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2020's calendar of community management #4486

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emmanuelle opened this issue Mar 3, 2020 · 36 comments
Closed

2020's calendar of community management #4486

emmanuelle opened this issue Mar 3, 2020 · 36 comments
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🤔 Planning 🔧 type: Maintenance Refactoring and maintenance of internals

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@emmanuelle
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emmanuelle commented Mar 3, 2020

As an experiment, we are trying to set up a rotating duty to take a first look at all contributions (PRs and issues) from the community, label them and ping relevant reviewers.

Scripts for generating the reports are available in this repository.

mar/2020

apr/2020

may/2020

jun/2020

jul/2020

ago/2020

sep/2020

oct/2020

nov/2020

  • 2020/10/26 - 2020/11/01:
  • 2020/11/02 - 2020/11/08: @alexdesiqueira
  • 2020/11/09 - 2020/11/15:
  • 2020/11/16 - 2020/11/22: @mkcor
  • 2020/11/23 - 2020/11/29: @rfezzani

dec/2020

  • 2020/11/30 - 2020/12/06: @grlee77
  • 2020/12/07 - 2020/12/13: @alexdesiqueira
  • 2020/12/14 - 2020/12/20:
  • 2020/12/21 - 2020/12/27:
  • 2020/12/28 - 2020/12/31: 🎉
@emmanuelle emmanuelle added the 🔧 type: Maintenance Refactoring and maintenance of internals label Mar 9, 2020
@emmanuelle emmanuelle pinned this issue Mar 25, 2020
@emmanuelle
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2020/04/06 - 2020/04/12

The script to generate the report below is on https://gist.github.com/emmanuelle/6937f6ad426754d40f5e9bcfdebd013d For now it's only a gist, you need to put your own Github token in the script. There is room for improvement in the script, in particular I use aggressive thresholds to cap the number of queried pull requests and issues (because it takes a lot of time) but we might miss some updates about very old PRs and issues.

Some other comments

  • The CI was broken at some point on OSX (some Tex issue) but started working again without us having to do anything, but now one of our tests is failing on all python 3.7 (Travis, Azure, Appveyor).
  • All PRs opened this week have been merged (or closed for a debugging PR) 🎉
  • It is possible to give your opinion in the RFC issue SKIP: in_place vs out kwarg #4563 about out vs inplace
  • I added the lists of PRs and issues with traffic (new comments or commits) last week since it can be good candidates for reviews if you find the time
  • I added a new label "solution: identified" for bug issues where a possible solution is explained. This could be useful for potential contributors. (Even if you don't have the time to work on an issue, explaining how it could be solved is useful).

Many thanks to all reviewers!!

new pull requests open last week

#4576 Remove importing skimage.transform as tf
#4575 section on registration in gallery
#4571 Remove binary specification from match_descriptors docstring
#4569 Strip backslash in sphinx 3.0.0
#4568 Bump Pywavelets min requirement to 1.1.1
#4565 Disable key check for texlive in travis-mac as a temporary workaround
#4562 Fix inconsistency in docstring (filters.median)
#4561 Remove "backport to 0.14" in github template
#4560 Do not enforce pil plugin in skimage.data

closed pull requests (not merged)

#4554 Debug plot directive

merged pull requests

#4576 Remove importing skimage.transform as tf
#4575 section on registration in gallery
#4571 Remove binary specification from match_descriptors docstring
#4569 Strip backslash in sphinx 3.0.0
#4568 Bump Pywavelets min requirement to 1.1.1
#4565 Disable key check for texlive in travis-mac as a temporary workaround
#4562 Fix inconsistency in docstring (filters.median)
#4561 Remove "backport to 0.14" in github template
#4560 Do not enforce pil plugin in skimage.data
#4512 Fix bool array save with imageio plugin
#4470 Fix bool array warping
#4438 Deprecate gray scale image support for rgb2gray
#4424 Add gray2rgba and deprecate RGBA support in gray2rgb
#4416 Fix profile_line interpolation errors
#4385 Document geometrical transformations in user guide
#4209 Refactor/move neighborhood utility functions in morphology

Older pull requests with new comments or commits

#4541 Broken plot in userguide fixed
#4531 Fixed automatic color generation in label2rgb function
#4528 Add example code for generating structuring elements.
#4508 API: Add cross_correlation regularization to register_translation
#4503 Move masked_register_translation from feature to registration
#4502 Move register_translation from skimage.feature to skimage.registration
#4496 Fix h_maxima/minima strange behaviors on floating point image input
#4435 3D Rank Filters WIP
#4418 Add nD support to colorconv module
#4380 Euler number and Crofton perimeter
#4307 Manage moments_hu output dtype
#4298 Manage iradon input and output data type
#4218 Add Minkowski distance metric support to corner_peak
#4165 Add function to remove near objects in nd-image
#4087 WIP: Allow regionprops to reuse objects
#4051 [WIP] Add distance transform function
#3850 Add mask support for slic
#3772 Compute histograms for multichannel images
#3614 removed tophat and bottomhat from filters.rank

new issues

#4577 CI fails on Azure for Default-Python-x64-Pre build
#4574 Built-images in data module don't work [Windows]
#4573 Broken CI on OSX
#4572 Avoid importing skimage.transform as tf
#4570 match_descriptors docstring describes descriptors too narrowly
#4567 Relax dimension requirements for structuring elements in morphology?
#4566 Signatures in dev API have backslashes before *
#4564 Broken travis CI for mac
#4563 SKIP: in_place vs out kwarg
#4559 Memory leak in CollectionViewer with repeated use
#4558 segmentation.find_boundaries: different results for different platforms

closed issues

#4574 Built-images in data module don't work [Windows]
#4573 Broken CI on OSX
#4572 Avoid importing skimage.transform as tf
#4570 match_descriptors docstring describes descriptors too narrowly
#4566 Signatures in dev API have backslashes before *
#4564 Broken travis CI for mac
#4553 Examples in doc/examples/registration are not displayed in the gallery
#4511 ValueError raised when bool array saving with imageio plugin
#4292 Rescaling boolean arrays yields plausible result or array of zeros depending on the scale factor
#4279 Interpolation error in measure.profile_line
#3699 Issues with regionprops
#3200 Should rgb2gray accept gray images?

older issues updated last week

#4557 Add origin argument for morpholgy function using structuring elements
#4538 Put our example data on a GitHub pages site
#4514 Specify that rgb2lab function is relative only to sRGB colorspace
#4454 Make travis fail on warnings
#4358 Status of regionprops PRs
#4294 Proposal: deprecate multichannel= in favour of channel_axis=
#4261 sdist review (Oct 2019)
#4105 Medial axis in 3D / Scale axis transform
#3850 Add mask support for slic
#3772 Compute histograms for multichannel images
#3614 removed tophat and bottomhat from filters.rank
#3049 Migrate to travis-ci.com
#2761 Generalised existing CLAHE implementation to support n dimensions
#2616 WIP: document our guidelines/coding conventions
#2613 SKIP: Consistency of multichannel parameter handling
#2604 SKIP: gray vs grey
#2592 peak_local_max fails to enforce min_distance

@jni
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jni commented Apr 20, 2020

Hi all!

Thanks to @emmanuelle this issue is going to get really long. =P See the output of her script below. I didn't reach her very high standard of merging every PR, but I reckon that's because people are being nitpicky about my brilliant #4585. =P Thanks @emmanuelle in particular for getting our CI green again, that's just excellent.

Could @scikit-image/core comment on the behaviour change picked up by @lagru in: https://github.com/scikit-image/scikit-image/pull/4585/files#r411019161

Thanks!

new pull requests open last week

#4593 Recommend cnp.import_array in contribution guide
#4592 [CI fix] add import_array in cython files where numpy is cimport-ed
#4591 Do not overwrite data module in plot_skeleton.py
#4590 Add convert to the API
#4589 [MRG] Fix Negative eigenvalue in inertia_tensor_eigvals due to floating point precision
#4587 DO NOT MERGE Fix empty image after skeletonize_3D
#4586 Revert "Skip extra deps on OSX (#3898)"
#4585 Update rescale_intensity to prevent under/overflow and produce proper output dtype
#4582 Sort naturally peaks coordinates of same amplitude in peak_local_max
#4579 update task in TODO.txt
#4578 Add note to remove option in doc config when numpydoc will be patched

closed pull requests (not merged)

#4586 Revert "Skip extra deps on OSX (#3898)"

merged pull requests

#4593 Recommend cnp.import_array in contribution guide
#4592 [CI fix] add import_array in cython files where numpy is cimport-ed
#4591 Do not overwrite data module in plot_skeleton.py
#4589 [MRG] Fix Negative eigenvalue in inertia_tensor_eigvals due to floating point precision
#4582 Sort naturally peaks coordinates of same amplitude in peak_local_max
#4579 update task in TODO.txt
#4578 Add note to remove option in doc config when numpydoc will be patched

Older pull requests with new comments or commits

#4528 Add example code for generating structuring elements.
#4502 Move register_translation from skimage.feature to skimage.registration
#4496 Fix h_maxima/minima strange behaviors on floating point image input
#4467 Complete deprecation of circle in morphsnakes
#4435 3D Rank Filters WIP
#4418 Add nD support to colorconv module
#4228 MAINT+DOC update RELEASE.txt
#4218 Add Minkowski distance metric support to corner_peak
#4165 Add function to remove near objects in nd-image
#3850 Add mask support for slic

new issues

#4595 Broken links in docs
#4594 Broken link in separate_stains docstring
#4588 Negative eigenvalue in inertia_tensor_eigvals due to floating point precision
#4584 imread published wheels, consider to revert a workaround in travis?
#4583 funky behavior of rescale_intensity
#4581 Merge connectivity resolving helper functions in morphology._util
#4580 corner_harris returns peaks in a non "natural" order when the peaks have the same amplitude

older issues updated last week

#4559 Memory leak in CollectionViewer with repeated use
#4557 Add origin argument for morpholgy function using structuring elements
#4540 Broken plot in userguide
#4486 Calendar of community management
#4154 Define standard common argument's names
#4105 Medial axis in 3D
#3850 Add mask support for slic
#3757 skeletonize_3d produces a zero array in certain conditions
#2616 WIP: document our guidelines/coding conventions

closed issues

#4588 Negative eigenvalue in inertia_tensor_eigvals due to floating point precision
#4584 imread published wheels, consider to revert a workaround in travis?
#4580 corner_harris returns peaks in a non "natural" order when the peaks have the same amplitude
#4577 CI fails on Azure for Default-Python-x64-Pre build
#4436 chroma subsampling not supported

@sciunto
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sciunto commented Apr 27, 2020

2020/4/20 - 2020/4/27

A good activity this week. An issue #4603 raised again the question how to decide the min version of requirements. @soupault opened a great issue (#4608) summarizing our current decisions and proposing policies for the different cases. This PR requires attention of @scikit-image/core in particular.

Kudos again to @soupault who fixed a ton of broken links in our code: #4600

@emmanuelle put the script to generate this report in a repository, so we can easily submit PRs.

