renaming to pybwa

.github/workflows/ci.yml

@@ -61,22 +61,22 @@ jobs:
     - name: Style checking
       shell: bash
       run: |
-        poetry run ruff format --check bwapy tests
+        poetry run ruff format --check pybwa tests
 
     - name: Run lint
       shell: bash
       run: |
-        poetry run ruff check bwapy tests
+        poetry run ruff check pybwa tests
 
     - name: Run mypy
       shell: bash
       run: |
-        poetry run mypy bwapy tests --config=pyproject.toml
+        poetry run mypy pybwa tests --config=pyproject.toml
 
     - name: Run pytest
       shell: bash
       run: |
-        poetry run python -m pytest --cov=bwapy --cov-report=xml --cov-branch 
+        poetry run python -m pytest --cov=pybwa --cov-report=xml --cov-branch 
 
     - name: Run docs
       shell: bash

.github/workflows/readthedocs.yaml

@@ -17,4 +17,4 @@ jobs:
     steps:
       - uses: readthedocs/actions/preview@v1
         with:
-          project-slug: "bwapy"
+          project-slug: "pybwa"

README.md

@@ -14,16 +14,16 @@
 [type-checking-link]:   http://mypy-lang.org/
 [pep-8-badge]:          https://img.shields.io/badge/code%20style-pep8-brightgreen.svg
 [pep-8-link]:           https://www.python.org/dev/peps/pep-0008/
-[code-coverage-badge]:  https://codecov.io/gh/fulcrumgenomics/bwapy/branch/main/graph/badge.svg
-[code-coverage-link]:   https://codecov.io/gh/fulcrumgenomics/bwapy
+[code-coverage-badge]:  https://codecov.io/gh/fulcrumgenomics/pybwa/branch/main/graph/badge.svg
+[code-coverage-link]:   https://codecov.io/gh/fulcrumgenomics/pybwa
 [license-badge]:        http://img.shields.io/badge/license-MIT-blue.svg
-[license-link]:         https://github.com/fulcrumgenomics/bwapy/blob/main/LICENSE
+[license-link]:         https://github.com/fulcrumgenomics/pybwa/blob/main/LICENSE
 
-# bwapy
+# pybwa
 
 Python language bindings for [bwa][bwa-link]
 
-See documentation on [bwapy.readthedocs.org][rtd-link].
+See documentation on [pybwa.readthedocs.org][rtd-link].
 
-[rtd-link]: http://bwapy.readthedocs.org/en/stable
+[rtd-link]: http://pybwa.readthedocs.org/en/stable
 [bwa-link]: https://github.com/lh3/bwa].

build.py

@@ -6,7 +6,7 @@
 import multiprocessing
 from pathlib import Path
 
-SOURCE_DIR = Path("bwapy")
+SOURCE_DIR = Path("pybwa")
 BUILD_DIR = Path("cython_build")
 compile_args = []
 link_args = []
@@ -16,13 +16,13 @@
 extra_objects = []  #glob.glob(os.path.join('bwa', '*.o'))
 h_files = []
 c_files = []
-for root_dir in ["bwa", "bwapy"]:
+for root_dir in ["bwa", "pybwa"]:
     h_files.extend(str(x) for x in Path(root_dir).rglob("*.h"))
     c_files.extend(str(x) for x in Path(root_dir).rglob("*.c") if x.name not in ['example.c', 'main.c'])
 
 libbwaindex_module = Extension(
-    name='bwapy.libbwaindex',
-    sources=['bwapy/libbwaindex.pyx'] + c_files,
+    name='pybwa.libbwaindex',
+    sources=['pybwa/libbwaindex.pyx'] + c_files,
     depends=h_files,
     extra_compile_args=compile_args,
     extra_link_args=link_args,
@@ -34,8 +34,8 @@
 )
 
 libbwaaln_module = Extension(
-    name='bwapy.libbwaaln',
-    sources=['bwapy/libbwaaln.pyx'] + c_files,
+    name='pybwa.libbwaaln',
+    sources=['pybwa/libbwaaln.pyx'] + c_files,
     depends=h_files,
     extra_compile_args=compile_args,
     extra_link_args=link_args,
@@ -47,8 +47,8 @@
 )
 
 libbwamem_module = Extension(
-    name='bwapy.libbwamem',
-    sources=['bwapy/libbwamem.pyx'] + c_files,
+    name='pybwa.libbwamem',
+    sources=['pybwa/libbwamem.pyx'] + c_files,
     depends=h_files,
     extra_compile_args=compile_args,
     extra_link_args=link_args,
@@ -106,7 +106,7 @@ def build():
 
     # Use Setuptools to collect files
     distribution = Distribution({
-        "name": "bwapy",
+        "name": "pybwa",
         'version': '0.0.1',  # FIXME
         'description': 'Todo',  # FIXME
         'long_description': 'FIXME',
@@ -116,9 +116,9 @@ def build():
         'license': 'MIT',
         'platforms': ['POSIX', 'UNIX', 'MacOS'],
         'classifiers': [_f for _f in CLASSIFIERS.split('\n') if _f],
-        'url': 'https://github.com/fulcrumgenomics/bwapy',
-        'packages': ['bwapy'],
-        'package_dirs': {'bwapy': 'bwapy'},
+        'url': 'https://github.com/fulcrumgenomics/pybwa',
+        'packages': ['pybwa'],
+        'package_dirs': {'pybwa': 'pybwa'},
         "ext_modules": extension_modules,
         "cmdclass": {
             "build_ext": cython_build_ext,

