Update instruction how to update contraints files #672

Czaki · 2025-04-14T08:16:29Z

References and relevant issues

closes #670

Description

After the most recent updates of constraints update, we could simplify this instrucition.

cnstt · 2025-04-14T08:48:56Z

docs/developers/coredev/release.md


 ```bash
-uv pip compile --python-version 3.11 --upgrade --output-file resources/constraints/constraints_py3.11_docs.txt pyproject.toml resources/constraints/version_denylist.txt resources/constraints/version_denylist_examples.txt ../docs/requirements.txt resources/constraints/pydantic_le_2.txt --extra pyqt5 --extra pyqt6 --extra pyside2 --extra pyside6_experimental --extra testing --extra testing_extra --extra optional


Shouldn't resources/constraints/version_denylist_examples.txt be kept (as in napari/napari#7788 ) ?

I have changed from docs to normal constraints, as docs are still on python 3.10.

Once we understand the source of problems in #7714 we may get docs constraints here.

I think this is now resolved as napari/napari#7714 is merged! Can we add this in here?

@melissawm I think bumping to 3.12 makes sense now that #7714 has landed.

docs/developers/coredev/release.md

TimMonko

Works locally now (with my comment), thanks!

TimMonko · 2025-04-14T16:50:42Z

docs/developers/coredev/release.md


 ```bash
-uv pip compile --python-version 3.11 --upgrade --output-file resources/constraints/constraints_py3.11_docs.txt pyproject.toml resources/constraints/version_denylist.txt resources/constraints/version_denylist_examples.txt ../docs/requirements.txt resources/constraints/pydantic_le_2.txt --extra pyqt5 --extra pyqt6 --extra pyside2 --extra pyside6_experimental --extra testing --extra testing_extra --extra optional
+uv pip compile --python-version 3.12 --output-file resources/constraints/constraints_py3.12.txt pyproject.toml resources/constraints/version_denylist.txt --extra pyqt6 --extra pyside2 --extra pyside6_experimental --extra testing --extra testing_extra --extra optional


this updates 3.12, we want to update docs though, right? I think this does that

Suggested change

uv pip compile --python-version 3.12 --output-file resources/constraints/constraints_py3.12.txt pyproject.toml resources/constraints/version_denylist.txt --extra pyqt6 --extra pyside2 --extra pyside6_experimental --extra testing --extra testing_extra --extra optional

uv pip compile --python-version 3.10 --output-file resources/constraints/constraints_py3.10_docs.txt pyproject.toml resources/constraints/version_denylist.txt --extra pyqt6 --extra pyside2 --extra pyside6_experimental --extra testing --extra testing_extra --extra optional

We can now use 3.12 here 🎉

psobolewskiPhD · 2025-05-13T23:06:08Z

@napari-bot make slimgallery

willingc · 2025-05-24T18:49:20Z

Team, let's try to land this doc pr this week.

Co-authored-by: Constantin Aronssohn <[email protected]>

Resolved by napari/napari #7714

willingc · 2025-07-18T03:33:21Z

@melissawm This worked fine for creating the constraint file for 3.12.

Running make docs with 3.12.11 threw a traceback when embedding hyperlinks:

embedding documentation hyperlinks...

Traceback (most recent call last):
  File "/Users/willingc/Code/repos-napari/napari-docs/.venv/lib/python3.12/site-packages/sphinx/events.py", line 98, in emit
    results.append(listener.handler(self.app, *args))
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/willingc/Code/repos-napari/napari-docs/.venv/lib/python3.12/site-packages/sphinx_gallery/docs_resolv.py", line 502, in embed_code_links
    _embed_code_links(app, gallery_conf, gallery_dir)
  File "/Users/willingc/Code/repos-napari/napari-docs/.venv/lib/python3.12/site-packages/sphinx_gallery/docs_resolv.py", line 341, in _embed_code_links
    doc_resolvers[this_module] = SphinxDocLinkResolver(
                                 ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/willingc/Code/repos-napari/napari-docs/.venv/lib/python3.12/site-packages/sphinx_gallery/docs_resolv.py", line 166, in __init__
    index = get_data(index_url, gallery_dir)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/willingc/Code/repos-napari/napari-docs/.venv/lib/python3.12/site-packages/sphinx_gallery/docs_resolv.py", line 50, in get_data
    search_index = shelve.open(cached_file)
                   ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/[email protected]/3.12.11/Frameworks/Python.framework/Versions/3.12/lib/python3.12/shelve.py", line 243, in open
    return DbfilenameShelf(filename, flag, protocol, writeback)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/[email protected]/3.12.11/Frameworks/Python.framework/Versions/3.12/lib/python3.12/shelve.py", line 227, in __init__
    Shelf.__init__(self, dbm.open(filename, flag), protocol, writeback)
                         ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/[email protected]/3.12.11/Frameworks/Python.framework/Versions/3.12/lib/python3.12/dbm/__init__.py", line 89, in open
    raise error[0]("db type could not be determined")
dbm.error: db type could not be determined

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/willingc/Code/repos-napari/napari-docs/.venv/lib/python3.12/site-packages/sphinx/cmd/build.py", line 337, in build_main
    app.build(args.force_all, args.filenames)
  File "/Users/willingc/Code/repos-napari/napari-docs/.venv/lib/python3.12/site-packages/sphinx/application.py", line 380, in build
    self.events.emit('build-finished', None)
  File "/Users/willingc/Code/repos-napari/napari-docs/.venv/lib/python3.12/site-packages/sphinx/events.py", line 109, in emit
    raise ExtensionError(
sphinx.errors.ExtensionError: Handler <function embed_code_links at 0x104129440> for event 'build-finished' threw an exception (exception: db type could not be determined)

Extension error (sphinx_gallery.docs_resolv):
Handler <function embed_code_links at 0x104129440> for event 'build-finished' threw an exception (exception: db type could not be determined)
make: *** [docs] Error 2

napari-docs on  update_constraints [$] via  v3.12.11 (napari-docs) took 3m26s

There were also several OMP: Info #276: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead. thrown on some notebook executions.