I tried to fix an issue in skeletonize3D based on a patch that have been submitted to the matlab implementation of this algorithm. I might not have fully understood the matlab code, but the modifications seem to be too drastic and lead to another incorrect behavior. Fiji still have the bug. I have not done the work to read carefully the paper to check the current implementation regarding the original algorithm.

I also investigated the loading page performances of our gallery. It turns out that the page is slow due to thumbnails. We merged a PR to reduce the resolution of thumbnails, which decreases by a factor 2 the image sizes, while keeping a correct rendering. I opened an issue on the sphinx-gallery tracker to raise this problem. Matplotlib and scikit-learn are also interested in better performances. One sphinx-gallery dev proposed a PR to use optipng (after @GaelVaroquaux's recommendations). This has to be tested.

I hope I did not missed any other important point.

2020/4/20 - 2020/4/27

New pull requests open last week

#4620 Add .mypy_cache to the gitignore
#4619 added one example to flood fill tutorial
#4617 Change math formatting in the docstrings
#4615 Fixed wrong behaviour of exposure.rescale_intensity for constant input.
#4614 Change label2rgb default background value from -1 to 0
#4613 Improve loading speed of our gallery by reducing the thumbnail size
#4612 Allow very large values in relabel_sequential
#4610 Add notes on deprecation warnings in marching_cube_* and gray2rgb
#4609 Fix register_translation warning message
#4607 Clarify error message when montaging multichannel nD images and multichannel=False
#4604 Update min required sphinx version for sphinx-copybutton
#4602 Fix typo in cython import_array
#4600 Fix broken and permanently moved links
#4599 Add example of natsort usage in documentation
#4598 Extended existing equalize_adapthist implementation (CLAHE) to N dimensions

Closed pull requests (not merged)

#4417 Fix rgb2gray docstring to show that 2-D arrays are allowed as inputs

Merged pull requests

#4620 Add .mypy_cache to the gitignore
#4617 Change math formatting in the docstrings
#4615 Fixed wrong behaviour of exposure.rescale_intensity for constant input.
#4613 Improve loading speed of our gallery by reducing the thumbnail size
#4610 Add notes on deprecation warnings in marching_cube_* and gray2rgb
#4609 Fix register_translation warning message
#4607 Clarify error message when montaging multichannel nD images and multichannel=False
#4604 Update min required sphinx version for sphinx-copybutton
#4602 Fix typo in cython import_array
#4600 Fix broken and permanently moved links
#4599 Add example of natsort usage in documentation
#4590 Rename convert to _convert, as it is a private function
#4585 Update rescale_intensity to prevent under/overflow and produce proper output dtype
#4528 Add example code for generating structuring elements.
#4502 Move register_translation from skimage.feature to skimage.registration
#4496 Fix h_maxima/minima strange behaviors on floating point image input
#4467 Complete deprecation of circle in morphsnakes

Older pull requests with new comments or commits

#4531 Fixed automatic color generation in label2rgb function
#4517 WIP: stub sphinx example to illustrate data type relevance
#4515 example: register rotation and scaling with no shared center
#4503 Move masked_register_translation from feature to registration
#4435 3D Rank Filters WIP

new issues

#4621 Does Difference of Gaussian need normalization?
#4618 flood_fill and flood are both in segmentation and morphology
#4616 Search links broken in dev documentation
#4611 Can't load most images from data package
#4608 RFC: Support cycle for the upstream and the downstream dependencies
#4606 Misleading "ValueError: Input array has to be either 3- or 4-dimensional" in montage
#4605 Check in CI whether we can bump the versions of the requirements
#4603 Documentation build failure with sphinx 2.4
#4601 Discuss gallery structure to bring out bioimaging examples.
#4597 equalize_adapthist border artifacts still present
#4596 exposure.equalize_adapthist can fail for constant inputs due to incorrect behavior in rescale_intensity

Older issues updated last week

#4594 Broken link in separate_stains docstring
#4544 Simplify the release process
#4507 Automatic color generation in the label2rgb function
#4486 Calendar of community management
#3015 WIP: Turn off relabelling in label2rgb
#2761 Generalised existing CLAHE implementation to support n dimensions

Closed issues

#4611 Can't load most images from data package
#4603 Documentation build failure with sphinx 2.4
#4596 exposure.equalize_adapthist can fail for constant inputs due to incorrect behavior in rescale_intensity
#4595 Broken links in docs
#4583 funky behavior of rescale_intensity
#4513 Add example of natsort usage in documentation
#4431 Add examples to docstring for structuring elements to visualize the shape
#4194 h_maxima/minima strange behaviors on floating point image input
#3014 Magic dimensionality guessing in gray2rgb

@emmanuelle
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2020/4/27 - 2020/5/4

Thank you @alexdesiqueira who did most of the work. Our CI is still failing because of Cython pre-release, I hope that they have a new pre-release coming soon because it's not nice to have a red CI. I hope that we can release 0.17 this week, I will take care of it with the help of @jni.

#4612 is I think ready and waiting for a second approval, it would be great if it could make it for the release.

2020/4/27 - 2020/5/4

New pull requests open last week

#4635 Update pooch registry with new file location
#4633 MAINT: remove unused cython file
#4632 add docstring examples for moments_hu and centroid
#4631 random walker: Display a warning when the probability is outsite [0,1] for a given tol
#4630 Random walker: minor corrections (typos, comments, added TODO task)
#4628 Fix deprecation warnings due to invalid escape sequences.
#4627 Userguide: add a visualization chapter

Closed pull requests (not merged)

#4587 DO NOT MERGE Fix empty image after skeletonize_3D

Merged pull requests

#4635 Update pooch registry with new file location
#4630 Random walker: minor corrections (typos, comments, added TODO task)
#4628 Fix deprecation warnings due to invalid escape sequences.
#4627 Userguide: add a visualization chapter
#4614 Change label2rgb default background value from -1 to 0
#4598 Extended existing equalize_adapthist implementation (CLAHE) to N dimensions
#4503 Move masked_register_translation from feature to registration

Older pull requests with new comments or commits

#4619 added one example to flood fill tutorial
#4612 Allow very large values in relabel_sequential
#4468 Added implementation of SSIM max/min algorithm from paper
#4435 3D Rank Filters WIP
#4418 Add nD support to colorconv module
#4390 Lddmm registration
#4342 Refactor canny edge detector
#4228 MAINT+DOC update RELEASE.txt
#4218 Add Minkowski distance metric support to corner_peak
#3883 move the location of fast_exp to help compilation with strange flags
#3651 Update image's luminance extraction to current recommendation.
#3316 Add benchmark suite for weiner and inverse functions
#3255 Add benchmarks for morphology.local_maxima

new issues

#4637 unsupervised_wiener for RGB images
#4636 win_size exceeds image extent. If the input is a multichannel (color) image, set multichannel=True.
#4634 Test for availability of the Pooch resources in CI
#4629 separate_stains output issue
#4626 Image Viewer produces two windows in Jupyter notebook
#4625 Optimize gallery images with optipng
#4624 [CI] Build broken with cython 3.0a3

Older issues updated last week

#4618 flood_fill and flood are both in segmentation and morphology
#3883 move the location of fast_exp to help compilation with strange flags
#3858 separate_stains output
#3651 Update image's luminance extraction to current recommendation.
#3316 Add benchmark suite for weiner and inverse functions
#3255 Add benchmarks for morphology.local_maxima
#3153 Python 3.7 Typing
#3009 Fixes for data types and other common sources of errors
#2698 RANSAC: Check for updates
#2360 Numerical inaccuracies with the random_walker

Closed issues

#4636 win_size exceeds image extent. If the input is a multichannel (color) image, set multichannel=True.
#4626 Image Viewer produces two windows in Jupyter notebook
#4597 equalize_adapthist border artifacts still present
#3324 Move restoration and color data to the combined data directory
#2761 Generalised existing CLAHE implementation to support n dimensions

@emmanuelle
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2020/5/4 - 2020/5/11

As you know last week was a release week and we're still in release-land with 0.17.2 coming up this week (meaning some backports of bug fixes for bugs introduced in 0.17). Apart from release stuff it'd be great to take a look at #3226 (pythran demo)

New pull requests open last week

#4678 Backport PR #4651 on branch v0.17.x (Fix doxstring and micro-optimization in SLIC)
#4676 Adding new default values to functions on doc/examples/segmentation/plot_ncut
#4670 [WIP] Make Pooch lazily create directories for python 3.7+
#4668 Add blind Richardson-Lucy deconvolution (supersedes #3524)
#4666 Optional pooch dependency
#4663 Setup longdesc markdown and switch to 0.18dev
#4662 Forget legacy data dir
#4661 Fix label2rgb
#4658 Add example for 3D adaptive histogram equalization (AHE)
#4655 equalize_adapthist: More efficient processing scheme with symmetrical padding
#4653 DOC: fix broken DOI links
#4652 Update version for release
#4651 Fix doxstring and micro-optimization in SLIC
#4650 Updates to plot_j_invariant.py
#4649 release notes for 0.17
#4648 Add first biology example: segmentation of human cells with mitosis.
#4646 Expose recently introduced map_array function in skimage.util
#4645 Fix ArrayMap test
#4644 Fix sphinx
#4643 Fix CI - cython 3.0a4
#4642 AffineTransform: Allow a single value for 'scale' to apply to both sx & sy
#4641 DOC: docstring enhancements for Marching cube and find_contours
#4640 Refactor ArrayMap.setitem to prevent memory allocation
#4639 Fix broken link
#4638 Misleading "ValueError: Input array has to be either 3- or 4-dimensional" in montage

Closed pull requests (not merged)

#4652 Update version for release
#4640 Refactor ArrayMap.setitem to prevent memory allocation
#4306 [WIP] Major cleanup to install instructions

Merged pull requests

#4676 Adding new default values to functions on doc/examples/segmentation/plot_ncut
#4666 Optional pooch dependency
#4663 Setup longdesc markdown and switch to 0.18dev
#4662 Forget legacy data dir
#4661 Fix label2rgb
#4653 DOC: fix broken DOI links
#4651 Fix doxstring and micro-optimization in SLIC
#4650 Updates to plot_j_invariant.py
#4649 release notes for 0.17
#4646 Expose recently introduced map_array function in skimage.util
#4645 Fix ArrayMap test
#4644 Fix sphinx
#4643 Fix CI - cython 3.0a4
#4642 AffineTransform: Allow a single value for 'scale' to apply to both sx & sy
#4641 DOC: docstring enhancements for Marching cube and find_contours
#4639 Fix broken link
#4638 Misleading "ValueError: Input array has to be either 3- or 4-dimensional" in montage

