Flatpak Handling by SethyM12 · Pull Request #99 · linuxmint/mintbackup

SethyM12 · 2026-02-16T13:45:27Z

A class was added that gives the ability to add and restore flatpaks.
Flatpaks installed on the system are added to the same list file as APT packages.
Then, that list file can be restored.

New features include flatpak backing up and restoring. Output file includes APT packages and Flatpaks.

hthienloc · 2026-02-21T04:26:10Z

Hi @SethyM12,

I noticed we are addressing the same issue. I have proposed a fix in PR #100, but since I do not currently have a machine running Linux Mint to perform a full live test, could you please verify if my approach works on your system?

Your feedback would be very helpful to ensure this gets resolved correctly.

SethyM12 · 2026-02-22T20:02:36Z

Hello @hthienloc,

I downloaded the source project from the issue you linked and ran the code. Unfortunately, trying to back up the installed apps causes the backup tool to crash. As of now, I am not able to diagnose the issue.

hthienloc · 2026-02-23T01:40:50Z

Thanks for testing the previous build @SethyM12 – I saw the freeze you mentioned.
I’ve fixed that issue in PR #101 and verified it runs through to completion on my side.
If you’d like to try again, feel free to pull that branch/build and give it another spin.

Copilot

Pull request overview

Adds Flatpak backup/restore capability to MintBackup’s software selection flow, aiming to include Flatpaks alongside APT packages.

Changes:

Adds Flatpak discovery during software backup and writes Flatpak entries into the generated .list file.
Introduces a new FlatpakHandler class to backup Flatpak apps/remotes to flatpaks.json and restore them later.
Includes various formatting-only cleanups in mintbackup.py.

Reviewed changes

Copilot reviewed 2 out of 3 changed files in this pull request and generated 7 comments.

File	Description
`usr/lib/linuxmint/mintbackup/mintbackup.py`	Adds Flatpak listing into the package selection UI/save file and triggers Flatpak restore after APT installs.
`usr/lib/linuxmint/mintbackup/flatpak_handler.py`	New helper to backup Flatpak remotes/apps to JSON and restore via `flatpak remote-add` / `flatpak install`.
`usr/lib/linuxmint/mintbackup/__pycache__/flatpak_handler.cpython-312.pyc`	Adds a compiled Python bytecode artifact to the repo (should not be committed).

Comments suppressed due to low confidence (1)

usr/lib/linuxmint/mintbackup/mintbackup.py:12

json is imported but never used in this file. Please remove the unused import (or use it) to avoid dead code and keep imports minimal.

import subprocess
import json

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Copilot · 2026-02-26T17:42:29Z

usr/lib/linuxmint/mintbackup/flatpak_handler.py

+            if app["installation"] == "user":
+                cmd.insert(2, "--user")


restore() only treats installation == "user" specially; system installs or named installations (as returned by Flatpak’s installation column) aren’t handled. This can cause restores to target the wrong installation or fail under a non-root run. Consider using --installation=... / --system appropriately based on the stored installation value.

Suggested change

if app["installation"] == "user":

cmd.insert(2, "--user")

installation = app.get("installation")

if installation == "user":

cmd.insert(2, "--user")

elif installation == "system":

cmd.insert(2, "--system")

elif installation:

# Named installation (as returned by flatpak list --columns=...,installation)

cmd.insert(2, installation)

cmd.insert(2, "--installation")

Copilot · 2026-02-26T17:42:29Z

usr/lib/linuxmint/mintbackup/mintbackup.py

+        # Backup Flatpaks in same directory
+        flatpak_handler = FlatpakHandler(BACKUP_DIR)
+        flatpak_handler.backup()
+


Flatpak state is being backed up to a separate flatpaks.json in BACKUP_DIR, but restore is driven by a user-selected .list file (self.package_source). If the .list file is moved to another machine or location, Flatpak restore will fail or restore the wrong selection because it still reads BACKUP_DIR/flatpaks.json. Consider storing Flatpak metadata alongside the selected list file (same directory / same basename) and restoring relative to self.package_source instead of BACKUP_DIR.

Copilot · 2026-02-26T17:42:30Z

usr/lib/linuxmint/mintbackup/mintbackup.py

+        apt_packages = []
+        flatpak_packages = []


flatpak_packages is collected during restore but never used, which makes the Flatpak selection logic dead code. Either remove it, or use it to drive Flatpak installation so the user’s selections in the list actually affect what gets restored.

