Update CythonExtension.cmake to include the `PyInterpreterState_Get…

…Id` patch on all Cython extensions
althonos · Oct 12, 2024 · 97b5c74 · 97b5c74
1 parent 200c1bb
commit 97b5c74
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Showing 6 changed files with 4 additions and 20 deletions.
diff --git a/src/pyhmmer/daemon.pyx b/src/pyhmmer/daemon.pyx
@@ -43,8 +43,6 @@ from pyhmmer.easel cimport Sequence, Alphabet, MSA, KeyHash
 from pyhmmer.errors import UnexpectedError, AllocationError, ServerError
 from pyhmmer.plan7 cimport Builder, TopHits, Pipeline, HMM, Background
 
-include "_getid.pxi"
-
 
 # --- Python imports ---------------------------------------------------------
 

diff --git a/src/pyhmmer/easel.pyx b/src/pyhmmer/easel.pyx
@@ -93,7 +93,6 @@ elif TARGET_SYSTEM == "Darwin" or TARGET_SYSTEM.endswith("BSD"):
     from .fileobj.bsd cimport fileobj_bsd_open as fopen_obj
 
 include "exceptions.pxi"
-include "_getid.pxi"
 
 # --- Python imports ---------------------------------------------------------
 

diff --git a/src/pyhmmer/errors.pyx b/src/pyhmmer/errors.pyx
@@ -6,8 +6,6 @@
 cimport libeasel
 cimport libeasel.alphabet
 
-include "_getid.pxi"
-
 statuscode = {
     libeasel.eslOK: "eslOK",
     libeasel.eslFAIL: "eslFAIL",

diff --git a/src/pyhmmer/plan7.pyx b/src/pyhmmer/plan7.pyx
@@ -194,7 +194,6 @@ elif TARGET_SYSTEM == "Darwin" or TARGET_SYSTEM.endswith("BSD"):
     from .fileobj.bsd cimport fileobj_bsd_open as fopen_obj
 
 include "exceptions.pxi"
-include "_getid.pxi"
 
 
 # --- Python imports ---------------------------------------------------------

diff --git a/src/scripts/cmake/CythonExtension.cmake b/src/scripts/cmake/CythonExtension.cmake
@@ -8,20 +8,9 @@ include(CheckSymbolExists)
 
 set(SAFE_CMAKE_REQUIRED_INCLUDES "${CMAKE_REQUIRED_INCLUDES}")
 set(CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES} ${Python_INCLUDE_DIRS})
-# set(PYINTERPRETER_STATE_SOURCE
-# "
-#   #include <stdint.h>
-#   #include <stdlib.h>
-#   #include <Python.h>
-
-#   int main(int argc, char *argv[]) {
-#     PyInterpreterState_GetID(NULL);
-#     return 0;
-#   }
-# ")
-# check_c_source_compiles("${PYINTERPRETER_STATE_SOURCE}" HAVE_PYINTERPRETERSTATE_GETID)
 check_symbol_exists(PyInterpreterState_GetID "stdint.h;stdlib.h;Python.h" HAVE_PYINTERPRETERSTATE_GETID)
 set(CMAKE_REQUIRED_INCLUDES "${SAFE_CMAKE_REQUIRED_INCLUDES}")
+set(PATCH_FILE "${CMAKE_CURRENT_LIST_DIR}/patch.pxi")
 
 # --- Detect implementation ----------------------------------------------------
 
@@ -92,7 +81,7 @@ macro(cython_extension _name)
       "Cythonizing ${_name}.pyx to ${_name}.c"
     COMMAND
       Python::Interpreter -m cython
-        "${CMAKE_CURRENT_SOURCE_DIR}/${_name}.pyx"
+        "${CMAKE_CURRENT_SOURCE_DIR}/${_name}.pyx" "${PATCH_FILE}"
         --output-file ${_name}.c
         --depfile
         -I "${CYTHON_HEADERS_DIR}"

diff --git a/src/pyhmmer/_getid.pxi → src/scripts/cmake/patch.pxi b/src/pyhmmer/_getid.pxi → src/scripts/cmake/patch.pxi
@@ -1,4 +1,5 @@
-# --- Patch for PyPy 3.9 -----------------------------------------------------
+# coding: utf-8
+# cython: language_level=3
 
 cdef extern from *:
     """