Commits · bf7c0e6ec144acfbc00794b787ae6081fbb55d1c · Martin Larralde / PyFastANI · GitLab

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Jun 13, 2021
- 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
- Add stub OpenMP headers to allow compiling on OSX · fe75f7ca
  Martin Larralde authored 3 years ago
  
  fe75f7ca
- Add OSX builds to the `test.yml` Actions workflow · cec1e886
  Martin Larralde authored 3 years ago
  
  cec1e886
- Make `test.yml` workflow install Boost::math before compiling · 26f9d2fa
  Martin Larralde authored 3 years ago
  
  26f9d2fa
- Compile and link against `boost::math` instead of the GSL to avoid licensing issues · b2b91b84
  Martin Larralde authored 3 years ago
  
  b2b91b84
- Add necessary stubs to `_utils.cpp` to avoid linking to `zlib` · 646c3227
  Martin Larralde authored 3 years ago
  
  646c3227
- Only run scikit-bio tests on CPython to avoid compiling with PyPy · b729875f
  Martin Larralde authored 3 years ago
  
  b729875f
- Fix tests to work with new versions of Biopython · eec01585
  Martin Larralde authored 3 years ago
  
  eec01585
- Fix outdated assertions in `pyfastani._fastani` Cython code · a240a18b
  Martin Larralde authored 3 years ago
  
  a240a18b
- Only test on Linux until GSL or Boost is vendored · ffade162
  Martin Larralde authored 3 years ago
  
  ffade162
- Fix `tests.test_mapper` to use generic paths instead of POSIX paths · aae5982c
  Martin Larralde authored 3 years ago
  
  aae5982c
- Add tests loading data with `skbio.io` and move tests in-source · 1cad5602
  Martin Larralde authored 3 years ago
  
  1cad5602
- Add `test.yml` Actions workflow to test and measure coverage · f3dc3ae2
  Martin Larralde authored 3 years ago
  
  f3dc3ae2
- Add a single unit test using the example genomes from FastANI · b83354d4
  Martin Larralde authored 3 years ago
  
  b83354d4
- Update `README.md` with a scikit-bio example in addition to Biopython · 18693fc9
  Martin Larralde authored 3 years ago
  
  18693fc9
- Update code to work with `numpy.ndarray` as sequence objects · f035b82e
  Martin Larralde authored 3 years ago
  
  f035b82e
- Refactor `Mapper.add_genome` to interally use the `_add_draft` Cython method · c3dee8db
  Martin Larralde authored 3 years ago
  
  c3dee8db
- Rewrite `Mapper._query_fragment` to avoid reallocating a new vector in the loop · ab525161
  Martin Larralde authored 3 years ago
  
  ab525161
- Add method to build reference from a draft genome · be0caa06
  Martin Larralde authored 3 years ago
  
  be0caa06
- Remove the `Parameters` class and directly configure in `Mapper.__init__` · cce3c6d8
  Martin Larralde authored 3 years ago
  
  cce3c6d8
- Update `.gitignore` to ignore Valgrind and `mprof` files · 6925750a
  Martin Larralde authored 3 years ago
  
  6925750a
- Add a `README.md` file to explain what's going on here · 276eae1d
  Martin Larralde authored 3 years ago
  
  276eae1d
- Ensure sequences are upper-case to avoid writing in read-only buffers · 39a10a8b
  Martin Larralde authored 3 years ago
  
  39a10a8b
- Add WIP implementation of a wrapper class to compute ANI mapping · 26257020
  Martin Larralde authored 3 years ago
  
  26257020
- Add basic Cython headers for the <fstream> header of the C++ standard library · 8d1539d1
  Martin Larralde authored 3 years ago
  
  8d1539d1
Jun 12, 2021
- Move `kseq_ptr_t` to the `_utils.hpp` helper header · 133e14e6
  Martin Larralde authored 3 years ago
  
  133e14e6
- Patch some FastANI constructors to prevent them from running additional methods · e54f5ccc
  Martin Larralde authored 3 years ago
  
  e54f5ccc
- Add partial headers for `kseq.h` without mapping to an actual stream · 9e87c093
  Martin Larralde authored 3 years ago
  
  9e87c093