Commits · 41cfdf1b849912a9e4dafa8d01c480f0cf3a5d24 · Martin Larralde / PyFastANI · GitLab

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Jun 19, 2021
- 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- Remove cache in GitHub Actions to fix outdated GCDA files crashing pipeline · 6f8d7676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
Jun 15, 2021
- Fix some Cython warnings in `pyfastani/__init__.pyx` · c9c49411
  Martin Larralde authored 3 years ago
  
  c9c49411
- Update examples in `README.md` to use the new type interface · b7250862
  Martin Larralde authored 3 years ago
  
  b7250862
- Add method to clear a `Sketch` from the sequences currently stored · c88a8ab2
  Martin Larralde authored 3 years ago
  
  c88a8ab2
- Rewrite interface using functional style to make the objects pseudo-immutable · a45ced2a
  Martin Larralde authored 3 years ago
  
  a45ced2a
- Release v0.1.2 · 14308966
  Martin Larralde authored 3 years ago
  
  v0.1.2
  
  14308966
Jun 14, 2021
- Relax the GIL in `Mapper._query_contigs` to allow multithreaded querying · 5dea6475
  Martin Larralde authored 3 years ago
  
  5dea6475
- Fix Actions and Codecov badges in `README.md` [ci skip] · 77122ddc
  Martin Larralde authored 3 years ago
  
  77122ddc
Jun 13, 2021
- Release v0.1.1 · 7e896e59
  Martin Larralde authored 3 years ago
  
  v0.1.1
  
  7e896e59
- Add `MANIFEST.in` file to fix sources missing from source distribution · bf7c0e6e
  Martin Larralde authored 3 years ago
  
  bf7c0e6e
- Use `load_tests` protocol in `pyfastani.tests` to run tests in site install · 290bdef4
  Martin Larralde authored 3 years ago
  
  290bdef4
- Fix links to Zenodo record in `setup.cfg` and `README.md` · c61fcdfa
  Martin Larralde authored 3 years ago
  
  c61fcdfa
- Release v0.1.0 · 782145f7
  Martin Larralde authored 3 years ago
  
  v0.1.0
  
  782145f7
- Implement querying with draft genomes and implement FastANI example as a test · e2c35832
  Martin Larralde authored 3 years ago
  
  e2c35832
- Add `CHANGELOG.md` template and prepare `README.md` for a PyPI release · 7783bb5d
  Martin Larralde authored 3 years ago
  
  7783bb5d
- Add a minimal FASTA parser to run tests without Biopython or scikit-bio · 3051ba2f
  Martin Larralde authored 3 years ago
  
  3051ba2f
- Remove test for PyPy 3.6 `manylinux` wheels from `package.yml` workflow · 244e76f2
  Martin Larralde authored 3 years ago
  
  244e76f2
- Remove Python 3.5 jobs from Actions workflows · 17606c1d
  Martin Larralde authored 3 years ago
  
  17606c1d
- Fix compilation error with `clang` on some older OSX versions · 49e21e2a
  Martin Larralde authored 3 years ago
  
  49e21e2a
- Update `package.yml` to install tests requirements before testing · 62cb5c9f
  Martin Larralde authored 3 years ago
  
  62cb5c9f
- Fix tests not being included in source distribution · b5b59ad9
  Martin Larralde authored 3 years ago
  
  b5b59ad9
- Add experimental `package.yml` Actions workflow to build `manylinux_2_24` wheels · e3db915c
  Martin Larralde authored 3 years ago
  
  e3db915c