add `uv` backend #172

jaimergp · 2025-08-11T09:54:49Z

This should result in (way) faster plugin installs.

codecov · 2025-08-11T10:29:02Z

Codecov Report

❌ Patch coverage is 96.38554% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 94.28%. Comparing base (b3908f6) to head (0e44be1).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
...napari_plugin_manager/base_qt_package_installer.py	93.87%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #172      +/-   ##
==========================================
+ Coverage   94.16%   94.28%   +0.12%     
==========================================
  Files          14       14              
  Lines        2159     2222      +63     
==========================================
+ Hits         2033     2095      +62     
- Misses        126      127       +1

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brisvag · 2025-08-29T09:57:17Z

Uhhhh I didn't see this, awesome!

brisvag

One thing I'm not clear on: uv is now a dependency, in what case would it be not available?

jaimergp · 2025-08-29T10:20:53Z

One thing I'm not clear on: uv is now a dependency, in what case would it be not available?

Almost never, but if the user manages to break their environment by removing uv for some reason, we handle that with a fallback. Also we need to note that depending on uv adds it to the napari env, which means that our uv would shadow the system one (if present) when the virtual/conda environment is active, and I'm not sure we are 100% onboard with that.

Czaki

@jaimergp Could you make a separate PR with rename enum from PIP to PIPI?

We may merge it fast and make this diff much cleaner.

src/napari_plugin_manager/base_qt_package_installer.py

Czaki · 2025-08-29T11:53:23Z

src/napari_plugin_manager/qt_package_installer.py

+    def constraints() -> Sequence[str]:
+        """
+        Version constraints to limit unwanted changes in installation.
+        """
+        return [f'napari=={_napari_version}']


The uv pip install --upgrade upgrade not only itself but also all its dependencies. But do not think about other packages installed in the environment.

So if a package depends on NumPy and Numba is installed, having only pinned napari means that the upgrade may end with a non-working environment, as import of Numba crashes.

Hm, do you think we could use --upgrade-package instead or a different --resolution strategy?

$ uv pip install --help [...] -U, --upgrade Allow package upgrades, ignoring pinned versions in any existing output file. Implies `--refresh` -P, --upgrade-package <UPGRADE_PACKAGE> Allow upgrades for a specific package, ignoring pinned versions in any existing output file. Implies `--refresh-package` --resolution <RESOLUTION> The strategy to use when selecting between the different compatible versions for a given package requirement [env: UV_RESOLUTION=] [possible values: highest, lowest, lowest-direct] [...]

And for clarity, does this affect pip install --upgrade too (without uv)?

Or is the suggestion to extend the constraints() list with all the dependencies of the currently installed napari version, and possibly all the plugins? Something like:

constraints = [f"napari=={napari.__version__}, *napari_plugins(exact_version=True)] for constraint in constraints: constraints.extend(get_dependencies(name_of(constraint), with_version_ranges=True)

As I remember, this is what Charlie advertised to me to use: --upgrade-package.

And for clarity, does this affect pip install --upgrade too (without uv)?

As far as I know, yes. Pip, do not update all dependencies of updated packages if the lower bound is below the currently installed version. (same for --upgrade-package).

Or is the suggestion to extend the constraints() list with all the dependencies of the currently installed napari version, and possibly all the plugins? Something like:

No. As it may block many updates when a plugin requires a newer version of its dependency.

As I remember, this is what Charlie advertised to me to use: --upgrade-package.

Ok, I'll change to using that flag!

As far as I know, yes. Pip, do not update all dependencies of updated packages if the lower bound is below the currently installed version. (same for --upgrade-package).

This is what I can find in the help:

-U, --upgrade Upgrade all specified packages to the newest available version. The handling of dependencies depends on the upgrade-strategy used. --upgrade-strategy <upgrade_strategy> Determines how dependency upgrading should be handled [default: only-if- needed]. "eager" - dependencies are upgraded regardless of whether the currently installed version satisfies the requirements of the upgraded package(s). "only-if-needed" - are upgraded only when they do not satisfy the requirements of the upgraded package(s).

@Czaki any word here?

src/napari_plugin_manager/qt_package_installer.py

src/napari_plugin_manager/base_qt_package_installer.py

psobolewskiPhD · 2025-08-29T13:17:56Z

Also we need to note that depending on uv adds it to the napari env, which means that our uv would shadow the system one (if present) when the virtual/conda environment is active, and I'm not sure we are 100% onboard with that.

So if someone had a system uv and they were used to using various uvx things then suddenly they'd be using uv from napari rather than their system uv? Would this create issues? Is there a way we could use uv programmatically, but not actually expose the binary?

jaimergp · 2025-08-29T14:09:21Z

So if someone had a system uv and they were used to using various uvx things then suddenly they'd be using uv from napari rather than their system uv?

In a shell with the napari env active, or in the napari console, yes.

Is there a way we could use uv programmatically, but not actually expose the binary?