Older pull requests with new comments or commits

#4633 MAINT: remove unused cython file
#4444 WIP: Move RAGs from future to segmentation
#4390 Lddmm registration
#4382 Hausdorff Distance (updated)
#4342 Refactor canny edge detector
#4298 Manage iradon input and output data type
#4126 morphology.rectangle() dimensions swapped, Fixes Issue #4125
#3524 Blind Richardson–Lucy deconvolution
#3329 Fix #3327: Add functionality for benchmark coverage
#3226 Tentative pythran support - demo

new issues

#4680 Reintroduce dtype.convert
#4679 Allow for calculation of single property in regionprops
#4677 BRIEF fails for float32 data type
#4675 ORB detection doesn't work on 32 bit float input
#4674 users are forced to upgrade their pip for 0.17
#4673 pip3 install failing on Ubuntu 18.04 + Python 3.6
#4672 INSTALL.rst confounds enduser installation with development instructions
#4671 Skipping tests that depend on pooch is confusing
#4669 test_hdx_rgb_roundtrip fails when running multithreaded?
#4667 ERROR - sudo pip3 install -U scikit-image
#4665 pooch is a hard requirement
#4664 PermissionError when creating data_dir when user doesn't have permissions
#4660 When running in multi-process Pooch tries to create a directory that already exist
#4659 data_dir always falling back to legacy_data_dir
#4657 Bugs in label2rgb
#4656 Master broken after commit bcd03b4
#4654 Broken doc examples using label2rgb
#4647 Update blacklisted versions for sphinx in requirement.txt

Older issues updated last week

#4629 separate_stains output issue
#4534 BUG: name of bg_color is not supported in skimage.color.label2rgb
#4486 Calendar of community management
#4259 Bump numpy to >= 1.16
#3620 Adding new ConicSectionModel?
#3577 rank filter maximum incorrect doc of output dtype
#3539 Port CI from AppVeyor to Azure
#3524 Blind Richardson–Lucy deconvolution
#3329 Fix #3327: Add functionality for benchmark coverage
#3226 Tentative pythran support - demo
#3124 Recursive Montage / ND Montage?
#3092 Failure in test_spacing_1 on 32-bit Linux builds
#3031 Use plane, row, col notation in all docstrings
#2993 Non-blocking ImageViewer
#2815 Restandardize handling of Multi-Image files
#2801 Choose 8 as opposed to default of 4-connectivity in measure.regionprops perimeter
#2740 Fit output in warp function
#2698 RANSAC: Check for updates
#2276 Use plane, row, col dimensions ordering as specified in the skimage conventions page

Closed issues

#4673 pip3 install failing on Ubuntu 18.04 + Python 3.6
#4665 pooch is a hard requirement
#4659 data_dir always falling back to legacy_data_dir
#4657 Bugs in label2rgb
#4656 Master broken after commit bcd03b4
#4654 Broken doc examples using label2rgb
#4616 Search links broken in dev documentation
#4606 Misleading "ValueError: Input array has to be either 3- or 4-dimensional" in montage
#4594 Broken link in separate_stains docstring
#3850 Add mask support for slic
#3824 J-invariant denoising
#3722 Consider returning segments starting from 1 from SLIC
#3684 test_adapthist_grayscale fails on linux 64 and conda
#1569 Consider adding mask support for SLIC

@alexdesiqueira
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2020/5/11 - 2020/5/17

Lots of new documentation and small fixes proposed, some backports and a discussion on our install docs — it would be interesting to have some thoughts from all @scikit-image/core to find a consensus and work on that quickly.

new pull requests open last week

#4725 [WIP] Fixing color/colorconv/separate_stains
#4724 Remove duplicate fused type definition
#4723 Improving register rotation example with notes and references
#4718 Backport PR #4713 on branch v0.17.x (Specify the encoding of files opened in the setup phase)
#4717 Add blind Richardson-Lucy deconvolution (supersedes #3524)
#4714 Anki xyz blind deconvolution
#4713 Specify the encoding of files opened in the setup phase
#4710 Backport PR #4702 on branch v0.17.x (release notes for 0.17.2)
#4709 Backport PR #4706 on branch v0.17.x (Fix gallery example mentioning deprecated argument)
#4708 Add pyramid_gaussian support for float32
#4706 Fix gallery example mentioning deprecated argument
#4704 [WIP] MNT: Use an image fetcher class instead of global variables.
#4703 Add exception for PermissionError at data_dir creation
#4702 release notes for 0.17.2
#4701 Backport PR #4696 on branch v0.17.x (Add pyramid_gaussian support for float32)
#4700 Backport PR #4697 on branch v0.17.x (Add ORB full float32 support)
#4699 Backport PR #4692 on branch v0.17.x (suppressing warnings from gallery examples)
#4698 Backport PR #4691 on branch v0.17.x (Perform todo tasks for 0.17!)
#4697 Add ORB full float32 support
#4696 Add pyramid_gaussian support for float32
#4694 Backport PR #4676 on branch v0.17.x (Adding new default values to functions on doc/examples/segmentation/plot_ncut)
#4693 Backport PR #4681 on branch v0.17.x (Reintroduced convert with a strong deprecation warning)
#4692 suppressing warnings from gallery examples
#4691 Perform todo tasks for 0.17!
#4690 Perform some todo tasks for 0.18
#4689 In release notes, better describe skimage's relationship to ecosystem
#4688 Backport PR #4684 on branch v0.17.x (Add ORB float32 support)
#4687 Backport PR #4685 on branch v0.17.x (Add BRIEF float32 support)
#4686 Backport PR #4683 on branch v0.17.x (Fix slic float32 support regression)
#4685 Add BRIEF float32 support
#4684 Add ORB float32 support
#4683 Fix slic float32 support regression
#4681 Reintroduced convert with a strong deprecation warning
#4678 Backport PR #4651 on branch v0.17.x (Fix doxstring and micro-optimization in SLIC)
#4676 Adding new default values to functions on doc/examples/segmentation/plot_ncut

closed pull requests (not merged)

#4714 Anki xyz blind deconvolution
#4701 Backport PR #4696 on branch v0.17.x (Add pyramid_gaussian support for float32)
#4668 Add blind Richardson-Lucy deconvolution (supersedes #3524)

merged pull requests

#4724 Remove duplicate fused type definition
#4718 Backport PR #4713 on branch v0.17.x (Specify the encoding of files opened in the setup phase)
#4713 Specify the encoding of files opened in the setup phase
#4710 Backport PR #4702 on branch v0.17.x (release notes for 0.17.2)
#4709 Backport PR #4706 on branch v0.17.x (Fix gallery example mentioning deprecated argument)
#4708 Add pyramid_gaussian support for float32
#4706 Fix gallery example mentioning deprecated argument
#4702 release notes for 0.17.2
#4700 Backport PR #4697 on branch v0.17.x (Add ORB full float32 support)
#4699 Backport PR #4692 on branch v0.17.x (suppressing warnings from gallery examples)
#4698 Backport PR #4691 on branch v0.17.x (Perform todo tasks for 0.17!)
#4697 Add ORB full float32 support
#4696 Add pyramid_gaussian support for float32
#4694 Backport PR #4676 on branch v0.17.x (Adding new default values to functions on doc/examples/segmentation/plot_ncut)
#4693 Backport PR #4681 on branch v0.17.x (Reintroduced convert with a strong deprecation warning)
#4692 suppressing warnings from gallery examples
#4691 Perform todo tasks for 0.17!
#4689 In release notes, better describe skimage's relationship to ecosystem
#4688 Backport PR #4684 on branch v0.17.x (Add ORB float32 support)
#4687 Backport PR #4685 on branch v0.17.x (Add BRIEF float32 support)
#4686 Backport PR #4683 on branch v0.17.x (Fix slic float32 support regression)
#4685 Add BRIEF float32 support
#4684 Add ORB float32 support
#4683 Fix slic float32 support regression
#4681 Reintroduced convert with a strong deprecation warning
#4678 Backport PR #4651 on branch v0.17.x (Fix doxstring and micro-optimization in SLIC)
#4676 Adding new default values to functions on doc/examples/segmentation/plot_ncut
#4666 Optional pooch dependency

Older pull requests with new comments or commits

#4670 [WIP] Make Pooch lazily create directories for python 3.7+
#4658 Add example for 3D adaptive histogram equalization (AHE)
#4648 Add first biology example: segmentation of human cells with mitosis.
#4631 random walker: Display a warning when the probability is outsite [0,1] for a given tol
#3524 Blind Richardson–Lucy deconvolution

new issues

#4722 cannot import name 'regionprops_table' from 'skimage.measure'
#4721 Install fails on rpi due to missing imagecodecs from tifffile
#4720 Error installing scikit-image
#4719 Pooch, usability, and the future of examples
#4716 Using rag_mean_color and merge_hierarchical with a custom weight_func uses default 'distance' or 'similarity' on first iteration?
#4715 Crash on specific computer
#4712 Measure region properties (scikit-image) on external images
#4711 single scale AffineTransform not supported
#4707 contradiction between example and docstring for active contour.
#4705 Unable to build on Jetson Nano (arm64): UnicodeDecodeError: 'ascii' codec ...
#4695 pyramid_gaussian doesn't support float32
#4682 slic float32 support regression
#4680 Reintroduce dtype.convert
#4679 Allow for calculation of single property in regionprops
#4677 BRIEF fails for float32 data type
#4675 ORB detection doesn't work on 32 bit float input

older issues updated last week

#4672 INSTALL.rst confounds enduser installation with development instructions
#4671 Skipping tests that depend on pooch is confusing
#4664 PermissionError when creating data_dir when user doesn't have permissions
#4647 Update blacklisted versions for sphinx in requirement.txt
#4629 separate_stains output issue
#4486 Calendar of community management
#3524 Blind Richardson–Lucy deconvolution

closed issues

#4722 cannot import name 'regionprops_table' from 'skimage.measure'
#4721 Install fails on rpi due to missing imagecodecs from tifffile
#4720 Error installing scikit-image
#4715 Crash on specific computer
#4705 Unable to build on Jetson Nano (arm64): UnicodeDecodeError: 'ascii' codec ...
#4695 pyramid_gaussian doesn't support float32
#4682 slic float32 support regression
#4680 Reintroduce dtype.convert
#4679 Allow for calculation of single property in regionprops
#4677 BRIEF fails for float32 data type
#4675 ORB detection doesn't work on 32 bit float input
#4674 users are forced to upgrade their pip for 0.17
#4667 ERROR - sudo pip3 install -U scikit-image
#4665 pooch is a hard requirement
#4660 When running in multi-process Pooch tries to create a directory that already exist

@lagru
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lagru commented May 25, 2020

2020/05/18 - 2020/05/24

This seemed like a productive week to me. Some highlights:

The gallery examples mentioned above and #4717 as well as #4734 might be good places to review if you find the time. And we still need someone to take over the community management this week (2020/05/25 - 2020/05/31)!

