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Probe-Particle / ppafm

Classical force field model for simulating atomic force microscopy images.
MIT License
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Unify the storage for examples #314

Open ondrejkrejci opened 1 day ago

ondrejkrejci commented 1 day ago

While working on # 233 and trying not to change the results there, I have found out that our examples are files are scattered all over the place - Zenodo, Dropbox, Mega ... The most of all, I do not like that the pyridineDensOverlap/run.sh needs sudo for mega tools. I am suggesting to move everything to Zenodo and adjust the examples accordingly. Let's discuss this,

NikoOinonen commented 1 day ago

Another thought about this: I made a while ago a Python function for easily downloading datasets in the GPU scripts here: https://github.com/Probe-Particle/ppafm/blob/12a90344f703da0278abe39bf067a81fafb95b70/ppafm/data.py#L47-L49 It downloads and unpacks a named dataset to a chosen location while printing a progress percentage, and skips the download if the destination already exists.

Maybe we could make a CLI command for this, something like

ppafm-download [DATASET_NAME] [SAVE_PATH]

This would somewhat simplify the code and avoid repeated downloads in the CLI scripts.

ProkopHapala commented 1 day ago

Question @ondrejkrejci @NikoOinonen @yakutovicha - so should I upload to zenodo directly the directory structure of the examples with the downloaded files? Perhaps that would be most easy to navigate ?

ondrejkrejci commented 1 day ago

I am not sure if it is possible. If so, then it is the easiest, otherwise I would rename those as 'directory-filename.tgz' so it is the same and easy to understand

NikoOinonen commented 18 hours ago

I think we want one compressed file per example, so that they can be downloaded individually. Also, we only need to upload the big files (.xsf), not the ones that only use an xyz geometry.