Upgrade scikit-image to v0.19.1 by oeway · Pull Request #2005 · pyodide/pyodide

oeway · 2021-11-28T18:23:30Z

Description

This PR upgrade the scikit-image package to v0.18.3.

Checklists

Add a CHANGELOG entry

rth · 2021-11-29T07:41:01Z

The blocker on updating scikit-image (and scikit-learn) was the outdated version of scipy we have #1464

What we could try, for instance, is to install scipy 0.17.1 locally with this version of scikit-image, see what test fails (pytest --pyargs skimage) and add backports for those if possible.

rth · 2022-01-03T22:09:03Z

I synced with main which should now have Scipy 1.7.3 thanks to Hood. Let's see if it builds now.

rth · 2022-01-04T00:07:11Z

skimage/_shared/geometry.c:645:10: fatal error: 'omp.h' file not found
#include <omp.h>
         ^~~~~~~
1 warning and 1 error generated

looks like some patches (or possibly env variables) to avoid building with OpenMP are still needed.

rth · 2022-01-04T21:26:59Z

pyodide-build/pyodide_build/buildpkg.py

+            "PYODIDE_ROOT",
+            "PYTHONINCLUDE",
+            "NUMPY_LIB",
+            "PYODIDE_PACKAGE_ABI",


It turns out the failure was because the fix I contributed upstream to scikit-image checked for the PYODIDE_PACKAGE_ABI variable, however, we deprecated it in favor of the PYODIDE. Re-adding that variable should fix the build.

It's nice that #2053 made it more explicit which environment variables we are passing down, but it does lead to some pain working out what is going on.

Agreed, I like that it's explicit now.

ryanking13 · 2022-01-05T00:23:15Z

docs/project/changelog.md


 ### packages

+- {{ Update }} Upgrade `scikit-image` to 0.19.1


Suggested change

- {{ Update }} Upgrade `scikit-image` to 0.19.1

- {{ Enhancement }} Upgrade `scikit-image` to 0.19.1

It looks like we are using enhancement badge for package update

Maybe it would make more sense to change them all to Update?

I agree. And I think we better rename Update tag to Upgrade or Version Up?

I agree we should indeed improve the changelog, I think it's simpler to just have a list, rather than an entry per package. Of course, major or long-awaited ones such as scipy still deserve their own changelog. For the rest I would rather spend time on some UI to list packages #977

hoodmane · 2022-01-05T00:46:31Z

Build failed with:

skimage/feature/brief_pythran.cpp:1:10: fatal error: 'pythonic/core.hpp' file not found
#include <pythonic/core.hpp>

rth · 2022-01-05T11:50:07Z

Build should be OK now.

An issue is that since 2019 scikit-image has a hard dependency on tifffile which itself depends on imagecodecs which has around 25 codecs dependencies. Currently patching to avoid tifffile import, which means that TIFF format won't work.

Another issue is that Chrome tests for scikit-image timeout though I cannot reproduce this locally.

rth · 2022-01-06T22:04:34Z

As far as I can tell it times out because scikit-image is quite large (23MB) and takes a while to load in CI. Locally it doesn't happen because of more CPU resources. This is in part due to it bundling image examples for skimage/data/ for around 7.6MB which will also be incompressible. So for now I'm going to skip Chrome as it was done before. A medium-term solution should be to add some mechanism to unvendor data files as a separate package (as we are doing for tests), possibly with some regex in meta.yaml.

oeway · 2022-01-07T08:35:40Z

@rth Great! thanks for taking care of this!

oeway added 3 commits November 27, 2021 22:19

Upgrade scikit-image to 0.18.3

375d515

Upgrade scikit-image to 0.18.3

60af7ae

Update changelog

312d940

rth mentioned this pull request Jan 3, 2022

Update to Scipy 1.7.3 #2065

Merged

Merge remote-tracking branch 'upstream/main' into upgrade-scikit-image

3750c6f

Re-add PYODIDE_PACKAGE_ABI to the env variables passed to setup.py

449bb03

rth reviewed Jan 4, 2022

View reviewed changes

rth added 3 commits January 4, 2022 22:29

Re-enable scikit-image tests in Chrome

de67a14

Make tifffile an optional dependency

937beac

Update to scikit-image 0.19.1

1357057

rth changed the title ~~Upgrade scikit-image to v0.18.3~~ Upgrade scikit-image to v0.19.1 Jan 4, 2022

rth marked this pull request as ready for review January 4, 2022 23:33

ryanking13 reviewed Jan 5, 2022

View reviewed changes

Add pythran to build dependencies

205f686

Skip scikit-image tests in CI

811f6a4

rth merged commit 4602ccf into pyodide:main Jan 6, 2022

ryanking13 mentioned this pull request Jun 23, 2022

PKG Add libtiff #2762

Merged

2 tasks

	- {{ Update }} Upgrade `scikit-image` to 0.19.1
	- {{ Enhancement }} Upgrade `scikit-image` to 0.19.1

Uh oh!

Conversation

oeway commented Nov 28, 2021 • edited by rth Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Description

Checklists

Uh oh!

rth commented Nov 29, 2021 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

rth commented Jan 3, 2022

Uh oh!

rth commented Jan 4, 2022

Uh oh!

rth Jan 4, 2022

Choose a reason for hiding this comment

Uh oh!

hoodmane Jan 4, 2022

Choose a reason for hiding this comment

Uh oh!

rth Jan 4, 2022

Choose a reason for hiding this comment

Uh oh!

ryanking13 Jan 5, 2022

Choose a reason for hiding this comment

Uh oh!

hoodmane Jan 5, 2022

Choose a reason for hiding this comment

Uh oh!

ryanking13 Jan 5, 2022

Choose a reason for hiding this comment

Uh oh!

rth Jan 5, 2022

Choose a reason for hiding this comment

Uh oh!

hoodmane commented Jan 5, 2022

Uh oh!

rth commented Jan 5, 2022

Uh oh!

rth commented Jan 6, 2022

Uh oh!

oeway commented Jan 7, 2022

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

oeway commented Nov 28, 2021 •

edited by rth

Loading

rth commented Nov 29, 2021 •

edited

Loading