new pull requests open last week

#4747 Turn checklist boxes into bullet points inside the pull request template
#4746 Highlight all source lines with HTML doc "source" links (sphinx.ext.linkcode)
#4745 Backport NumPy deprecation fixes to v0.17.x
#4744 Fix plotting error in j-invariant denoising tutorial
#4742 Backport PR #4740 on branch v0.17.x (Unwrap decorators before resolving link to source (sphinx.ext.linkcode))
#4740 Unwrap decorators before resolving link to source (sphinx.ext.linkcode)
#4739 gallery example on trainable segmentation
#4738 Add pooch in requirements/test.txt
#4737 Backport PR #4733 on branch v0.17.x (Add versionadded for new scalar type support for "scale" param in transform.AffineTransform)
#4735 Fix Ci failures related to array ragged input numpy deprecation
#4734 Add Phansalkar local threshold algorithm
#4733 Add versionadded for new scalar type support for "scale" param in transform.AffineTransform
#4731 Fix CI failures related to conversion of np.floating to dtype
#4730 Blacklist cython version 0.29.18

closed pull requests (not merged)

none

merged pull requests

#4746 Highlight all source lines with HTML doc "source" links (sphinx.ext.linkcode)
#4745 Backport NumPy deprecation fixes to v0.17.x
#4744 Fix plotting error in j-invariant denoising tutorial
#4742 Backport PR #4740 on branch v0.17.x (Unwrap decorators before resolving link to source (sphinx.ext.linkcode))
#4740 Unwrap decorators before resolving link to source (sphinx.ext.linkcode)
#4737 Backport PR #4733 on branch v0.17.x (Add versionadded for new scalar type support for "scale" param in transform.AffineTransform)
#4735 Fix Ci failures related to array ragged input numpy deprecation
#4733 Add versionadded for new scalar type support for "scale" param in transform.AffineTransform
#4731 Fix CI failures related to conversion of np.floating to dtype
#4730 Blacklist cython version 0.29.18
#4725 Fixing color/colorconv/separate_stains
#4690 Perform some todo tasks for 0.18
#4631 random walker: Display a warning when the probability is outsite [0,1] for a given tol

Older pull requests with new comments or commits

#4717 Add blind Richardson-Lucy deconvolution (supersedes #3524)
#4658 Add example for 3D adaptive histogram equalization (AHE)
#4648 Add first biology example: segmentation of human cells with mitosis.
#4435 3D Rank Filters WIP
#4390 Lddmm registration
#4382 Hausdorff Distance (updated)

new issues

#4748 Sphinx gallery issues
#4743 Wrong MSE computation in the SSIM code example
#4741 Turn checkmarks in pull request templates into bullet points
#4736 Blob finding runtime warning
#4732 warp on rotated image provides wrong results
#4729 RuntimeWarning in blob.py (division by zero)
#4728 does scikit-image have C or C++ version code?
#4727 Broken CI on py3.8 and Windows following Cython 0.29.18 release
#4726 Add ..versionchanged:: tags to all API changes from 0.17

older issues updated last week

#4707 contradiction between example and docstring for active contour.
#4672 INSTALL.rst confounds enduser installation with development instructions
#4621 Does Difference of Gaussian need normalization?
#4486 Calendar of community management
#3990 Trivial image check for peak_local_max
#3892 some edge points not included in points_in_poly result
#3547 Allow animations in the documentation
#2546 skimage.color.rgb2hed scale not between (-1,1)

closed issues

#4732 warp on rotated image provides wrong results
#4728 does scikit-image have C or C++ version code?
#4727 Broken CI on py3.8 and Windows following Cython 0.29.18 release
#4712 Measure region properties (scikit-image) on external images
#4711 single scale AffineTransform not supported
#4629 separate_stains output issue
#3858 separate_stains output
#2360 Numerical inaccuracies with the random_walker
#2221 docs link to decorator rather than function itself

@rfezzani
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rfezzani commented Jun 1, 2020

2020/05/25 - 2020/05/31

Last week looks like a quite week compared to the previous weeks, but as the following highlights shows, things are going very well:

There is no one in charge for the community management this week, we are still looking for a last minute volunteer ;)

new pull requests open last week

#4762 [WIP] wip on viz libraries
#4761 Deprecate min_size in remove_small_objects
#4760 Refactor and fix peack_local_max
#4758 forbid dask 2.17.0 to fix CI
#4753 Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max
#4752 Deprecate indices in peak_local_max
#4751 Optimize peak_local_max trivial image test
#4750 Rewrite INSTALL instructions for python novices

closed pull requests (not merged)

#4751 Optimize peak_local_max trivial image test
#4738 Add pooch in requirements/test.txt

merged pull requests

#4758 forbid dask 2.17.0 to fix CI

Older pull requests with new comments or commits

#4747 Turn checklist boxes into bullet points inside the pull request template
#4739 [WIP] trainable segmentation (algorithm + gallery example)
#4734 Add Phansalkar local threshold algorithm
#4717 Add blind Richardson-Lucy deconvolution (supersedes #3524)
#4658 Add example for 3D adaptive histogram equalization (AHE)
#4648 Add first biology example: segmentation of human cells with mitosis.
#4435 3D Rank Filters WIP
#4390 Lddmm registration
#4201 Add rescale_local_mean
#4161 Add the iterative Lucas-Kanade (iLK) optical flow method

new issues

#4759 Arctan2 being passed arguments in wrong order in Approximate_polygon
#4757 CI broken following dask 2.17.0 release
#4756 Peaks may not be detected in peak_local_max when label is provided
#4755 ImportError in skimage.exposure
#4754 Compiling from sources (?)
#4749 Deprecate edge cases in peak_local_max

older issues updated last week

#4748 Sphinx gallery issues
#4741 Turn checkmarks in pull request templates into bullet points
#4672 INSTALL.rst confounds enduser installation with development instructions
#3990 Trivial image check for peak_local_max
#2592 peak_local_max fails to enforce min_distance

closed issues

#4757 CI broken following dask 2.17.0 release
#4755 ImportError in skimage.exposure
#4754 Compiling from sources (?)
#2758 peak_local_max takes a very long time to complete

@alexdesiqueira
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2020/06/01 - 2020/06/08

Not too much activity this week, but several issues related to Mac/Win were described.

new pull requests open last week

#4771 Fix random_walker regression
#4767 Handle NaNs in phase_cross_correlation

closed pull requests (not merged)

none

merged pull requests

none

Older pull requests with new comments or commits

#4739 [WIP] trainable segmentation (algorithm + gallery example)
#4717 Add blind Richardson-Lucy deconvolution (supersedes #3524)
#4648 Add first biology example: segmentation of human cells with mitosis.
#4390 Lddmm registration
#4382 Hausdorff Distance (updated)

new issues

#4783 [feature request] skimage.feature.greycomatrix should add support for different distances
#4782 test_free_reference fails on ppc64le with python 3.6
#4781 test_ellipse_rotated fails on python3.8
#4780 Getting "ImportError: DLL load failed: The specified module could not be found."
#4779 sigma_range not used in denoiser calibration examples
#4778 test_hed_rgb_float_roundtrip fails on ppc64le python 3.8
#4777 test_uint16 fails on win
#4776 test_hed_rgb_roundtrip fails on osx with python3.8 and ppc64le with python 3.6
#4775 test_hdx_rgb_roundtrip fail son osx with python 3.8
#4774 test_end_points fails on ppc64le with python 3.6, 3.7, 3.8
#4773 test_RGB fails on ppc64le with python 3.7
#4772 test_periodic_reference fails on ppc64le python 3.7 (conda feedstock)
#4770 segmentation.random_walker error, masking problem
#4769 _masked_phase_cross_correlation: is it truly a phase cross-correlation?
#4768 Broken tests on ppc64le
#4766 Missing attribute 'offsets' in skimage.graph.MCP_Geometric
#4765 Is cross_correlate_masked() now superseded by phase_cross_correlation() with kwargs?
#4764 API inconsistency: phase_cross_correlation does not return error & phasediff
#4763 phase_cross_correlation with NaN pixels returns an invalid result

older issues updated last week

#4486 Calendar of community management
#3306 What's the use of tform.inverse() in transform.PiecewiseAffineTransform?
#1131 Tracing the boundary curve of an image region

closed issues

#4765 Is cross_correlate_masked() now superseded by phase_cross_correlation() with kwargs?

@alexdesiqueira
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2020/06/09 - 2020/06/15

This week we merged an awesome biology example and fixed random_walker.

new pull requests open last week

#4792 Remove unused variable in j invariant docs
#4788 try to fix ci which is broken because of pyqt5 last version

closed pull requests (not merged)

none

merged pull requests

#4792 Remove unused variable in j invariant docs
#4788 try to fix ci which is broken because of pyqt5 last version
#4771 Fix random_walker regression
#4747 Turn checklist boxes into bullet points inside the pull request template
#4648 Add first biology example: segmentation of human cells with mitosis.

Older pull requests with new comments or commits

#4767 Handle NaNs in phase_cross_correlation
#4761 Deprecate min_size in remove_small_objects
#4390 Lddmm registration
#4121 Crofton perimeter and Euler number

new issues

#4791 Another missing attribute 'reduce_cython'
#4790 how to mark object centroid in the video
#4789 how to read properties in regionprops
#4787 label2rgb only color the contour not the area
#4786 Backport bugfix #4771
#4785 test_fixed_reference fails on ppc64le with python 3.7
#4784 segmentation.random_walker bug with float32 image, masking and 'bf' optimization

older issues updated last week

#4783 [feature request] skimage.feature.greycomatrix should add support for different distances
#4780 Getting "ImportError: DLL load failed: The specified module could not be found."
#4768 Broken tests on ppc64le
#4622 Feature: Weighted phase unwrapping
#4499 SIFT patent expired
#4486 Calendar of community management

closed issues

#4791 Another missing attribute 'reduce_cython'
#4790 how to mark object centroid in the video
#4789 how to read properties in regionprops
#4787 label2rgb only color the contour not the area
#4785 test_fixed_reference fails on ppc64le with python 3.7
#4782 test_free_reference fails on ppc64le with python 3.6
#4781 test_ellipse_rotated fails on python3.8
#4779 sigma_range not used in denoiser calibration examples
#4778 test_hed_rgb_float_roundtrip fails on ppc64le python 3.8
#4777 test_uint16 fails on win
#4776 test_hed_rgb_roundtrip fails on osx with python3.8 and ppc64le with python 3.6
#4774 test_end_points fails on ppc64le with python 3.6, 3.7, 3.8
#4770 segmentation.random_walker error, masking problem
#4741 Turn checkmarks in pull request templates into bullet points

@rfezzani
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2020/06/15 - 2020/06/22

Last week highlights:

new pull requests open last week

#4795 [WIP] added expand_labels
#4794 [wip] add type annotations in some modules in skimage.segmentation
#4793 include all md files in manifest.in
#4792 Remove unused variable in j invariant docs

closed pull requests (not merged)

none

merged pull requests

#4792 Remove unused variable in j invariant docs

Older pull requests with new comments or commits

#4767 Handle NaNs in phase_cross_correlation
#4761 Deprecate min_size in remove_small_objects
#4752 Deprecate indices in peak_local_max
#4739 [WIP] trainable segmentation (algorithm + gallery example)
#4723 Improving register rotation example with notes and references
#4658 Add example for 3D adaptive histogram equalization (AHE)
#4619 added one example to flood fill tutorial
#4390 Lddmm registration
#4382 Hausdorff Distance (updated)
#4379 Feret diameter

new issues

#4797 API: replace array by image in measure.find_contours()
#4796 Cannot upload by imread() files containing char "–"

older issues updated last week

#4780 Getting "ImportError: DLL load failed: The specified module could not be found."
#4622 Feature: Weighted phase unwrapping
#4486 Calendar of community management
#3538 Rolling Ball/Sliding Paraboloid Algorithm for background estimation
#3153 Python 3.7 Typing
#3070 Allow passing callable for high and low threshold of Canny
#3009 Fixes for data types and other common sources of errors
#1131 Tracing the boundary curve of an image region

closed issues

#4796 Cannot upload by imread() files containing char "–"
#4779 sigma_range not used in denoiser calibration examples

@emmanuelle
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An average level of activity last week I'd say. The CI is currently broken because of matplotlib pre-release which is annoying, I opened #4805 to discuss our general CI process related to pre-releases. Several open PRs have a good momentum but need some input, for example #4767, #4794, #4739, #4444.

