scoring-matrices - npm Package Compare versions

Comparing version 0.3.3 to 0.3.4

.github/workflows/test.yml

@@ -36,2 +36,5 @@ name: Test
           python-impl: CPython
+        - python-version: 3.14
+          python-release: v3.14
+          python-impl: CPython
         - python-version: pypy-3.9
@@ -96,2 +99,5 @@ python-release: v3.9
           python-impl: CPython
+        - python-version: '3.14'
+          python-release: v3.14
+          python-impl: CPython
         - python-version: pypy-3.9
@@ -156,2 +162,5 @@ python-release: v3.9
           python-impl: CPython
+        - python-version: '3.14'
+          python-release: v3.14
+          python-impl: CPython
         - python-version: pypy-3.9
@@ -158,0 +167,0 @@ python-release: v3.9

CHANGELOG.md

@@ -9,5 +9,21 @@ # Changelog
 ## [Unreleased]
-[Unreleased]: https://github.com/althonos/scoring-matrices/compare/v0.3.3...HEAD
+[Unreleased]: https://github.com/althonos/scoring-matrices/compare/v0.3.4...HEAD
 
 
+## [v0.3.4] - 2026-01-18
+[v0.3.4]: https://github.com/althonos/scoring-matrices/compare/v0.3.3...v0.3.4
+
+### Added
+- New `buffer` attribute to `ScoringMatrix` exposing a unique read-only `memoryview`.
+- `PFASUM31`, `PFAM43` and `PFASUM60` matrices ([#6](https://github.com/althonos/scoring-matrices/pull/6), by [@apcamargo](https://github.com/apcamargo)).
+- `EDNAFULL` nucleotide matrix ([#7](https://github.com/althonos/scoring-matrices/pull/7), by [@apcamargo](https://github.com/apcamargo)).
+
+### Changed
+- Compile wheel in Python Limited API mode for Python 3.11 and later.
+
+### Fixed
+- Issue with `pickle` protocol 5 causing issues with `ScoringMatrix` pickling.
+- Ensure documentation is built with extension in debug mode on ReadTheDocs.
+
+
 ## [v0.3.3] - 2025-08-13
@@ -14,0 +30,0 @@ [v0.3.3]: https://github.com/althonos/scoring-matrices/compare/v0.3.2...v0.3.3

COPYING

 MIT License
 
-Copyright (c) 2024 Martin Larralde <[e-mail]>
+Copyright (c) 2024-2026 Martin Larralde <[e-mail]>
 
@@ -5,0 +5,0 @@ Permission is hereby granted, free of charge, to any person obtaining a copy

PKG-INFO

 Metadata-Version: 2.2
 Name: scoring-matrices
-Version: 0.3.3
+Version: 0.3.4
 Summary: Dependency free, Cython-compatible scoring matrices to use with biological sequences.
@@ -9,3 +9,3 @@ Keywords: bioinformatics,sequence,substitution,matrix,score
          
-         Copyright (c) 2024 Martin Larralde <[e-mail]>
+         Copyright (c) 2024-2026 Martin Larralde <[e-mail]>
          
@@ -44,2 +44,3 @@ Permission is hereby granted, free of charge, to any person obtaining a copy
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Programming Language :: Python :: Implementation :: CPython
@@ -46,0 +47,0 @@ Classifier: Programming Language :: Python :: Implementation :: PyPy

pyproject.toml

@@ -7,3 +7,3 @@ [build-system]
 name = "scoring-matrices"
-version = "0.3.3"
+version = "0.3.4"
 description = "Dependency free, Cython-compatible scoring matrices to use with biological sequences."
@@ -32,2 +32,3 @@ readme = "README.md"
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Programming Language :: Python :: Implementation :: CPython",
@@ -53,2 +54,4 @@ "Programming Language :: Python :: Implementation :: PyPy",
 build-dir = "build/{build_type}"
+wheel.py-api = "cp311"
+wheel.expand-macos-universal-tags = true
 editable.rebuild = true
@@ -65,2 +68,6 @@ editable.verbose = false
 
