Add GUI extra in auto-updater; support uv by C-Achard · Pull Request #3346 · DeepLabCut/DeepLabCut

C-Achard · 2026-05-26T14:35:46Z

Scope

Introduces support for multiple installer backends (such as uv instead of justpip)
Added GUI extra since the auto-update process runs only there

Adds new utility functions for building update commands, refactors the update process to try preferred installers first with fallbacks, and adds tests for these.

Automated summary

Update backend improvements:

Added package_specs_for_update and build_update_commands utility functions in deeplabcut/gui/utils.py to generate the correct package specifications (ensuring deeplabcut is updated with [gui] extra) and to build a prioritized list of installer commands, preferring uv if available and always falling back to pip ([deeplabcut/gui/utils.pyR239-R292](https://github.com/DeepLabCut/DeepLabCut/pull/3346/files#diff-4279538071ed35262d378e598eb69f5d2e1aced94717f42138692f0d8c718e3cR239-R292)).
Refactored the update process in deeplabcut/gui/window.py to use the new backend selection logic, attempting each backend in order and providing more informative error messages and logs for each attempt ([[1]](https://github.com/DeepLabCut/DeepLabCut/pull/3346/files#diff-4dbcd4272a9f0fb80775a2e54ed8d52f229695085258e5b5d0172f05870a3772L344-R380), [[2]](https://github.com/DeepLabCut/DeepLabCut/pull/3346/files#diff-4dbcd4272a9f0fb80775a2e54ed8d52f229695085258e5b5d0172f05870a3772R336-R358), [[3]](https://github.com/DeepLabCut/DeepLabCut/pull/3346/files#diff-4dbcd4272a9f0fb80775a2e54ed8d52f229695085258e5b5d0172f05870a3772L408-L429), [[4]](https://github.com/DeepLabCut/DeepLabCut/pull/3346/files#diff-4dbcd4272a9f0fb80775a2e54ed8d52f229695085258e5b5d0172f05870a3772R418-R444), [[5]](https://github.com/DeepLabCut/DeepLabCut/pull/3346/files#diff-4dbcd4272a9f0fb80775a2e54ed8d52f229695085258e5b5d0172f05870a3772R404-R409)).

Testing and reliability:

Added a new test suite tests/gui/test_auto_update.py to verify that package specs are built correctly and that the update command selection logic works as intended, including backend prioritization and fallback behavior ([tests/gui/test_auto_update.pyR1-R143](https://github.com/DeepLabCut/DeepLabCut/pull/3346/files#diff-fe6347302c05d4e806136ae254f592f3a74c323a95a79724b435dd5c0d83c75eR1-R143)).

Dependency management:

Ensured that updates to DeepLabCut via the GUI always include the [gui] extra, keeping GUI dependencies in sync and reducing the risk of mismatched versions ([deeplabcut/gui/utils.pyR239-R292](https://github.com/DeepLabCut/DeepLabCut/pull/3346/files#diff-4279538071ed35262d378e598eb69f5d2e1aced94717f42138692f0d8c718e3cR239-R292)).

Add utilities to construct package specs and installer commands (supporting uv then pip) and import shutil/sys. Update MainWindow to run update commands in sequence: store a queue of backends, start each with _start_next_update_command, accumulate attempt outputs and backend names, and retry fallbacks when one backend fails. Improve error messages and logging, adjust progress/cleanup behavior, and surface a consolidated failure dialog if no backend succeeds.

Add unit tests for deeplabcut.gui.utils functions package_specs_for_update and build_update_commands. Tests verify package_specs_for_update adds the GUI extra to 'deeplabcut', preserves other packages, and strips surrounding whitespace. Tests for build_update_commands assert backend ordering and that 'uv' is used when available, the exact command arguments (including use of sys.executable), and that a pip fallback is always present; monkeypatching of shutil.which is used to simulate installer availability.

Copilot

Pull request overview

This PR refactors the GUI auto-updater to support multiple installer backends, preferring uv when available with a pip fallback, and ensures DeepLabCut updates from the GUI always include the [gui] extra so GUI dependencies stay in sync.

