pyseqalignment 0.1.2__tar.gz → 0.1.3__tar.gz

{pyseqalignment-0.1.2/src/pyseqalignment.egg-info → pyseqalignment-0.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyseqalignment
-Version: 0.1.2
+Version: 0.1.3
 Summary: pySeqAlign -- sequence alignment with Prolog-style distance functions and ILP learning
 Author-email: Andreas Karwath <a.karwath@bham.ac.uk>
 License-Expression: MIT
@@ -313,15 +313,31 @@ For reference, other notable systems in the field include:
 
 The pure-Python aligners are fine for typical use. For heavy workloads (e.g.
 boosting that re-aligns thousands of sequence pairs per iteration), an optional
-**C++ affine-gap Needleman-Wunsch** kernel is provided. It is NOT built by default
-(the core stays pure Python); build it once with a C++ compiler + pybind11:
+**C++ affine-gap Needleman-Wunsch** kernel is provided.
+
+**It is compiled automatically at install time** (best effort). The package is
+distributed as an sdist, so `pip install pyseqalignment` builds from source and
+tries to compile the accelerator for your Python/ABI/platform using a C++
+compiler + pybind11 (pulled in as a build dependency). On macOS/Linux with a
+compiler present this "just works"; if no compiler is available the install
+still succeeds and the library falls back to the pure-Python aligner. Check with:
+
+```python
+from pyseqalign.accel import cpp_available
+print(cpp_available())   # True if the accelerator compiled at install
+```
+
+If you installed without a compiler and later want the accelerator, install one
+(Xcode Command Line Tools on macOS, `build-essential` on Debian/Ubuntu) and
+either reinstall (`pip install --force-reinstall --no-binary :all: pyseqalignment`)
+or build it in place once:
 
 ```bash
 pip install pybind11
 src/pyseqalign/cpp/build_cpp_aligner.sh          # or: PY=$(which python) src/.../build_cpp_aligner.sh
 ```
 
-This compiles the extension into the `pyseqalign` package. Then:
+Either way it compiles the extension into the `pyseqalign` package. Then:
 
 ```python
 from pyseqalign.accel import cpp_available, load

{pyseqalignment-0.1.2 → pyseqalignment-0.1.3}/README.md

@@ -275,15 +275,31 @@ For reference, other notable systems in the field include:
 
 The pure-Python aligners are fine for typical use. For heavy workloads (e.g.
 boosting that re-aligns thousands of sequence pairs per iteration), an optional
-**C++ affine-gap Needleman-Wunsch** kernel is provided. It is NOT built by default
-(the core stays pure Python); build it once with a C++ compiler + pybind11:
+**C++ affine-gap Needleman-Wunsch** kernel is provided.
+
+**It is compiled automatically at install time** (best effort). The package is
+distributed as an sdist, so `pip install pyseqalignment` builds from source and
+tries to compile the accelerator for your Python/ABI/platform using a C++
+compiler + pybind11 (pulled in as a build dependency). On macOS/Linux with a
+compiler present this "just works"; if no compiler is available the install
+still succeeds and the library falls back to the pure-Python aligner. Check with:
+
+```python
+from pyseqalign.accel import cpp_available
+print(cpp_available())   # True if the accelerator compiled at install
+```
+
+If you installed without a compiler and later want the accelerator, install one
+(Xcode Command Line Tools on macOS, `build-essential` on Debian/Ubuntu) and
+either reinstall (`pip install --force-reinstall --no-binary :all: pyseqalignment`)
+or build it in place once:
 
 ```bash
 pip install pybind11
 src/pyseqalign/cpp/build_cpp_aligner.sh          # or: PY=$(which python) src/.../build_cpp_aligner.sh
 ```
 
-This compiles the extension into the `pyseqalign` package. Then:
+Either way it compiles the extension into the `pyseqalign` package. Then:
 
 ```python
 from pyseqalign.accel import cpp_available, load

{pyseqalignment-0.1.2 → pyseqalignment-0.1.3}/pyproject.toml

@@ -1,12 +1,14 @@
 [build-system]
-requires = ["setuptools>=68.0"]
+# pybind11 is a build-time dep so the OPTIONAL C++ aligner can be compiled at
+# install time (best-effort; see setup.py). It is not a runtime dependency.
+requires = ["setuptools>=68.0", "pybind11>=2.10"]
 build-backend = "setuptools.build_meta"
 
