Commits · 0274126e536fe274aedbb1ec224b8ae27f4be1b1 · Martin Larralde / PyFastANI · GitLab

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Nov 15, 2021
- Add unit tests for protein-mode ANI using homologous BGCs from MIBiG · 0274126e
  Martin Larralde authored 3 years ago
  
  0274126e
- Use the C-API in `Sketch.minimizers` to allocate a list of the right size · 98f1104a
  Martin Larralde authored 3 years ago
  
  98f1104a
- Add support for using `Sketch` and `Mapper` with protein sequences · 82084d21
  Martin Larralde authored 3 years ago
  
  82084d21
Jul 11, 2021
- Use simple tuple serialization to pickle minimizers in `Mapper` · c064eee4
  Martin Larralde authored 3 years ago
  
  c064eee4
Jul 10, 2021
- Add tests to make sure results are consistent through pickling · 0cf1e94a
  Martin Larralde authored 3 years ago
  
  0cf1e94a
- Implement `__getstate__` and `__setstate__` for `Sketch` and `Mapper` · e1f5201d
  Martin Larralde authored 3 years ago
  
  e1f5201d
- Implement `__getstate__` and `__setstate__` for `Hit` and `MinimizerInfo` · f74fa347
  Martin Larralde authored 3 years ago
  
  f74fa347
- Add a property to access the minimizers of `Sketch` or `Mapper` · 2642ca11
  Martin Larralde authored 3 years ago
  
  2642ca11
Jun 20, 2021
- Make classes final and prevent direct instantiation of `Mapper` · dc7f482f
  Martin Larralde authored 3 years ago
  
  dc7f482f
- Release v0.2.1 · 0f388a0f
  Martin Larralde authored 3 years ago
  
  v0.2.1
  
  0f388a0f
- Add missing Cython headers to source distribution · 3f0c75a3
  Martin Larralde authored 3 years ago
  
  3f0c75a3
Jun 19, 2021
- Release v0.2.0 · f6b6dfa1
  Martin Larralde authored 3 years ago
  
  v0.2.0
  
  f6b6dfa1
- Fix missing defines in compilation of `cpu_features` library · 33cd43de
  Martin Larralde authored 3 years ago
  
  33cd43de
- Update `MANIFEST.in` to vendor the `cpu_features` sources · 7acb214b
  Martin Larralde authored 3 years ago
  
  7acb214b
- Fix invalid detection of x86_64 platform in `sequtils.c` · 918c7801
  Martin Larralde authored 3 years ago
  
  918c7801
- Fix typo with `reverse_complement` argument names being swapped in `sequtils.c` · 5beb83f6
  Martin Larralde authored 3 years ago
  
  5beb83f6
- Use Google's `cpu_features` for cross-platform runtime detection of CPU features · 838add64
  Martin Larralde authored 3 years ago
  
  838add64
- Update `.gitignore` and add missing C files · 445e044a
  Martin Larralde authored 3 years ago
  
  445e044a
- Rewrite `build_clib` command in `setup.py` to attempt compiling platform-specific code · fde8a9b8
  Martin Larralde authored 3 years ago
  
  fde8a9b8
- Reorganize platform-specific code to allow independent compiling · 3ce1a799
  Martin Larralde authored 3 years ago
  
  3ce1a799
- Fix default implementation of the FASTA reader · 8e5851af
  Martin Larralde authored 3 years ago
  
  8e5851af
- Add a minimal SIMD-accelerated FASTA parser for tests and CLI · 41cfdf1b
  Martin Larralde authored 3 years ago
  
  41cfdf1b
Jun 18, 2021
- Remove cache in GitHub Actions to fix outdated GCDA files crashing pipeline · 6f8d7676
  Martin Larralde authored 3 years ago
  
  6f8d7676
- Fix `std::unique` requiring function pointers in OSX · dcf90bdc
  Martin Larralde authored 3 years ago
  
  dcf90bdc
- Manually define `std::unique` with concrete types to fix issue with Clang · 4ab56195
  Martin Larralde authored 3 years ago
  
  4ab56195
Jun 17, 2021
- Add type annotation files for Cython classes · a41a8dca
  Martin Larralde authored 3 years ago
  
  a41a8dca
- Fix some Cython warnings in `pyfastani/_fastani.pyx` · 0d34a85f
  Martin Larralde authored 3 years ago
  
  0d34a85f
- Explicitly cast a void pointer as `char*` before doing arithmetic · a9faa952
  Martin Larralde authored 3 years ago
  
  a9faa952
- Expose internal `Parameters` as properties in `Sketch` and `Mapper` · b7c4913b
  Martin Larralde authored 3 years ago
  
  b7c4913b
- Add small unit tests for `pyfastani.Sketch` behaviours without data dependency · a1147089
  Martin Larralde authored 3 years ago
  
  a1147089
- Use smaller structs to emulate a `kseq_t` and improve on indexing of query fragments · 2347d978
  Martin Larralde authored 3 years ago
  
  2347d978
- Make implementation of `_query_draft` work with strings without copying · 681cd224
  Martin Larralde authored 3 years ago
  
  681cd224
- Fix integer underflow in `_add_minimizers` causing wrong minimizers to be extracted · 33fe1f9b
  Martin Larralde authored 3 years ago
  
  33fe1f9b
- Fix buffer overflow caused by index underflow in `_read_nucl` · ed488a62
  Martin Larralde authored 3 years ago
  
  ed488a62
- Add tests to read the sequence from both `str` and bytes in `pyfastani.tests` · ee3cf544
  Martin Larralde authored 3 years ago
  
  ee3cf544
- Disable fail-fast in `test.yml` Actions workflow to simplify debugging · 81d3821f
  Martin Larralde authored 3 years ago
  
  81d3821f
- Use `const` qualifiers in some functions to help the compiler · 8853a7e4
  Martin Larralde authored 3 years ago
  
  8853a7e4
Jun 16, 2021
- Add missing Cython headers for the new PyUnicode API · 9fd4ab21
  Martin Larralde authored 3 years ago
  
  9fd4ab21
- Use a lookup table to compute the complement with IUPAC support · 3657ed2b
  Martin Larralde authored 3 years ago
  
  3657ed2b
- Rewrite `Sketch._add_draft` to allow reading directly from Unicode sequences · 62a18dba
  Martin Larralde authored 3 years ago
  
  62a18dba