biosimulators no longer working on macOS

[fbergmann]

Running the bio simulator, just freezes whenever the StandardOutputErrorCapturer is used. When I run without log file, it works, however no output is produced. so

        config = bio_copasi.get_config()
        config.LOG=True
        config.DEBUG=True
        config.VERBOSE=True
        results, log = bio_copasi.exec_sedml_docs_in_combine_archive(
            omexfile, 
            outdir, 
            config=config, 
            fix_copasi_generated_combine_archive=False)

freezes the program, needing for the python process to be killed. while

        config = bio_copasi.get_config()
        config.LOG=False
        config.DEBUG=True
        config.VERBOSE=True
        results, log = bio_copasi.exec_sedml_docs_in_combine_archive(
            omexfile, 
            outdir, 
            config=config, 
            fix_copasi_generated_combine_archive=False)

works fine, however it does not produce any output, and there is a warning message:

StandardOutputNotLoggedWarning: Standard output and error could not be logged because capturer is not installed. To install capturer, install BioSimulators utils with the `logging` option (`pip install biosimulators-utils[logging]`).

it would be nice if output could be produced without needing capturer.

[AlexPatrie]

Just curious: what Python version were you using?

[fbergmann]

I have been using python 3.11.3 but it also happens with the default macOS 3.9.6. It is pretty much independent on the python version. I think it is an issue with the capturer library.

[AlexPatrie]

I ask because I have noticed that bio_copasi v. 0.1.25 installs with Python3.11, with the newest bio_copasi version being 0.1.35. When using Python 3.7, the latest version is fetched.

[fbergmann]

I've created an issue with the utils package, as the problem comes from there. It would still be nice, if the simulator could work even without logging.

[fbergmann]

trying to get the biosimulator running locally, I still find the same issue. if I try to execute it, or run tests, everything just freezes. @AlexPatrie I notice there are 2 draft PRs still open in utils about this ... it would be great if we could leave this issue open until it really is resolved.

[AlexPatrie]

@fbergmann I realized that I was referencing another issue when closing this PR originally. Thanks for the clarification.