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nordvpn-client
Unofficial NordVPN client - an excuse to practice Common Lisp and a way to manage my VPN on Fedora Silverblue
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InfluxDB
Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
All I'm missing is great IDE support because most don't support flatpak well, but it's still usable. No idea what you need for data science as I don't do it, but everything else you mentioned works great (except for Windows 11 VMs because the libosinfo merge request that is required hasn't been merged yet (link), so GNOME Boxes doesn't create a VM with UEFI support. Win10 works though)
Not sure what you mean by the second sentence, but there's a PR to add Rstudio to Flathub, so you'll just have to wait until that is accepted (or use it in toolbox until then)
And currently, it's not possible for flatpaks to talk to your GPG agent, so if you have git commit signing enabled you can't use your IDE's git gui (there's a PR for this, but it's been dead for a while)
Related posts
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XZ backdoor story – Initial analysis
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FOSS software is probably less likely to abuse this, but it just depends how ruthless the publisher is, a lot of people desire to be successful and it's human nature to look for advantages to put yourself above others in competitive environments.
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Flathub – The Linux App Store
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Flatpak Subtle Welcome UI Update
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Bforartists Flatpak, coming soon to Flathub