Commits · f6abd16c86078834b31a51c99628fedad791c8f4 · Martin Larralde / pyhmmer · GitLab

17 May, 2022 2 commits
- Rewrite `pyhmmer.hmmer` threading code with a `Deque` to record query order · f6abd16c
  Martin Larralde authored May 18, 2022
  
  f6abd16c
- Use `os.cpu_count` instead of `multiprocessing.cpu_count` in `pyhmmer.hmmer` · c3d6ce03
  Martin Larralde authored May 18, 2022
  
  c3d6ce03
20 Apr, 2022 1 commit
- Add type stubs for `pyhmmer.daemon` and fix remaining `mypy` errors · 6e716e33
  Martin Larralde authored Apr 20, 2022
  
  6e716e33
03 Mar, 2022 1 commit
- Refactor `SequenceFile` to set digital mode right from constructor · 108566ba
  Martin Larralde authored Mar 03, 2022
  
  108566ba
24 Dec, 2021 2 commits
- Fix some type issues in `pyhmmer.plan7` and `pyhmmer.hmmer` · 928c1164
  Martin Larralde authored Dec 24, 2021
  
  928c1164
- Update `pyhmmer.hmmer` to use the `PipelineSearchTargets` collection when possible · fa110a5b
  Martin Larralde authored Dec 24, 2021
  
  fa110a5b
15 Dec, 2021 1 commit
- Update CLI to use pressed models in `hmmsearch` if available · a28d65bf
  Martin Larralde authored Dec 15, 2021
  
  a28d65bf
13 Dec, 2021 3 commits
- Remove overloaded signatures replaced by generics in `pyhmmer.hmmer` · 79652698
  Martin Larralde authored Dec 13, 2021
  
  79652698
- Improve documentation in `pyhmmer.hmmer` where applicable · 6343fa47
  Martin Larralde authored Dec 13, 2021
  
  6343fa47
- Update type annotations in `pyhmmer.hmmer` to allow `Profile` and `OptimizedProfile` where possible · 9991646f
  Martin Larralde authored Dec 13, 2021
  
  9991646f
11 Nov, 2021 1 commit
- Update `nhmmer` type hints and documentation in `pyhmmer.hmmer` · 4da9cbfe
  Martin Larralde authored Nov 11, 2021
  
  4da9cbfe
10 Nov, 2021 1 commit
- Update `pyhmmer.hmmer.nhmmer` to use the new `LongTargetsPipeline` class · b3e3d168
  Martin Larralde authored Nov 10, 2021
  
  b3e3d168
01 Nov, 2021 1 commit
- Add tests for `pyhmmer.hmmer.nhmmer` using a BGC from MIBiG · a9bac565
  Martin Larralde authored Nov 01, 2021
  
  a9bac565
27 Sep, 2021 3 commits
- Remove the `map_alignments` option from `pyhmmer.hmmer.hmmalign` · 28435ac2
  Martin Larralde authored Sep 28, 2021
  
  28435ac2
- Add `versionadded` directive to documentation to new `plan7` classes · 024bc8f7
  Martin Larralde authored Sep 27, 2021
  
  024bc8f7
- Implement `pyhmmer.hmmalign` function with a basic CLI and unit tests · 57e939ae
  Martin Larralde authored Sep 27, 2021
  
  57e939ae
19 Aug, 2021 1 commit
- Improve `pyhmmer.hmmer` to ensure background threads exit on a `KeyboardInterrupt` · e055d8f0
  Martin Larralde authored Aug 19, 2021
  
  e055d8f0
08 Jun, 2021 1 commit
- Add `Hit.best_domain` property mapping to the highest-scoring domain of a hit · 541eda52
  Martin Larralde authored Jun 08, 2021
  
  541eda52
11 May, 2021 1 commit
- Add documentation for some undocumented attributes in `pyhmmer.plan7` · 6338057e
  Martin Larralde authored May 11, 2021
  
