Pip Installation on Mac OS

[wcwest]

There is an issue when installing omero-py on a MacOS when using Pip. Although the preferred installer is Conda, pip is required when deploying to AWS using elastic beanstalk. The issue comes up when zero-ice is being installed as a dependency for Omero. Apparently there is a conflict located in the file, SecBase.h on Mac, where the structs SecKey and SecCertificate are initialized. Zeroc-ice > 3.7 attempts to redefine these structs which produces an error. Using zero-ice >= 3.7 causes a downstream error during a function call that required=s 5 inputs however this version calls the function with 9 inputs. The error is 'error: typedef redefinition with different types'

[jburel]

Thanks for the issue. Zeroc-ice 3.7 is not supported. I assume you installed it separately. I have installed omero-py in a virtual environment on a new M1 using pip and everything works as expected.

[wcwest]

Thanks for responding quickly to this issue. I need to add a clarification to the ticket. The issue isn’t really deployment to AWS but in our shop, we currently do development work on our local laptops. In this case we are using MacBook Pros with the Monterey OS (version 12). It is in this environment we are encountering the issue using pip.

Thanks again,

bw

[jburel]

I am running Monterey 12.0.1 too. I assume you have installed Zeroc 3.7 via Homebrew. This will not work since it is not compatible with the version supported by omero-py see https://github.com/ome/omero-py/blob/master/setup.py#L222

[wcwest]

Hi Jean-Marie,

Yes, I tried installing zeroc 3.7 independently and it did not work. There is a method that version is not compatible with in the Omero-py package. I also tried to pip install Omero-py which attempted to load zeroc 3.6.5 however this failed due to the issues I mentioned when I created the ticket. Were you able to find a workable solution to installing on Mac Monterey?

Thanks again,

bw

From: jean-marie burel @.> Reply-To: ome/omero-py @.> Date: Wednesday, February 9, 2022 at 12:21 AM To: ome/omero-py @.> Cc: Bill West @.>, Author @.***> Subject: Re: [ome/omero-py] Pip Installation on Mac OS (Issue #317)

I am running Monterey 12.0.1 too. I assume you have installed Zeroc 3.7 via Homebrew. This will not work since it is not compatible with the version supported by omero-py see https://github.com/ome/omero-py/blob/master/setup.py#L222https://urldefense.com/v3/__https:/github.com/ome/omero-py/blob/master/setup.py*L222__;Iw!!LLK065n_VXAQ!yxs-bmjgzP9VinWGhzZoZV_WWV_4K9sd5n4-2CbUll_umY9oUu4kUgdnn4_dKaHE$

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/ome/omero-py/issues/317*issuecomment-1033477036__;Iw!!LLK065n_VXAQ!yxs-bmjgzP9VinWGhzZoZV_WWV_4K9sd5n4-2CbUll_umY9oUu4kUgdnn7TAHeD7$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/ALEQBIQVRWUY4VINJFIWZ5TU2IPYFANCNFSM5NYEXLHA__;!!LLK065n_VXAQ!yxs-bmjgzP9VinWGhzZoZV_WWV_4K9sd5n4-2CbUll_umY9oUu4kUgdnn0Jll_RW$. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.com/v3/__https:/apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675__;!!LLK065n_VXAQ!yxs-bmjgzP9VinWGhzZoZV_WWV_4K9sd5n4-2CbUll_umY9oUu4kUgdnn6H-bm3i$ or Androidhttps://urldefense.com/v3/__https:/play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign*3Dnotification-email*26utm_medium*3Demail*26utm_source*3Dgithub__;JSUlJSU!!LLK065n_VXAQ!yxs-bmjgzP9VinWGhzZoZV_WWV_4K9sd5n4-2CbUll_umY9oUu4kUgdnn3xGjdef$. You are receiving this because you authored the thread.Message ID: @.***>

[wcwest]

Hi Jean-Marie,

I was able to install the omero-py package on my MacBook Pro using the Mamba installer. I’m not sure why this worked and Conda and Pip did not but for now, this solves my issue. You may be able to use this solution for others using the Mac OS who might be experiencing this issue.

Thanks,

Bill West

From: "West, William" @.> Date: Wednesday, February 9, 2022 at 8:39 AM To: ome/omero-py @.> Subject: Re: [ome/omero-py] Pip Installation on Mac OS (Issue #317)

Hi Jean-Marie,

Yes, I tried installing zeroc 3.7 independently and it did not work. There is a method that version is not compatible with in the Omero-py package. I also tried to pip install Omero-py which attempted to load zeroc 3.6.5 however this failed due to the issues I mentioned when I created the ticket. Were you able to find a workable solution to installing on Mac Monterey?

Thanks again,

bw

From: jean-marie burel @.> Reply-To: ome/omero-py @.> Date: Wednesday, February 9, 2022 at 12:21 AM To: ome/omero-py @.> Cc: Bill West @.>, Author @.***> Subject: Re: [ome/omero-py] Pip Installation on Mac OS (Issue #317)

I am running Monterey 12.0.1 too. I assume you have installed Zeroc 3.7 via Homebrew. This will not work since it is not compatible with the version supported by omero-py see https://github.com/ome/omero-py/blob/master/setup.py#L222https://urldefense.com/v3/__https:/github.com/ome/omero-py/blob/master/setup.py*L222__;Iw!!LLK065n_VXAQ!yxs-bmjgzP9VinWGhzZoZV_WWV_4K9sd5n4-2CbUll_umY9oUu4kUgdnn4_dKaHE$

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/ome/omero-py/issues/317*issuecomment-1033477036__;Iw!!LLK065n_VXAQ!yxs-bmjgzP9VinWGhzZoZV_WWV_4K9sd5n4-2CbUll_umY9oUu4kUgdnn7TAHeD7$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/ALEQBIQVRWUY4VINJFIWZ5TU2IPYFANCNFSM5NYEXLHA__;!!LLK065n_VXAQ!yxs-bmjgzP9VinWGhzZoZV_WWV_4K9sd5n4-2CbUll_umY9oUu4kUgdnn0Jll_RW$. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.com/v3/__https:/apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675__;!!LLK065n_VXAQ!yxs-bmjgzP9VinWGhzZoZV_WWV_4K9sd5n4-2CbUll_umY9oUu4kUgdnn6H-bm3i$ or Androidhttps://urldefense.com/v3/__https:/play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign*3Dnotification-email*26utm_medium*3Demail*26utm_source*3Dgithub__;JSUlJSU!!LLK065n_VXAQ!yxs-bmjgzP9VinWGhzZoZV_WWV_4K9sd5n4-2CbUll_umY9oUu4kUgdnn3xGjdef$. You are receiving this because you authored the thread.Message ID: @.***>

[jburel]

Thanks @wcwest for the update. We will add that information in a troubleshooting section

[afermg]

Just to add that we are experiencing the same issue in multiple MacOS computers (both M1 and non-M1). We use poetry to deploy our software, so using mamba is not quite an option. Is there any plan to support zeroc-ice>=3.7? Thanks

[jburel]

We have no plan at the moment to support zeroc-ice>=3.7

[sbesson]

Cross-linking to https://www.glencoesoftware.com/blog/2023/12/08/ice-binaries-for-omero.html. A number of pre-built Python wheel packages for Ice 3.6.5 are available, some of them being used by this repository to test the various Python versions. This includes recent versions of Python (up to 3.11) and OSX on both arm64 and x64_64 architectures. There is a long-term goal to either upgrade or revisit the Ice dependency but we are definitely talking of a multi-month project. I expect these packages allow to address the installation issue immediately