SKIP 3 — Transitioning to scikit-image 1.0

Author

Juan Nunez-Iglesias <juan.nunez-iglesias@monash.edu>

Status

Final

Type

Standards Track

Created

2021-07-15

Resolved

2021-09-13

Resolution

Rejected

Version effective

None

Abstract

scikit-image is preparing to release version 1.0. This is potentially an opportunity to clean up the API, including backwards incompatible changes. Some of these changes involve changing return values without changing function signatures, which can ordinarily only be done by adding an otherwise useless keyword argument (such as new_return_style=True) whose default value changes over several releases. The result is still a backwards incompatible change, but made over a longer time period.

Despite being in beta and in a 0.x series of releases, scikit-image is used extremely broadly, and any backwards incompatible changes are likely to be disruptive. This SKIP proposes a process to ensure that the community is aware of upcoming changes, and can adapt their libraries or their declared scikit-image version dependencies accordingly.

Motivation and Scope

scikit-image has grown organically over the past 12 years, with functionality being added by a broad community of contributors from different backgrounds. This has resulted in various parts of the API being inconsistent: for example, skimage.transform.warp inverts the order of coordinates, so that a translation of (45, 32) actually moves the values in a NumPy array by 32 along the 0th axis, and 45 along the 1st, but only in 2D.

Additionally, as our user base has grown, it has become apparent that certain early API choices turned out to be more confusing than helpful. For example, scikit-image will automatically convert images to various data types, rescaling them in the process. A uint8 image in the range [0, 255] will automatically be converted to a float64 image in [0, 1]. This might initially seem reasonable, but, for consistency, uint16 images in [0, 65535] are rescaled to [0, 1] floats, and uint16 images with 12-bit range in [0, 4095], which are common in microscopy, are rescaled to [0, 0.0625]. These silent conversions have resulted in much user confusion.

Changing this convention would require adding a preserve_range= keyword argument to almost all scikit-image functions, whose default value would change from False to True over 4 versions. Eventually, the change would be backwards-incompatible, no matter how gentle we made the deprecation curve.

Given the accumulation of potential API changes that have turned out to be too burdensome and noisy to fix with a standard deprecation cycle, principally because they involve changing function outputs for the same inputs, it makes sense to make all those changes in a transition to version 1.0 – semantic versioning, which we use, explicitly allows breaking API changes on major version updates 6. However, we must acknowledge that (1) an enormous number of projects depend on scikit-image and would thus be affected by backwards incompatible changes, and (2) it is not yet common practice in the scientific Python community to put upper version bounds on dependencies, so it is very unlikely that anyone used scikit-image<1.* in their dependency list (though this is slowly changing 5).

Given the above, we need to come up with a way to notify all our users that this change is coming, while also allowing them to silence any warnings once they have been noted.

Detailed description

It is beyond the scope of this document to list all of the proposed API changes for scikit-image 1.0, many of which have yet to be decided upon. Indeed, the scope and ambition of the 1.0 transition could grow if this SKIP is accepted. The SKIP instead proposes a mechanism for warning users about upcoming breaking changes. A meta-issue tracking the proposed changes can be found on GitHub, scikit-image/scikit-image#5439 7. Some examples are briefly included below for illustrative purposes:

  • Stop rescaling input arrays when the dtype must be coerced to float.

  • Stop swapping coordinate axis order in different contexts, such as drawing or warping.

  • Allow automatic return of non-NumPy types, so long as they are coercible to NumPy with numpy.asarray.

  • Harmonizing similar parameters in different functions to have the same name; for example, we currently have random_seed, random_state, seed, or sample_seed in different functions, all to mean the same thing.

  • Changing measure.regionprops to return a dictionary instead of a list.

  • Combine functions that have the same purpose, such as watershed, slic, or felzenschwalb, into a common namespace. This would make it easier for new users to find out which functions they should try out for a specific task.

The question is, how do we make this transition while causing as little disruption as possible?

