Commits · 252f5db09b4ea008fab79f057c9866dbb812f00f · Martin Larralde / pyrodigal · GitLab

15 Mar, 2022 10 commits
- Return double precision numbers from `Node._intergenic_mod` functions · 252f5db0
  Martin Larralde authored Mar 15, 2022
  
  252f5db0
- Disable coverage measurement since it takes too long · d6654d1c
  Martin Larralde authored Mar 15, 2022
  
  d6654d1c
- Use original Prodigal code instead of the generic filter when SIMD is unavailable · 1327832f
  Martin Larralde authored Mar 15, 2022
  
  1327832f
- Make `ConnectionScorer._index` a no-op when using Prodigal backend · 7cec8f63
  Martin Larralde authored Mar 15, 2022
  
  7cec8f63
- Add option to use original Prodigal code in `ConnectionScoring` for testing · f3f6e717
  Martin Larralde authored Mar 15, 2022
  
  f3f6e717
- Rewrite `dprog.score_connection` as a `ConnectionScorer` static method · d6af8598
  Martin Larralde authored Mar 15, 2022
  
  d6af8598
- Add `const` qualifier where possible for C function arguments · 33ed2a05
  Martin Larralde authored Mar 15, 2022
  
  33ed2a05
- Fix some repeated calls to `_mer_ndx` in `TrainingInfo._update_motif_counts` · 34044ae5
  Martin Larralde authored Mar 15, 2022
  
  34044ae5
- Add functions to compute the intergenic node modifier as `Node` static methods · 9c177488
  Martin Larralde authored Mar 15, 2022
  
  9c177488
- Use a generic implementation of the connection scoring filter for unsupported CPUs · 1c2f9b89
  Martin Larralde authored Mar 15, 2022
  
  1c2f9b89
14 Mar, 2022 8 commits
- Remove the `embedsignature` Cython directive from `_pyrodigal.pyx` · b54cfb82
  Martin Larralde authored Mar 14, 2022
  
  b54cfb82
- Fix memory leak caused by memory not being freed in `calc_most_gc_frame` · a284c96b
  Martin Larralde authored Mar 14, 2022
  
  a284c96b
- Fix `Gene.translate` ignoring the `unknown_residue` argument value · b068dd94
  Martin Larralde authored Mar 14, 2022
  
  b068dd94
- Use `nucleotide` enum values defined in `_sequence.h` · 36d98238
  Martin Larralde authored Mar 14, 2022
  
  36d98238
- Use bit-twiddling instead of LUT to complement nucleotides when possible in `_sequence.h` · d81ce87c
  Martin Larralde authored Mar 14, 2022
  
  d81ce87c
- Implement `_mer_ndx` in `_sequence.h` so that it can be inlined · 1287df62
  Martin Larralde authored Mar 14, 2022
  
  1287df62
- Inline functions used for nucleotide matching using an additional C header · ad36a0cd
  Martin Larralde authored Mar 14, 2022
  
  ad36a0cd
- Fix bug causing `Nodes.copy` to fail when copying an empty collection · 59010c3c
  Martin Larralde authored Mar 14, 2022
  
  59010c3c
12 Mar, 2022 15 commits
- Update type hints in `pyrodigal/_pyrodigal.pyi` with newest version of API · bc10f6db
  Martin Larralde authored Mar 12, 2022
  
  bc10f6db
- Implement `Sequence.__str__` to get a string back from a sequence · 8bc8fae0
  Martin Larralde authored Mar 12, 2022
  
  8bc8fae0
- Fix rendering of some docstrings in `pyrodigal.Genes` · e43e2c9f
  Martin Larralde authored Mar 12, 2022
  
  e43e2c9f
- Remove `Pyrodigal` class in preparation for `v0.7.0` · 86819cb5
  Martin Larralde authored Mar 12, 2022
  
  86819cb5
- Fix `Nodes._calc_orf_gc` causing sequence memory to be read after buffer end · d7568f3b
  Martin Larralde authored Mar 12, 2022
  
  d7568f3b
- Disable fail-fast in `test.yml` Actions workflow to simplify debugging · c9478c32
  Martin Larralde authored Mar 12, 2022
  
  c9478c32
- Use a more compact data structure to store gene data in memory · fb22da04
  Martin Larralde authored Mar 12, 2022
  
  fb22da04
- Build `Gene._score_data` and `Gene._gene_data` on demand instead of allocating... · aa01348e
  Martin Larralde authored Mar 12, 2022
```
Build `Gene._score_data` and `Gene._gene_data` on demand instead of allocating strings for every gene
```
  aa01348e
- Turn `add_genes` into a method of `Genes` objects · 3f3eaac6
  Martin Larralde authored Mar 12, 2022
  
  3f3eaac6
- Make `Gene` constructor require `Sequence`, `TrainingInfo` and `Nodes` objects · 57591368
  Martin Larralde authored Mar 12, 2022
  
  57591368
- Merge `Genes` and `Predictions` classes to make public API less complicated · 4b4c0636
  Martin Larralde authored Mar 12, 2022
  
  4b4c0636
- Rewrite `Prediction.rbs_motif` and `Prediction.rbs_spacer` to avoid reading string data · 61e84d65
  Martin Larralde authored Mar 12, 2022
  
  61e84d65
- Add `__repr__` methods for some types missing one · acd9b764
  Martin Larralde authored Mar 12, 2022
  
  acd9b764
- Mark some `ConnectionScorer` functions as raising no exception · ba1d5a4f
  Martin Larralde authored Mar 12, 2022
  
  ba1d5a4f
- Add `Sequence.shine_dalgarno` method with unit tests prior to refactoring · 12b6b5f6
  Martin Larralde authored Mar 12, 2022
  
  12b6b5f6
11 Mar, 2022 7 commits
- Attempt fixing circular import by including version tag directly in `_pyrodigal.pyx` · 52a3246b
  Martin Larralde authored Mar 11, 2022
  
  52a3246b
- Fix `Predictions.write_scores` not sorting nodes by STOP position · 709c81b6
  Martin Larralde authored Mar 11, 2022
  
  709c81b6
- Add `Predictions.write_scores` to write the start scores in tabular format like Prodigal · 17a1aec5
  Martin Larralde authored Mar 11, 2022
  
  17a1aec5
- Port `record_overlapping_starts` and `tweak_final_starts` to allow customizing overlap · 9a2cc19a
  Martin Larralde authored Mar 11, 2022
  
  9a2cc19a
- Continue refactoring some training functions into `TrainingInfo` · 5bf9b0ec
  Martin Larralde authored Mar 11, 2022
  
  5bf9b0ec
- Turn `calc_dicodon_gene` into a `TrainingInfo` method · 532e7cd2
  Martin Larralde authored Mar 11, 2022
  
  532e7cd2
- Make `Nodes._find_genes_meta` work without having to hold the GIL · e5353cc2
  Martin Larralde authored Mar 11, 2022
  
  e5353cc2