Typing: Fully type 5 more files #6361

Carreau · 2023-10-22T07:38:14Z

This updates a number of files to be fully typed,

I'll note that some of the dynamic nature of napari (like all the proxy stuff) cannot be well types as we can't express the typing informations yet.

I keep this small for quick/easy review, and hopping to decrease the number fo conflicts.

Carreau · 2023-11-08T10:50:15Z

restarting test.

codecov · 2023-11-08T15:07:08Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (7405c53) 92.23% compared to head (c03d3e3) 92.20%.
Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #6361      +/-   ##
==========================================
- Coverage   92.23%   92.20%   -0.03%     
==========================================
  Files         601      601              
  Lines       53231    53398     +167     
==========================================
+ Hits        49097    49236     +139     
- Misses       4134     4162      +28

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andy-sweet · 2023-11-21T19:01:28Z

I merged #6356, so you should be able to merge in its commit from main, resolve conflicts, then mark this as ready for review.

Carreau · 2023-11-21T19:13:58Z

I merged #6356, so you should be able to merge in its commit from main, resolve conflicts, then mark this as ready for review.

Thanks, I rebased, as there are a few PRs on top of this one, and merging tend to make things even more complicated.

brisvag · 2023-11-22T09:08:27Z

napari/_vispy/utils/gl.py

        if dtype_ == np.uint16 and dtype.itemsize > 2:
-            dtype_ = np.float32
+            dtype_ = np.float32  # type: ignore [assignment]


why is this necessary btw?

Imho a problem in mypy type inference:

error: Incompatible types in assignment (expression has type "type[floating[Any]]", variable has type "type[dtype[Any]]") [assignment]

I tried various combinaison above, to no success, and AFAIC, I dont se why X[floating[Y]] can't be assinged to X[dtype[Y]]

wait, maybe I can try a union. Also maybe we can refactor the try-except with dtype.kind in 'ifub' ?

Ok, find a way to do it with a union. That does not get rid of the cast, but it's better. thanks

fix types of utils/naming type napari/utils/info.py update types in napari/utils/_proxies.py fully type napari/layers/utils/plane.py fully type napari/_vispy/utils/gl.py typalias refix napari/utils/naming.py test typing extension on 3.8/3.9 typo fix type remove double define to str as we can't subscript on 3.8 fix types

andy-sweet

Sorry this has been approved and open for a while. I almost just clicked the merge button, but I noticed a couple of things that didn't make sense. Happy to expedite this getting merged to unblock other PRs once those questions are resolved.

napari/_vispy/utils/gl.py

andy-sweet · 2023-12-01T17:23:57Z

pyproject.toml

@@ -370,6 +370,7 @@ module = [
    "napari.layers.utils.interactivity_utils",
    "napari.layers.vectors._vector_utils",
    "napari.resources._icons",
+    "napari.utils.color",


Why was this added here?

Typing can have ripple effects, as if mypy sometime achieve to infer further it finds issues. It is likely to be fixed in one of my subsequents PRs relying on this one that are drafts.

In particular in this case:

(many of....): error: Variable "napari._pydantic_compat.Color" is not valid as a type [valid-type] (many of....): note: See https://mypy.readthedocs.io/en/stable/common_issues.html#variables-vs-type-aliases ... napari/utils/theme.py:141: error: Item Color? of str | Color? has no attribute "startswith" [union-attr] napari/utils/theme.py:142: error: Item Color? of str | Color? has no attribute "lstrip" [union-attr]

Thanks for clarifying!

napari/_vispy/utils/gl.py

andy-sweet

This has been approved for a while, is very safe, and blocks other PRs, so I'm going to merge this now instead of doing the usual ready to merge + 24 hours.

Carreau · 2023-12-04T16:58:12Z

Thanks

…

On Mon, Dec 4, 2023 at 17:57 Andy Sweet ***@***.***> wrote: Merged #6361 <#6361> into main. — Reply to this email directly, view it on GitHub <#6361 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACR5TY7WMIYUCBALIUXDRDYHX6ILAVCNFSM6AAAAAA6KW2OD6VHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJRGE2DCOJSGEZDOMY> . You are receiving this because you authored the thread.Message ID: ***@***.***>

Carreau · 2023-12-05T08:03:11Z

Also from this comment I assumed that we would hold any other merge, so should this have been merged ?

@Czaki ?

Czaki · 2023-12-05T08:12:45Z

This PR is not touching files that I'm waiting for someone to review.

