From c0c193c0aaf38055b996ae0f60e61c6d1d0cf178 Mon Sep 17 00:00:00 2001
From: Adrian Altenhoff <adrian.altenhoff@inf.ethz.ch>
Date: Wed, 27 Nov 2024 09:23:21 +0100
Subject: [PATCH] remove cpyoma.pxd from repo, go back to cython<3

---
 pyopa/backend/cpyopa.pxd | 47 ----------------------------------------
 pyproject.toml           |  2 +-
 2 files changed, 1 insertion(+), 48 deletions(-)
 delete mode 100644 pyopa/backend/cpyopa.pxd

diff --git a/pyopa/backend/cpyopa.pxd b/pyopa/backend/cpyopa.pxd
deleted file mode 100644
index 05939a9..0000000
--- a/pyopa/backend/cpyopa.pxd
+++ /dev/null
@@ -1,47 +0,0 @@
-cdef extern from "Python_extension.h":
-    ctypedef struct ProfileByte:
-        pass
-    ctypedef struct ProfileShort:
-        pass
-
-    double c_align_scalar_reference_local(double* matrix, const char *s1, int ls1, const char *s2, int ls2,
-                               double gap_open, double gap_ext, double threshold)
-    double c_align_profile_byte_sse_local(ProfileByte* profile, const char *s2, int ls2,
-                                         double gap_open, double gap_ext, double threshold)
-    double c_align_profile_short_sse_local(ProfileShort* profile, const char *s2, int ls2,
-                                          double gap_open, double gap_ext, double threshold)
-
-    ProfileByte* c_create_profile_byte_sse_local(const char* query, int query_len, signed char* matrix)
-    ProfileShort* c_create_profile_short_sse_local(const char* query, int query_len, signed short* matrix)
-
-    void c_free_profile_byte_sse_local(ProfileByte* profile)
-    void c_free_profile_short_sse_local(ProfileShort* profile)
-
-    double c_align_double_local(double* matrix, const char *s1, int ls1, const char *s2, int ls2, double gap_open,
-                          double gap_ext, double threshold, int* max1, int* max2)
-    double c_align_double_global(double* matrix, const char *s1, int ls1, const char *s2, int ls2,
-                                 double gap_open, double gap_ext)
-    int c_align_strings(double* matrix, char *s1, int len1, char *s2, int len2, double escore, char *o1,
-                        char *o2, double maxerr, double gap_open, double gap_ext)
-
-
-cdef extern from "EstimatePam.h":
-    ctypedef struct DayMatrix:
-        pass
-
-    DayMatrix* createDayMatrices(double* gapOpen, double* gapExt,
-        double* pamDistances, long long* matrix_pointers, int DMSLen)
-    void EstimatePam(char* o1, char* o2, int len, DayMatrix* DMS, int DMSLen,
-            double* logPAM1, double* result)
-    void freeDayMatrices(DayMatrix* DMS, int DMSLen)
-    void CreateOrigDayMatrix(double* log_pam1, double pam, double* new_matrix)
-
-
-cdef extern from "DynProgr_sse_double.h":
-    ctypedef struct ProfileDouble:
-        pass
-
-    double align_double_local(ProfileDouble* profileDouble, const char *s2, int ls2, double gap_open,
-        double gap_ext, double threshold, int* max1, int* max2)
-    ProfileDouble* createProfileDoubleSSE(const char* s1, int ls1, double* matrix)
-    void free_profile_double_sse(ProfileDouble* profile)
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 201217e..6e2d5c7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,6 +3,6 @@ requires = [
     # setuptools, wheel and Cython are needed for the setup.py based build
     "setuptools>=59.2.0",
     "wheel>=0.37.0",
-    "Cython<4.0",
+    "Cython<3.0",
     "numpy",
 ]