Patch auditwheel to fix libstem.so rpath issue

pypa/auditwheel#136 results in pure C++ libraries not getting patched
by auditwheel. This is a problem for us, since our pure C++ library,
libstem.so, needs its rpath patched for hdf5.

pypa/auditwheel#283 fixes this issue, but is not yet merged. Until
it gets merged and added to quay.io/pypa/manylinux2010_x86_64,
we will patch auditwheel inside quay.io/pypa/manylinux2010_x86_64 to
include this fix.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

.github/workflows/build_wheels.yml

@@ -7,7 +7,7 @@ env:
   CIBW_SKIP: "cp27-* pp* *-manylinux_i686 *-win32"
 
   # This has some of the software we need pre-installed on it
-  CIBW_MANYLINUX_X86_64_IMAGE: openchemistry/stempy_manylinux2010_x86_64
+  CIBW_MANYLINUX_X86_64_IMAGE: openchemistry/stempy_wheel_builder
 
   # Need to do some setup before repairing the wheel on linux...
   CIBW_REPAIR_WHEEL_COMMAND_LINUX: bash scripts/github-actions/repair_command_linux.sh

scripts/github-actions/docker/Dockerfile

@@ -12,3 +12,13 @@ RUN VERSION=3.19.4 && \
   wget -q https://github.com/Kitware/CMake/releases/download/v$VERSION/cmake-$VERSION-Linux-x86_64.sh && \
   bash cmake-$VERSION-Linux-x86_64.sh --skip-license --prefix=/usr/local && \
   rm cmake-$VERSION-Linux-x86_64.sh
+
+# Apply the code patch from https://github.com/pypa/auditwheel/pull/283
+# This allows for non-python dependencies to get their RPATHs patched, which
+# we need so that libstem.so can get patched for HDF5
+# FIXME: when https://github.com/pypa/auditwheel/pull/283 is merged and
+# a part of quay.io/pypa/manylinux2010_x86_64, we can remove these lines.
+COPY auditwheel_pr_283.patch /
+RUN cd /opt/_internal/tools/lib/python3.7/site-packages && \
+  patch -p1 < /auditwheel_pr_283.patch && \
+  rm /auditwheel_pr_283.patch

scripts/github-actions/docker/auditwheel_pr_283.patch

@@ -0,0 +1,24 @@
+diff --git a/auditwheel/wheel_abi.py b/auditwheel/wheel_abi.py
+index 69f83ce..7875f6e 100644
+--- a/auditwheel/wheel_abi.py
++++ b/auditwheel/wheel_abi.py
+@@ -118,10 +118,16 @@ def get_wheel_elfdata(wheel_fn: str):
+             # we should walk its elftree.
+             if basename(fn) not in needed_libs:
+                 full_elftree[fn] = nonpy_elftree[fn]
+-                full_external_refs[fn] = lddtree_external_references(
+-                    nonpy_elftree[fn], ctx.path)
+
+-    log.debug(json.dumps(full_elftree, indent=4))
++            # Even if a non-pyextension ELF file is not needed, we
++            # should include it as an external references, because
++            # they might also require external libraries.
++            full_external_refs[fn] = lddtree_external_references(
++                nonpy_elftree[fn], ctx.path)
++
++    log.debug('full_elftree:\n%s', json.dumps(full_elftree, indent=4))
++    log.debug('full_external_refs (will be repaired):\n%s',
++              json.dumps(full_external_refs, indent=4))
+
+     return (full_elftree, full_external_refs, versioned_symbols,
+             uses_ucs2_symbols, uses_PyFPE_jbuf)

scripts/github-actions/docker/build_and_push.sh

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
 image_base=quay.io/pypa/manylinux2010_x86_64
-tag=openchemistry/stempy_manylinux2010_x86_64
+tag=openchemistry/stempy_wheel_builder
 
 docker build . -t $tag --build-arg BASE_IMAGE=$image_base
 docker push $tag