Commits · e851e474fb10f18e350f147d8bd70861b36b5001 · Martin Larralde / pyhmmer · GitLab

28 Sep, 2021 2 commits
- Release v0.4.7 · e851e474
  Martin Larralde authored Sep 28, 2021
  
  e851e474
- Add unit tests for `plan7.Traces` and implement `plan7.Traces.__eq__` · 35a4637f
  Martin Larralde authored Sep 28, 2021
  
  35a4637f
27 Sep, 2021 18 commits
- Fix some `cpdef` methods silencing exceptions in `plan7.pyx` and `easel.pyx` · 268ba291
  Martin Larralde authored Sep 28, 2021
  
  268ba291
- Add missing documentation for `hmmalign` function in the API docs · 8dcdc03b
  Martin Larralde authored Sep 28, 2021
  
  8dcdc03b
- Remove the `map_alignments` option from `pyhmmer.hmmer.hmmalign` · 28435ac2
  Martin Larralde authored Sep 28, 2021
  
  28435ac2
- Avoid using C-level API of `array.array` for PyPy compatibility · e09e961b
  Martin Larralde authored Sep 28, 2021
  
  e09e961b
- Allow creating an empty `Vector` without arguments to `__init__` · 5104da64
  Martin Larralde authored Sep 27, 2021
  
  5104da64
- Implement out-of-band pickling for `pyhmmer.easel.Matrix` · d91756ad
  Martin Larralde authored Sep 27, 2021
  
  d91756ad
- Refactor common code in `pyhmmer.easel.Matrix` subclasses · 4ee950c5
  Martin Larralde authored Sep 27, 2021
  
  4ee950c5
- Implement out-of-band pickling for `Vector` and refactor `Vector.zeros` · 3ef08543
  Martin Larralde authored Sep 27, 2021
  
  3ef08543
- Add `Matrix.format` property and optimize `Vector.__init__` to use `memcpy` when possible · 002b5955
  Martin Larralde authored Sep 27, 2021
  
  002b5955
- Use the Cython `array` API to `memcpy` data when pickling `pyhmmer.easel` types · d44b7816
  Martin Larralde authored Sep 27, 2021
  
  d44b7816
- Refactor `TraceAligner` to keep a pointer buffer until deallocation · 677d2995
  Martin Larralde authored Sep 27, 2021
  
  677d2995
- Add `versionadded` directive to documentation to new `plan7` classes · 024bc8f7
  Martin Larralde authored Sep 27, 2021
  
  024bc8f7
- Add build dependencies to `docs/requirements.txt` for RTD to build the extension locally · 12fae679
  Martin Larralde authored Sep 27, 2021
  
  12fae679
- Implement `pyhmmer.hmmalign` function with a basic CLI and unit tests · 57e939ae
  Martin Larralde authored Sep 27, 2021
  
  57e939ae
- Allow calling `TraceAligner.align_traces` with an empty array of traces · ea824160
  Martin Larralde authored Sep 27, 2021
  
  ea824160
- Add basic unit tests for `pyhmmer.plan7.TraceAligner` · e584246f
  Martin Larralde authored Sep 27, 2021
  
  e584246f
- Add several classes to `pyhmmer.plan7` to report tracebacks for HMM/sequence alignment · 4750558e
  Martin Larralde authored Sep 27, 2021
  
  4750558e
- Add Cython header files for the `tracealign.c` HMMER functions · 522e0e9e
  Martin Larralde authored Sep 27, 2021
  
  522e0e9e
10 Sep, 2021 8 commits
- Update the graph in the *Performance* page with v0.4.5 benchmark [ci skip] · f78943d1
  Martin Larralde authored Sep 10, 2021
  
  f78943d1
- Fix formatting issue with the docstring of `plan7.Cutoffs.as_vector` · 3a1740ee
  Martin Larralde authored Sep 10, 2021
  
  3a1740ee
- Release v0.4.6 · a7d97832
  Martin Larralde authored Sep 10, 2021
  
  a7d97832
- Make `Offsets`, `Cutoffs` and `EvalueParameters` public types of `plan7` · b5b8b2a1
  Martin Larralde authored Sep 10, 2021
  
  b5b8b2a1
- Fix formatting of `plan7.HMM` docstrings · 25587de0
  Martin Larralde authored Sep 10, 2021
  
  25587de0
- Fix typo in `plan7.Pipeline.bit_cutoffs.setter` assertion · 06cbce46
  Martin Larralde authored Sep 10, 2021
  
  06cbce46
- Improve documentation of `plan7.Pipeline` parameters and type hints · 960e9a24
  Martin Larralde authored Sep 10, 2021
  
  960e9a24
- Allow using model-specific thresholding options in `plan7.Pipeline` · 9d171eba
  Martin Larralde authored Sep 10, 2021
  
  9d171eba
02 Sep, 2021 2 commits
- Add a hint about running the HMMER pipeline in slow/max mode · 9bc45fb8
  Martin Larralde authored Sep 02, 2021
  
  9bc45fb8
- Add keyword arguments and properties to configure E-value thresholds of `plan7.Pipeline` objects · cedcebad
  Martin Larralde authored Sep 02, 2021
  
  cedcebad
01 Sep, 2021 1 commit
- Add results for the proGenomes comparative benchmark of`v0.4.5` · 6f10acd6
  Martin Larralde authored Sep 01, 2021
  
  6f10acd6
29 Aug, 2021 1 commit
- Refactor common code of vector operations into `easel.Vector` · 01239f7f
  Martin Larralde authored Aug 29, 2021
  
  01239f7f
28 Aug, 2021 6 commits
- Update `Matrix` and `Vector` docstrings with thrown exceptions · 8a0b43e5
  Martin Larralde authored Aug 29, 2021
  
  8a0b43e5
- Drop use of `PyBuffer_FillContiguousStrides` for PyPy compatibility · b7bed5f9
  Martin Larralde authored Aug 27, 2021
  
  b7bed5f9
- Rewrite `HMM.__getstate__` and `HMM.__setstate__` as `cpdef` methods · 8269d9c8
  Martin Larralde authored Aug 27, 2021
  
  8269d9c8
- Make `HMM.__setstate__` expect typed memoryviews instead of concrete types for numerical data · 97f4c293
  Martin Larralde authored Aug 27, 2021
  
  97f4c293
- Update `easel.pyx` to mark all `Vector` and `Matrix` memories as C-contiguous · 3225256b
  Martin Larralde authored Aug 27, 2021
  
  3225256b
- Fix `HMM.__setstate__` writing optional composition line to NULL memory · 9f064bf1
  Martin Larralde authored Aug 27, 2021
  
  9f064bf1
27 Aug, 2021 1 commit
- Fix `HMM.__setstate__` not setting a null byte when copying string attributes · 1573764c
  Martin Larralde authored Aug 27, 2021
  
  1573764c
24 Aug, 2021 1 commit
- Fix buffer overflow in `plan7.HMM.__getstate__` when reading the `map` attribute · a7427888
  Martin Larralde authored Aug 24, 2021
  
  a7427888