bidscoin pip install fails on apple silicon #189
Comments
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Mhhh, I did make a port to qt6 some time ago, but I didn't make it default
because it looked less good (on Linux). Can you test to see if that would
work for you?
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Op vr 30 jun. 2023 03:31 schreef dkp ***@***.***>:
*Describe the bug*
bidscoin environment creation fails on Apple Silicon (though it worked on
my intel mac).
The install hangs here:
Collecting PyQt5>=5.12.1 (from bidscoin)
Using cached PyQt5-5.15.9.tar.gz (3.2 MB)
Installing build dependencies ... done
StackOverflow reports that pyqt5 is not compatible with the ARM
architecture, but pyqt6 IS compatible.
https://stackoverflow.com/questions/71046800/how-to-install-pyqt5-on-m1-arm64-architecture
*To reproduce*
On Apple Silicon:
conda create -n bidscoin python=3.10
conda activate bidscoin
pip install bidscoin[all]
*Expected behavior*
I hoped it would install ; (
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See the qt6 branch comments in this issue:
#131
…_____________________
Sent from my phone
Op vr 30 jun. 2023 03:31 schreef dkp ***@***.***>:
*Describe the bug*
bidscoin environment creation fails on Apple Silicon (though it worked on
my intel mac).
The install hangs here:
Collecting PyQt5>=5.12.1 (from bidscoin)
Using cached PyQt5-5.15.9.tar.gz (3.2 MB)
Installing build dependencies ... done
StackOverflow reports that pyqt5 is not compatible with the ARM
architecture, but pyqt6 IS compatible.
https://stackoverflow.com/questions/71046800/how-to-install-pyqt5-on-m1-arm64-architecture
*To reproduce*
On Apple Silicon:
conda create -n bidscoin python=3.10
conda activate bidscoin
pip install bidscoin[all]
*Expected behavior*
I hoped it would install ; (
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Wow. I think it may just have worked!
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Could it be that you have both PyQt5 and PyQt6 installed? Or did you install the qt6 branch in it's own new environment? |
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I think this library error is a bit out of my scope, @bendhouseart have you perhaps seen this? |
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My Python knowledge is wobbly. Maybe you can help me understand where to go from here. Honestly, i can't say in PyQt5 is lurking somewhere. I cloned the qt6 branch: I tried creating a venv and building there with Outside a virtual env has the same problems. |
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I think installing bidscoin-qt6 in a virtual environment, as you did, should just work. I don't own a mac, so I can't replicate your issue myself, but I'll try to find a colleague with a mac who can test this out for me. In the meantime, perhaps this is of help? |
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Thank you for the suggestions. I tried the regular bidscoin distribution on linux (intel) the other day and got errors there too (though completely different): I'll probably try apptainer on our HPC next, but it may be a little while before I get to it. I'll let you know how it goes. I appreciate your willingness to help. |
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I have never seen this message and have no idea what could be the cause of it. I'll look into it tomorrow... |
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That traits error seems rather fundamental, can you install other packages without error? E.g. |
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Aha, thank you for your patience. Problem solved on Linux. There were two factors, I think:
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You mean that you have to install it in a (e.g. conda) virtual environment? Sure, that is not just true for BIDScoin, but for any python library you install
Although I have seen this clunky conda behaviour too in the past, it is certainly not true in general (in other OS / anaconda versions it works just fine) |
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Which Linux version is that? Some old CentOS version by any chance? |
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This is ubuntu 22.0.2: I've always set up conda for myself, so I was not aware of what issues might ensue from a global install. |
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Thanks, I didn't know that. Glad you figured that out :) |
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Well, maybe there is some way around the problem, I just don't know what that is yet. |
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Just got back from summer break, so apologies for the late reply.
Hi @marcelzwiers don't recall running into the specific errors in the attached text file. But, happy to test this out on Apple Silicon for you and @dkp Currently getting hanging doing the install w/ dependencies for pyqt5 via python 3.10: That said, installing from here Really frustrating when even the example in their docs fails miserably. But, that's to be expected I think when the docs are a year out of date at least: If I roll back to rumel.yaml version 0.17.0 I no longer get that error: It might be worth rolling back to an earlier version of this library or ditching it for pyYAML or something else. @marcelzwiers I'm going to fiddle around with the |
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Alright, moving over discussion from mattermost to here so it's more visible. Turns out I wasn't just "tired and out of it" |
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@bendhouseart Well, I also have trouble running tox with python 3.11, but that's because of [tool.poetry.dependencies]
python = ">=3.8,<=3.11.1"It would make my life easier if you would relax it a bit and take out the point release (I think that's a harmless thing to do): Here's the error: py311: install_package_deps> python -I -m pip install 'pypet2bids>=1.0.12'
ERROR: Ignored the following versions that require a different python version: 0.0.10 Requires-Python >3.7.1,<3.10; 0.0.11 Requires-Python >3.7.1,<3.10; 0.0.12 Requires-Python >3.7.1,<3.10; 0.0.13 Requires-Python >3.7.1,<3.10; 0.0.14 Requires-Python >3.7.1,<3.10; 0.0.15 Requires-Python >3.7.1,<3.10; 0.0.4 Requires-Python >3.7.1,<3.10; 0.0.6 Requires-Python >3.7.1,<3.10; 0.0.7 Requires-Python >3.7.1,<3.10; 0.0.8 Requires-Python >3.7.1,<3.10; 0.0.9 Requires-Python >3.7.1,<3.10; 1.0.0 Requires-Python >3.7.1,<3.10; 1.0.10 Requires-Python >=3.8,<3.11; 1.0.12 Requires-Python >=3.8,<=3.11.1; 1.0.2 Requires-Python >3.7.1,<3.10; 1.0.5 Requires-Python >=3.8,<3.11; 1.0.7 Requires-Python >=3.8,<3.11; 1.0.8 Requires-Python >=3.8,<3.11; 1.0.9 Requires-Python >=3.8,<3.11; 1.1.0 Requires-Python >=3.8,<=3.11.1; 1.1.1 Requires-Python >=3.8,<=3.11.1; 1.1.2 Requires-Python >=3.8,<=3.11.1; 1.2.2 Requires-Python >=3.8,<=3.11.1; 1.2.3 Requires-Python >=3.8,<=3.11.1
ERROR: Could not find a version that satisfies the requirement pypet2bids>=1.0.12 (from versions: 1.0.4)
ERROR: No matching distribution found for pypet2bids>=1.0.12 |
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@bendhouseart I chose ruamel.yaml over pyyaml because pyyaml still doesn't support the 10 year old release of yaml v1.2. Generally, it has been very good to me, including supporting writing back the comments (which I think pyyaml just drops). Which version of ruamel.yaml wasn't working for you? I suspect it is the compiled part (see |
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@bendhouseart Perhaps you can file a ruamel.yaml ticket? I think the author is very responsive to good tickets |
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@bendhouseart I've been reading up a bit on how to use python on MacOS and learned that you probably don't want to use |
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Ok, I managed to borrow a brand new M2 MacBook pro (out of the box). I did the following
So no ruamel.yaml error and no pyqt6 error. It seems to me the problems are caused by homebrew |
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I'm closing this issue because it is due to the user installation. Feel free to re-open it if needed |
Describe the bug
bidscoin environment creation fails on Apple Silicon (though it worked on my intel mac).
The install hangs here:
StackOverflow reports that pyqt5 is not compatible with the ARM architecture, but PyQt6 IS compatible:
https://stackoverflow.com/questions/71046800/how-to-install-pyqt5-on-m1-arm64-architecture
To reproduce
On Apple Silicon:
Expected behavior
I hoped it would install ; (
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