feat: use pybwa

README.md

@@ -47,9 +47,7 @@
 
 ## Recommended Installation
 
-The package `prymer` requires installation of [interactive `bwa`](https://github.com/fulcrumgenomics/bwa-aln-interactive).
-
-To satisfy these requirements, it is recommended to install using [bioconda](https://bioconda.github.io/):
+It is recommended to install using [bioconda](https://bioconda.github.io/):
 
 ```console
 mamba install -c bioconda prymer

docs/installation-and-developers-documentation.md

@@ -0,0 +1,89 @@
+# Installation and Developer's Documentation
+
+## Recommended Installation
+
+It is recommended to install using [bioconda](https://bioconda.github.io/):
+
+```console
+mamba install -c bioconda prymer
+```
+
+## Installation for Development and Release
+
+1. Install the environment manager [`mamba`](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html)
+2. Install the Python build tool [`poetry`](https://python-poetry.org/docs/#installing-with-the-official-installer)
+
+    ```console
+    mamba env create -y -f prymer.yml
+    ```
+
+3. Activate the environment:
+
+    ```console
+    mamba activate prymer
+    ```
+
+4. Configure `poetry` to install into pre-existing virtual environments:
+
+    ```console
+    poetry config virtualenvs.create false
+    ```
+
+5. Install `prymer` into the virtual environment:
+
+    ```console
+    poetry install
+    ```
+
+## Checking the Build
+
+Use `poetry` to test your code.
+
+```console
+poetry run pytest
+```
+
+Note that `poetry run pytest` will run `mypy` checks, `ruff` checks, `pytest` unit tests, and will provide a unit test coverage report.
+However, `pytest` will neither run the ruff formatter nor apply `ruff`'s automatic lint fixes, which can be done by calling `ruff` directly. 
+
+```console
+poetry run ruff format && poetry run ruff check --fix
+```
+
+## Building the Documentation
+
+Use `mkdocs` to build and serve the documentation.
+
+```console
+poetry run mkdocs build && poetry run mkdocs serve
+```
+
+## Creating a Release on PyPi
+
+1. Clone the repository recursively and ensure you are on the `main` (un-dirty) branch
+2. Checkout a new branch to prepare the library for release
+3. Bump the version of the library to the desired SemVer with `poetry version #.#.#`
+4. Commit the version bump changes with a Git commit message like `chore(release): bump to #.#.#`
+5. Push the commit to the upstream remote, open a PR, ensure tests pass, and seek reviews
+6. Squash merge the PR
+7. Tag the new commit on the main branch of the origin repository with the new SemVer
+
+> [!NOTE]
+> This project follows [Semantic Versioning](https://semver.org/).
+> In brief:
+> 
+> * `MAJOR` version when you make incompatible API changes
+> * `MINOR` version when you add functionality in a backwards compatible manner
+> * `PATCH` version when you make backwards compatible bug fixes
+
+GitHub Actions will take care of the remainder of the deployment and release process with:
+
+1. Unit tests will be run for safety-sake
+2. A source distribution will be built
+3. Multi-arch multi-Python binary distributions will be built
+4. Assets will be deployed to PyPi with the new SemVer
+5. A [Conventional Commit](https://www.conventionalcommits.org/en/v1.0.0/)-aware changelog will be drafted
+6. A GitHub release will be created with the new SemVer and the drafted changelog
+
+> [!IMPORTANT]
+> Consider editing the changelog if there are any errors or necessary enhancements.

prymer.yml

@@ -3,5 +3,4 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - bioconda::bwa-aln-interactive=0.7.18
   - conda-forge::python>=3.11.*

prymer/model.py

@@ -212,7 +212,7 @@ def from_string(cls, line: str) -> "Span":
                 strand = Strand(strand_symbol[0])
             except ValueError as e:
                 raise ValueError(
-                    "Did not find valid strand information; " f"received {strand_symbol}"
+                    f"Did not find valid strand information; received {strand_symbol}"
                 ) from e
         elif len(parts) == 2:
             refname, range_ = parts

prymer/offtarget/__init__.py

@@ -1,12 +1,12 @@
-from prymer.offtarget.bwa import BwaAlnInteractive
+from prymer.offtarget.bwa import Bwa
 from prymer.offtarget.bwa import BwaHit
 from prymer.offtarget.bwa import BwaResult
 from prymer.offtarget.bwa import Query
 from prymer.offtarget.offtarget_detector import OffTargetDetector
 from prymer.offtarget.offtarget_detector import OffTargetResult
 
 __all__ = [
-    "BwaAlnInteractive",
+    "Bwa",
     "Query",
     "BwaHit",
     "BwaResult",