Commits · f7a37a3b200fa0193c91419764382bb2ec0ebf51 · Martin Larralde / PyHMMER · GitLab

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Oct 08, 2024
- Overload `SequenceFile.read_block` with concrete `SequenceBlock` types · f7a37a3b
  Martin Larralde authored 5 months ago
  
  f7a37a3b
- Make `SequenceFile` generic on the sequence type · c59025e0
  Martin Larralde authored 5 months ago
  
  c59025e0
- Use faster `PyUnicode` functions to decode fixed-sized strings of `HMM` and `Profile` · 5433c1a8
  Martin Larralde authored 5 months ago
  
  5433c1a8
- Fix type annotations for Python 3.8 to 3.10 · c2fb99e4
  Martin Larralde authored 5 months ago
  
  c2fb99e4
- Add `SequenceFile` as an accepted type for most `hmmer` functions · 21600453
  Martin Larralde authored 5 months ago
  
  21600453
- Fix detection of alphabet from arbitrary queries in `phmmer` and `hmmscan` · f4f81a18
  Martin Larralde authored 5 months ago
  
  f4f81a18
- Reorganize detection and handling of alphabets in `pyhmmer.hmmer` · 950e7238
  Martin Larralde authored 5 months ago
  
  950e7238
- Fix type annotations for `LongTargetsPipeline` specific options and properties · f8e443de
  Martin Larralde authored 5 months ago
  
  f8e443de
- Use new `TypedDict` API to a typing information to `pyhmmer.hmmer` functions · 5ec54584
  Martin Larralde authored 5 months ago
  
  5ec54584
- Release v0.10.15 · 274cee30
  Martin Larralde authored 5 months ago
  
  v0.10.15
  
  274cee30
- Fix rendering of `TopHits.query` doctest · 127d95ab
  Martin Larralde authored 5 months ago
  
  127d95ab
- Disable detection of CPU float behaviour in `setup.py` · 88a66e28
  Martin Larralde authored 5 months ago
  
  88a66e28
- Merge pull request #78 from althonos/top-hits-query · b2627eb0
  Martin Larralde authored 5 months ago
  
  Record query object in every `TopHits` object.
  b2627eb0
- Fix handling of `TopHits` in `pyhmmer.daemon.Client` · 41c377e6
  Martin Larralde authored 5 months ago
  
  41c377e6
- Fix use of deprecated `TopHits` properties in documentation · a13e32aa
  Martin Larralde authored 5 months ago
  
  a13e32aa
- Fix use of deprecated `TopHits` properties in pyhmmer.tests · 85c532e4
  Martin Larralde authored 5 months ago
  
  85c532e4
- Add deprecation warnings to old `TopHits` query properties · 5ad28e24
  Martin Larralde authored 5 months ago
  
  5ad28e24
- Fix type annotations in `pyhmmer.hmmer` to pass the query type transparently · 54259b60
  Martin Larralde authored 5 months ago
  
  54259b60
- Fix type hints in `pyhmmer.hmmer` · e64bb172
  Martin Larralde authored 5 months ago
  
  e64bb172
- Make `TopHits` generic over the query type · 371d1a50
  Martin Larralde authored 5 months ago
  
  371d1a50
- Require a query when creating a `TopHits` object · af126fbb
  Martin Larralde authored 5 months ago
  
  af126fbb
Oct 07, 2024
- Add type annotations for `TopHits.query` property · e444ee4b
  Martin Larralde authored 5 months ago
  
  e444ee4b
- Fix recording of query in `TopHits` obtained from a daemon `Client` · eb94ef97
  Martin Larralde authored 5 months ago
  
  eb94ef97
- Update `TopHits` to reference the query it was created with · 40c1cfed
  Martin Larralde authored 5 months ago
  
  40c1cfed
Jul 18, 2024
- Fix outdated SSH key type in `package.yml` Actions workflow [ci skip] · e8f254c8
  Martin Larralde authored 8 months ago
  
  e8f254c8
Jul 16, 2024
- Fix styling of logo in dark-mode in documentation index [ci skip] · 1584d40d
  Martin Larralde authored 8 months ago
  
  1584d40d
- Add explicit module names to API reference section of the docs [ci skip] · b8e84e20
  Martin Larralde authored 8 months ago
  
  b8e84e20
- Fix permissions in `package.yml` Actions workflow [ci skip] · 1892211c
  Martin Larralde authored 8 months ago
  
  1892211c
- Fix SSH deployment to AUR [ci skip] · 64c993be
  Martin Larralde authored 8 months ago
  
  64c993be
- Release v0.10.14 · 580f8842
  Martin Larralde authored 8 months ago
  
  v0.10.14
  
  580f8842
- Fix inverted titles in HMMER section of API reference [ci skip] · 0d64caf2
  Martin Larralde authored 8 months ago
  
  0d64caf2
- Update symlink to latest benchmark [ci skip] · 91c16f80
  Martin Larralde authored 8 months ago
  
  91c16f80
- Merge branch 'docs-pydata' · b4042058
  Martin Larralde authored 8 months ago
  
  b4042058
- Fix remaining issues in documentation [ci skip] · 9bb027ea
  Martin Larralde authored 8 months ago
  
  9bb027ea
- Add `favicon` to website [ci skip] · 522ef649
  Martin Larralde authored 8 months ago
  
  522ef649
- Fix missing `__init__` signatures for most Cython types · 1a82b0aa
  Martin Larralde authored 8 months ago
  
  1a82b0aa
- Fix some remaining issues in Sphinx documentation [ci skip] · aed6b51b
  Martin Larralde authored 8 months ago
  
  aed6b51b
- Add logo and copyright links to documentation [ci skip] · 6523fb9a
  Martin Larralde authored 8 months ago
  
  6523fb9a
Jul 15, 2024
- Fix broken references in `pyhmmer` docstrings [ci skip] · bca6571c
  Martin Larralde authored 8 months ago
  
  bca6571c
- Add copyright notice section with Easel and HMMER licensing [ci skip] · b800eb70
  Martin Larralde authored 8 months ago
  
  b800eb70