+[[tool.scikit-build.overrides]]
+if.env.READTHEDOCS = "True"
+cmake.build-type = "Debug"
+
 [[tool.scikit-build-overrides]]
@@ -67,0 +74,0 @@ if.env.SCCACHE = true

src/scoring_matrices/lib.pxd

@@ -5,4 +5,4 @@ # distutils: language = c
 cdef class ScoringMatrix:
-    cdef readonly str name
-    cdef readonly str alphabet
+    cdef readonly str        name
+    cdef readonly str        alphabet
 
@@ -9,0 +9,0 @@ cdef size_t        _size

src/scoring_matrices/lib.pyi

@@ -47,2 +47,4 @@ import typing
     def name(self) -> Optional[str]: ...
+    @property
+    def buffer(self) -> Optional[memoryview]: ...
     @typing.overload
@@ -49,0 +51,0 @@ def __getitem__(self, item: int) -> List[float]: ...

src/scoring_matrices/lib.pyx

@@ -8,3 +8,4 @@ # distutils: language = c
 from cpython.buffer cimport PyBUF_FORMAT, PyBUF_READ, PyBUF_WRITE
-from cpython.memoryview cimport PyMemoryView_FromMemory
+from cpython.memoryview cimport PyMemoryView_FromMemory, PyMemoryView_GET_BUFFER
+from cpython.pycapsule cimport PyCapsule_New
 
@@ -29,2 +30,7 @@ from libc.math cimport INFINITY, lrintf
     """A scoring matrix to use for biological sequence alignments.
+
+    Attributes:
+        alphabet (`str`): The alphabet of the scoring matrix.
+        name (`str` or `None`): The name of the scoring matrix, if any.
+
     """
@@ -43,3 +49,3 @@
         VTML or BENNER matrix series. See the :doc:`Matrices </guide/matrices>`
-        page of the documentation for a comprehensive list. 
+        page of the documentation for a comprehensive list.
 
@@ -58,3 +64,3 @@ Arguments:
             The `ScoringMatrix.BUILTIN_MATRICES` frozenset contains the names
-            of every available matrix, which can be useful for checking 
+            of every available matrix, which can be useful for checking
             allowed matrix names::
@@ -65,3 +71,3 @@
                 >>> arg = parser.add_argument(
-                ...     "--matrix", 
+                ...     "--matrix",
                 ...     choices=ScoringMatrix.BUILTIN_MATRICES,
@@ -129,6 +135,6 @@ ...     default="BLOSUM62"
     def from_diagonal(
-        cls, 
-        object diagonal, 
-        float mismatch_score=0.0, 
-        str alphabet not None = DEFAULT_ALPHABET, 
+        cls,
+        object diagonal,
+        float mismatch_score=0.0,
+        str alphabet not None = DEFAULT_ALPHABET,
         str name = None
@@ -141,3 +147,3 @@ ):
                 matrix, used to score character matches.
-            mismatch_score (`float`): The mismatch score to use for 
+            mismatch_score (`float`): The mismatch score to use for
                 every mismatches.
@@ -174,3 +180,3 @@ alphabet (`str`): The alphabet to use with the scoring matrix.
         cls,
-        float match_score = 1.0, 
+        float match_score = 1.0,
         float mismatch_score = -1.0,
@@ -214,3 +220,3 @@ str alphabet not None = DEFAULT_ALPHABET,
         """__init__(self, matrix, alphabet="ARNDCQEGHILKMFPSTWYVBZX", name=None)\n--\n
-        
+
         Create a new scoring matrix.
@@ -243,6 +249,6 @@
         """
-        cdef ssize_t i
-        cdef ssize_t j
-        cdef float   x
-        cdef size_t  size = len(alphabet)
+        cdef ssize_t    i
+        cdef ssize_t    j
+        cdef float      x
+        cdef size_t     size = len(alphabet)
 
@@ -252,3 +258,3 @@ if len(alphabet) != len(set(alphabet)):
         if len(matrix) != size:
-            raise ValueError("Matrix must contain one row per alphabet letter")
+            raise ValueError(f"Matrix must contain one row per alphabet letter, got {len(matrix)}")
 
