MintUpdate does not automatically update Flatpak

[sk8board]

Describe the bug

• MintUpdate does not automatically update Flatpak.

Screenshots

To Reproduce
Steps to reproduce the behavior:

• The Update Manager automatically performs updates every morning when I first use the computer. After the automated updates are completed, the Update Manager icon shows updates are available. When I check the available updates, only Flatpak updates are available.

Expected behavior

• I expect all updates to be installed after the automated update is performed.

Distribution:

• Linux Mint MATE 22.2
• I am using a fresh install of MATE 22.2, not an update from 22.1.

Software version:
See Help > About in Update Manager.

• mintUpdate 7.1.1

Logs:
Copy & paste the log output from Update Manager > View > Information here.

2025.09.26@12:30 ++ Launching Update Manager
2025.09.26@12:30 ++ Auto-refresh disabled in preferences, automatic refresh thread stopped
2025.09.26@12:30 ++ Inhibited power management
2025.09.26@12:30 ++ Checking for updates
2025.09.26@12:30 ++ Refresh finished
2025.09.26@12:30 ++ System is up to date
2025.09.26@12:30 ++ Resumed power management
2025.09.26@12:35 ++ Inhibited power management
2025.09.26@12:35 ++ Checking for updates
2025.09.26@12:35 ++ System is up to date
2025.09.26@12:35 ++ Refresh finished
2025.09.26@12:35 ++ Resumed power management

Crash report:
If you are reporting a crash, please run mintupdate from a terminal window, reproduce the crash and copy & paste any output from the terminal window here.

• no crash

Additional context
Add any other context about the problem you think might be relevant.

• no additional information

Locale:
If the problem is with text not getting displayed correctly, paste the output of the terminal command locale.

• no problem with text

[sk8board]

The problem appears to be that automatic_upgrades.py only uses mintupdate-cliand does not use flatpakUpdater.py.

mintupdate/usr/lib/linuxmint/mintUpdate/automatic_upgrades.py

Lines 43 to 46 in 51007ad

	# Run mintupdate-cli through systemd-inhibit
	cmd = ["/bin/systemd-inhibit", '--why="Performing automatic updates"',
	'--who="Update Manager"', "--what=shutdown", "--mode=block",
	"/usr/bin/mintupdate-cli", "upgrade", "--refresh-cache", "--yes"]

Also, automatic_upgrades.py does not use the "Update Flatpaks automatically" slider button from the UI.

[sk8board]

I noticed the UI states, "Performed when you log in".

Apparently the design intent is that Flatpaks are updated during log-in rather than when Mint Updates are performed.

If a user never logs-out (which is my use case), then Flatpaks will never be updated automatically.

@clefebvre Could you help by explaining why Flatpak Update Automation performs updates at log-in rather than when Mint Updates are automatically performed?

For a uniform update scheme, could we simply add the following lines of code to automatic_upgrades.py?

cmd = ["/bin/systemd-inhibit", '--why="Performing automatic updates"',
       '--who="Update Manager"',  "--what=shutdown", "--mode=block",
       "/usr/bin/mintupdate-launcher"]
subprocess.run(cmd, stdout=log, stderr=log)

This code calls mintupdate-launcher which purges unused Flatpaks

mintupdate/usr/bin/mintupdate-launcher

Lines 80 to 87 in 51007ad

	try:
	print("Purging unused flatpaks")
	out = subprocess.run(
	[
	"flatpak", "uninstall", "--unused", "-y"
	],
	stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
	print(out.stdout.decode())

as well as updates Flatpaks if the "auto-update-flatpaks" boolean setting is enabled.

mintupdate/usr/bin/mintupdate-launcher

Lines 91 to 99 in 51007ad

	if settings.get_boolean("auto-update-flatpaks"):
	print("Updating flatpaks")
	try:
	# Update flatpaks
	out = subprocess.run(
	[
	"flatpak", "update", "-y"
	],
	stdout=subprocess.PIPE, stderr=subprocess.STDOUT)