DO NOT MERGE: Minimal example for representation

[ziw-liu]

Produce a source distribution by:

1. Clone the repo
2. Checkout this branch
3. Delete Git by running rm -rf ./.git

Then test if the no-git version in the shared drive:

• installation works with a pared-down version
• training and prediction works with the example file

[Soorya19Pradeep]

@ziw-liu , I tried doing a fresh installation. I am getting the following error:

(dynaclr) soorya.pradeep@SFO-IT0358 viscy % pip install -e ".[visual,metrics]"
Obtaining file:///Users/soorya.pradeep/Documents/GitHub/Dynaclr/viscy
Installing build dependencies ... done
Checking if build backend supports build_editable ... done
Getting requirements to build editable ... done
Preparing editable metadata (pyproject.toml) ... done
Collecting iohub==0.1.0 (from viscy==0.3.0a1)
Using cached iohub-0.1.0-py3-none-any.whl.metadata (6.5 kB)
INFO: pip is looking at multiple versions of viscy to determine which version is compatible with other requirements. This could take a while.
ERROR: Could not find a version that satisfies the requirement torch>=2.4.1 (from viscy) (from versions: 1.11.0, 1.12.0, 1.12.1, 1.13.0, 1.13.1, 2.0.0, 2.0.1, 2.1.0, 2.1.1, 2.1.2, 2.2.0, 2.2.1, 2.2.2)
ERROR: No matching distribution found for torch>=2.4.1

[ziw-liu]

@Soorya19Pradeep Seems like you are testing on macOS. Can you share the output of this:

python -c "import platform; print(platform.machine())"

It is likely that you are running Python in x86 emulation mode. As explained in readme, you need the arm64 (native) build of Python for torch to work.

Can you also test on Linux?

[ziw-liu]

@Soorya19Pradeep also if you are using conda, it's helpful to look at the output of conda info to make sure that arm64 is used instead of x86_64.

[Soorya19Pradeep]

@ziw-liu , I tried it on an HPC OnDemand session. It does work there.
conda info does show x86_64.

(dynaclr) soorya.pradeep@SFO-IT0358 viscy % conda info

 active environment : dynaclr
active env location : /opt/miniconda3/envs/dynaclr
        shell level : 2
   user config file : /Users/soorya.pradeep/.condarc

populated config files :
conda version : 4.11.0
conda-build version : not installed
python version : 3.9.19.final.0
virtual packages : __osx=10.16=0
__unix=0=0
__archspec=1=x86_64
base environment : /opt/miniconda3 (writable)
conda av data dir : /opt/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/osx-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /opt/miniconda3/pkgs
/Users/soorya.pradeep/.conda/pkgs
envs directories : /opt/miniconda3/envs
/Users/soorya.pradeep/.conda/envs
platform : osx-64
user-agent : conda/4.11.0 requests/2.27.1 CPython/3.9.19 Darwin/21.5.0 OSX/10.16
UID:GID : 502:20
netrc file : None
offline mode : False