Commits · 968376a38257ef70adf740835e10e212a5b9bc17 · Martin Larralde / pyhmmer · GitLab

04 Mar, 2021 3 commits
- Release v0.2.2 · 968376a3
  Martin Larralde authored Mar 04, 2021
  
  968376a3
- Disable Python deployments from GitLab-CI · 20b9f3d5
  Martin Larralde authored Mar 04, 2021
  
  20b9f3d5
- Fix `Upload` stage of the `package.yml` Actions workflow · 68c670e8
  Martin Larralde authored Mar 04, 2021
  
  68c670e8
03 Mar, 2021 3 commits
- Only run `coverage` statistics collection on CPython implementations · fff008ff
  Martin Larralde authored Mar 03, 2021
  
  fff008ff
- Add GitHub Actions workflow to build on Linux and OSX · db7ccc90
  Martin Larralde authored Mar 03, 2021
  
  db7ccc90
- Reseed the RNG in `plan7.Builder` when building a new HMM · 79c54a5b
  Martin Larralde authored Mar 03, 2021
  
  79c54a5b
29 Jan, 2021 5 commits
- Release v0.2.1 · 83556881
  Martin Larralde authored Jan 29, 2021
  
  83556881
- Fix outdated badges in documentation index page · 3fcc437c
  Martin Larralde authored Jan 29, 2021
  
  3fcc437c
- Remove unused Travis-CI and AppVeyor configuration files · 8bc73512
  Martin Larralde authored Jan 29, 2021
  
  8bc73512
- Add the `pyhmmer.plan7.HMM.checksum` property · 9a58ff75
  Martin Larralde authored Jan 29, 2021
  
  9a58ff75
- Add more project URLs to `setup.cfg` [ci skip] · ed0fc493
  Martin Larralde authored Jan 29, 2021
  
  ed0fc493
22 Jan, 2021 1 commit
- Update `hmmsearch` benchmarks with CPU count up to 12 · 1eeb23ee
  Martin Larralde authored Jan 22, 2021
  
  1eeb23ee
21 Jan, 2021 12 commits
- Release v0.2.0 · a0743b01
  Martin Larralde authored Jan 21, 2021
  
  a0743b01
- Add section about `hmmer-py` to `README.md` [ci skip] · 858f853b
  Martin Larralde authored Jan 21, 2021
  
  858f853b
- Merge pull request #2 from althonos/phmmer · bc193166
  Martin Larralde authored Jan 21, 2021
```
Add code to allow `phmmer` search pipelines
```
  bc193166
- Add a simple test for the `SequenceFile.guess_alphabet` method · 0fcdd68d
  Martin Larralde authored Jan 21, 2021
  
  0fcdd68d
- Refactor the database search loop in `pyhmmer.plan7.Pipeline` · 777dbb98
  Martin Larralde authored Jan 21, 2021
  
  777dbb98
- Use `sq.n` instead of `sq.L` to extract `Sequence` length · 97114849
  Martin Larralde authored Jan 21, 2021
  
  97114849
- Fix `SequenceFile.__next__` not working when in digital mode · 17c8be94
  Martin Larralde authored Jan 21, 2021
  
  17c8be94
- Release GIL more often in `pyhmmer.easel` code · b8381048
  Martin Larralde authored Jan 21, 2021
  
  b8381048
- Fix type annotations of `pyhmmer.easel.Sequence` properties · 2f3bdb29
  Martin Larralde authored Jan 21, 2021
  
  2f3bdb29
- Fix indentation issue in `Pipeline.clear` preventing domaindef reuse · fe393339
  Martin Larralde authored Jan 21, 2021
  
  fe393339
- Make `plan7` code release GIL more often when interfacing with `libhmmer` · 5fa3a0f8
  Martin Larralde authored Jan 21, 2021
  
  5fa3a0f8
- Remove broken coordinate properties on `Domain` objects · 410e8e66
  Martin Larralde authored Jan 21, 2021
  
  410e8e66
20 Jan, 2021 14 commits
- Add test to check consistency of `pyhmmer.phmmer` with HMMER3 · cc3da660
  Martin Larralde authored Jan 21, 2021
  
  cc3da660
- Fix method in 'Active Site' example of documentation · 0e378fd6
  Martin Larralde authored Jan 20, 2021
  
  0e378fd6
- 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
- Improve `README.md` and add benchmarks as graphs instead of table · 65aa90d5
  Martin Larralde authored Jan 20, 2021
  
  65aa90d5
- Add documentation to the `pyhmmer.hmmer` method · 1763843e
  Martin Larralde authored Jan 20, 2021
  
  1763843e
- Update benchmarks with new runs using Pfam v33.1 · 9a3e1057
  Martin Larralde authored Jan 20, 2021
  
  9a3e1057
- 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
- Add method signatures to all methods of `pyhmmer.easel` · b82df9c9
  Martin Larralde authored Jan 20, 2021
  
  b82df9c9
- Add method signatures to all methods of `pyhmmer.plan7` · 92403db1
  Martin Larralde authored Jan 20, 2021
  
  92403db1
- Add an entry for `pyhmmer.plan7.Builder` in the documentation · 1b404f08
  Martin Larralde authored Jan 20, 2021
  
  1b404f08
- Improve documentation of the `pyhmmer.plan7` module · 1e9a1f30
  Martin Larralde authored Jan 20, 2021
  
  1e9a1f30
- Mark the `random` functions of `libeasel` as `nogil` in Cython headers · 414eb4e9
  Martin Larralde authored Jan 20, 2021
  
  414eb4e9
19 Jan, 2021 2 commits
- Add a simple test running `pyhmmer.phmmer` in `tests.test_hmmer` · 8fbc3a9d
  Martin Larralde authored Jan 19, 2021
  
  8fbc3a9d
- Make `pyhmmer.plan7.Builder.build` release the GIL when building · f94b6ab1
  Martin Larralde authored Jan 19, 2021
  
  f94b6ab1