New pull requests open last week

#4809 Let biomed example load image data with Pooch.
#4807 Change SSIM code example to use real MSE
#4806 API change: Replace array by image in measure.find_contour
#4804 Add TODO task for sphinx-gallery>=0.9.0 to remove enforced thumbnail_size
#4803 Fix runtime warning in blob.py
#4800 Use optipng to compress images/thumbnails in our gallery
#4798 Remove additional "::" to make plot directive work.

Merged pull requests

#4803 Fix runtime warning in blob.py
#4798 Remove additional "::" to make plot directive work.
#4795 Add expand_labels function to dilate segments while avoiding overlaps
#4793 include all md files in manifest.in

Older pull requests with new comments or commits

#4794 [wip] add type annotations in some modules in skimage.segmentation
#4767 Handle NaNs in phase_cross_correlation
#4750 Rewrite INSTALL instructions for python novices
#4739 [WIP] trainable segmentation (algorithm + gallery example)
#4444 WIP: Move RAGs from future to segmentation
#4435 3D Rank Filters WIP
#4390 Lddmm registration
#4382 Hausdorff Distance (updated)
#4121 Crofton perimeter and Euler number

new issues

#4808 skimage/feature/censure_cy.c:16073:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? *type = tstate->exc_type;
#4805 dev doc is not deployed when pre build is failing on Travis
#4802 AttributeError: 'tuple' object has no attribute 'rgb2hsv'
#4801 Monitor the decision taken by sphinx-gallery dev on the thumbnail size in future release
#4799 Prerelease builds broken by matplotlib 3.3.0rc1

Older issues updated last week

#4797 API: replace array by image in measure.find_contours()
#4748 Sphinx gallery issues
#4486 Calendar of community management
#4121 Crofton perimeter and Euler number

Closed issues

#4802 AttributeError: 'tuple' object has no attribute 'rgb2hsv'
#4729 RuntimeWarning in blob.py (division by zero)
#4540 Broken plot in userguide
#1780 maximum Feret diameter in regionprops

@jni
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jni commented Jul 6, 2020

Hello all! And hello @alexdesiqueira, thanks for picking SciPy week to be on call, a brave move! 😅

Here's the summary for last week from @emmanuelle's script. Note that I've modified it to do Monday to Monday at midnight UTC, rather than at whatever time the current maintainer decides to run it. (I'll submit a PR for this tomorrow.) This will make sure that issues etc are always caught by a run of the script.

I'm also going to curate the output to display PRs and issues opened and closed in the same week as crossed out, which should give a better sense of how we are doing on response time. And I'll comment on PRs/issues inline below.

Long term, I want to modify the script to produce some data analysis about how we are doing. Response time, sentiment, etc. Ambitious perhaps but I think it would be both motivating and informative!

Ok enough planning:

2020/6/29 - 2020/7/6

New pull requests open last week

#4823 Richardson-Lucy deconv: add optional filtering, work in > 2d (:point_left: this one just got in during the weekend and I haven't had a chance to comment, can someone take a look?)
#4820 Change feret_diameter to feret_diameter_max (:point_left: needs discussion!)
#4819 Simplify equivalent_diameter function (:point_left: mrg+1)
#4815 Ensure assert messages from Cython rank filters are informative (:point_left: super simple, should be quick review+merge!)
#4812 Tweak threshold_otsu error checking - closes #4811 (:point_left: very close and waiting for second review.)
#4810 allow passing extra measurement functions to regionprops and regionprops_table (:point_left: this is very exciting imho and almost ready, just needs some CI to get fixed! Help appreciated tracking it down!)
#4809 Let biomed example load image data with Pooch.

Closed pull requests (not merged)

none

Merged pull requests

#4809 Let biomed example load image data with Pooch.
#4807 Change SSIM code example to use real MSE
#4806 API change: Replace array by image in measure.find_contour
#4804 Add TODO task for sphinx-gallery>=0.9.0 to remove enforced thumbnail_size
#4795 Add expand_labels function to dilate segments while avoiding overlaps (:point_left: some nice new functionality!)
#4752 Deprecate indices in peak_local_max

Older pull requests with new comments or commits

#4794 add type annotations in some modules in skimage.segmentation (:point_left: this needs comments from the team. What do people think? Do we like type annotations enough to add them everywhere? Or do we want to go with the harder-to-maintain-but-cleaner-to-read annotation stub files?)
#4753 Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max
#4750 Rewrite INSTALL instructions for python novices (:point_left: sphinx issues, otherwise 100% ready, so if anyone has an inclination to flex their sphinx muscles, this is a great candidate to push over the line!)
#4739 [WIP] trainable segmentation (algorithm + gallery example)
#4723 Improving register rotation example with notes and references (:point_left: just merged!)
#4717 Add blind Richardson-Lucy deconvolution (supersedes #3524)
#4619 added one example to flood fill tutorial (:point_left: just merged this now while making these notes! :joy:)
#4444 WIP: Move RAGs from future to segmentation (:point_left: I still need to work on debugging this one...!)
#4435 3D Rank Filters WIP

new issues

#4824 Distance-based discrete interpolation in affine transformation
#4822 DeprecationWarning using segmentation.slic
#4821 regionprops: rename equivalent_diameter -> equivalent_diameter_area (:point_left: needs discussion)
#4818 Does skimage.feature.haar_like_feature computes all the features?
#4817 rename feret_diameter -> max_feret_diameter ? (:point_left: needs discussion)
#4816 skimage.image's ransac function does not handle well when best_inliers are all False
#4814 IndexError when calling hough_line_peaks (:point_left: significant bug)
#4813 Make level parameter optional in measure.find_contours
#4811 threshold_otsu check for single-colour is slow on large arrays
#4808 skimage/feature/censure_cy.c:16073:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? *type = tstate->exc_type;

Older issues updated last week

#4805 dev doc is not deployed when pre build is failing on Travis
#4622 Feature: Weighted phase unwrapping
#4199 Work on Transonic for scikit-image kernels: need small help
#3412 Is it possible to plot half-ellipses?

Closed issues

#4808 skimage/feature/censure_cy.c:16073:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? *type = tstate->exc_type;
#4801 Monitor the decision taken by sphinx-gallery dev on the thumbnail size in future release
#4797 API: replace array by image in measure.find_contours()
#1780 maximum Feret diameter in regionprops

PS

Going through these notes manually, rather than just posting the output, led me to merge two PRs that might have just sat there for months. So it's a really good exercise to go through these slowly at the end of a shift!

Also, thanks to those two merges, we merged 8 PRs this week but 7 were opened, so we are net negative for PRs! 🎉 For issues we are +5 so there is some work to be done! 😬

Again, good luck @alexdesiqueira this week! 😊

@alexdesiqueira
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2020/07/06 - 2020/07/14

Lots of work this week due to our SciPy 2020 sprint. Again, we'd like to thank everyone for your time, discussions and contributions!

new pull requests open last week

#4847 [WIP] Adding @eldad-a's ridge directed ring detector
#4846 DOC: Add a link to Mayavi example for mesh decimation
#4845 DOC: Autoformat docstrings in io.*.py
#4844 fix the issue where ransac fails if all the inliers are false and add tests
#4843 Github action to build docs
#4841 Change structure_tensor to use row/col-notation instead of x/y.
#4840 handle color string mapping correctly
#4839 Update docstring for rgb2lab
#4838 Silence a few RuntimeWarnings in the test suite
#4837 Silence several warnings in the test suite
#4834 MAINT: import Iterable from collections.abc (Python 3.9 compatibility)
#4828 Fix equalize_adapthist (CLAHE) for clip value 1.0, fix docstrings
#4826 style: be explicit when stacking arrays
#4825 DOC: update subpackage descriptions
#4823 Richardson-Lucy deconv: add optional filtering, work in > 2d

closed pull requests (not merged)

#4508 API: Add cross_correlation regularization to register_translation

merged pull requests

#4846 DOC: Add a link to Mayavi example for mesh decimation
#4845 DOC: Autoformat docstrings in io.*.py
#4841 Change structure_tensor to use row/col-notation instead of x/y.
#4839 Update docstring for rgb2lab
#4838 Silence a few RuntimeWarnings in the test suite
#4837 Silence several warnings in the test suite
#4834 MAINT: import Iterable from collections.abc (Python 3.9 compatibility)
#4826 style: be explicit when stacking arrays
#4825 DOC: update subpackage descriptions
#4820 Change feret_diameter to feret_diameter_max
#4819 Simplify equivalent_diameter function
#4815 Ensure assert messages from Cython rank filters are informative
#4812 Tweak threshold_otsu error checking - closes #4811
#4810 allow passing extra measurement functions to regionprops and regionprops_table
#4723 Improving register rotation example with notes and references
#4619 added one example to flood fill tutorial

Older pull requests with new comments or commits

#4800 Use optipng to compress images/thumbnails in our gallery
#4794 add type annotations in some modules in skimage.segmentation
#4739 [WIP] trainable segmentation (algorithm + gallery example)
#4658 Add example for 3D adaptive histogram equalization (AHE)
#4655 equalize_adapthist: More efficient processing scheme with symmetrical padding
#4435 3D Rank Filters WIP
#4390 Lddmm registration
#3772 Compute histograms for multichannel images
#3590 WIP NEW histogram backprojection
#3544 Affine Image Registration

new issues

#4848 Numpy deprecation warning in convert_to_float()
#4842 [doc] width and height order
#4836 pyiodide compatibility
#4835 KeyError: 'ellipse'
#4833 measure.label speed
#4832 Future of graph cuts
#4831 Work on structure_tensor: gallery example, row/col notation, port to 3D
#4830 Key error when using skimage.measure.find_contours
#4829 equalize_adapthist rescales intensities based on global min/max
#4827 equalize_adapthist returns input image for clip value of 1.0
#4824 Distance-based discrete interpolation in affine transformation

older issues updated last week

#4822 DeprecationWarning using segmentation.slic
#4818 Does skimage.feature.haar_like_feature computes all the features?
#4814 IndexError when calling hough_line_peaks
#4813 Make level parameter optional in measure.find_contours
#4805 dev doc is not deployed when pre build is failing on Travis
#4759 Arctan2 being passed arguments in wrong order in Approximate_polygon
#4736 Blob finding runtime warning
#4622 Feature: Weighted phase unwrapping
#4558 segmentation.find_boundaries: different results for different platforms
#4537 Feature request: mesh decimation algorithm
#4534 BUG: name of bg_color is not supported in skimage.color.label2rgb
#4488 Add a link to forum at the bottom of gallery examples
#4486 Calendar of community management
#4455 Add definitions to glossary for disk and perimeter
#4454 Make travis fail on warnings
#4294 Proposal: deprecate multichannel= in favour of channel_axis=
#4284 regionprops_table behaves differently than regionprops list on no-regions found
#3772 Compute histograms for multichannel images
#3590 WIP NEW histogram backprojection
#3547 Allow animations in the documentation
#3544 Affine Image Registration
#3538 Rolling Ball/Sliding Paraboloid Algorithm for background estimation
#3412 Is it possible to plot half-ellipses?
#3384 Missing scientific (domain-specific) images and corresponding examples and tutorials
#2987 WIP: Adds 3D structure tensor capability
#2720 Attempting to build documentation on circle-ci
#2613 SKIP: Consistency of multichannel parameter handling
#2563 Warning in local binary pattern if image dtype is not integer
#1131 Tracing the boundary curve of an image region

closed issues

#4848 Numpy deprecation warning in convert_to_float()
#4835 KeyError: 'ellipse'
#4817 rename feret_diameter -> max_feret_diameter ?
#4811 threshold_otsu check for single-colour is slow on large arrays
#4624 [CI] Build broken with cython 3.0a3
#4514 Specify that rgb2lab function is relative only to sRGB colorspace
#4466 Feature suggestion: passing user-defined measurement functions to regionprops
#1706 added ridge-directed-ring-detector + demo notebook

PS.

