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BiAPoL / blog

Most of us study and work at the Bio-image Analysis Technology Development group at the DFG Cluster of Excellence “Physics of Life” at the TU Dresden. We blog about image data science, knowledge exchange and research data management in the life sciences.
https://biapol.github.io/blog/
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Install devbio napari on an arm64 mac #52

Closed thawn closed 1 year ago

thawn commented 2 years ago

Since Robert Muench asked for help with installing devbio-napari on an arm64 mac, I thought I write down my way to get this to work as a blog article.

@haesleinhuepf did you maybe find an easier way?

The way I describe allows to have both the arm64 and the i386 versions in parallel, which makes it a bit complicated - but allows to run python code that works on arm64 natively.

haesleinhuepf commented 2 years ago

Thanks @thawn for this blog post! Before merging it I'd like to wait for the potential fixes here:

psobolewskiPhD commented 2 years ago

Bah, something in devbio-napari has PyQt5 as a hard depend rather than qtpy so you can't easily work around the lack of pyqt5 for arm64 on pip by installing pyqt from conda-forge. What a bummer. Edit: oh and imagecodecs

psobolewskiPhD commented 2 years ago

I've found the PyQt culprit: it's PlatyMatch. I will see if I can make a PR there to fix it, just sanity checking on zulip that I understand things correctly.

psobolewskiPhD commented 2 years ago

PR made: https://github.com/juglab/PlatyMatch/pull/7 This should make PlatyMatch pip installable on arm64 M1.

thawn commented 2 years ago

@psobolewskiPhD kudos for the PlayMatch PR :-)

thawn commented 2 years ago

wait for the potential fixes here: https://github.com/haesleinhuepf/devbio-napari/issues/23

I am a bit worried, that the simpleitk migration to arm64 might not come in time for our course. Also, the rosetta installation requires sudo, which means that some students that do not have admin rights will need assistance from the IT department. Therefore, I would like to give the students with an arm64 system the chance to install devbio-napari with help from the IT in the week before the course.

I am perfectly fine with sending them the link to this branch, without merging the article. However, I was wondering if @haesleinhuepf found an installation method that is a bit simpler (i.e. not requiring sudo)

psobolewskiPhD commented 2 years ago

Also pure conda install should be working soon too! I think this is the only holdup: https://github.com/conda-forge/simpleitk-feedstock/pull/27#pullrequestreview-1128790505

thawn commented 1 year ago

obsolete because native arm64 installation works now