Changes:

Added package_specs_for_update and build_update_commands utilities to generate update package specs (including deeplabcut[gui]) and a prioritized installer command list.
Refactored the GUI update flow to sequentially try each backend and aggregate per-backend failure output for clearer diagnostics.
Added unit tests validating package spec generation and backend command selection.

Reviewed changes

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

File	Description
`deeplabcut/gui/utils.py`	Adds helpers to build package specs (injecting `[gui]`) and generate backend-specific update commands (uv → pip).
`deeplabcut/gui/window.py`	Updates GUI auto-update execution to try backends in order and improve logging/error reporting across attempts.
`tests/gui/test_auto_update.py`	Adds tests for package spec normalization and backend command prioritization/fallback behavior.

Comments suppressed due to low confidence (1)

tests/gui/test_auto_update.py:38

The parameterization includes two identical {"uv": "/mock/bin/uv"} cases expecting the same backend order. This duplicates test work without increasing coverage; remove the redundant entry to keep the test intent clear.

        ({}, ["pip"]),
        ({"uv": "/mock/bin/uv"}, ["uv", "pip"]),
        (
            {"uv": "/mock/bin/uv"},
            ["uv", "pip"],
        ),

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Initialize _update_process_output to an empty list when tearing down the update process to avoid carrying over stale output after process deletion. Also make the GUI auto-update test skip when PySide6 is not installed by adding pytest.importorskip("PySide6") to tests/gui/test_auto_update.py, preventing failures in environments without the GUI dependency.

Copilot

Pull request overview

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

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

Add robust handling for the update QProcess to avoid races and leaks. Introduces _disconnect_update_process to safely disconnect signals, updates _drain_update_process_output to accept a process (and resolve sender()), and adds sender checks in error/finished handlers so only the current process is handled. Ensures signals are disconnected before deleteLater and prevents acting on stale or unrelated processes.

Copilot

Pull request overview

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

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

Copilot

Pull request overview

Copilot reviewed 3 out of 3 changed files in this pull request and generated no new comments.

deruyter92

Good fix! Just some minor comments and suggestions.

deruyter92 · 2026-06-03T07:51:58Z

+        if not self._start_next_update_command():
+            self._cleanup_update_process()
+            QtWidgets.QMessageBox.warning(
+                self,
+                "Update failed",
+                "No available installer backend was found.",
+            )
+


build_update_commands unconditionally appends the pip fallback so the list if never empty. This means that this code is unreachable, correct?

deruyter92 · 2026-06-03T07:56:47Z

+        if process is not self._update_process:
+            return

-    def _drain_update_process_output(self):
-        if self._update_process is None:
+        if process is None:
            return



The second condition is only met when (simulataneous) self._update_process is None AND process is None. Consider changing to:

Suggested change

if process is not self._update_process:

return

def _drain_update_process_output(self):

if self._update_process is None:

if process is None:

return

if process is None or process is not self._update_process:

return

deruyter92 · 2026-06-03T07:58:01Z

+        process = self.sender()
+        if process is not self._update_process:
+            return
+
        if self._closing:
            self._cleanup_update_process()
            return

-        if self._update_process is None:
+        if process is None:
            return


Suggested change

process = self.sender()

if process is not self._update_process:

return

if self._closing:

self._cleanup_update_process()

return

if self._update_process is None:

if process is None:

return

process = self.sender()

if process is None or process is not self._update_process:

return

if self._closing:

self._cleanup_update_process()

return

deruyter92 · 2026-06-03T07:59:47Z

-            if output:
-                self.logger.error(output)
+
+            self._cleanup_update_process()


calls _progress_bar.hide() again. Maybe better to remove in one of both places to avoid confusion.

deruyter92 · 2026-06-03T08:07:54Z

+        self._disconnect_update_process(process)
+        self._update_process.deleteLater()


Currently this only works because the guard (process is not self._update_process → return). Safer is process.deleteLater() like in _on_update_process_finished:

Suggested change

self._disconnect_update_process(process)

self._update_process.deleteLater()

self._disconnect_update_process(process)

process.deleteLater()

deruyter92 · 2026-06-03T08:23:05Z

+def package_specs_for_update(packages: list[str]) -> list[str]:
+    """Return package specs to install for GUI updates.
+
+    DeepLabCut itself should be updated with the GUI extra so GUI dependencies
+    are kept in sync.
+    """
+    specs = []
+
+    for package in packages:
+        normalized = package.strip()
+
+        if normalized == "deeplabcut":
+            specs.append("deeplabcut[gui]")
+        else:
+            specs.append(normalized)
+
+    return specs
+
+
+def build_update_commands(packages: list[str]) -> list[tuple[str, str, list[str]]]:
+    """Build installer commands, ordered from preferred to fallback.
+
+    Returns tuples of:
+
+        (backend_name, program, arguments)
+
+    The order is:
+      1. uv, if available
+      2. current-interpreter pip fallback
+    """


Small nitpick:

These functions seem designed as a generic public function for building normalized package specs install commands, but in practice they only work for very specific input (e.g. case-sensitive exact match for "deeplabcut"). Also they are specifically intended for the auto-update flow, not general GUI utilities. Maybe make these functions private or document this somehow, e.g.:

Suggested change

def package_specs_for_update(packages: list[str]) -> list[str]:

"""Return package specs to install for GUI updates.

DeepLabCut itself should be updated with the GUI extra so GUI dependencies

are kept in sync.

"""

specs = []

for package in packages:

normalized = package.strip()

if normalized == "deeplabcut":

specs.append("deeplabcut[gui]")

else:

specs.append(normalized)

return specs

def build_update_commands(packages: list[str]) -> list[tuple[str, str, list[str]]]:

"""Build installer commands, ordered from preferred to fallback.

Returns tuples of:

(backend_name, program, arguments)

The order is:

1. uv, if available

2. current-interpreter pip fallback

"""

DLCPackage: TypeAlias = Literal["deeplabcut", "napari-deeplabcut"]

def _package_specs_for_update(packages: list[DLCPackage]) -> list[str]:

"""Return package specs to install for GUI updates.

DeepLabCut itself should be updated with the GUI extra so GUI dependencies

are kept in sync.

"""

specs = []

for package in packages:

normalized = package.strip()

if normalized == "deeplabcut":

specs.append("deeplabcut[gui]")

else:

specs.append(normalized)

return specs

def _build_update_commands(packages: list[DLCPackage]) -> list[tuple[str, str, list[str]]]:

"""Build installer commands, ordered from preferred to fallback.

Returns tuples of:

(backend_name, program, arguments)

The order is:

1. uv, if available

2. current-interpreter pip fallback

"""

C-Achard added 2 commits May 26, 2026 16:32

C-Achard requested a review from Copilot May 26, 2026 14:35

C-Achard self-assigned this May 26, 2026

C-Achard linked an issue May 26, 2026 that may be closed by this pull request

Dependency mismatch when upgrading from rc14 to 3.0.0 (pydantic, napari) #3343

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2 tasks

C-Achard added enhancement New feature or request GUI issues relating to GUI labels May 26, 2026

Copilot started reviewing on behalf of C-Achard May 26, 2026 14:36 View session

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Comment thread tests/gui/test_auto_update.py

Comment thread deeplabcut/gui/window.py Outdated

C-Achard requested a review from Copilot May 27, 2026 07:57

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Comment thread deeplabcut/gui/window.py Outdated

Comment thread tests/gui/test_auto_update.py Outdated

C-Achard and others added 2 commits May 27, 2026 16:37

Remove duplicate test

faeb05d

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C-Achard requested a review from Copilot May 28, 2026 09:09

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Comment thread tests/gui/test_auto_update.py

Comment thread deeplabcut/gui/window.py

Separate failed output for update retries

5298ced

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C-Achard requested a review from Copilot May 28, 2026 09:18

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C-Achard marked this pull request as ready for review May 28, 2026 13:41

Update window.py

defdc96

C-Achard requested a review from deruyter92 May 28, 2026 13:42

deruyter92 approved these changes Jun 3, 2026

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		self._disconnect_update_process(process)
		self._update_process.deleteLater()

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C-Achard commented May 26, 2026

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