sassy 0.2.1

Approximate string matching using SIMD
Documentation 
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# Sassy Python Bindings

🐍 The python bindings for Sassy

## Installation

**Pip.**
```bash
pip install sassy-rs
```
(as sassy was already taken we chose sassy-rs)

**From source.**
In the root of the repository, run: 
```bash
maturin develop --features python
```
You need Maturin for this, see [maturin](https://github.com/PyO3/maturin):


## Usage

A simple usage is as follows:

``` python
import sassy
pattern = b"ATCGATCG"
text = b"GGGGATCGATCGTTTT"
# alphabet: ascii, dna, uipac
searcher = sassy.Searcher("dna")
matches = searcher.search(pattern, text, k=1)
for i, match in enumerate(matches):
    print(f"Match {i+1}:")
    print(f"    Start: {match.text_start}")
    print(f"    End: {match.text_end}")
    print(f"    Cost: {match.cost}")
    print(f"    Strand: {match.strand}")
    print(f"    CIGAR: {match.cigar}")
```

This finds 3 matches:

``` text
Match 1:
    Start: 4
    End: 12
    Cost: 0
    Strand: +
    CIGAR: 8=
Match 2:
    Start: 6
    End: 14
    Cost: 1
    Strand: -
    CIGAR: 6=X=
Match 3:
    Start: 2
    End: 10
    Cost: 1
    Strand: -
    CIGAR: X7=
```

Further options are `sassy.Searcher(alpha=0.5)` to allow overhang alignments,
and `sassy.Searcher("dna", rc=False)` to disable reverse complements for DNA
or IUPAC strings. `searcher.search` is the simple function to search one pattern
in one text, while `searcher.search_many` takes multiple patterns and multiple
texts and searches each pattern in each text, possibly in multiple threads.

See [sassy/example.py](sassy/example.py) for a larger example.

## Type Hints

This package ships [PEP 561](https://peps.python.org/pep-0561/) type stubs (`sassy/py.typed` + `sassy/sassy.pyi`) so that type checkers and IDEs can provide autocomplete and type checking out of the box.

See [sassy/example_typed.py](sassy/example_typed.py) for a typed example that exercises all public APIs.

Running the example requires the sassy package be installed in your environment.

To install muatrin and the package in an isolated environment, then run the typed example you can use a single [`uv`](https://docs.astral.sh/uv/) command:
```console
uv run \
    --with maturin \
    sh -c 'maturin develop && python python/sassy/example_typed.py'
```

Running type checking on the type example requires mypy be installed in your environment.

To install mypy in an isolated environment then run type checking on the typed example you can use a single [`uv`](https://docs.astral.sh/uv/) command:
```console
uv run \
    --with mypy \
    sh -c 'mypy python/sassy/example_typed.py'
```

**Note on auto-generation.** The `.pyi` stubs are currently maintained by hand.
PyO3's [type stub introspection](https://pyo3.rs/main/type-stub.html) is a work-in-progress and does not yet support the function-based `#[pymodule]` declaration used here.
Maturin does not generate stubs itself — it only packages them.
Until PyO3 introspection matures, the manual stubs are the most reliable approach and should be kept in sync with `src/python.rs` when the API changes.

## Troubleshooting


**1. I could install `sassy-rc` but no modules/functions are found.**

When creating an issue please include the output of `print(dir(sassy))` if you were able to install `sassy-rs` but no functions/modules were found. 

Your output might look like:
```python
['__all__', '__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__']
```
Whereas it should look like:
```python
['Searcher', '__all__', '__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', 'features', 'sassy']
```

**2. Other sassy issues.**

If you were able to install sassy, but have other issues please also add the output of `sassy.features()`.