Pr1

.pre-commit-config.yaml

@@ -14,12 +14,12 @@ repos:
       - id: requirements-txt-fixer
 
   - repo: https://github.com/Spill-Tea/addlicense-pre-commit
-    rev: v1.1.2
+    rev: v1.1.3
     hooks:
       - id: addlicense
         language: golang
         exclude: ^docs/
         args: [
           -f, LICENSE,
           ]
-        types_or: [ python ]
+        types_or: [ python, cython, c ]

src/designer_dna/_oligos.pyx

@@ -37,7 +37,11 @@ cdef extern from "Python.h":
     bytes PyUnicode_AsUTF8String(object)
     Py_ssize_t PyBytes_GET_SIZE(object)
 
-cimport common
+from common cimport (
+    StringView,
+    str_to_view,
+    to_str
+)
 
 cdef extern from "oligos.h":
     const unsigned char DNA[0x100]
@@ -92,14 +96,14 @@ cdef void c_complement(char* sequence, Py_ssize_t length, unsigned char[] table)
 
     for j in range(idx):
         end = (length - 1) - j
-        sequence[j] = table[<unsigned char> sequence[j]]
-        sequence[end] = table[<unsigned char> sequence[end]]
+        sequence[j] = table[<ssize_t> sequence[j]]
+        sequence[end] = table[<ssize_t> sequence[end]]
 
     if length % 2:
-        sequence[idx] = table[<unsigned char> sequence[idx]]
+        sequence[idx] = table[<ssize_t> sequence[idx]]
 
 
-cdef void v_complement(common.StringView view, bint dna):
+cdef void v_complement(StringView view, bint dna):
     """Handle complement on StringView directly, in place."""
     if dna:
         c_complement(view.ptr, view.size, DNA)
@@ -124,10 +128,10 @@ cpdef str complement(str sequence, bint dna = True):
             complement("ATGC", False) == "UACG"
 
     """
-    cdef common.StringView view = common.str_to_view(sequence)
+    cdef StringView view = str_to_view(sequence)
     v_complement(view, dna)
 
-    return common.to_str(view)
+    return to_str(view)
 
 
 cdef void c_reverse_complement(
@@ -148,14 +152,14 @@ cdef void c_reverse_complement(
 
     while end_ptr > sequence:
         sequence[0], end_ptr[0] = (
-            table[<unsigned char> end_ptr[0]],
-            table[<unsigned char> sequence[0]]
+            table[<ssize_t> end_ptr[0]],
+            table[<ssize_t> sequence[0]]
         )
         end_ptr -= 1
         sequence += 1
 
     if length % 2:
-        sequence[0] = table[<unsigned char> sequence[0]]
+        sequence[0] = table[<ssize_t> sequence[0]]
 
 
 cpdef str reverse_complement(str sequence, bint dna = True):
@@ -175,14 +179,14 @@ cpdef str reverse_complement(str sequence, bint dna = True):
             reverse_complement("ATGC", False) == "GCAU"
 
     """
-    cdef common.StringView view = common.str_to_view(sequence)
+    cdef StringView view = str_to_view(sequence)
 
     if dna:
         c_reverse_complement(view.ptr, view.size, DNA)
     else:
         c_reverse_complement(view.ptr, view.size, RNA)
 
-    return common.to_str(view)
+    return to_str(view)
 
 
 cdef void _center(
@@ -224,8 +228,8 @@ cpdef str palindrome(str sequence, bint dna = True):
 
     """
     cdef:
-        common.StringView seq = common.str_to_view(sequence)
-        common.StringView com = common.str_to_view(sequence)
+        StringView seq = str_to_view(sequence)
+        StringView com = str_to_view(sequence)
         Py_ssize_t i, left, right, current, length = 0, start = 0, end = 0
 
     v_complement(com, dna)
@@ -263,7 +267,7 @@ cpdef int stretch(str sequence):
 
     """
     cdef:
-        common.StringView view = common.str_to_view(sequence)
+        StringView view = str_to_view(sequence)
         Py_ssize_t j
         int longest = 0, current = 0
         char prev = view.ptr[0]
@@ -327,7 +331,7 @@ cpdef int nrepeats(str sequence, int n):
 
     """
     cdef:
-        common.StringView view = common.str_to_view(sequence)
+        StringView view = str_to_view(sequence)
         Py_ssize_t t = <Py_ssize_t> n
         Py_ssize_t v = view.size // t
         Py_ssize_t i, j, k

src/designer_dna/headers/oligos.h

@@ -1,31 +1,33 @@
-// BSD 3-Clause License
-
-// Copyright (c) 2025, Spill-Tea
-
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-
-// 1. Redistributions of source code must retain the above copyright notice, this
-//    list of conditions and the following disclaimer.
-
-// 2. Redistributions in binary form must reproduce the above copyright notice,
-//    this list of conditions and the following disclaimer in the documentation
-//    and/or other materials provided with the distribution.
-
-// 3. Neither the name of the copyright holder nor the names of its
-//    contributors may be used to endorse or promote products derived from
-//    this software without specific prior written permission.
-
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-// DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+/*
+ * BSD 3-Clause License
+ *
+ * Copyright (c) 2025, Spill-Tea
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ *    list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * 3. Neither the name of the copyright holder nor the names of its
+ *    contributors may be used to endorse or promote products derived from
+ *    this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
 
 #ifndef __LDPY_LDHELPERS_H
 #define __LDPY_LDHELPERS_H