Build and test on Windows

.github/workflows/ci.yml

@@ -13,10 +13,14 @@ jobs:
   build:
     name: ${{ matrix.os }} ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        # bash also on windows, e.g. for the dist/*.tar.gz glob
+        shell: bash
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest, macos-latest, windows-latest]
         python-version: ["3.10", "3.11", "3.12", "3.13", "3.14", "3.15"]
     steps:
     - uses: actions/checkout@v7

.github/workflows/wheels.yml

@@ -26,8 +26,8 @@ jobs:
           - ubuntu-24.04-arm    # linux aarch64
           - macos-15-intel      # macos x86_64
           - macos-latest        # macos arm64
-          # tests are failing for now on windows.
-          # - windows-latest
+          - windows-latest      # windows x86_64
+          - windows-11-arm      # windows arm64
 
     steps:
       - uses: actions/checkout@v7

CHANGELOG.md

@@ -15,6 +15,9 @@ changes are released with the following version.
   ([#29](https://github.com/DessimozLab/pyopa/pull/29)).
 - Wheels for Linux aarch64 and for Python 3.14 and 3.15
   ([#27](https://github.com/DessimozLab/pyopa/pull/27)).
+- Wheels for Windows x86_64 and arm64 (Python 3.11 or newer on arm64, as
+  numpy has no Windows arm64 wheels for Python 3.10); Windows is tested in
+  CI ([#33](https://github.com/DessimozLab/pyopa/pull/33)).
 
 ### Changed
 - Requires Python 3.10 or newer; no more wheels for Python 3.6 to 3.9.
@@ -53,6 +56,9 @@ changes are released with the following version.
   matrices while `estimate_many_pam` is running; using freed matrices
   raises a `RuntimeError` instead of crashing
   ([#28](https://github.com/DessimozLab/pyopa/pull/28)).
+- `align_double` truncated pointers on 64-bit Windows, where `long` is
+  32 bits ([#33](https://github.com/DessimozLab/pyopa/pull/33)).
+- Compiler warnings about implicit conversions with MSVC ([#33](https://github.com/DessimozLab/pyopa/pull/33)).
 
 ## 0.8.6 - 2025-04-24
 

c_source/DynProgr_sse_byte.c

@@ -120,7 +120,7 @@ EXPORT double swps3_alignmentByteSSE_lin(ProfileByte * query, const char * db,
 
 	__m128i vMinimums = _mm_set1_epi32(0);
 
-	__m128i vDelFixed = _mm_set1_epi8(-options->gapOpen);
+	__m128i vDelFixed = _mm_set1_epi8((char) -options->gapOpen);
 	__m128i vBias = _mm_set1_epi8(query->bias);
 
 	__m128i vMaxScore = vMinimums; /* vMaxScore = [0,0] */
@@ -265,8 +265,8 @@ EXPORT double swps3_alignmentByteSSE(ProfileByte * query, const char * db,
 
 	__m128i vMinimums = _mm_set1_epi32(0);
 
-	__m128i vDelIncr = _mm_set1_epi8(-options->gapExt);
-	__m128i vDelFixed = _mm_set1_epi8(-options->gapOpen);
+	__m128i vDelIncr = _mm_set1_epi8((char) -options->gapExt);
+	__m128i vDelFixed = _mm_set1_epi8((char) -options->gapOpen);
 	__m128i vBias = _mm_set1_epi8(query->bias);
 
 	__m128i vMaxScore = vMinimums; /* vMaxScore = [0,0] */

c_source/DynProgr_sse_double.c

@@ -7,12 +7,14 @@
 
 /* According to http://stackoverflow.com/questions/1919183/how-to-allocate-and-free-aligned-memory-in-c */
 