  6338057e
10 May, 2021 1 commit
- Add a page explaining pyHMMER performance tricks to the docs · 3f9e55c9
  Martin Larralde authored May 11, 2021
  
  3f9e55c9
09 May, 2021 3 commits
- Rewrite multithreaded loop in `pyhmmer.hmmer` to reduce memory consumption · 878c553b
  Martin Larralde authored May 09, 2021
  
  878c553b
- Fix some type annotations in `pyhmmer.hmmer` · 0a0822c9
  Martin Larralde authored May 09, 2021
  
  0a0822c9
- Update synchronization code in `pyhmmer.hmmer` to yield `TopHits` in order · 086c4fac
  Martin Larralde authored May 09, 2021
  
  086c4fac
08 May, 2021 1 commit
- Improve threading code in `pyhmmer.hmmer` to yield results iteratively · da26f5cc
  Martin Larralde authored May 08, 2021
  
  da26f5cc
15 Mar, 2021 1 commit
- Improve workflow of workers in single-thread mode in `pyhmmer.hmmer` · 1c956f61
  Martin Larralde authored Mar 15, 2021
  
  1c956f61
10 Mar, 2021 2 commits
- Add `pyhmmer.hmmer.nhmmer` method to search nucleic sequences · b5f2e56d
  Martin Larralde authored Mar 10, 2021
  
  b5f2e56d
- Refactor `pyhmmer.hmmer` to avoid duplicating code between `hmmsearch` and `phmmer` · 3bfb25fa
  Martin Larralde authored Mar 10, 2021
  
  3bfb25fa
08 Mar, 2021 1 commit
- Directly read input sequences in digital mode in `pyhmmer.hmmer` minimal CLI · 457b5eae
  Martin Larralde authored Mar 08, 2021
  
  457b5eae
07 Mar, 2021 1 commit
- Add `versionadded` directive to documentation of items added after `v0.1.0` · 1ac333dc
  Martin Larralde authored Mar 07, 2021
  
  1ac333dc
20 Jan, 2021 5 commits
- Use `psutil` to detect the thread count for `phmmer` and `hmmsearch` · 6c85dd93
  Martin Larralde authored Jan 20, 2021
  
  6c85dd93
- Hardcode `pyhmmer.hmmer.phmmer` to use `Alphabet.amino` · f103f5f0
  Martin Larralde authored Jan 20, 2021
  
  f103f5f0
- Add documentation to the `pyhmmer.hmmer` method · 1763843e
  Martin Larralde authored Jan 20, 2021
  
  1763843e
- Relax type annotations for `sequences` in `hmmsearch` and `phmmer` functions · 069ad754
  Martin Larralde authored Jan 20, 2021
  
  069ad754
- Fix type annotations in `pyhmmer.hmmer` · b41a1c67
  Martin Larralde authored Jan 20, 2021
  
  b41a1c67
19 Jan, 2021 4 commits
- Add `phmmer` implementation to `pyhmmer.hmmer` module · e49f36bc
  Martin Larralde authored Jan 19, 2021
  
  e49f36bc
- Rewrite parts of `hmmer.py` to be agnostic over the query type · 158accae
  Martin Larralde authored Jan 19, 2021
  
  158accae
- Fix small typing issues found by `mypy` · 837a639f
  Martin Larralde authored Jan 19, 2021
  
  837a639f
- Rename `Pipeline.search` to `Pipeline.search_hmm` for consistency · bc2cb91a
  Martin Larralde authored Jan 19, 2021
  
  bc2cb91a
16 Jan, 2021 1 commit
- Remove option to use an existing `TopHits` instance in `Pipeline.search` · f0be52d7
  Martin Larralde authored Jan 17, 2021
  
  f0be52d7
01 Dec, 2020 1 commit
- Make `pyhmmer.hmmsearch` run in the main thread if `cpus` argument is `1` · 523fe43b
  Martin Larralde authored Dec 01, 2020
  
  523fe43b