10000 Fix wheels' bundled libcurl.so incompatibility with Debian [HACK] · pysam-developers/pysam@b18dde8 · GitHub
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jmarshalljmarshall
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Fix wheels' bundled libcurl.so incompatibility with Debian [HACK]
Linux wheels are (currently) built on AlmaLinux, so the libcurl.so bundled into the wheel follows Alma/Red Hat/Fedora conventions for the location of its certificate bundle. This fails when the wheel is used on a Debian/Ubuntu platform with a different convention for this location. When not overridden by $CURL_CA_BUNDLE, work around this by specifying the expected Debian bundle location if the Red Hat one isn't present. Fixes #1257 via a hacky work around. (Take care to preserve this patch when importing HTSlib in future.)
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‎htslib/hfile_libcurl.c

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Original file line numberDiff line numberDiff line change
@@ -34,6 +34,7 @@ DEALINGS IN THE SOFTWARE. */
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#ifndef _WIN32
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# include <sys/select.h>
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#endif
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#include <sys/stat.h>
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#include <assert.h>
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#include "hfile_internal.h"
@@ -1246,6 +1247,19 @@ libcurl_open(const char *url, const char *modes, http_headers *headers)
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if (env_curl_ca_bundle) {
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err |= curl_easy_setopt(fp->easy, CURLOPT_CAINFO, env_curl_ca_bundle);
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}
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#if defined __linux__ && defined BUILDING_WHEEL
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else {
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// Linux wheels are (currently) built on AlmaLinux, so the libcurl.so bundled
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// into the wheel follows Alma/Red Hat/Fedora conventions for the location of
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// its certificate bundle. This fails when the wheel is used on a Debian/Ubuntu
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// platform with a different convention for this location. When not overridden
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// by $CURL_CA_BUNDLE, work around this by specifying the expected Debian bundle
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// location if the Red Hat one isn't present.
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struct stat st;
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if (stat("/etc/pki", &st) < 0 && errno == ENOENT)
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err |= curl_easy_setopt(fp->easy, CURLOPT_CAINFO, "/etc/ssl/certs/ca-certificates.crt");
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}
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#endif
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}
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err |= curl_easy_setopt(fp->easy, CURLOPT_USERAGENT, curl.useragent.s);
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if (fp->headers.callback) {

‎setup.py

Lines changed: 9 additions & 1 deletion
Original file line number< EF71 /th>Diff line numberDiff line change
@@ -186,6 +186,10 @@ def set_compiler_envvars():
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del os.environ[var]
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def format_macro_option(name, value):
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return f"-D{name}={value}" if value is not None else f"-D{name}"
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def configure_library(library_dir, env_options=None, options=[]):
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configure_script = os.path.join(library_dir, "configure")
@@ -532,6 +536,9 @@ def run(self):
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define_macros = []
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if os.environ.get("CIBUILDWHEEL", "0") == "1":
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define_macros.append(("BUILDING_WHEEL", None))
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suffix = sysconfig.get_config_var('EXT_SUFFIX')
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internal_htslib_libraries = [
@@ -567,7 +574,8 @@ def prebuild_libchtslib(ext, force):
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# TODO Eventually by running configure here, we can set these
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# extra flags for configure instead of hacking on ALL_CPPFLAGS.
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args = " ".join(ext.extra_compile_args)
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run_make(["ALL_CPPFLAGS=-I. " + args + " $(CPPFLAGS)", "lib-static"])
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defines = " ".join([format_macro_option(*pair) for pair in ext.define_macros])
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run_make(["ALL_CPPFLAGS=-I. " + args + " " + defines + " $(CPPFLAGS)", "lib-static"])
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else:
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log.warning("skipping 'libhts.a' (already built)")
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