+#include <stdint.h>
 #include "Python_extension.h"
 #include "DynProgr_sse_double.h"
 
 void *aligned_malloc(int align, int size) {
 	char *mem = malloc(size + align + sizeof(char*));
-	char **ptr = (char**) ((long) (mem + align + sizeof(char*)) & ~(align - 1));
+	/* uintptr_t, as long is only 32 bits on 64-bit Windows */
+	char **ptr = (char**) ((uintptr_t) (mem + align + sizeof(char*)) & ~(uintptr_t) (align - 1));
 	ptr[-1] = mem;
 	return ptr;
 }

c_source/DynProgr_sse_short.c

@@ -102,7 +102,7 @@ EXPORT double swps3_alignmentShortSSE_lin(ProfileShort * query, const char * db,
 
 	__m128i vMinimums = _mm_set1_epi16(0x8000);
 
-	__m128i vDelFixed = _mm_set1_epi16(options->gapOpen);
+	__m128i vDelFixed = _mm_set1_epi16((short) options->gapOpen);
 	__m128i vBias = _mm_set1_epi16(query->bias);
 
 	__m128i vMaxScore = vMinimums; /* vMaxScore = [0,0] */
@@ -254,8 +254,8 @@ EXPORT double swps3_alignmentShortSSE(ProfileShort * query, const char * db,
 
 	__m128i vMinimums = _mm_set1_epi16(0x8000);
 
-	__m128i vDelIncr = _mm_set1_epi16(options->gapExt);
-	__m128i vDelFixed = _mm_set1_epi16(options->gapOpen);
+	__m128i vDelIncr = _mm_set1_epi16((short) options->gapExt);
+	__m128i vDelFixed = _mm_set1_epi16((short) options->gapOpen);
 	__m128i vBias = _mm_set1_epi16(query->bias);
 
 	__m128i vMaxScore = vMinimums; /* vMaxScore = [0,0] */

c_source/EstimatePam.c

@@ -610,7 +610,7 @@ DayMatrix* createDayMatrices(double* gapOpen, double* gapExt,
 #ifdef PY_DEBUG
 		printf("Creating day matrix:\n");
 		printf("FixedDel = %f\nIncDel = %f\nPamNumber = %f\n", gapOpen[i], gapExt[i], pamDistances[i]);
-		printf("Simi at %lx:\n", (long)matrix_pointers[i]);
+		printf("Simi at %p:\n", (void*) matrix_pointers[i]);
 		for(k = 0; k < MATRIX_DIM; ++k) {
 			printf("\t[");
 			for(l = 0; l < MATRIX_DIM; ++l) {

c_source/Python_extension.c

@@ -34,8 +34,8 @@ void debug_alignment(char* name, void* profile, const char* s2, int ls2,
 		Options* options) {
 	char* dns2 = denormalize(s2, ls2);
 	printf(
-			"Aligning %s: profile = %lu, s2 = %s, len(s2) = %d, gapOpen = %f, gapExt = %f, threshold = %f\n",
-			name, (unsigned long) profile, dns2, ls2, options->gapOpen,
+			"Aligning %s: profile = %p, s2 = %s, len(s2) = %d, gapOpen = %f, gapExt = %f, threshold = %f\n",
+			name, profile, dns2, ls2, options->gapOpen,
 			options->gapExt, options->threshold);
 	free(dns2);
 }
@@ -46,8 +46,8 @@ void debug_profile(char* name, void* pb, const char* q, int queryLen,
 	int i, j;
 
 	printf(
-			"Successfully created %s profile at %lu from query = %s, len(query) = %d\n",
-			name, (unsigned long) pb, query, queryLen);
+			"Successfully created %s profile at %p from query = %s, len(query) = %d\n",
+			name, pb, query, queryLen);
 	printf("The matrix used for the %s profile: \n", name);
 
 	for (i = 0; i < 26; ++i) {
@@ -114,13 +114,13 @@ ProfileShort* c_create_profile_short_sse_local(const char* query, int queryLen,
 
 void c_free_profile_byte_sse_local(ProfileByte* profile) {
 #ifdef PY_DEBUG
-	printf("Freeing BYTE profile at %lu\n", (unsigned long)profile);
+	printf("Freeing BYTE profile at %p\n", (void*) profile);
 #endif
 	swps3_freeProfileByteSSE(profile);
 }
 void c_free_profile_short_sse_local(ProfileShort* profile) {
 #ifdef PY_DEBUG
-	printf("Freeing SHORT profile at %lu\n", (unsigned long)profile);
+	printf("Freeing SHORT profile at %p\n", (void*) profile);
 #endif
 	swps3_freeProfileShortSSE(profile);
 }
@@ -189,7 +189,8 @@ int c_align_strings(double* matrix, char *s1, int len1, char *s2, int len2,
 
 	/* equal length, try to see if there is a match without deletions */
 	if (len1 == len2 && s1 != s2) {
-		for (i = tot = 0; i < len1; i++)
+		tot = 0;
+		for (i = 0; i < len1; i++)
 			tot += matrix[s1[i] * MATRIX_DIM + s2[i]];
 		if (tot >= escore) {
 			for (i = 0; i < len1; i++) {
@@ -216,14 +217,14 @@ int c_align_strings(double* matrix, char *s1, int len1, char *s2, int len2,
 
 	/* reverse strings */
 	if (s1 - s2 >= 0 && s2 + len2 - s1 > 0) {
-		j = MMAX(s1 - s2 + len1, len2);
+		j = (int) MMAX(s1 - s2 + len1, len2);
 		tprs1 = (char*) malloc(j * sizeof(char));
 		for (i = 0; i < j; i++)
 			tprs1[j - 1 - i] = s2[i];
 		prs1 = tprs1 + (j + s2 - s1 - len1);
 		prs2 = tprs1 + (j - len2);
 	} else if (s2 - s1 >= 0 && s1 + len1 - s2 > 0) {
-		j = MMAX(s2 - s1 + len2, len1);
+		j = (int) MMAX(s2 - s1 + len2, len1);
 		tprs1 = (char*) malloc(j * sizeof(char));
 		for (i = 0; i < j; i++)
 			tprs1[j - 1 - i] = s1[i];

pyopa/backend/pyopa.pyx

@@ -313,8 +313,8 @@ cpdef align_strings(s1, s2, env, is_global=False, provided_alignment=None):
 
     cdef np.ndarray[np.double_t,ndim=2] matrix = env.float64_matrix
 
-    max_len = cpyopa.c_align_strings(<double*> matrix.data, s1.encode('utf-8'), len(s1),
-                                    s2.encode('utf-8'), len(s2), provided_alignment[0], o1, o2, 0.5e-4, env.gap_open, env.gap_ext)
+    max_len = cpyopa.c_align_strings(<double*> matrix.data, s1.encode('utf-8'), <int> len(s1),
+                                    s2.encode('utf-8'), <int> len(s2), provided_alignment[0], o1, o2, 0.5e-4, env.gap_open, env.gap_ext)
 
     o1_p = [0] * max_len
     o2_p = [0] * max_len
@@ -343,7 +343,7 @@ def align_double(s1, s2, env, stop_at_threshold=False, is_global=False, calculat
     profile1.create_profile_double(s1, env.float64_matrix)
 
     if is_global:
-        res = c_align_double_normalized_global(env.float64_matrix, s1.s_norm.encode('utf-8'), len(s1), s2.s_norm.encode('utf-8'), len(s2),
+        res = c_align_double_normalized_global(env.float64_matrix, s1.s_norm.encode('utf-8'), <int> len(s1), s2.s_norm.encode('utf-8'), <int> len(s2),
                              env.gap_open, env.gap_ext)
         if calculate_ranges :
             res.extend([0, 0])
@@ -380,7 +380,7 @@ def align_scalar_reference_local(s1, s2, env):
     :param env: the AlignmentEnvironment to be used
     :return: the exact scalar score
     """
-    return c_align_scalar_normalized_reference_local(env.float64_matrix, s1.s_norm.encode('utf-8'), len(s1), s2.s_norm.encode('utf-8'), len(s2),
+    return c_align_scalar_normalized_reference_local(env.float64_matrix, s1.s_norm.encode('utf-8'), <int> len(s1), s2.s_norm.encode('utf-8'), <int> len(s2),
                                      env.gap_open, env.gap_ext, env.threshold)
 