But every merged PR with typing increases hardness of cherry-picking, so increases some probability that some bug will be introduced.

andy-sweet · 2023-12-05T16:46:56Z

This PR is not touching files that I'm waiting for someone to review.

But every merged PR with typing increases hardness of cherry-picking, so increases some probability that some bug will be introduced.

Sorry! I didn't see that message. Will hold off on merges over the next week or so, or until the release seems to have stabilized.

Carreau · 2023-12-05T16:58:50Z

No worries, it is also for me to understand what need to be done, as right now I feel 0.4.19 is starting to seriously impair work on the main branch. So maybe we need everyone to focus on 0.4.19 and push it over the line.

Czaki · 2023-12-05T20:04:39Z

I have hope that only one PR is left for 0.4.19 #6439. But it touches fragile part of code (rendering). And do not have big number of reviewing core-devs

Carreau · 2023-12-05T21:08:53Z

I still see a few things tagged 0.4.19, 4prs, 2 PRs drafts and 2 issues: https://github.com/napari/napari/milestone/38, should they be retagged ?

Czaki · 2023-12-05T22:51:43Z

2 of these PR are against 0.4.19, so no cherry-picking problems. Two drafts, are an alternative solution for a single problem that requires #6439 to be merged. Then it could be quickly solved.

* main: (80 commits) Check in LabelColormap that fewer than 2**16 colors are requested (napari#6540) Fix label color shuffling by also updating colormap size (napari#6460) Add `_block_refresh()` to layers (napari#6525) MNT: Use `partial` in samples menu to avoid leaking (napari#6538) Update performance and reduce memory usage for big Labels layer in direct color mode (napari#6439) Reset single step and decimals on reset range slider in popup (napari#6523) Add copy operator to fix memory benchmarks (napari#6530) Restore quit shortcut (napari#6526) Fix problem with invalidate cache (napari#6520) [pre-commit.ci] pre-commit autoupdate (napari#6505) Pass key event from Main window to our internal mechanism (napari#6419) Typing: Fully type 5 more files (napari#6361) Do not use native dialog for reset shortcuts (napari#6493) Use views rather than CPU-based hashing for 8- and 16-bit Labels data (napari#6467) Add import lint back to CI (napari#6506) Type napari.layers.image helper sub-modules (napari#6499) Bugfix: ensure gamma and opacity are floats (napari#6498) FIX: Remove `None` default from `_remove_dock_widget` (napari#6481) Add testing_extra and optional dependencies when creating constraints (napari#6487) Run test suite with optional dependencies and fix tests when `triangle` is installed (napari#6488) ...

Carreau added maintenance PR with maintance changes, typing PR that focus on typing improvement labels Oct 22, 2023

github-actions bot added the qt Relates to qt label Oct 22, 2023

Carreau force-pushed the more-typing-III branch 4 times, most recently from 2372fb3 to 84dad07 Compare October 22, 2023 10:44

Carreau force-pushed the more-typing-III branch from cb45464 to 75a2cf3 Compare November 6, 2023 18:28

Carreau force-pushed the more-typing-III branch from 15bbf83 to db2143d Compare November 8, 2023 14:15

Carreau force-pushed the more-typing-III branch 2 times, most recently from 823949c to 252dbde Compare November 13, 2023 10:13

Carreau force-pushed the more-typing-III branch 4 times, most recently from 21e6dcf to e328c25 Compare November 21, 2023 14:14

Carreau force-pushed the more-typing-III branch from e328c25 to 092f7e7 Compare November 21, 2023 19:07

Carreau marked this pull request as ready for review November 21, 2023 19:11

Carreau changed the title ~~Typing: Even more typing (on top of #6352 and #6356)~~ Typing: Fully type 5 more files Nov 21, 2023

Carreau added this to the 0.5 milestone Nov 21, 2023

brisvag approved these changes Nov 22, 2023

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Carreau force-pushed the more-typing-III branch from 092f7e7 to be9cf75 Compare November 22, 2023 10:36

Carreau force-pushed the more-typing-III branch from be9cf75 to afaeb95 Compare November 28, 2023 14:09

andy-sweet reviewed Dec 1, 2023

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Carreau commented Dec 3, 2023

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andy-sweet approved these changes Dec 4, 2023

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andy-sweet merged commit 6e0d23a into napari:main Dec 4, 2023
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andy-sweet modified the milestones: 0.5, 0.5.0 Dec 4, 2023

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Typing: Fully type 5 more files #6361

Typing: Fully type 5 more files #6361

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Typing: Fully type 5 more files #6361

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