docs/index.md

@@ -1,9 +1,9 @@
-# bwapy
+# pybwa
 
 Python bindings for BWA
 
 ## Documentation Contents
 
 * [Installation](installation-and-developers-documentation.md)
-* [API](reference/bwapy/index.md)
+* [API](reference/pybwa/index.md)
 

docs/installation-and-developers-documentation.md

@@ -2,7 +2,7 @@
 
 ## Recommended Installation
 
-The package `bwapy` requires cloning [`bwa`](https://github.com/lh3/bwa) into the source directory.
+The package `pybwa` requires cloning [`bwa`](https://github.com/lh3/bwa) into the source directory.
 
 ```console
 git clone [email protected]:lh3/bwa.git

mkdocs.yml

@@ -1,5 +1,5 @@
-site_name: bwapy
-site_url: https://bwapy.readthedocs.io/en/latest/
+site_name: pybwa
+site_url: https://pybwa.readthedocs.io/en/latest/
 use_directory_urls: false
 theme:
   name: material
@@ -11,7 +11,7 @@ theme:
   navstyle: dark
   include_sidebar: true
   collapse_navigation: false
-repo_url: https://github.com/fulcrumgenomics/bwapy
+repo_url: https://github.com/fulcrumgenomics/pybwa
 plugins:
   - autorefs:
       resolve_closest: true

bwapy.yml → pybwa.yml

@@ -1,4 +1,4 @@
-name: bwapy
+name: pybwa
 channels:
   - defaults
   - conda-forge

pybwa/__init__.py

@@ -0,0 +1,3 @@
+from pybwa.libbwaaln import *  # noqa: F403
+from pybwa.libbwaindex import *  # noqa: F403
+from pybwa.libbwamem import *  # noqa: F403

bwapy/libbwaaln.pyi → pybwa/libbwaaln.pyi

@@ -4,7 +4,7 @@ from typing import List
 from pysam import AlignedSegment
 from pysam import FastxRecord
 
-from bwapy.libbwaindex import BwaIndex
+from pybwa.libbwaindex import BwaIndex
 
 class BwaAlnOptions:
     def __init__(self, max_hits: int = 3) -> None: ...

bwapy/libbwaaln.pyx → pybwa/libbwaaln.pyx

@@ -7,8 +7,8 @@ from libc.stdint cimport uint8_t
 from libc.stdlib cimport calloc, free
 from libc.string cimport strncpy
 from pysam import FastxRecord, AlignedSegment
-from bwapy.libbwaindex cimport force_bytes
-from bwapy.libbwaindex cimport BwaIndex
+from pybwa.libbwaindex cimport force_bytes
+from pybwa.libbwaindex cimport BwaIndex
 
 
 __all__ = [
@@ -17,7 +17,7 @@ __all__ = [
 ]
 
 cdef class BwaAlnOptions:
-    """The container for options for [`BwaAln`][bwapy.BwaAln]."""
+    """The container for options for [`BwaAln`][pybwa.BwaAln]."""
     cdef gap_opt_t * _delegate
 
     _max_hits: int

bwapy/libbwamem.pyi → pybwa/libbwamem.pyi

@@ -5,7 +5,7 @@ from typing import List
 from pysam import AlignedSegment
 from pysam import FastxRecord
 
-from bwapy.libbwaindex import BwaIndex
+from pybwa.libbwaindex import BwaIndex
 
 # class syntax
 @enum.unique

bwapy/libbwamem.pyx → pybwa/libbwamem.pyx

@@ -4,7 +4,7 @@ from typing import List
 from libc.string cimport memset, memcpy
 from libc.stdlib cimport calloc, free
 import enum
-from bwapy.libbwaindex cimport BwaIndex
+from pybwa.libbwaindex cimport BwaIndex
 from pysam import FastxRecord, AlignedSegment
 
 __all__ = [
@@ -25,7 +25,7 @@ class BwaMemMode(enum.Enum):
 
 
 cdef class BwaMemOptions:
-    """The container for options for [`BwaMem`][bwapy.BwaMem]."""
+    """The container for options for [`BwaMem`][pybwa.BwaMem]."""
     _ignore_alt: bool
     _mode: BwaMemMode | None
     cdef mem_opt_t* _options
@@ -201,7 +201,7 @@ cdef class BwaMemOptions:
 
 
 cdef class BwaMemOptionsBuilder(BwaMemOptions):
-    """The container for options for [`BwaMem`][bwapy.BwaMem]."""
+    """The container for options for [`BwaMem`][pybwa.BwaMem]."""
     cdef mem_opt_t* _options0
 
     def __init__(self, options: BwaMemOptions | None = None):

pyproject.toml

@@ -1,14 +1,14 @@
 [tool.poetry]
-name = "bwapy"
+name = "pybwa"
 version = "0.0.1-dev"
 description = "Python bindings for BWA"
 authors = ["Nils Homer"]
 license = "MIT"
 readme = "README.md"
-homepage = "https://github.com/fulcrumgenomics/bwapy"
-repository = "https://github.com/fulcrumgenomics/bwapy"
+homepage = "https://github.com/fulcrumgenomics/pybwa"
+repository = "https://github.com/fulcrumgenomics/pybwa"
 keywords = ["bioinformatics"]
-packages = [{ include = "bwapy" }]
+packages = [{ include = "pybwa" }]
 classifiers = [
 	"Development Status :: 3 - Alpha",
 	"Environment :: Console",
@@ -23,7 +23,7 @@ classifiers = [
 ]
 include = [
 	"LICENSE",
-	{ path = "bwapy/**/*.so", format = "wheel" },
+	{ path = "pybwa/**/*.so", format = "wheel" },
 	{ path = "**/*.so", format = "wheel" },
 	{ path = "*.so", format = "wheel" },
 	#{ path = "*.so", format = "wheel" }