add macos runner

[jamesmkrieger]

Hopefully this works

[jamesmkrieger]

For some reason, this doesn't trigger checks

[jamesmkrieger]

ok, now this runs!

[jamesmkrieger]

@jamesmkrieger, right above line 33 can you add conda init bash and try it again? Please try conda init bash before the conda activate line. (please see: https://gemini.google.com/app/36fc43d7a25f69ee)

I tried that many ways and it didn't like it. I now have it sourcing the bashrc or bash_profile after and then it seems fine

[jamesmkrieger]

ok, suggestions how to fix the library gfortran not found problem?

[jamesmkrieger]

ok, suggestions how to fix the library gfortran not found problem?

I think it might work to use -L and specify instead as at https://clang.llvm.org/docs/CrossCompilation.html

[jamesmkrieger]

ok, suggestions how to fix the library gfortran not found problem?

I think it might work to use -L and specify instead as at https://clang.llvm.org/docs/CrossCompilation.html

oh, I didn't get that right

[AnthonyBogetti]

AI is saying to add conda install -c conda-forge gfortran, maybe try that?

[AnthonyBogetti]

With maybe also (after installing gfortran through conda):

  - name: Find gfortran library
    shell: bash -l {0}
    run: |
      GFORTRAN_LIB=$(find /Users/runner/miniconda3 -name libgfortran.dylib)
      echo "GFORTRAN_LIB=$GFORTRAN_LIB" >> $GITHUB_ENV

  - name: Install dependencies
    shell: bash -l {0}
    run: |
      export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${GFORTRAN_LIB%/*}"
      pip install mmtf-python scikit-learn
      pip install .

[jamesmkrieger]

AI is saying to add conda install -c conda-forge gfortran, maybe try that?

we already have that and I've tried adding libgfortran too

[jamesmkrieger]

With maybe also (after installing gfortran through conda):

  - name: Find gfortran library
    shell: bash -l {0}
    run: |
      GFORTRAN_LIB=$(find /Users/runner/miniconda3 -name libgfortran.dylib)
      echo "GFORTRAN_LIB=$GFORTRAN_LIB" >> $GITHUB_ENV

  - name: Install dependencies
    shell: bash -l {0}
    run: |
      export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${GFORTRAN_LIB%/*}"
      pip install mmtf-python scikit-learn
      pip install .

this seems worth a try though. Thanks

[jamesmkrieger]

Actually that has to go together with everything else after sourcing the bash_profile

[jamesmkrieger]

Actually that has to go together with everything else after sourcing the bash_profile

or maybe it works because of being sent into the github env

[AnthonyBogetti]

@jamesmkrieger, I'll have a deeper look into this on Monday if you aren't able to get it. I'll try a few things on my Mac too.

[jamesmkrieger]

@jamesmkrieger, I'll have a deeper look into this on Monday if you aren't able to get it. I'll try a few things on my Mac too.

thank you. Sounds good. Have a good weekend. I'll stop for now too

We've got to a different error now at least

ld: duplicate LC_RPATH '@loader_path' in '/Users/runner/miniconda3/envs/test/lib/libgfortran.5.dylib'

[jamesmkrieger]

We probably want to have one for macos-13 that is intel too

[AnthonyBogetti]

Hi @jamesmkrieger, I did work a little bit on this last week but didn't make any progress. I will see what I can do this week.

[jamesmkrieger]

Thank you