@jni:

Going through these notes manually, rather than just posting the output, led me to merge two PRs that might have just sat there for months. So it's a really good exercise to go through these slowly at the end of a shift!

This is a great idea! I tried that in the past, but I couldn't do it effectively yet. I'll try to add it to my process as well.

@emmanuelle
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2020/7/13 - 2020/7/20

It was the week just after the scipy sprint, so quite a lot of activity. #4844, #4847, #4850, #4852 and #4853 are open PRs resulting from the sprint, so let's keep an eye on them (I think #4844 and #4852 can be merged quite soon). #4850 needs a review (3D tutorial).

Our CI is currently broken due to a matplotlib bug with PYTHONOPTIMIZE=2 (see #4854).

There have been interesting discussions in #4794 about type annotations, I'm thinking of organizing a dev meeting which would discuss specifically this topic.

Please also take a look at the list of "Older pull requests with new comments or commits", some of them would need a round of review.

New pull requests open last week

#4853 WIP: Add a boundary tracing algorithm
#4852 Dev/GitHub action doc build
#4851 added rolling ball algorithm example
#4850 Port 3D image processing tutorial into gallery.
#4849 DOC: autoformat docstrings of segmentation/*.py

Closed pull requests (not merged)

#4843 Github action to build docs

Merged pull requests

#4849 DOC: autoformat docstrings of segmentation/.py
#4845 DOC: Autoformat docstrings in io.
.py
#4840 handle color string mapping correctly
#4823 Richardson-Lucy deconv: add optional filtering, work in > 2d
#4820 Change feret_diameter to feret_diameter_max

Older pull requests with new comments or commits

#4847 [WIP] Adding @eldad-a's ridge directed ring detector
#4844 fix the issue where ransac fails if all the inliers are false and add tests
#4828 Fix equalize_adapthist (CLAHE) for clip value 1.0, fix docstrings
#4800 Use optipng to compress images/thumbnails in our gallery
#4794 add type annotations in some modules in skimage.segmentation
#4761 Deprecate min_size in remove_small_objects
#4760 Refactor and fix peack_local_max
#4739 trainable segmentation (algorithm + gallery example)
#4717 Add blind Richardson-Lucy deconvolution (supersedes #3524)
#4390 Lddmm registration
#4165 Add function to remove near objects in nd-image
#3544 Affine Image Registration

new issues

#4854 CI fails with PYTHONOPTIMIZE >= 1 due to matplotlib code using docstring
#4848 Numpy deprecation warning in convert_to_float()

Older issues updated last week

#4836 pyiodide compatibility
#4486 Calendar of community management
#4165 Add function to remove near objects in nd-image
#3544 Affine Image Registration
#3538 Rolling Ball/Sliding Paraboloid Algorithm for background estimation
#3384 Missing scientific (domain-specific) images and corresponding examples and tutorials

Closed issues

#4848 Numpy deprecation warning in convert_to_float()
#4817 rename feret_diameter -> max_feret_diameter ?
#4534 BUG: name of bg_color is not supported in skimage.color.label2rgb

@alexdesiqueira
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2020/7/20 - 2020/7/27

This week we merged the great 3D AHE example and some documentation on how to contribute with a gallery example. Thanks @m-albert @mkcor!

new pull requests open last week

#4861 Update min req for pillow due to CVE-2020-10379 and co.
#4859 WIP Restandardize handling of Multi-Image files (rebased #2815)
#4857 Document how to contribute a gallery example.

closed pull requests (not merged)

none

merged pull requests

#4857 Document how to contribute a gallery example.
#4658 Add example for 3D adaptive histogram equalization (AHE)

Older pull requests with new comments or commits

#4853 WIP: Add a boundary tracing algorithm
#4852 Dev/GitHub action doc build
#4851 New: add rolling ball algorithm for background substraction
#4850 Port 3D image processing tutorial into gallery.
#4847 [WIP] Adding @eldad-a's ridge directed ring detector
#4844 fix the issue where ransac fails if all the inliers are false and add tests
#4828 Fix equalize_adapthist (CLAHE) for clip value 1.0, fix docstrings
#4800 Use optipng to compress images/thumbnails in our gallery
#4794 add type annotations in some modules in skimage.segmentation
#4760 Refactor and fix peack_local_max
#4750 Rewrite INSTALL instructions for python novices
#4655 equalize_adapthist: More efficient processing scheme with symmetrical padding
#4435 3D Rank Filters WIP
#4390 Lddmm registration

new issues

#4860 Pillow security alert
#4858 Proposal: new feature for morphology.skeletonize
#4856 Problem in variation of infromation, should we ignore 0 in pred?
#4855 Proposal: speed up regionprops region finding

older issues updated last week

#4486 Calendar of community management
#3538 Rolling Ball/Sliding Paraboloid Algorithm for background estimation
#3120 Trying to accelerate slic

closed issues

none

@sciunto
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sciunto commented Aug 10, 2020

2020/8/3 - 2020/8/10

Nice features of the week. We now have doc builds for PRs by @emmanuelle . A 3D dataset has been contributed this week by @GenevieveBuckley which is extremely valuable. I noted also the nice ongoing contribution #4851 by @FirefoxMetzger on background substraction, which received a lot of comments already and for which we must converge anytime soon.

We also have several PRs/issues for documentation and performance issues.

New pull requests open last week

#4905 expand the benchmarking section of the developer docs
#4904 Fix and improve entropy example
#4903 WIP: accelerate the masked slic superpixels algorithm
#4901 minor refactoring in phase_cross_correlation
#4898 Changelog back-log
#4897 Minor edit for proper doc rendering
#4896 [WIP] Sphinx gallery thumbnailsoptim
#4893 added script for plausible analytics
#4892 Contributor guide: add info about gitlab repository for data
#4891 Fix benchmarks so they can be run on older scikit-image commits
#4888 Fix Incorrect documentation for skimage.util.img_as_int Issue
#4886 Raise ValueError if NaN found in phase_cross_correlation result

Closed pull requests (not merged)

#4896 [WIP] Sphinx gallery thumbnailsoptim
#4882 [WIP] Circleci doc
#4767 Handle NaNs in phase_cross_correlation

Merged pull requests

#4897 Minor edit for proper doc rendering
#4888 Fix Incorrect documentation for skimage.util.img_as_int Issue
#4886 Raise ValueError if NaN found in phase_cross_correlation result
#4881 build doc on circle ci and link artifact
#4875 Fix variation_of_information
#4872 DOC: Clarify condition on unique vertices returned by marching cubes
#4862 Add default level parameter in measure.find_contours
#4852 Build and deploy dev/master documentation using GitHub Actions
#4850 Port 3D image processing tutorial into gallery.
#4633 MAINT: remove unused cython file

Older pull requests with new comments or commits

#4880 Richardson-Lucy deconvolution: allow single-precision computation
#4878 Add pre-commit configuration and instructions
#4877 Use matplotlib's infinite axline to demonstrate hough transform
#4873 Remove unmaintained wiki page link in contributor guidelines
#4871 Alternative wording for install guide PR #4750
#4863 DOC: First pass at format conversion, rst -> myst
#4861 Update min req for pillow due to CVE-2020-10379 and co.
#4853 WIP: Add a boundary tracing algorithm
#4851 New: add rolling ball algorithm for background substraction
#4800 Use optipng to compress images/thumbnails in our gallery
#4750 Rewrite INSTALL instructions for python novices
#4739 trainable segmentation (algorithm + gallery example)
#4435 3D Rank Filters WIP
#4390 Lddmm registration
#4380 Euler number and Crofton perimeter

new issues

#4902 slic is much slower when using a mask
#4900 IndexError with util.apply_parallel
#4899 Update contributing / core dev notes with more information about CI
#4895 Reversed values in entropy example
#4894 Algorithm to remove padding / find largest valid sub-image given a mask
#4890 Sporadic pooch failures in CI
#4889 Add a note in our documentation/on website saying that we have a gitlab repo
#4887 Incorrect documentation for skimage.util.img_as_int
#4885 Differences between random_noise and numpy.random.poisson
#4884 Incorrect deprecation message for draw.circle
#4883 skimage.segmentation.slic crashes when passed NaNs

Older issues updated last week

#4831 Work on structure_tensor: gallery example, row/col notation, port to 3D
#4822 DeprecationWarning using segmentation.slic
#4537 Feature request: mesh decimation algorithm
#4083 Explore performance of parallel Richardson-Lucy deconvolution
#3384 Missing scientific (domain-specific) images and corresponding examples and tutorials
#3120 Trying to accelerate slic

Closed issues

#4887 Incorrect documentation for skimage.util.img_as_int
#4856 Problem in variation of infromation, should we ignore 0 in pred?
#4842 [doc] width and height order
#4813 Make level parameter optional in measure.find_contours
#4805 dev doc is not deployed when pre build is failing on Travis
#4763 phase_cross_correlation with NaN pixels returns an invalid result
#4736 Blob finding runtime warning
#2720 Attempting to build documentation on circle-ci

@emmanuelle
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2020/8/10 - 2020/8/17

Quite a busy week for mid-August standard. Alex is introducing a new eagle image and replacing the camera man image by a new one due to license issues. This change might cause some tests to fail, so please pay attention to #4913.

#4851 (rolling ball for background substraction) is ready for a round of review. #4390 (lddmm registration) also saw new activity and the API needs to be discussed for this new feature. #4739 (trainable segmentation) is also awaiting a review.

For the coming week we don't have anybody yet registered to be in charge, and same for the following weeks. For this week I can follow up but only until Thursday and then I'm on vacation for 10 days, so we'd need someone else to take over starting from Friday (or for the whole week depending on their availability).