I need to look into how it is packaged, but my intuition tells me that we would only be able to do that by not depending on it in pyproject.toml, but handling the download/install ourselves (e.g. an internal environment?) or by vendoring it (ew).

Co-authored-by: Grzegorz Bokota <[email protected]>

jaimergp · 2025-08-29T14:40:56Z

Could you make a separate PR with rename enum from PIP to PIPI?

We amy merge it fast and make this diff much cleaner.

See #176. Once that's in I'll rebase here.

dalthviz · 2025-09-29T18:07:03Z

Hi there, so gave this a check on Windows and, as long as you install uv on the napari env, seems like things are working as expected 👍 However, just to be sure, the idea here is to always have uv available from the napari env (making it a dependency), right?

jaimergp · 2025-10-02T08:27:11Z

the idea here is to always have uv available from the napari env (making it a dependency), right?

Yes, it's added as a dependency in pyproject.toml.

willingc

Thanks @jaimergp. I think we should add pixi as well since it creates a nicer experience when using GPUs. It doesn't need to be this PR. 😄

Czaki · 2025-10-02T14:26:13Z

If we add uv to dependencies, why keep the pip backend?

jaimergp · 2025-10-02T15:07:38Z

I'd like to keep it for a while in case it helps with debugging, workarounds, and other annoying tasks in case uv reveals some rough edges we didn't know about.

Czaki · 2025-10-02T15:09:54Z

I check some uv documentation. I'm not a fan of adding it as a default dependency, as it will shadow the global one and need separate updates.

jaimergp · 2025-10-02T15:12:12Z

I think we should add pixi as well since it creates a nicer experience when using GPUs.

I'd like to do that too, but the inability to specify an arbitrary environment location will make integration with the installation root problematic. I can think of hacky workarounds (e.g. having an empty project folder somewhere where we maintain the necessary lockfiles and then using pixi-install-to-prefix to link the packages)

jaimergp · 2025-10-02T15:14:01Z

I check some uv documentation. I'm not a fan of adding it as a default dependency, as it will shadow the global one and need separate updates.

We can go back to the behaviour of only using the uv backend if it's in PATH, or auto-install it on first use to a private, non-PATH location.

jaimergp · 2025-10-02T15:27:41Z

Added it as an extra so folks can install it with napari-plugin-manager[uv].

Czaki · 2025-10-02T16:29:59Z

Added it as an extra so folks can install it with napari-plugin-manager[uv].

You need to add it also to testing dependencies.

Czaki

Looks really good. A few small questions.

Czaki · 2025-10-07T10:41:09Z

tox.ini


 deps =
    napari_repo: git+https://github.com/napari/napari.git
-extras = testing


As there is no skip for uv tests I prefer to add uv to testing extras.

Using napari-plugin-manager[uv] in testing extras.

Czaki · 2025-10-07T10:51:10Z

src/napari_plugin_manager/qt_package_installer.py

+        """
+        Version constraints to limit unwanted changes in installation.
+        """
+        return [f'napari=={_napari_version}']


Hm. So the only risk for now is if the environment has Numba installed and the plugin needs a NumPy newer than the installed one. But it is a problem as well for pip.

Czaki · 2025-10-07T10:54:49Z

src/napari_plugin_manager/_tests/test_installer_process.py

+        if tool == NapariPipInstallerTool
+        else '_python_executable',
        lambda *a: 'not-a-real-executable',


Why we can not unify this?

Czaki · 2025-10-07T10:55:13Z

src/napari_plugin_manager/_tests/test_installer_process.py

+    if tool == NapariPipInstallerTool:
+        monkeypatch.setattr(
+            NapariPipInstallerTool,
+            'origins',
+            ('https://pypi.org/simple',),
+        )


Why is this if is needed? Why we cannot uify this?

jaimergp added 2 commits August 11, 2025 11:54

add uv backend

7b66870

pre-commit

bc35f59

brisvag reviewed Aug 29, 2025

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Czaki reviewed Aug 29, 2025

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jaimergp and others added 2 commits August 29, 2025 16:20

Apply suggestions from code review

ab0e8e1

Co-authored-by: Grzegorz Bokota <[email protected]>

default to uv

c276e31

jaimergp mentioned this pull request Aug 29, 2025

Rename PIP enums to PYPI #176

Merged

jaimergp mentioned this pull request Aug 30, 2025

Add missing type hints #177

Merged

jaimergp added 4 commits August 30, 2025 12:45

Merge branch 'main' of github.com:napari/napari-plugin-manager into uv

273c11d

Merge branch 'main' into uv

f37f9e5

adjust return types

7854098

use --upgrade-package in uv

4bef3e8

jaimergp requested a review from Czaki September 2, 2025 08:28

willingc approved these changes Oct 2, 2025

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Only use uv backend if uv is in PATH

de2bc7c

Prefer uv installed in the env

0e44be1

Czaki reviewed Oct 7, 2025

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add uv backend #172

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add uv backend #172

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add `uv` backend #172

add `uv` backend #172

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