 cpdef generate_env(log_pam1_env, new_pam, threshold=85.0):
@@ -534,7 +534,7 @@ cdef class AlignmentProfile:
         if self._c_profileByte is not NULL:
             cpyopa.c_free_profile_byte_sse_local(self._c_profileByte)
 
-        self._c_profileByte = cpyopa.c_create_profile_byte_sse_local(query.encode('utf-8'), len(query), <signed char*> matrix.data)
+        self._c_profileByte = cpyopa.c_create_profile_byte_sse_local(query.encode('utf-8'), <int> len(query), <signed char*> matrix.data)
 
 
     cpdef create_profile_short(self, query, np.ndarray[np.int16_t,ndim=2] matrix):
@@ -554,7 +554,7 @@ cdef class AlignmentProfile:
         if self._c_profileShort is not NULL:
             cpyopa.c_free_profile_short_sse_local(self._c_profileShort)
 
-        self._c_profileShort = cpyopa.c_create_profile_short_sse_local(query.encode('utf-8'), len(query),
+        self._c_profileShort = cpyopa.c_create_profile_short_sse_local(query.encode('utf-8'), <int> len(query),
                                                                       <signed short*> matrix.data)
 
 
@@ -574,7 +574,7 @@ cdef class AlignmentProfile:
         if self._c_profileDouble is not NULL:
             cpyopa.free_profile_double_sse(self._c_profileDouble)
 
-        self._c_profileDouble = cpyopa.createProfileDoubleSSE(query.encode('utf-8'), len(query), <double*> matrix.data)
+        self._c_profileDouble = cpyopa.createProfileDoubleSSE(query.encode('utf-8'), <int> len(query), <double*> matrix.data)
 
 
     cpdef align_byte(self, s2, env):
@@ -589,7 +589,7 @@ cdef class AlignmentProfile:
 
         s2 = s2.s_norm
 
-        ret = cpyopa.c_align_profile_byte_sse_local(self._c_profileByte, s2.encode('utf-8'), len(s2),
+        ret = cpyopa.c_align_profile_byte_sse_local(self._c_profileByte, s2.encode('utf-8'), <int> len(s2),
                                                    env.int8_gap_open, env.int8_gap_ext, env.threshold)
         #do not scale back DBL_MAX
         if ret >= sys.float_info.max:
@@ -610,7 +610,7 @@ cdef class AlignmentProfile:
         s2 = s2.s_norm
 
         ret = cpyopa.c_align_profile_short_sse_local(self._c_profileShort,
-                                                    s2.encode('utf-8'), len(s2), env.int16_gap_open, env.int16_gap_ext, env.threshold)
+                                                    s2.encode('utf-8'), <int> len(s2), env.int16_gap_open, env.int16_gap_ext, env.threshold)
         #do not scale back DBL_MAX
         if ret >= sys.float_info.max:
             return ret
@@ -641,7 +641,7 @@ cdef class AlignmentProfile:
 
         if threshold is None:
             threshold = env.threshold if stop_at_threshold else sys.float_info.max
-        res = cpyopa.align_double_local(self._c_profileDouble, s2.encode('utf-8'), len(s2),
+        res = cpyopa.align_double_local(self._c_profileDouble, s2.encode('utf-8'), <int> len(s2),
                                        env.gap_open, env.gap_ext, threshold, max1, max2)
 
         ret.append(res)
@@ -778,7 +778,7 @@ cdef class MutipleAlEnv:
         Q2 = Q @ Q
         Q3 = Q @ Q2
 