 [project]
 # PyPI distribution name (the import package is `pyseqalign`; the name
 # `pyseqalign` was blocked by PyPI's similarity guard vs. an existing project).
 name = "pyseqalignment"
-version = "0.1.2"
+version = "0.1.3"
 description = "pySeqAlign -- sequence alignment with Prolog-style distance functions and ILP learning"
 readme = "README.md"
 license = "MIT"

pyseqalignment-0.1.3/setup.py

@@ -0,0 +1,58 @@
+"""Best-effort build of the optional C++ affine-gap aligner.
+
+pySeqAlign's core is pure Python. The C++ aligner (``pyseqalign.cpp_aligner``)
+is an OPTIONAL accelerator (~100-270x faster, identical results). We try to
+compile it at install time on any platform that has a C++ compiler + pybind11;
+if that fails (no compiler, no pybind11, unsupported platform, ...) the install
+STILL SUCCEEDS and the library transparently falls back to the pure-Python
+aligner -- see ``pyseqalign.accel``.
+
+This is why the project publishes an sdist (not a pure-Python wheel): pip builds
+from source on the target machine, giving every install a chance to compile the
+accelerator locally for its own Python/ABI/platform.
+"""
+
+from __future__ import annotations
+
+import sys
+
+from setuptools import Extension, setup
+from setuptools.command.build_ext import build_ext
+
+# Only build on POSIX (macOS/Linux); the hand-tuned flags below are GCC/Clang.
+_CPP = 'src/pyseqalign/cpp/cpp_aligner.cpp'
+ext_modules: list[Extension] = []
+if sys.platform != 'win32':
+    try:
+        import pybind11
+        ext_modules = [
+            Extension(
+                'pyseqalign.cpp_aligner',
+                [_CPP],
+                include_dirs=[pybind11.get_include()],
+                language='c++',
+                optional=True,  # setuptools won't fail the build if this ext won't compile
+                extra_compile_args=['-O3', '-std=c++14'],
+            )
+        ]
+    except Exception as exc:  # pybind11 missing -> skip the accelerator
+        print(f'pyseqalign: skipping optional C++ aligner ({exc}); pure-Python fallback.')
+
+
+class BestEffortBuildExt(build_ext):
+    """Compile the accelerator if possible; never break the install if not."""
+
+    def run(self) -> None:
+        try:
+            super().run()
+        except Exception as exc:  # pragma: no cover - depends on build env
+            print(f'pyseqalign: optional C++ aligner not built ({exc}); pure-Python fallback.')
+
+    def build_extension(self, ext) -> None:
+        try:
+            super().build_extension(ext)
+        except Exception as exc:  # pragma: no cover - depends on build env
+            print(f'pyseqalign: optional C++ aligner not built ({exc}); pure-Python fallback.')
+
+
+setup(ext_modules=ext_modules, cmdclass={'build_ext': BestEffortBuildExt})

{pyseqalignment-0.1.2 → pyseqalignment-0.1.3}/src/pyseqalign/__init__.py

@@ -4,7 +4,7 @@ from pyseqalign.core.alignment import AlignmentResult, LocalAlignmentResult
 from pyseqalign.core.needleman_wunsch import NeedlemanWunsch
 from pyseqalign.core.smith_waterman import SmithWaterman
 
-__version__ = "0.1.0"
+__version__ = "0.1.3"
 
 __all__ = [
     "SmithWaterman",

{pyseqalignment-0.1.2 → pyseqalignment-0.1.3/src/pyseqalignment.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyseqalignment
-Version: 0.1.2
+Version: 0.1.3
 Summary: pySeqAlign -- sequence alignment with Prolog-style distance functions and ILP learning
 Author-email: Andreas Karwath <a.karwath@bham.ac.uk>
 License-Expression: MIT
@@ -313,15 +313,31 @@ For reference, other notable systems in the field include:
 
 The pure-Python aligners are fine for typical use. For heavy workloads (e.g.
 boosting that re-aligns thousands of sequence pairs per iteration), an optional
-**C++ affine-gap Needleman-Wunsch** kernel is provided. It is NOT built by default
-(the core stays pure Python); build it once with a C++ compiler + pybind11:
+**C++ affine-gap Needleman-Wunsch** kernel is provided.
+
+**It is compiled automatically at install time** (best effort). The package is
+distributed as an sdist, so `pip install pyseqalignment` builds from source and
+tries to compile the accelerator for your Python/ABI/platform using a C++
+compiler + pybind11 (pulled in as a build dependency). On macOS/Linux with a
+compiler present this "just works"; if no compiler is available the install
+still succeeds and the library falls back to the pure-Python aligner. Check with:
+
+```python
+from pyseqalign.accel import cpp_available
+print(cpp_available())   # True if the accelerator compiled at install
+```
+
+If you installed without a compiler and later want the accelerator, install one
+(Xcode Command Line Tools on macOS, `build-essential` on Debian/Ubuntu) and
+either reinstall (`pip install --force-reinstall --no-binary :all: pyseqalignment`)
+or build it in place once:
 
 ```bash
 pip install pybind11
 src/pyseqalign/cpp/build_cpp_aligner.sh          # or: PY=$(which python) src/.../build_cpp_aligner.sh
 ```
 
-This compiles the extension into the `pyseqalign` package. Then:
+Either way it compiles the extension into the `pyseqalign` package. Then:
 
 ```python
 from pyseqalign.accel import cpp_available, load

{pyseqalignment-0.1.2 → pyseqalignment-0.1.3}/src/pyseqalignment.egg-info/SOURCES.txt

@@ -1,6 +1,7 @@
 LICENSE
 README.md
 pyproject.toml
+setup.py
 src/pyseqalign/__init__.py
 src/pyseqalign/accel.py
 src/pyseqalign/core/__init__.py