New pull requests open last week

#4924 OpenMP support in MSVC
#4922 Adding data/eagle.png
#4921 Replace words with racial connotations
#4920 Declare build dependencies
#4913 Replacing data/camera.png due to copyright
#4912 Use sparse cross-correlation to accelerate local thresholding functions
#4910 Block sphinx versions for which links from search engine are broken
#4909 Add versionchanged tag for new opt param in measure.find_contours()
#4908 Fix draw.circle/disk deprecation message, fixes #4884
#4907 Fix edge filters do not respect padding mode
#4906 Fix deprecation message in draw.circle()

Closed pull requests (not merged)

#4906 Fix deprecation message in draw.circle()

Merged pull requests

#4921 Replace words with racial connotations
#4909 Add versionchanged tag for new opt param in measure.find_contours()
#4908 Fix draw.circle/disk deprecation message, fixes #4884
#4907 Fix edge filters do not respect padding mode
#4905 expand the benchmarking section of the developer docs
#4904 Fix and improve entropy example
#4901 minor refactoring in phase_cross_correlation
#4893 added script for plausible analytics
#4892 Contributor guide: add info about gitlab repository for data
#4891 Fix benchmarks so they can be run on older scikit-image commits
#4873 Remove unmaintained wiki page link in contributor guidelines
#4863 DOC: First pass at format conversion, rst -> myst

Older pull requests with new comments or commits

#4903 WIP: accelerate the masked slic superpixels algorithm
#4898 Changelog back-log
#4880 Richardson-Lucy deconvolution: allow single-precision computation
#4861 Update min req for pillow due to CVE-2020-10379 and co.
#4851 New: add rolling ball algorithm for background substraction
#4800 Use optipng to compress images/thumbnails in our gallery
#4390 Lddmm registration

new issues

#4923 CI fails with PYTHONOPTIMIZE=2 due to ipywidgets
#4919 scikit-image is not installable from source
#4918 Memory corruption in flood_fill
#4917 hough_line_peaks does not respect min_distance argument
#4916 A short book has been created from your examples
#4915 rgb2gray should work on gray image
#4914 Proposing a substitute for cameraman
#4911 OpenMP build not supported for MSVC

Older issues updated last week

#4900 IndexError with util.apply_parallel (RGB images)
#4883 skimage.segmentation.slic crashes when passed NaNs
#4876 Terminology: n_jobs vs num_workers vs ncpu etc.
#4647 Update blacklisted versions for sphinx in requirement.txt
#4486 Calendar of community management
#4270 Windows Build of 0.16.2 on python 3.6 seems to be incompatible with numpy 1.15.4
#3927 camera(man) image must be removed for license issues
#3384 Missing scientific (domain-specific) images and corresponding examples and tutorials
#2429 2D image warping via thin-plate splines

Closed issues

#4916 A short book has been created from your examples
#4914 Proposing a substitute for cameraman
#4889 Add a note in our documentation/on website saying that we have a gitlab repo
#4884 Incorrect deprecation message for draw.circle
#4854 CI fails with PYTHONOPTIMIZE >= 1 due to matplotlib code using docstring

@alexdesiqueira
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Lots of infrastructure work this week. Also, data/eagle.png is now available 🎉

new pull requests open last week

#4939 Add fluorescence microscopy images to data registry.
#4937 Backport PR #4930 on branch v0.17.x (CI: Skip doc build for PYTHONOPTIMIZE=2)
#4936 Backport PR #4879 on branch v0.17.x (new matomo config)
#4935 Backport PR #4861 on branch v0.17.x (Update min req for pillow due to CVE-2020-10379 and co.)
#4932 MAINT: remove numpydoc option, issue fixed in numpydoc 1.0
#4931 MAINT: Remove custom fused type in skimage/morphology/_max_tree.pyx
#4930 CI: Skip doc build for PYTHONOPTIMIZE=2
#4929 Improve description of h_maxima and h_minima functions (#4928)
#4927 Fixes to apply_parallel for functions working with multichannel data
#4926 swap rectangle variable names
#4924 OpenMP support in MSVC

closed pull requests (not merged)

none

merged pull requests

#4936 Backport PR #4879 on branch v0.17.x (new matomo config)
#4935 Backport PR #4861 on branch v0.17.x (Update min req for pillow due to CVE-2020-10379 and co.)
#4932 MAINT: remove numpydoc option, issue fixed in numpydoc 1.0
#4931 MAINT: Remove custom fused type in skimage/morphology/_max_tree.pyx
#4930 CI: Skip doc build for PYTHONOPTIMIZE=2
#4922 Add new high resolution grayscale image data/eagle.png
#4880 Richardson-Lucy deconvolution: allow single-precision computation
#4861 Update min req for pillow due to CVE-2020-10379 and co.
#4844 fix the issue where ransac fails if all the inliers are false and add tests
#4800 Use optipng to compress images/thumbnails in our gallery

Older pull requests with new comments or commits

#4920 Declare build dependencies
#4913 [WIP] Replacing data/camera.png due to copyright
#4912 Use sparse cross-correlation to accelerate local thresholding functions
#4910 Block sphinx versions for which links from search engine are broken
#4903 accelerate the masked slic superpixels algorithm
#4898 Changelog back-log
#4878 Add pre-commit configuration and instructions
#4871 Alternative wording for install guide PR #4750
#4859 WIP Restandardize handling of Multi-Image files (rebased #2815)
#4853 WIP: Add a boundary tracing algorithm
#4851 New: add rolling ball algorithm for background substraction
#4847 [WIP] Adding @eldad-a's ridge directed ring detector
#4828 Fix equalize_adapthist (CLAHE) for clip value 1.0, fix docstrings
#4762 [WIP] wip on viz libraries
#4435 3D Rank Filters WIP
#4390 Lddmm registration
#4126 morphology.rectangle() dimensions swapped, Fixes Issue #4125

new issues

#4938 skimage.draw.polygon segmentation fault with np.nan
#4934 ipywidgets somehow making Travis fail on py3.6
#4933 Deprecate skivi
#4928 morphology.extrema.h_maxima and h_minima: slightly confusing function descriptions
#4925 width and height swapped in morphology.rectangle

older issues updated last week

#4919 scikit-image is not installable from source
#4915 rgb2gray should work on gray image
#4900 IndexError with util.apply_parallel (RGB images)
#4869 image description in docstring: towards uniformity?
#4786 Backport bugfix #4771
#4748 Sphinx gallery issues
#4647 Update blocked versions for sphinx in requirement.txt
#4537 Feature request: mesh decimation algorithm
#4486 Calendar of community management
#4407 array or ndarray as argument type documentation?
#4259 Bump numpy to >= 1.16
#4126 morphology.rectangle() dimensions swapped, Fixes Issue #4125
#4081 Consider deprecating viewer and skivi
#3846 Identifying scikit-image incompatibilities with dask input arrays

closed issues

#4934 ipywidgets somehow making Travis fail on py3.6
#4933 Deprecate skivi
#4925 width and height swapped in morphology.rectangle
#4923 CI fails with PYTHONOPTIMIZE=2 due to ipywidgets
#4895 Reversed values in entropy example
#4860 Pillow security alert
#4816 skimage.image's ransac function does not handle well when best_inliers are all False
#4799 Prerelease builds broken by matplotlib 3.3.0rc1
#4625 Optimize gallery images with optipng
#3853 References formatting is broken in plot_segmentations

@rfezzani
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Last week was quite productive with two bug fixes merged! Thanks to @sciunto we also now deprecate skivi 🎉 I would be very happy if we keep moving on this way and soon deprecate skimage.io and skimage.viewer 😉.

I just finally want to bring your attention to a decision to be taken concerning edge cases of peak_local_max

new pull requests open last week

#4953 Add (interactive) slice explorer in plotly.
#4952 Provide a public method for iradon_filters
#4951 Add missing datasets to public API
#4950 DRAFT: Iradon filter tests 2020
#4948 Fix corrupt floodfill
#4947 modify development version string to allow use with NumpyVersion
#4946 Start example using 3D multichannel image.
#4945 PERF: improve label speed for bool input by using the scipy.ndimage implementation
#4943 Fix draw.polygon segfault caused by 0d input
#4942 MAINT: remove deprecated parameter neighbors in measure.label()
#4941 Deprecate qt and skivi plugins in skimage.io
#4939 Add fluorescence microscopy images to data registry.

closed pull requests (not merged)

#4950 DRAFT: Iradon filter tests 2020
#4670 [WIP] Make Pooch lazily create directories for python 3.7+

merged pull requests

#4947 modify development version string to allow use with NumpyVersion
#4945 PERF: improve label speed for bool input by using the scipy.ndimage implementation
#4943 Fix draw.polygon segfault caused by 0d input
#4942 MAINT: remove deprecated parameter neighbors in measure.label()
#4941 Deprecate qt and skivi plugins in skimage.io
#4926 swap rectangle variable names

Older pull requests with new comments or commits

#4937 Backport PR #4930 on branch v0.17.x (CI: Skip doc build for PYTHONOPTIMIZE=2)
#4920 Declare build dependencies
#4912 Use sparse cross-correlation to accelerate local thresholding functions
#4910 Block sphinx versions for which links from search engine are broken
#4853 WIP: Add a boundary tracing algorithm
#4851 New: add rolling ball algorithm for background substraction
#4828 Fix equalize_adapthist (CLAHE) for clip value 1.0, fix docstrings
#4760 Refactor and fix peak_local_max
#4753 Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max
#4435 3D Rank Filters WIP
#4390 Lddmm registration
#4215 WIP Accelerate fundamental functions with OpenCL using gputools

new issues

#4949 Unable to install on Nvidia Xavier. Stuck at 100%.
#4944 Is filled_area in measure.regionprop wrong? -> regionprop fails to fill a shape
#4940 Add a way to drop rows / columns of un-dividable 2D arrays using 'block_reduce'
#4938 skimage.draw.polygon segmentation fault with np.nan

older issues updated last week

#4918 Memory corruption in flood_fill
#4917 hough_line_peaks does not respect min_distance argument
#4915 rgb2gray should work on gray image
#4830 Key error when using skimage.measure.find_contours
#4749 Deprecate edge cases in peak_local_max
#4486 Calendar of community management
#4407 array or ndarray as argument type documentation?
#4215 WIP Accelerate fundamental functions with OpenCL using gputools
#4081 Consider deprecating viewer and skivi
#3099 iradon filter function
#2616 WIP: document our guidelines/coding conventions
#1131 Tracing the boundary curve of an image region

closed issues

#4938 skimage.draw.polygon segmentation fault with np.nan
#4833 measure.label speed
#4126 morphology.rectangle() dimensions swapped, Fixes Issue #4125
#4125 BUG: morphology.rectangle() dimensions swapped

@sciunto
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sciunto commented Sep 7, 2020

2020/8/31 - 2020/9/7

During this first week of september, the activity was lower than usual. We had a broken CI for two reasons. With @hmaarrfk we worked on fixing it. There is still issues with OSX jobs on travis caused by a timeout. We added a verbose flag to the command, which helps from time to time, but is not always sufficient. We were unsuccessful applying correctly travis_wait, we must try again. See #4955

I noted activities around PRs on 3D data sets by @mkcor and @hmaarrfk

I also made triage on old issues.

