Exclude argument not excluding library

[Jake-Moss]

Describe the bug
When providing the --exclude argument to exclude libarrow and libarrow_python from the wheel delocate.libsana still claims it is unable to find the library instead of ignoring it.

To Reproduce
This fails within our CI using pypa/cibuildwheel@v2.16.5, specifically our repair-wheel-command is

[tool.cibuildwheel.macos]
archs = ["x86_64"]
environment = { CC="gcc-12", CXX="g++-12" }
repair-wheel-command = "delocate-wheel -vv --exclude arrow --require-archs {delocate_archs} -w {dest_dir} -v {wheel}"

I've tried plenty of variations of --exclude arrow, --exclude libarrow --exclude libarrow_python and such, the docs and #106 lead me to believe that this should be excluding based on substring presence.

Expected behavior
Similarly to auditwheel, the libarrow and libarrow_python should be excluded from the repair attempt.

Wheels used
I don't have access to a MacOs system to recreate the wheel but the relevant branch is AequilibraE/aequilibrae#510
We're attempting to link against the pyarrow Cython and arrow C++ APIs using Cython.

Platform:

• OS version: macos-12
• Delocate version: 0.10.7

Additional context
I've attached the full logs of a failed CI run, the relevant section is Build wheels or the Build wheels on macos-latest/4_Build wheels.txt file. Here's a small section as well

2024-02-27T00:09:05.7946960Z ERROR:delocate.libsana:
2024-02-27T00:09:05.7947870Z @rpath/libarrow_python.dylib not found:
2024-02-27T00:09:05.7950530Z   Needed by: /private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmp9dd8xlza/wheel/aequilibrae/paths/route_choice.cpython-39-darwin.so
2024-02-27T00:09:05.7951850Z   Search path:
2024-02-27T00:09:05.7952360Z     @loader_path
2024-02-27T00:09:05.7953250Z     /usr/local/Cellar/gcc@12/12.3.0/lib/gcc/12/gcc/x86_64-apple-darwin21/12
2024-02-27T00:09:05.7954320Z     /usr/local/Cellar/gcc@12/12.3.0/lib/gcc/12/gcc
2024-02-27T00:09:05.7955080Z     /usr/local/Cellar/gcc@12/12.3.0/lib/gcc/12
2024-02-27T00:09:05.7957100Z ERROR:delocate.libsana:@rpath/libarrow_python.dylib not found, requested by /private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmp9dd8xlza/wheel/aequilibrae/paths/route_choice.cpython-39-darwin.so
2024-02-27T00:09:05.7958850Z ERROR:delocate.libsana:
2024-02-27T00:09:05.7959460Z @rpath/libarrow.1500.dylib not found:
2024-02-27T00:09:05.7960930Z   Needed by: /private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmp9dd8xlza/wheel/aequilibrae/paths/route_choice.cpython-39-darwin.so
2024-02-27T00:09:05.7962320Z   Search path:
2024-02-27T00:09:05.7962830Z     @loader_path
2024-02-27T00:09:05.7963700Z     /usr/local/Cellar/gcc@12/12.3.0/lib/gcc/12/gcc/x86_64-apple-darwin21/12
2024-02-27T00:09:05.7964620Z     /usr/local/Cellar/gcc@12/12.3.0/lib/gcc/12/gcc
2024-02-27T00:09:05.7965350Z     /usr/local/Cellar/gcc@12/12.3.0/lib/gcc/12

logs_11438.zip

[HexDecimal]

Looks like exclusion is performed too late in the process of finding a library. It's done after rpaths are resolved which causes the error seen here.

I think copy_filt_func should probably be called in the tree_libs or get_dependencies function. In fact, it should probably be moved there entirely.

[mattip]

We may have come across this in scipy. We have this situation:

• We use a package that packages openblas, which already uses delocate to pull in libgfortran.
• The scipy wheel build also uses a fortran compiler installed in the build environment, it has its own libgfortran. Some of the shared objects (one of them is arpack) use both fortran code and openblas code.
• A "bare" call of delocate complains that these shared objects use two libgfortran shared objects: the one from the gfortran compiler and the one from openblas.
• Using -exclude "solves" the complaint, but does not properly -change the dylib loader command in arpack: it leaves the full build path of libgfortran in place. While dlocate does pack a libgfortran into the .dylibs directory of the wheel, the arpack shared object does not see that one.

I think copy_filt_func should probably be called in the tree_libs or get_dependencies function. In fact, it should probably be moved there entirely.

I don't know the code base. Is this something I could easily try?

[HexDecimal]

• A "bare" call of delocate complains that these shared objects use two libgfortran shared objects: the one from the gfortran compiler and the one from openblas.

• Using -exclude "solves" the complaint, but does not properly -change the dylib loader command in arpack: it leaves the full build path of libgfortran in place. While dlocate does pack a libgfortran into the .dylibs directory of the wheel, the arpack shared object does not see that one.

This sounds like a complex case slightly unrelated to this issue. It sounds correct that --exclude would skip the libgfortran dylib and then not know how to deal with the path to it afterwards. What is your expectation for this situation?

If the extra paths you're referring to are rpaths then --sanitize-rpaths will remove any absolute and relative paths from arpack and any other bundled dylibs, leaving only the special @loader_path paths. This might resolve the issue when combined with --exclude, but I'm not completely sure.

Otherwise the dylibs need to link to the same libgfortran before they are delocated. Either by compiling them to point to a single library in the first place or by modifying the dylibs with install_name_tool before running Delocate.

[mattip]

What is your expectation for this situation?

Right, when trying to write in words the algorithm, I came to the conclusion that you are correct: -exclude is not the right option for the scipy use case.

modifying the dylibs with install_name_tool before running Delocate

This was the solution we chose.

Sorry for hijacking this issue.

[mattip]

I am still willing to try to make a PR to solve this issue, if help is needed.