write permission mishaps

[ZLLentz]

• With the environment write-protected, certain basic commands like conda list give annoying warnings.
  • These can so far be mitigated by opening up write permissions in that specific directory.
• I'm somewhat worried about __pycache__ folders, do these get created properly in a write-protected env?
• A write-protected environment cannot be conda-packed and conda-unpacked properly.

[ZLLentz]

conda list example:

(pcds-5.8.4)zlentz@psbuild-rhel7-03:~/.../pcds-envs/scripts(master -)$ conda list
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(188): Could not remove or rename /cds/home/z/zlentz/miniconda3/envs/pcds-5.8.4/conda-meta/httpx-0.27.0-pyhd8ed1ab_0.json.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(188): Could not remove or rename /cds/home/z/zlentz/miniconda3/envs/pcds-5.8.4/conda-meta/pydantic-2.5.3-pyhd8ed1ab_0.json.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(188): Could not remove or rename /cds/home/z/zlentz/miniconda3/envs/pcds-5.8.4/conda-meta/event-model-1.20.0-pyhd8ed1ab_0.json.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(188): Could not remove or rename /cds/home/z/zlentz/miniconda3/envs/pcds-5.8.4/conda-meta/anyio-4.3.0-pyhd8ed1ab_0.json.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(188): Could not remove or rename /cds/home/z/zlentz/miniconda3/envs/pcds-5.8.4/conda-meta/urllib3-2.2.1-pyhd8ed1ab_0.json.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(188): Could not remove or rename /cds/home/z/zlentz/miniconda3/envs/pcds-5.8.4/conda-meta/httpcore-1.0.5-pyhd8ed1ab_0.json.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(188): Could not remove or rename /cds/home/z/zlentz/miniconda3/envs/pcds-5.8.4/conda-meta/epicscorelibs-7.0.7.99.0.0-py39h7eddda4_1.json.  Please remove this file manually (you may need to reboot to free file handles)
# packages in environment at /cds/home/z/zlentz/miniconda3/envs/pcds-5.8.4:

[tangkong]

Was the environment not write protected before? I don't recall getting errors like this in the past

[ZLLentz]

I think this has been happening for a while, but not since the first env. It's been write-protected since the start but this cropped up somewhere in 5.7.something iirc

[ZLLentz]

Adding a new case to the description: an environment that has been write-protected and then conda-pack -ed cannot be unpacked properly. I ran into this today because for the first time in a while I had created environments in my home area via the "apply release" script (to test the script) rather than from the yaml file or as the originating template for the environment release.

[ZLLentz]

The conda-meta directory is the one that causes issues when write-protected for the purposes of the conda list output. Giving this directory write permissions is enough to fix the problem.