This document proposes releasing 0.19 as the final 0.x series release, then immediately releasing a nearly identical 0.20 release that warns users about breaking changes in 1.0, thus giving them an opportunity to pin their scikit-image dependency to 0.19.x. The warning would also point users to a transition guide to prepare their code for 1.0. See Implementation for details.

This approach ensures that all users get ample warning, and a chance to ensure that their scripts and libraries will continue to work after 1.0 is released. Users who don’t have the time or inclination to make the transition will be able to pin their dependencies correctly. Those who prefer to be on the cutting edge will also be able to plan around the 1.0 release and update their code correctly, in sync with scikit-image.

Implementation

The details of the proposal are as follows:

  • scikit-image 0.19 will be the final true 0.x release. It contains some new features, bug fixes, and several API changes following on from deprecations in 0.17.

  • shortly after 0.19, we release 0.20, which is identical except that it emits a warning at import time. The warning reads something like the following: “scikit-image 1.0 will be released later this year and will contain breaking changes. To ensure your code keeps running, please install scikit-image<=0.19.*. To silence this warning but still depend on scikit-image after 1.0 is released, install scikit-image!=0.20.*.” The warning also contains a link for further details, and instructions for managing the dependency in both conda and pip environments.

  • After 0.20, we make all the API changes we need, without deprecation cycles. Importantly, for every API change, we add a line to a “scikit-image 1.0 transition guide” in the documentation, which maps every changed functionality in the library from its old form to its new form. These changes are tracked on a GitHub issue 7 and in the 1.0 milestone 8.

  • Once the transition has happened in the repository, we release 1.0.0a0, an alpha release which contains a global warning pointing to the transition guide, as well as all of the new functionality. We also release 0.21, which contains the same warning but is functionally identical to 0.19. This gives authors who chose to pin to scikit-image!=0.20.* a chance to make the migration to 1.0.

  • After at least one month, we release 1.0.

  • We continue to maintain a 0.19.x branch with bug fixes for a year, in order to give users time to transition to the new API.

Backward compatibility

This proposal breaks backwards compatibility in numerous places in the library.

Alternatives

New package naming

Instead of breaking compatibility in the scikit-image package, we could leave that package at 0.19, and release a new package, e.g. scikit-image1, which starts at 1.0 and imports as skimage1. This would obviate the need for users to pin their scikit-image version — users depending on skimage 0.x would be able to use that library “in perpetuity.”

Ultimately, the core developers felt that this approach could unnecessarily fragment the community, between those that continue using 0.19 and those that shift to 1.0. Ultimately, the transition of downstream code to 1.0 would be equally painful as the proposed approach, but the pressure to make the switch would be decreased, as everyone installing scikit-image would still get the old version.

Continuous deprecation over multiple versions

This transition could occur gradually over many versions. For example, for functions automatically converting and rescaling float inputs, we could add a preserve_range keyword argument that would initially default to False, but the default value of False would be deprecated, with users getting a warning to switch to True. After the switch, we could (optionally) deprecate the argument, arriving, after a further two releases, at the same place: scikit-image no longer rescales data automatically, there are no unnecessary keyword arguments lingering all over the API.

Of course, this kind of operation would have to be done simultaneously over all of the above proposed changes.

Ultimately, the core team felt that this approach generates more work for both the scikit-image developers and the developers of downstream libraries, for dubious benefit: ultimately, later versions of scikit-image will still be incompatible with prior versions, although over a longer time scale.

Not making the proposed API changes

Another possibility is to reject backwards incompatible API changes outright, except in extreme cases. The core team feels that this is essentially equivalent to pinning the library at 0.19.

Discussion

In early July 2021, the core team held a series of meetings to discuss this approach. The minutes of this meeting are in the scikit-image meeting notes repository 9.

Ongoing discussion will happen on the user forum 10, the developer forum 11, and GitHub discussion 7. Specific links to relevant posts will be added to this document before acceptance.