-        self._pam_model.nlam = len(active)
+        self._pam_model.nlam = <int> len(active)
         for i in range(26):
             self._pam_model.lam[i] = lam[i] if i < len(active) else 0.0
             for j in range(26):
@@ -799,7 +799,7 @@ cdef class MutipleAlEnv:
     def create_day_matrices(self, envs):
         self.free()
 
-        self.dms_len = len(envs)
+        self.dms_len = <int> len(envs)
         cdef np.ndarray[np.double_t, ndim=1, mode="c"] gap_open = np.empty(shape=(self.dms_len + 1))
         cdef np.ndarray[np.double_t, ndim=1, mode="c"] gap_ext = np.empty(shape=(self.dms_len + 1))
         cdef np.ndarray[np.double_t, ndim=1, mode="c"] pam_dist = np.empty(shape=(self.dms_len + 1))
@@ -830,7 +830,7 @@ cdef class MutipleAlEnv:
             raise RuntimeError('The day matrices have been freed')
 
         cdef double result[3]
-        cpyopa.EstimatePamEigen(s1.s_norm.encode('utf-8'), s2.s_norm.encode('utf-8'), len(s1),
+        cpyopa.EstimatePamEigen(s1.s_norm.encode('utf-8'), s2.s_norm.encode('utf-8'), <int> len(s1),
                                 self._c_dayMatrices, self.dms_len, &self._pam_model, result)
         return [result[0], result[1], result[2]]
 
@@ -849,7 +849,7 @@ cdef class MutipleAlEnv:
         cdef double result[3]
         cdef np.ndarray[np.double_t, ndim=2, mode="c"] logpam = self.log_pam1.float64_matrix
 
-        cpyopa.EstimatePam(s1.s_norm.encode('utf-8'), s2.s_norm.encode('utf-8'), len(s1),
+        cpyopa.EstimatePam(s1.s_norm.encode('utf-8'), s2.s_norm.encode('utf-8'), <int> len(s1),
                           self._c_dayMatrices, self.dms_len, <double*> logpam.data, result)
         return [result[0], result[1], result[2]]
 
@@ -871,7 +871,7 @@ cdef class MutipleAlEnv:
         if n < 2:
             raise ValueError('Must pass atleast 2 sequences!')
 
-        cdef int seq_len = len(seqs[0])
+        cdef int seq_len = <int> len(seqs[0])
         for i in range(1, n):
             if len(seqs[i]) != seq_len:
                 raise ValueError('All lengths must be equal!')

pyproject.toml

@@ -51,8 +51,9 @@ include = ["pyopa*"]
 [tool.cibuildwheel]
 build-frontend = "build[uv]"
 build-verbosity = 1
-# the Cython extension is not declared free-threading compatible yet
-skip = ["cp3*t-*"]
+# the Cython extension is not declared free-threading compatible yet;
+# no 32-bit windows wheels; numpy has no windows arm64 wheels for Python 3.10
+skip = ["cp3*t-*", "*-win32", "cp310-win_arm64"]
 test-groups = ["test"]
 test-command = "pytest -v {project}/test"
 # fail instead of silently building wheels without parallel support
@@ -64,3 +65,7 @@ before-all = "bash tools/build_libomp_macos.sh /tmp/libomp"
 # set explicitly: before-all otherwise gets MACOSX_DEPLOYMENT_TARGET=10.9 from
 # cibuildwheel, but libomp needs >= 10.15 (and arm64 needs >= 11.0 anyway)
 environment = { PYOPA_REQUIRE_OPENMP = "1", OPENMP_PREFIX = "/tmp/libomp", MACOSX_DEPLOYMENT_TARGET = "11.0" }
+
+[tool.cibuildwheel.windows]
+# bundle the MSVC OpenMP runtime (vcomp140.dll)
+repair-wheel-command = "uvx delvewheel repair -w {dest_dir} {wheel}"