Commit 24a5f7d2 authored by Martin Larralde's avatar Martin Larralde
Browse files

Release v0.6.1

parent ccbb58cd
Pipeline #34989 failed with stage
in 4 minutes and 25 seconds
......@@ -6,7 +6,28 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
## [Unreleased]
[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.6.0...HEAD
[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.6.1...HEAD
## [v0.6.1] - 2022-06-28
[v0.6.1]: https://github.com/althonos/pyhmmer/compare/v0.6.0...v0.6.1
### Added
- `pickle` protocol support for `TopHits` objects, using the HMMER network serialization.
- `TopHits.write` method to write hits to a file in tabular format.
- `query_name` and `query_accession` properties to `TopHits` objects to access the name and accession of the query that produced the hits.
### Fixed
- Extraction of filename from file-like objects in the `HMMFile` constructor.
- Use `os.cpu_count` instead of `multiprocessing.cpu_count` where applicable to preserve OS scheduling.
- Wrong return type in docstring of `HMM.insert_emissions`.
- `TopHits.searched_nodes` returning the searched number of residues instead of the searched number of model nodes.
- Unsound decoding of pickled `MatrixF` or `VectorF` when data comes from a source of different endianness.
### Changed
- Rewrite `pyhmmer.hmmer` threading code using `Deque` instead of `collections.Queue` to store the queries and results.
- Reduce memory consumption of `pyhmmer.hmmer` by reducing the number of semaphores and event flags used concurrently.
- Make `pyhmmer.hmmer` main threads block on query insertion rather than result retrieval to make sure worker threads are never idling.
## [v0.6.0] - 2022-05-01
......
......@@ -26,7 +26,7 @@ from .hmmer import hmmalign, hmmsearch, hmmpress, nhmmer, phmmer
__author__ = "Martin Larralde <martin.larralde@embl.de>"
__license__ = "MIT"
__version__ = "0.6.0"
__version__ = "0.6.1"
__all__ = [
errors.__name__,
easel.__name__,
......
......@@ -197,6 +197,9 @@ cdef class Alignment:
Attributes:
domain (`Domain`): The domain this alignment corresponds to.
.. versionadded:: 0.6.1
`pickle` protocol support.
"""
# --- Magic methods ------------------------------------------------------
......@@ -1318,6 +1321,9 @@ cdef class Domain:
alignment (`~pyhmmer.plan7.Alignment`): The alignment of this domain
to a target sequence.
.. versionadded:: 0.6.1
`pickle` protocol support.
"""
# --- Magic methods ------------------------------------------------------
......@@ -1625,6 +1631,10 @@ cdef class EvalueParameters:
cdef class Hit:
"""A high-scoring database hit found by the comparison pipeline.
.. versionadded:: 0.6.1
`pickle` protocol support.
"""
# --- Magic methods ------------------------------------------------------
......@@ -6288,6 +6298,9 @@ cdef class TopHits:
>>> hits[0].name
b'938293.PRJEB85.HG003687_113'
.. versionadded:: 0.6.1
`pickle` protocol support.
"""
# --- Magic methods ------------------------------------------------------
......
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