Fix bad -pthread default when cross-compiling

Also, switch to using cross_compiling=yes instead of patching
./configure in place, which allows us to move rerunning autoconf to
right before running ./configure, avoiding the risk of patching
./configure.ac too late.

See astral-sh#599.

Author: geofft

cpython-unix/build-cpython.sh

@@ -306,17 +306,6 @@ else
     patch -p1 -i "${ROOT}/patch-python-configure-add-enable-static-libpython-for-interpreter-${PYTHON_MAJMIN_VERSION}.patch"
 fi
 
-# We patched configure.ac above. Reflect those changes.
-autoconf
-
-# configure assumes cross compiling when host != target and doesn't provide a way to
-# override. Our target triple normalization may lead configure into thinking we
-# aren't cross-compiling when we are. So force a static "yes" value when our
-# build system says we are cross-compiling.
-if [ -n "${CROSS_COMPILING}" ]; then
-  patch -p1 -i ${ROOT}/patch-force-cross-compile.patch
-fi
-
 # BOLT instrumented binaries segfault in some test_embed tests for unknown reasons.
 # On 3.12 (minimum BOLT version), the segfault causes the test harness to
 # abort and BOLT optimization uses the partial test results. On 3.13, the segfault
@@ -582,6 +571,14 @@ else
 fi
 
 if [ -n "${CROSS_COMPILING}" ]; then
+    # configure assumes cross compiling when host != target and doesn't
+    # provide a way to override. Our target triple normalization may
+    # lead configure into thinking we aren't cross-compiling when we
+    # are. So force a static "yes" value when our build system says we
+    # are cross-compiling.
+    # See also https://savannah.gnu.org/support/?110348
+    CONFIGURE_FLAGS="${CONFIGURE_FLAGS} cross_compiling=yes"
+
     # configure doesn't like a handful of scenarios when cross-compiling.
     #
     # getaddrinfo buggy test fails for some reason. So we short-circuit it.
@@ -598,8 +595,18 @@ if [ -n "${CROSS_COMPILING}" ]; then
     if [ "${PYBUILD_PLATFORM}" != "macos" ]; then
         CONFIGURE_FLAGS="${CONFIGURE_FLAGS} ac_cv_working_tzset=yes"
     fi
+
+    # Also, it cannot detect whether the compiler supports -pthread or
+    # not, and conservatively defaults to no, which is not the right
+    # default on relatively modern compilers.
+    CONFIGURE_FLAGS="${CONFIGURE_FLAGS} ac_cv_pthread=yes"
+
+    # TODO: There are probably more of these, see #399.
 fi
 
+# We patched configure.ac above. Reflect those changes.
+autoconf
+
 CFLAGS=$CFLAGS CPPFLAGS=$CFLAGS LDFLAGS=$LDFLAGS \
     ./configure ${CONFIGURE_FLAGS}
 

cpython-unix/build.py

@@ -562,21 +562,34 @@ def python_build_info(
     bi["object_file_format"] = object_file_format
 
     # Determine allowed libaries on Linux
+    libs = extra_metadata["python_config_vars"].get("LIBS", "").split()
     mips = target_triple.split("-")[0] in {"mips", "mipsel"}
     linux_allowed_system_libraries = LINUX_ALLOW_SYSTEM_LIBRARIES.copy()
     if mips and version == "3.13":
         # See https://github.com/astral-sh/python-build-standalone/issues/410
         linux_allowed_system_libraries.add("atomic")
     riscv = target_triple.split("-")[0] in {"riscv64"}
     if riscv:
-        # RISC-V binary often comes with libatomic on old GCC versions
+        # On older GCC versions, RISC-V sub-word atomic operations require a
+        # helper function found in libatomic. To facilitate this, GCC <15 adds
+        # "-latomic" to the definition of "-pthread". We think it's generally
+        # reasonable on RISC-V systems (but not all Linux systems in general)
+        # to expect a libatomic system library is installed.
+        #
+        # Because "-latomic" is implicitly added by "-pthread", it may not be
+        # found in the LIBS sysconfig variable, but we need to pretend it is so
+        # that it gets into PYTHON.json (in particular, so that the validation
+        # script accepts this dependency).
+        #
         # See https://github.com/riscvarchive/riscv-gcc/issues/12
         # https://github.com/riscvarchive/riscv-gcc/issues/337
         # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=86005
+        # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=104338
+        # https://github.com/gcc-mirror/gcc/commit/203f3060dd363361b172f7295f42bb6bf5ac0b3b
         linux_allowed_system_libraries.add("atomic")
+        libs.append("-latomic")
 
     # Add in core linking annotations.
-    libs = extra_metadata["python_config_vars"].get("LIBS", "").split()
     skip = False
     for i, lib in enumerate(libs):
         if skip: