Commit 898083a2 authored by Martin Larralde's avatar Martin Larralde
Browse files

Release v0.3.1

parent 64112a13
Pipeline #22977 passed with stage
in 5 minutes and 7 seconds
......@@ -6,18 +6,26 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
## [Unreleased]
[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.3.0...HEAD
[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.3.1...HEAD
## [v0.3.1] - 2021-05-08
[v0.3.1]: https://github.com/althonos/pyhmmer/compare/v0.3.0...v0.3.1
### Added
- `Pipeline.scan_seq` method to query a database of profiles with one or more sequences.
- `transition_probabilities`, `match_emissions`, `insert_emissions` properties to the `HMM` class, providing access to the numerical parameters of the HMM.
- `consensus_structure` and `consensus_accessibility` properties to the `HMM` class to get consensus lines from the source alignment if the HMM was created from a MSA.
- `nseq` and `nseq_effective` properties to the `HMM` class to get the number of training sequences and effective sequences used to build the HMM.
### Changed
- `HMM.checksum` is now `None` if the `p7H_CHKSUM` flag is not set.
- `Builder` methods will now record `sys.argv` when creating a HMM.
### Fixed
- `HMM.write(..., binary=False)` crashing on HMMs without a consensus line. ([#5](https://github.com/althonos/pyhmmer/issues/5)). Fixed upstream in ([EddyRivasLab/HMMER#236](https://github.com/EddyRivasLab/hmmer/pull/236)).
- `Pipeline.reset` mishandling the `Z` and `domZ` values if those were detected from the number of targets.
- `pyhmmer.hmmer` functions will not block until all results have been collected anymore when run in multithreaded mode.
## [v0.3.0] - 2021-03-11
......
......@@ -20,12 +20,12 @@ from . import errors
from . import easel
from . import plan7
from .hmmer import hmmsearch, hmmpress, phmmer
from .hmmer import hmmsearch, hmmpress, nhmmer, phmmer
__author__ = "Martin Larralde <martin.larralde@embl.de>"
__license__ = "MIT"
__version__ = "0.3.0"
__version__ = "0.3.1"
__all__ = [
errors.__name__,
easel.__name__,
......@@ -33,6 +33,7 @@ __all__ = [
hmmsearch.__name__,
hmmpress.__name__,
phmmer.__name__,
nhmmer.__name__,
]
# Small addition to the docstring: we want to show a link redirecting to the
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