Copilot · 2026-02-26T17:42:30Z

usr/lib/linuxmint/mintbackup/mintbackup.py

        client = aptkit.simpleclient.SimpleAPTClient(self.main_window)
        client.set_cancelled_callback(self.on_apt_install_finished)
        client.set_finished_callback(self.on_apt_install_finished)
-        client.install_packages(packages)
+        client.install_packages(apt_packages)


If the selection contains only Flatpaks, apt_packages can be empty and client.install_packages(apt_packages) may not execute any transaction/callback, which can prevent Flatpaks from being restored. Handle the empty-APT case explicitly (e.g., run Flatpak restore directly when apt_packages is empty).

Copilot · 2026-02-26T17:42:30Z

usr/lib/linuxmint/mintbackup/flatpak_handler.py

+                "flatpak", "install", "-y",
+                app["origin"],
+                f"{app['app_id']}//{app['branch']}"
+            ]
+
+            if app["installation"] == "user":
+                cmd.insert(2, "--user")
+


backup() records an arch field for each app, but the restore install command doesn’t use it. Either pass the arch through on install (e.g., --arch=...) or stop storing arch to avoid misleading backup data and potential restore mismatches on non-default architectures.

Suggested change

"flatpak", "install", "-y",

app["origin"],

f"{app['app_id']}//{app['branch']}"

]

if app["installation"] == "user":

cmd.insert(2, "--user")

"flatpak", "install", "-y"

]

# Use the same installation scope as in the backup

if app.get("installation") == "user":

cmd.append("--user")

# If an architecture was recorded, pass it through to flatpak

arch = app.get("arch")

if arch:

cmd.append(f"--arch={arch}")

cmd.extend([

app["origin"],

f"{app['app_id']}//{app['branch']}"

])

Copilot · 2026-02-26T17:42:31Z

usr/lib/linuxmint/mintbackup/mintbackup.py

+                    if name.startswith("flatpak:"):
+                        flatpak_ref = name.replace("flatpak:", "")
+                        status = "%s\n<small>Flatpak application</small>" % flatpak_ref
+                        model.append([True, status, True, flatpak_ref])


Flatpak lines from the .list file are detected via name.startswith("flatpak:"), but you then store flatpak_ref (with the prefix removed) in column 3. Later installation code checks row[3].startswith("flatpak:"), so Flatpaks loaded here will never be recognized for installation. Keep a consistent identifier format between load and install (either keep the prefix in column 3 or adjust the install check).

Suggested change

model.append([True, status, True, flatpak_ref])

model.append([True, status, True, name])

Copilot · 2026-02-26T17:42:31Z

usr/lib/linuxmint/mintbackup/mintbackup.py

    def on_apt_install_finished(self, transaction, exit_state):
+        # Restore flatpaks after apt finishes
+        flatpak_handler = FlatpakHandler(BACKUP_DIR)
+        flatpak_handler.restore()
+


on_apt_install_finished() restores Flatpaks unconditionally even when the APT transaction is cancelled or fails (this callback is registered for both cancelled and finished). Please gate Flatpak restore on a successful exit_state (and/or only run it from the finished callback) to avoid applying Flatpak changes after a failed APT operation.

SethyM12 added 4 commits February 9, 2026 09:14

Beginning flatpak functionality

ca06fdd

Trying my best

e8de20c

flatpaks appear in backup file

98797cc

Extra docs

cdca5a1

New features include flatpak backing up and restoring. Output file includes APT packages and Flatpaks.

hthienloc mentioned this pull request Feb 23, 2026

feat: Add support for listing and restoring Flatpak applications. #101

Open

Remove metadata :(

5ad0da3

Copilot AI review requested due to automatic review settings February 26, 2026 17:36

Copilot started reviewing on behalf of SethyM12 February 26, 2026 17:36 View session

Copilot AI reviewed Feb 26, 2026

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Flatpak Handling#99

Flatpak Handling#99
SethyM12 wants to merge 5 commits intolinuxmint:masterfrom
SethyM12:master

SethyM12 commented Feb 16, 2026

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hthienloc commented Feb 21, 2026

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-            if app["installation"] == "user":
-                cmd.insert(2, "--user")
+            installation = app.get("installation")
+            if installation == "user":
+                cmd.insert(2, "--user")
+            elif installation == "system":
+                cmd.insert(2, "--system")
+            elif installation:
+                # Named installation (as returned by flatpak list --columns=...,installation)
+                cmd.insert(2, installation)
+                cmd.insert(2, "--installation")

	model.append([True, status, True, flatpak_ref])
	model.append([True, status, True, name])

Conversation

SethyM12 commented Feb 16, 2026

Uh oh!

hthienloc commented Feb 21, 2026

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SethyM12 commented Feb 22, 2026

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