Resolution

This SKIP was discussed most extensively in a thread on the mailing list in July 2021 12. In the end, many and core developers felt that this plan posed too big a risk of either changing code behavior silently or eroding goodwill in the community, or both. Matthew Brett wrote 13:

I’m afraid I wasn’t completely sure whether the 1.0 option would result in breaking what I call the Konrad Hinsen rule for scientific software:

“”” Under (virtually) no circumstances should new versions of a scientific package silently give substantially different results for the same function / method call from a previous version of the package. “””

Matthew further wrote 14 that if we don’t break the Hinsen rule, but instead break users’ unpinned scripts, we will lose a lot of goodwill from the community:

If you make all these break (if they are lucky) or give completely wrong results, it’s hard to imagine you aren’t going to cause significant damage to the rest-of-iceberg body of users who are not on the mailing list.

Riadh Fezzani, one of our core developers, felt strongly that SemVer 6 was sufficient to protect users 15:

In scikit-image, we adopted the semantic versioning as it is largely adopted in the engineering community. This convention manages API breaking and that’s what we are doing by releasing v1.0

Even taking this view, though, it cannot address the issue of external scikit-image “documentation”, such as a decade’s worth of accumulated StackOverflow answers, that would be made obsolete by a breaking 1.0 release, as pointed out by Josh Warner 16:

It’s also worth considering that there is a substantial corpus of scikit-image teaching material out there. The majority we do not control, so cannot be updated or edited. The first hits on YouTube for tutorials are not the most recent, but older ones with lots of views.

Nor can it address the issue of gradually migrating a code base from the old API to the new API, as pointed out by Tom Caswell 17:

Put another way, you do not want to put a graduate student in the position of saying “I _want_ to use the new API, but I have 10k LoC of inherited code using the old API …..”.

Ultimately, all these concerns add up to a compelling case to rejecting the SKIP. Juan Nunez-Iglesias wrote on the mailing list 18:

My proposal going forward is to reject SKIP-3 and create a SKIP-4 proposing the skimage2 package.

The SKIP is therefore rejected.

References and Footnotes

All SKIPs should be declared as dedicated to the public domain with the CC0 license 1, as in Copyright, below, with attribution encouraged with CC0+BY 2.

1(1,2)

CC0 1.0 Universal (CC0 1.0) Public Domain Dedication, https://creativecommons.org/publicdomain/zero/1.0/

2(1,2)

https://dancohen.org/2013/11/26/cc0-by/

3

https://pandas.pydata.org/pandas-docs/stable/whatsnew/v1.0.0.html#backwards-incompatible-api-changes

4

https://docs.scipy.org/doc/scipy/reference/release.1.0.0.html

5(1,2)

https://github.com/scipy/scipy/pull/12862

6(1,2)

https://semver.org/

7(1,2,3)

https://github.com/scikit-image/scikit-image/discussions/5651

8

https://github.com/scikit-image/scikit-image/milestones/1.0

9

https://github.com/scikit-image/meeting-notes/blob/main/2021/july-api-meetings.md

10

https://forum.image.sc/tag/scikit-image

11

https://discuss.scientific-python.org/c/contributor/skimage

12

https://mail.python.org/archives/list/scikit-image@python.org/thread/DSV6PEYVJ4RZRUWWV5SBNF7FFRERTSCF/

13

https://mail.python.org/archives/list/scikit-image@python.org/message/UYARUQM5LBWXIAWBAPNHIQIDRKUUDTEK/

14

https://mail.python.org/archives/list/scikit-image@python.org/message/63ZGG7DY5SWVM62XASHMCPFAG6KPJCMT/

15

https://mail.python.org/archives/list/scikit-image@python.org/message/HXI7YVCN6IFF5TL54JBP5QRUDHKTTYRR/

16

https://mail.python.org/archives/list/scikit-image@python.org/message/HRZGMOJLD2WDIO3JXQV3PRWKIUOVOF7P/

17

https://mail.python.org/archives/list/scikit-image@python.org/message/GFXBQYKDACDCH7BGNEGOU7LKHR2LPFX6/

18

https://mail.python.org/archives/list/scikit-image@python.org/message/5J4W63BXFQTT4GHPTZFH3AM4QHAXOW5R/