If you installed the LUKS variant of byzantium from scratch then I believe that is known, intentional and annoying behaviour. You are expected to expand the partition immediately after the install.
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So, until this last journey into mounting a non-native image to copy over files, the only changes I’ve made to the primary software package are the updates - once manually, but the rest through the Purism GUI. And I haven’t done any manual re-partitioning. But seeing the LUKS partition sure does make it seem like that’s what is on my device. But I’m supposing the LUKS variant doesn’t go in on one of the updates, so it would have to have been a “factory” install choice.
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IMO, this is most likely related to the fact that you powered on, for the very first time, your Librem 5 with the almost empty BPP-L503 battery and your Librem 5 turned off without allowing to PureOS to auto-expand its related partitions? After recharging your phone battery you continued using it without “by itself” expanded partitions, without taking care about data space available to/after your specific case “factory” PureOS installation.
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This is misleading information. Users are expected and encouraged to check if auto-expanding of two PureOS partitions happened (if ever such non-expanding of partitions thing happens, with initially turning on Librem 5 under its original power supply connected, for example). In other words, regularly and usually there is no need to expand partitions by any new Librem 5 phone user.
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That would make sense then. Any reason not to use the native “Disks” GUI preloaded on the LIbrem 5?
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I think that gnome-disks is very useful application and complementing Librem 5 features just fine. One implementation example is kindly confirmed here:
Another DE usage is shown here:
To include that the second option here might be executed under CLI as well:
https://manpages.debian.org/testing/gnome-disk-utility/gnome-disks.1.en.html
Gnome-disks had the the resize option greyed out. Maybe because it just opens up with user privileges? I was going to try and open the GUI using sudo from the terminal, but while I was in there, I decided to just try and do it manually. Sequence to expand the LUKS partition went something like this:
(all with sudo)
parted —pretend-input-tty /dev/mmcblk0 resizepart 2 100%
partx -u /dev/mmcblk0
cryptsetup resize /dev/mapper/crypt_root
resize2fs /dev/mapper/crypt_root
df suggests that it worked, although it looks kind of funny in gnome-disks now. Maybe just needs a reboot. But maybe I don’t reboot and enjoy the phone for awhile in case I totally screwed something up that will manifest on reboot.
Update - I went ahead and let it update and reboot. Worked fine, and now it looks normal in gnome-disks. Now root has expanded to the rest of the drive and no more out of space errors.
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I get the same error about 500-800MB remaining depending on the day.
Btw in gnome browser i cannot uploaad images to the forum which is a bummer.
@N8W all lines together at once or line after line? Id rather not brick my phone that early in its life 
i have done that on Sailfish OS twice while trying to resize root partition, that was even without encryption.
I would say: always line after line so that you stop if something isn’t right.
Note that the forum has butchered the parted command option. It should be
---pretend-input-tty
and is a hidden (undocumented) option.
Edit: For clarity, confirming, the option is preceded by 3 dashes i.e. relatively non-standard. Not 1, not 2, but 3.
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3 dashes? (10 chars)
Yes.
hmmm doesnt seem to work for me:
sudo parted ---pretend-input-tty /dev/mmcblk0 resizepart 2 100%
Information: You may need to update /etc/fstab
My drives are both defined by UUID= in fstab.
Just “information”, not “error”? (…and I don’t think you will need to update /etc/fstab for this particular operation)
Got it thank at the end it states:
sudo resize2fs /dev/mapper/crypt_root resize2fs 1.46.2 (28-Feb-2021) The filesystem is already 7513088 (4k) blocks long. Nothing to do!
Is that what showed up for you too?
Here related and useful pre-steps (warm-up ones) that are informational only and easily executed directly within (non-encrypted) Librem 5 CLI (no big difference output):
sudo partx --show /dev/sda
sudo parted ---pretend-input-tty /dev/sda print
sudo parted /dev/sda print
While not in need, not from my side tested one (that includes yes):
sudo parted -a optimal ---pretend-input-tty resizepart X Yes 100%
Therefore here posting related link to the non-interactive parted usage, explanation actually.
Sorry, I’ve been away a few days. I’m glad others answered questions.
Curious question: did your mmcblk0 appear to have a bunch of free space at the end like mine did when you checked in gnome disks?
To confirm some of the previous answers: yes each a separate line (with sudo in front); yes three dashes - It was a weird one… sorry I didn’t notice that the forum had “auto-incorrected” my dashes.
Next: “You may need to update /etc/fstab” was the same notice I got. I believe it means that the partition was expanded out successfully, but the command is worried fstab wouldn’t know it yet? I believe the partx -u command updates the kernel to know the partition was expanded, so maybe it tips-off fstab? I did not update fstab separately, and it worked fine.
In the end, I do not believe I got the note that the filesystem was already that long. Did part -u and cryptsetup commands run successfully?
I’m curious what your gnone disks thinks about your partions now?
Yes all commands ran successfully gnome looks identical to before. I believe my case might be different, the file system warnings start because i have less than 1GB of space left in root. The Luks partition has 2.3Gb free, the file partition 1 has 275MB free, and the unallocated free space has 5.2Mb free.
I think my case is related to root running out of space literally. Too bad that usage the app cant access it so i can visually see which folder is sucking up all the space.
You should probably have more than 2.3 GB free in the Luks partition, since the total drive space is bigger than 31 GB. On my phone, that was the the “root” of my problem. I think root is actually in the Luks partition.
If you’ve taken some pictures with the phone, maybe try moving those pictures off of that drive (Home Pictures directory), and onto your SD card. If that frees up enough space to stop the error, your issue could still could be the same as mine.
I also had 5.2 Mb free at the front end of the drive (and still do). But I had 27 GB unallocated at the end as well, which is now fixed. When I was using the terminal to check for space, I would miss that fact, since 27123123123 is tough to distinguish from 2712312312 at a quick glance. I would still like to see a screen capture (or pic upload, since your drive is out of space) of the 31 GB drive from the Disks application.