Commits · a13e32aa71967e80d972dadaec62aa5140bff68e · Martin Larralde / PyHMMER · GitLab

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Oct 08, 2024
- Fix use of deprecated `TopHits` properties in documentation · a13e32aa
  Martin Larralde authored 5 months ago
  
  a13e32aa
Jul 16, 2024
- Fix some remaining issues in Sphinx documentation [ci skip] · aed6b51b
  Martin Larralde authored 8 months ago
  
  aed6b51b
Jul 10, 2024
- Reorganize documentation to use the PyData theme · e9b8d526
  Martin Larralde authored 8 months ago
  
  e9b8d526
Jun 19, 2024
- Fix resource links in `fetchmgs.ipynb` example notebook · 04a516b1
  Martin Larralde authored 9 months ago
  
  04a516b1
Apr 20, 2024
- Replace `t2pks.hmm` with `RREFam` in documentation [ci skip] · c5234e58
  Martin Larralde authored 11 months ago
  
  c5234e58
Mar 28, 2024
- Add more rules to `.gitignore` files [ci skip] · 75b4b02f
  Martin Larralde authored 1 year ago
  
  75b4b02f
Mar 13, 2024
- Fix typo in documentation [ci skip] · 31671a7d
  Martin Larralde authored 1 year ago
  
  31671a7d
Jan 20, 2024
- Add Bakta and Pharokka to the documentation [ci skip] · 12ab83c2
  Martin Larralde authored 1 year ago
  
  12ab83c2
Aug 16, 2023
- Update `HMMFiles` recipe to avoid opening all files [ci skip] · cd23dbcd
  Martin Larralde authored 1 year ago
  
  cd23dbcd
May 19, 2023
- Add Model-Angelo to the publications page of the docs [ci skip] · fcc00121
  Martin Larralde authored 1 year ago
  
  fcc00121
Apr 14, 2023
- Fix documentation configuration to build for Sphinx 5+ · 83e75967
  Martin Larralde authored 1 year ago
  
  83e75967
- Add suggestion from #24 by @zdk123 to the documentation · a1b21597
  Martin Larralde authored 1 year ago
  
  a1b21597
Mar 24, 2023
- Fix iterative search example not using up-to-date API [ci skip] · e3b73222
  Martin Larralde authored 2 years ago
  
  e3b73222
- Add disclaimer about target pre-loading in the performance tips [ci skip] · dac0df14
  Martin Larralde authored 2 years ago
  
  dac0df14
Mar 13, 2023
- Fix rendering of iterative search example [ci skip] · b4e282e4
  Martin Larralde authored 2 years ago
  
  b4e282e4
Dec 08, 2022
- Update HMM build example from documentation (#28) [ci skip] · b9afd399
  Martin Larralde authored 2 years ago
  
  b9afd399
Dec 03, 2022
- Update documentation examples to use new inclusion flags for `Hit` objects · 9ef1b9af
  Martin Larralde authored 2 years ago
  
  9ef1b9af
Dec 02, 2022
- Add a some performance tips and fix some classes missing from the documentation · de8599f1
  Martin Larralde authored 2 years ago
  
  de8599f1
Dec 01, 2022
- Update notebook examples in the documentation with an example of `SequenceFile` targets · 2b673d7a
  Martin Larralde authored 2 years ago
  
  2b673d7a
Nov 28, 2022
- Use `SequenceFile.read_block` where applicable in the documentation · 1dcc3745
  Martin Larralde authored 2 years ago
  
  1dcc3745
Nov 05, 2022
- Add notice about copyright to `embed_hmms` example [ci skip] · f8efc375
  Martin Larralde authored 2 years ago
  
  f8efc375
- Warn about PyPI size limits in the `embed_hmms` documentation example · 53aae587
  Martin Larralde authored 2 years ago
  
  53aae587
- Add an example on how to create a Python package with internal HMM files · 5732a489
  Martin Larralde authored 2 years ago
  
  5732a489
- Update notebook examples in the documentation to use up-to-date API · 2a5f3a9c
  Martin Larralde authored 2 years ago
  
  2a5f3a9c
Aug 12, 2022
- List some dependent projects in the `examples` page of the documentation [ci skip] · ce98b291
  Martin Larralde authored 2 years ago
  
  ce98b291
Jun 28, 2022
- Add an example use of `TopHits.write` to the example notebooks [ci skip] · ccbb58cd
  Martin Larralde authored 2 years ago
  
  ccbb58cd
May 01, 2022
- Fix rendering of iterative search example [ci skip] · c188b947
  Martin Larralde authored 2 years ago
  
  c188b947
- Update examples to display alignments of results with `print` · 3fd18532
  Martin Larralde authored 2 years ago
  
  3fd18532
Apr 30, 2022
- Use `bytes` instead of `str` for name in `TextSequence` example (#20) · 7913ed64
  tmsincomb authored 2 years ago
  
  Unverified
  
  7913ed64
Apr 27, 2022
- Add an example notebook showing how to use the iterative search · 3d782876
  Martin Larralde authored 2 years ago
  
  3d782876
Mar 14, 2022
- Update documentation in preparation for next release · d067b78b
  Martin Larralde authored 3 years ago
  
  d067b78b
Mar 03, 2022
- Remove uses of `SequenceFile.set_digital` from the example notebooks · f879a408
  Martin Larralde authored 3 years ago
  
  f879a408
Nov 11, 2021
- Rewrite the `fetchMGs` example to filter results with bitscore cutoffs · 60d507a8
  Martin Larralde authored 3 years ago
  
  60d507a8
Oct 01, 2021
- Add an example based on `fetchMGs` showing how to find marker genes · 72fa1f63
  Martin Larralde authored 3 years ago
  
  72fa1f63
Aug 14, 2021
- Update wrong class in `msa_to_hmm` example · 78095467
  Martin Larralde authored 3 years ago
  
  78095467
Jul 22, 2021
- Update `msa_to_hmm` example notebook to pre-load reference sequences · fc3abd27
  Martin Larralde authored 3 years ago
  
  fc3abd27
Jun 06, 2021
- Fix `msa_to_hmm.ipynb` example not building with `v0.4.0` · 86a5e920
  Martin Larralde authored 3 years ago
  
  86a5e920
May 10, 2021
- Add a page explaining pyHMMER performance tricks to the docs · 3f9e55c9
  Martin Larralde authored 3 years ago
  
  3f9e55c9
Mar 10, 2021
- Add example to build a HMM from a multiple sequence alignment · 8104fc16
  Martin Larralde authored 4 years ago
  
  8104fc16
Mar 09, 2021
- Improve index page in HTML documentation and update active-site example · 9e4063c2
  Martin Larralde authored 4 years ago
  
  9e4063c2