chore: Wheels for MacOS and ARM Linux

[pgarrison]

• I followed the How to structure your PR.

Fixes #57
Fixes #82
Fixes bioio-devs/bioio-czi#51

Context

pylibrczirw does not provide wheels for MacOS or ARM Linux. In some installation contexts, build dependencies like cmake are unavailable, which makes pylibczirw unusable. Specifically, this is an issue downstream for bioio-czi.

Changes

Added 3 new build artifacts: x86-64 MacOS, ARM64 MacOS, and ARM64 Linux, with MacOS-specific build logic in setup.py.

Testing

I only tested the ARM64 MacOS wheel, since that's the hardware I have. I was able to install the wheel and import pylibCZIrw.

Review notes

I strongly recommend also merging my PR #84 so that CI continues to work past the end of the month.

[sebi06]

Hi @pgarrison - I will check why I cannot approve this with my account ... (sorry for the delay)

[DaveyJonesBitPail]

Approved from sec eng considerations w/ recommendation to make openssl lib and version more transparent to ensure consistency and try to dial down versions used in shipped packages to properly audit

[pgarrison]

All lint errors should now be resolved.

My contributions are covered under the corporate CLA signed by the Allen Institute.

[sebi06]

@pgarrison and @DaveyJonesBitPail what is still missing to merge this and make a new release for pylibCZIrw?

[DaveyJonesBitPail]

@pgarrison and @DaveyJonesBitPail what is still missing to merge this and make a new release for pylibCZIrw?

from the security standpoint there are no further requirements.

Looking at the failing linux build it looks like a vcpkg-related CI issue. VCPKG_INSTALLATION_ROOT ought to be set appropriately OOB however....

[pgarrison]

(I think I fixed the install and tested on my fork; waiting on CI to re-run)

[pgarrison]

None of the CI jobs failed, but many were cancelled? They don't appear to be cancelled due to a timeout. Perhaps they were cancelled manually?

Can one of the maintainers try re-triggering CI? If that doesn't resolve it, debugging this may require more direct support from one of the maintainers.

Edit: It appears the canceled jobs are due to the windows-2019 runner being removed. Getting CI to run now depends on my PR #84.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.56%. Comparing base (cc17eb3) to head (5426686).

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #85   +/-   ##
=======================================
  Coverage   96.56%   96.56%           
=======================================
  Files           1        1           
  Lines         379      379           
  Branches       51       51           
=======================================
  Hits          366      366           
  Misses          7        7           
  Partials        6        6           

Components	Coverage Δ
pylibczirw_python	96.56% <ø> (ø)
pylibczirw_c	∅ <ø> (∅)

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[pgarrison]

Notes on current build errors:

• The main error appears to be a missing std::atomic.

CMake Error at libs/libCZIrw/cmake/CheckForAdditionalLibsRequiredForAtomic.cmake:59 (message):
    Unable to compile code which uses 'atomic'.

• The code with this test lives here
• Github actions log shows The CXX compiler identification is AppleClang 15.0.0.15000100 for macOS-x86_64 and The CXX compiler identification is AppleClang 15.0.0.15000309 for macOS-arm64
• I was able to compile and run the test function (linked above) on my macOS-arm64 machine with clang -std=c++11 test.cxx. The test was successful (returns 0). I tested against Apple clang version 16.0.0 (clang-1600.0.26.6).
• cmake uses CXX_STANDARD to control which C++ standard the compiler uses. Although this variable is set in many places (e.g., libCZIrw/Src/libCZI/CMakeLists.txt), I don't see any setting that would affect libs/libCZIrw/cmake/CheckForAdditionalLibsRequiredForAtomic.cmake.