@@ -285,29 +291,5 @@ self.alphabet = alphabet
         assert self._matrix != NULL
-
-        # use out-of-band pickling (only supported since protocol 5, see
-        # https://docs.python.org/3/library/pickle.html#out-of-band-buffers)
-        if protocol >= 5:
-            matrix = pickle.PickleBuffer(self)
-        else:
-            matrix = list(self)
+        matrix = list(self)
         return (type(self), (matrix, self.alphabet, self.name))
 
-    def __getbuffer__(self, Py_buffer* buffer, int flags):
-        assert self._data != NULL
-
-        if flags & PyBUF_FORMAT:
-            buffer.format = b"f"
-        else:
-            buffer.format = NULL
-        buffer.buf = self._data
-        buffer.internal = NULL
-        buffer.itemsize = sizeof(float)
-        buffer.len = self._nitems * sizeof(float)
-        buffer.ndim = 2
-        buffer.obj = self
-        buffer.readonly = 1
-        buffer.shape = <Py_ssize_t*> &self._shape
-        buffer.suboffsets = NULL
-        buffer.strides = NULL
-
     def __len__(self):
@@ -373,4 +355,22 @@ return self._size
 
+    def __getbuffer__(self, Py_buffer* buffer, int flags):
+        assert self._data != NULL
+
+        if flags & PyBUF_FORMAT:
+            buffer.format = b"f"
+        else:
+            buffer.format = NULL
+        buffer.buf = self._data
+        buffer.internal = NULL
+        buffer.itemsize = sizeof(float)
+        buffer.len = self._nitems * sizeof(float)
+        buffer.ndim = 2
+        buffer.obj = self
+        buffer.readonly = 1
+        buffer.shape = <Py_ssize_t*> &self._shape
+        buffer.suboffsets = NULL
+        buffer.strides = NULL
+
     # --- Private methods ------------------------------------------------------
-    
+
     cdef int _allocate(self, size_t size) except 1 nogil:
@@ -509,3 +509,3 @@ cdef size_t i
         assert self._data != NULL
-        
+
         cdef size_t i
@@ -527,3 +527,3 @@ cdef float  m = -INFINITY
         Arguments:
-            alphabet (`str`): The new alphabet to use for the columns. It 
+            alphabet (`str`): The new alphabet to use for the columns. It
                 must be a subset of ``self.alphabet``.
@@ -530,0 +530,0 @@

src/scripts/cmake/CythonExtension.cmake

@@ -1,2 +0,2 @@
-find_package(Python COMPONENTS Interpreter Development.Module REQUIRED)
+find_package(Python COMPONENTS Interpreter Development.Module ${SKBUILD_SABI_COMPONENT} REQUIRED)
 get_property(PYTHON_EXTENSIONS_SOURCE_DIR GLOBAL PROPERTY PYTHON_EXTENSIONS_SOURCE_DIR)
@@ -97,3 +97,9 @@
   endif()
-  python_add_library(${_target} MODULE WITH_SOABI ${EXTENSION_SOURCES})
+  if((NOT "${SKBUILD_SABI_VERSION}" STREQUAL "") AND (NOT CMAKE_BUILD_TYPE STREQUAL Debug))
+    message(STATUS "Building in Limited API mode for Python: ${SKBUILD_SABI_VERSION}")
+    python_add_library(${_target} MODULE WITH_SOABI USE_SABI "${SKBUILD_SABI_VERSION}" ${EXTENSION_SOURCES})
+  else()
+    message(STATUS "Building in latest API mode for Python: ${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}")
+    python_add_library(${_target} MODULE WITH_SOABI ${EXTENSION_SOURCES})
+  endif()
   set_target_properties(${_target} PROPERTIES OUTPUT_NAME ${_name})
@@ -122,7 +128,2 @@ set_target_properties(${_target} PROPERTIES CXX_STANDARD 17)
   message(DEBUG "Install folder for extension ${_name}: ${_dest_folder}")
-
-  # Add the targets to the list of Cython extensions
-  get_property(_ext GLOBAL PROPERTY PYRODIGAL_CYTHON_EXTENSIONS)
-  list(APPEND _ext ${_target})
-  set_property(GLOBAL PROPERTY PYRODIGAL_CYTHON_EXTENSIONS ${_ext})
 endmacro()

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Total package byte prevSize

305767

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Number of package files

117

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Lines of code

326

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