Reran after installing optional-numba. Got the spinning ball of doom after hitting the first OMP output on my M1 mac.

psobolewskiPhD · 2025-07-18T23:25:03Z

I don't have 3.12 handy right now, but ran in my 3.13 docs env.
make docs completed, but with some seg faults on exit -- alas, i sometimes see those when using and exiting napari.
Which triangulation backend do you have @willingc ? I'm running fastest available and bermuda
I dont see OMP warnings.

edit: note: make html is the full build command.

psobolewskiPhD · 2025-07-18T23:25:57Z

napari info:

napari: 0.6.2rc1.dev71+g0294fad15
Platform: macOS-14.5-arm64-arm-64bit-Mach-O
System: MacOS 14.5
Python: 3.13.3 | packaged by conda-forge | (main, Apr 14 2025, 20:44:30) [Clang 18.1.8 ]
Qt: 6.9.0
PyQt6: 6.9.0
NumPy: 2.2.6
SciPy: 1.15.3
Dask: 2025.5.1
VisPy: 0.15.2
magicgui: 0.10.0
superqt: 0.7.3
in-n-out: 0.2.1
app-model: 0.3.1
psygnal: 0.13.0
npe2: 0.7.9
pydantic: 2.11.5

OpenGL:
  - PyOpenGL: 3.1.9
  - GL version:  2.1 Metal - 88.1
  - MAX_TEXTURE_SIZE: 16384
  - GL_MAX_3D_TEXTURE_SIZE: 2048

Screens:
  - screen 1: resolution 1680x1050, scale 2.0

Optional:
  - numba: 0.61.2
  - triangle: 20250106
  - napari-plugin-manager: 0.1.6
  - bermuda: 0.1.4
  - PartSegCore not installed

Experimental Settings:
  - Async: False
  - Autoswap buffers: False
  - Triangulation backend: Fastest available

Settings path:
  - /Users/piotrsobolewski/Library/Application Support/napari/napari-dev_a1eb8b76ba95fa16ad06e26097b46b8455dfbf0b/settings.yaml

Launch command:
  - /Users/piotrsobolewski/Dev/miniforge3/envs/napari-dev/bin/napari --info

Plugins:
  - napari-animation: 0.0.8 (2 contributions)
  - napari-skimage: 0.5.0 (64 contributions)
  - napari: 0.6.2.dev11+g6371fffe9 (84 contributions)
  - napari-tiff: 0.1.5.dev1+gebf2362 (2 contributions)
  - napari-svg: 0.2.1 (2 contributions)
  - napari-console: 0.1.3 (0 contributions)

Czaki · 2025-07-19T13:37:19Z

What is currently blocking?

psobolewskiPhD · 2025-07-19T14:10:45Z

I think nothing, per se.
I think Carol just tried to build the docs using py312 constraints and they crashed, but I think making the constraints worked.
But building docs with py312 is a different issue & Pr.

willingc · 2025-07-20T18:01:12Z

Let's land this. I was able to clean and regenerate. All seems well.

Update instruction how to update contraints files

eaee6d2

github-actions bot added the documentation Improvements or additions to documentation label Apr 14, 2025

github-actions bot assigned Czaki Apr 14, 2025

cnstt previously requested changes Apr 14, 2025

View reviewed changes

TimMonko approved these changes Apr 14, 2025

View reviewed changes

TimMonko reviewed Apr 14, 2025

View reviewed changes

psobolewskiPhD added 2 commits April 27, 2025 17:57

Merge branch 'main' into update_constraints

d4ecade

Merge branch 'main' into update_constraints

a07e8e0

willingc and others added 2 commits July 17, 2025 13:43

Update docs/developers/coredev/release.md

b7cae9a

Co-authored-by: Constantin Aronssohn <[email protected]>

Update docs/developers/coredev/release.md

f223b90

Co-authored-by: Constantin Aronssohn <[email protected]>

willingc added this to the 0.6.3 milestone Jul 17, 2025

willingc approved these changes Jul 20, 2025

View reviewed changes

willingc merged commit 80e18d1 into napari:main Jul 20, 2025
8 checks passed


		```bash
		uv pip compile --python-version 3.11 --upgrade --output-file resources/constraints/constraints_py3.11_docs.txt pyproject.toml resources/constraints/version_denylist.txt resources/constraints/version_denylist_examples.txt ../docs/requirements.txt resources/constraints/pydantic_le_2.txt --extra pyqt5 --extra pyqt6 --extra pyside2 --extra pyside6_experimental --extra testing --extra testing_extra --extra optional

	uv pip compile --python-version 3.12 --output-file resources/constraints/constraints_py3.12.txt pyproject.toml resources/constraints/version_denylist.txt --extra pyqt6 --extra pyside2 --extra pyside6_experimental --extra testing --extra testing_extra --extra optional
	uv pip compile --python-version 3.10 --output-file resources/constraints/constraints_py3.10_docs.txt pyproject.toml resources/constraints/version_denylist.txt --extra pyqt6 --extra pyside2 --extra pyside6_experimental --extra testing --extra testing_extra --extra optional

Update instruction how to update contraints files #672

Update instruction how to update contraints files #672

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Czaki commented Apr 14, 2025

References and relevant issues

Description

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