Commit 83d762bf authored by Martin Larralde's avatar Martin Larralde
Browse files

Release v0.4.0

parent 7b98a345
Pipeline #23445 failed with stage
in 4 minutes and 53 seconds
......@@ -138,6 +138,7 @@ jobs:
docs:
environment: ReadTheDocs
runs-on: ubuntu-latest
name: Rebuild stable docs
needs:
- upload
steps:
......
......@@ -61,6 +61,8 @@ jobs:
run: python -m pip install -r ci/requirements.txt
- name: Build C extension
run: python setup.py build_ext --inplace --debug
- name: Install test requirements
run: python -m pip install -r tests/requirements.txt
- name: Test with coverage
run: python -m coverage run -m unittest discover -vv
- name: Upload to Codecov
......@@ -129,6 +131,8 @@ jobs:
run: OPENBLAS="$(brew --prefix openblas)" python -m pip install -r ci/requirements.txt
- name: Build C extension
run: python setup.py build_ext --inplace --debug
- name: Install test requirements
run: python -m pip install -r ci/requirements.txt
- name: Test with coverage
run: python -m coverage run -m unittest discover -vv
- name: Upload to Codecov
......
......@@ -6,7 +6,37 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
## [Unreleased]
[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.3.1...HEAD
[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.4.0...HEAD
## [v0.4.0] - 2021-06-05
[v0.4.0]: https://github.com/althonos/pyhmmer/compare/v0.3.1...v0.4.0
### Added
- Linear algebra primitives to expose 1D (`Vector`) and 2D (`Matrix`) contiguous buffers containing numerical values to `pyhmmer.easel`.
- Documentation for the `Z` and `domZ` parameters of the `pyhmmer.plan7.Pipeline` constructor.
- `pyhmmer.errors.AlphabetMismatch` exception deriving from `ValueError` to specifically report mismatching Easel alphabets where applicable.
- `scale` and `normalize` methods to `pyhmmer.plan7.HMM` objects.
- Property to access `pyhmmer.plan7.Background` residue frequencies as a `VectorF` object.
- Property to access `pyhmmer.plan7.HMM` mean residue composition as a `VectorF` object.
- Property to access `pyhmmer.plan7.HMM` probabilities and emissions as `MatrixF` objects.
- `ssv_filter` methods to `pyhmmer.plan7.OptimizedProfile` to get the SSV filter score of the profile for a given sequence.
- Several additional properties to access the `pyhmmer.plan7.OptimizedProfile` internals.
### Removed
- Unused `report_e` parameter of `pyhmmer.plan7.Pipeline` constructor.
- `pyhmmer.plan7.TopHits.clear` method which could lead to segfault if it was called while a `Hit` is being held.
### Changed
- Multithreaded loop in `pyhmmer.hmmer` to reduce memory consumption while still yielding hits in order.
- `pyhmmer.easel.DigitalSequence.sequence` property is now a `VectorU8`.
### Fixed
- Type annotations in `pyhmmer.hmmer`.
- Potential double free in `pyhmmer.plan7.HMM.command_line` property setter.
- Minor floating-point precision issues in `pyhmmer.plan7.Builder` constructor.
- Segfault in `TextMSA.digitize` caused by `esl_msa_Copy` not digitizing on-the-fly like `esl_sq_Copy`.
- Exceptions not being raised in some methods of `pyhmmer.plan7.Profile` and `pyhmmer.plan7.TopHits`.
## [v0.3.1] - 2021-05-08
......
......@@ -3,9 +3,6 @@ setuptools >=46.4
wheel >=0.35.0
cython ~=0.29.16
# test dependencies
-r ../tests/requirements.txt
# run dependencies
psutil ~=5.0
......@@ -15,4 +12,3 @@ codecov ~=2.0
# deployment dependencies
auditwheel
......@@ -25,7 +25,7 @@ from .hmmer import hmmsearch, hmmpress, nhmmer, phmmer
__author__ = "Martin Larralde <martin.larralde@embl.de>"
__license__ = "MIT"
__version__ = "0.3.1"
__version__ = "0.4.0"
__all__ = [
errors.__name__,
easel.__name__,
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment