of
Sketch.index
to type stubs. - PyPy builds failing on missing
PyInterpreterState_GetID
function.
v0.4.1 - 2022-08-20
Changed
- Use lists instead of arrays to store state of
Minimizers
when pickling. - Skip serialization of minimizer index to reduce total state size.
- Make
Mapper.query_draft
andMapper.query_genome
return hits sorted by identity in descending order.
v0.4.0 - 2022-08-04
Added
- Multi-threaded computation of fragment mapping in
Mapper.query_draft
andMapper.query_genome
.
Fixed
- NEON-specific compile flags in
setup.py
for Aarch64 target platforms. - Broken compilation for Arm platforms because of missing header guards.
v0.3.1 - 2022-07-22
Added
- Slightly improve documentation in some classes.
- Sphinx documentation for the project hosted on ReadTheDocs.
- Links and instructions to install package from the Bioconda channel.
v0.3.0 - 2022-07-17
Added
-
pickle
protocol implementation toMapper
andSketch
via__getstate__
and__setstate__
. -
Minimizers
class to access the minimizers of aSketch
orMapper
object.
Changed
- Make
Sketcher
andMapper
final. - Prevent direct instantiation of
Mapper
objects. - Update
Mapper._query_draft
to recycle memory between fragments. - Vendor
Boost::math
headers (v1.79
) to allow compiling without depdendencies.
Fixed
- Broken compilation of
_fastani
extension module asuniversal2
binaries on MacOS.
v0.2.1 - 2021-06-20
Fixed
- Missing header files in the
tar.gz
distribution, preventing compilation of the wheel from source.
v0.2.0 - 2021-06-20
Added
-
Sketch.clear
method to remove all sequences currently in aSketch
and reset the list of minimizers. - SIMD code to read and reverse-complement the input sequences efficiently on supported platforms (x86-64 with SSE2 or SSSE3, and ARM with NEON).
Changed
- Split the
Sketch
type in two depending on whether the object is at the sketching stage (Sketch
) or at the querying stage (Mapper
). -
Sketch.add_genome
,Sketch.add_draft
,Mapper.query_genome
andMapper.query_draft
can now be passed a Unicode string for the sequence.
Fixed
- Integer underflow causing minimizers out of the block window to be added to the final minimizers list.
v0.1.2 - 2021-06-15
Changed
- Querying functions now release GIL to allow efficient parallel querying.
v0.1.1 - 2021-06-13
Fixed
- Source distribution missing Cython and C++ sources, thus preventing compilation.
v0.1.0 - 2021-06-13
Initial release.