New pull requests open last week

#4963 Fix typo.
#4962 Alias for data.chelsea: data.cat()
#4960 Fix CI: ban sphinx-gallery 0.8.0
#4959 TEST - DO NOT MERGE remove lily
#4957 PERF: faster Hog computation
#4956 CI: Add verbose option to avoid travis timeout for OSX install script
#4954 Deprecate viewer and skivi script, will be removed in 0.20
#4953 Add (interactive) slice explorer in plotly.

Closed pull requests (not merged)

#4959 TEST - DO NOT MERGE remove lily
#4750 Rewrite INSTALL instructions for python novices

Merged pull requests

#4963 Fix typo.
#4960 Fix CI: ban sphinx-gallery 0.8.0
#4956 CI: Add verbose option to avoid travis timeout for OSX install script
#4954 Deprecate viewer and skivi script, will be removed in 0.20
#4945 PERF: improve label speed for bool input by using the scipy.ndimage implementation
#4939 Add fluorescence microscopy images to data registry.
#4937 Backport PR #4930 on branch v0.17.x (CI: Skip doc build for PYTHONOPTIMIZE=2)
#4929 Improve description of h_maxima and h_minima functions (#4928)
#4927 Fixes to apply_parallel for functions working with multichannel data
#4912 Use sparse cross-correlation to accelerate local thresholding functions
#4871 Alternative wording for install guide PR #4750

Older pull requests with new comments or commits

#4951 Add missing datasets to public API
#4948 Fix corrupt floodfill
#4913 [WIP] Replacing data/camera.png due to copyright
#4903 accelerate the masked slic superpixels algorithm
#4853 WIP: Add a boundary tracing algorithm
#4851 New: add rolling ball algorithm for background substraction
#4753 Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max
#4399 Boost Haar feature calculation for meeting training and real-time inference request
#4390 Lddmm registration
#4214 Usage of util.apply_parallel in tutorial_parallelization.rst.
#3524 Blind Richardson–Lucy deconvolution
#3386 Example batch processing

new issues

#4961 Raster-to-vector conversion of color images using scikit-image.
#4958 CI failure, path issue for windows in gallery
#4955 Random frequent CI failures due to tex and travis timeout

Older issues updated last week

#4944 measure.regionprop fails to fill a circle, filled_area is wrong
#4917 hough_line_peaks does not respect min_distance argument
#4537 Feature request: mesh decimation algorithm
#4486 Calendar of community management
#4214 Usage of util.apply_parallel in tutorial_parallelization.rst.
#3927 camera(man) image must be removed for license issues
#3524 Blind Richardson–Lucy deconvolution
#3386 Example batch processing
#2239 Moments documentation is confusing to users
#1131 Tracing the boundary curve of an image region

Closed issues

#4961 Raster-to-vector conversion of color images using scikit-image.
#4958 CI failure, path issue for windows in gallery
#4955 Random frequent CI failures due to tex and travis timeout
#4949 Unable to install on Nvidia Xavier. Stuck at 100%.
#4928 morphology.extrema.h_maxima and h_minima: slightly confusing function descriptions
#4900 IndexError with util.apply_parallel (RGB images)
#4833 measure.label speed
#4822 DeprecationWarning using segmentation.slic
#4780 Getting "ImportError: DLL load failed: The specified module could not be found."
#4081 Consider deprecating viewer and skivi
#3328 Coverage low hanging fruits

@jni
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jni commented Sep 14, 2020

Hi @alexdesiqueira! Here's the report for this week. =) We're -2 on PRs (:tada:) but +1 on issues (:disappointed:). Pretty good week though. :blush:

Note: I manually edited the report below to mark the PRs that were opened and closed this week.

2020/9/7 - 2020/9/14

New pull requests open last week

#4973 forbid latest version of pyqt MERGED
#4972 Fix floodfill segmentation fault MERGED
#4970 MAINT: Remove conditional import on networkx MERGED
#4968 MAINT: remove unused imports MERGED
#4967 Small enhancement in "Contour finding" example: Removed unused variable n MERGED
#4966 Accelerate gamma_adjust for uint8 images MERGED
#4965 CI: Use Travis wait improved to avoid timeout for OSX builds MERGED
#4964 Delegate standard images load to imageio

Closed pull requests (not merged)

none

Merged older pull requests

#4962 Alias for data.chelsea: data.cat()
#4948 Fix corrupt floodfill
#4903 accelerate the masked slic superpixels algorithm

Older pull requests with new comments or commits

#4957 PERF: faster Hog computation
#4953 Add (interactive) slice explorer in plotly.
#4952 Provide a public method for iradon_filters
#4951 Add missing datasets to public API
#4913 [WIP] Replacing data/camera.png due to copyright
#4851 New: add rolling ball algorithm for background substraction
#4761 Deprecate min_size in remove_small_objects
#4760 Refactor and fix peak_local_max
#4753 Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max
#4739 trainable segmentation (algorithm + gallery example)
#4435 3D Rank Filters WIP
#4390 Lddmm registration
#4380 Euler number and Crofton perimeter
#4291 New threshold_tpoint function
#4161 Add the iterative Lucas-Kanade (iLK) optical flow method
#3772 Compute histograms for multichannel images

new issues

#4971 Write a piece of documentation on data.download_all() in the install procedure
#4969 Tackle remaining todo tasks for 0.18

Older issues updated last week

#4902 slic is much slower when using a mask
#4890 Sporadic pooch failures in CI
#4486 Calendar of community management
#4291 New threshold_tpoint function
#4161 Add the iterative Lucas-Kanade (iLK) optical flow method
#3772 Compute histograms for multichannel images
#2704 Gabor filters are not 3-D compatible
#2698 RANSAC: Check for updates
#2239 Moments documentation is confusing to users

Closed issues

#4918 Memory corruption in flood_fill

@alexdesiqueira
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2020/9/14 – 2020/9/21

I'd consider not too much movement this week (although I was taking care of #4913, so didn't see too much outside that 🙂 ). We had our Atlantic meeting today — with @emmanuelle @jni @grlee77 @lagru @sciunto and myself — preparing for 0.18. Great to see you all!

new pull requests open last week

#4974 Remove warnings/explicit settings on feature, restoration
#4973 forbid latest version of pyqt

closed pull requests (not merged)

none

merged pull requests

#4973 forbid latest version of pyqt
#4966 Accelerate gamma_adjust for uint8 images

Older pull requests with new comments or commits

#4953 Add (interactive) slice explorer in plotly.
#4952 Provide a public method for iradon_filters
#4951 Add missing datasets to public API
#4913 Replacing data/camera.png due to copyright
#4760 Refactor and fix peak_local_max
#4753 Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max
#4739 trainable segmentation (algorithm + gallery example)
#4444 WIP: Move RAGs from future to segmentation
#4435 3D Rank Filters WIP
#4390 Lddmm registration
#4380 Euler number and Crofton perimeter
#4161 Add the iterative Lucas-Kanade (iLK) optical flow method

new issues

#4979 TypeError: unexpected keyword argument: img_num
#4978 skimage.feature.peak_local_max problem
#4977 Error using scikit-image
#4976 graph module goal_reached method not implemented?
#4975 Faster SLIC implementation

older issues updated last week

#4971 Write a piece of documentation on data.download_all() in the install procedure
#4969 Tackle remaining todo tasks for 0.18
#4855 Proposal: speed up regionprops region finding
#4486 Calendar of community management
#4161 Add the iterative Lucas-Kanade (iLK) optical flow method
#3538 Rolling Ball/Sliding Paraboloid Algorithm for background estimation

closed issues

#4978 skimage.feature.peak_local_max problem
#4977 Error using scikit-image
#4976 graph module goal_reached method not implemented?
#4902 slic is much slower when using a mask

@emmanuelle
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2020/9/21 - 2020/9/28

Not a lot of new PRs this week, but I think this is because the core team is busy trying to merge existing ones (the "Older pull requests with new comments or commits") for the 0.18 milestone https://github.com/scikit-image/scikit-image/pulls?q=is%3Aopen+is%3Apr+milestone%3A0.18

We need someone for next week!

New pull requests open last week

#4986 try to fix timeout problem with circleci MERGED
#4984 Add instructions to download the entire dataset
#4983 Docstring improvements for label and regionprops_label CLOSED
#4981 3D rank filters (ctd', follow up of 4435) CLOSED

Closed pull requests (not merged)

#4981 3D rank filters (ctd', follow up of 4435)

Merged pull requests

#4986 try to fix timeout problem with circleci
#4983 Docstring improvements for label and regionprops_label
#4974 Remove warnings/explicit settings on feature, restoration
#4920 Declare build dependencies

Older pull requests with new comments or commits

#4924 OpenMP support in MSVC
#4913 Replacing data/camera.png due to copyright
#4851 New: add rolling ball algorithm for background substraction
#4739 trainable segmentation (algorithm + gallery example)
#4444 WIP: Move RAGs from future to segmentation
#4390 Lddmm registration
#4380 Euler number and Crofton perimeter
#4161 Add the iterative Lucas-Kanade (iLK) optical flow method
#4087 WIP: Allow regionprops to reuse objects
#3883 move the location of fast_exp to help compilation with strange flags

new issues

#4987 Pyinstaller cannot implement scikit-image
#4985 Issue in Structural_Similarity and SSIM MATLAB implementation
#4982 ImportError: cannot import name 'phase_cross_correlation' from 'skimage.registration'
#4980 phase_cross_correlation does not work with 3D arrays and masks

Older issues updated last week

#4883 skimage.segmentation.slic crashes when passed NaNs
#4764 API inconsistency: phase_cross_correlation does not return error & phasediff
#4486 Calendar of community management
#4161 Add the iterative Lucas-Kanade (iLK) optical flow method
#4087 WIP: Allow regionprops to reuse objects
#3883 move the location of fast_exp to help compilation with strange flags

Closed issues

#4985 Issue in Structural_Similarity and SSIM MATLAB implementation
#4982 ImportError: cannot import name 'phase_cross_correlation' from 'skimage.registration'
#4969 Tackle remaining todo tasks for 0.18
#4919 scikit-image is not installable from source

@mkcor
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mkcor commented Oct 5, 2020

2020/9/28 - 2020/10/4

This has been my first week as the person in charge, yay! I'm not sure I've followed everything as closely as I should have; the beginning of the week was pretty quiet.

PS: Just so you know, the utility script for this weekly update spit out "2020/9/28 - 2020/10/5" as the title for this post, and I shamelessly edited to "2020/9/28 - 2020/10/4" (meant to fix the inconsistency, but then I ran out of GitHub API pokes, even though I generated a token, but didn't export it, and anyway... next time). 😉

New pull requests open last week

#5006 Refactoring: threshold methods with histogram parameters
#5003 Update sphinx mapping for sklearn and numpy
#5002 [WIP] Make structure_tensor support 3d
#5001 Update docstring for random_noise function
#4999 Update Hough ellipse
#4997 Let tifffile.imread handle additional keyword arguments
#4992 Catch leftover typos in INSTALL file.
#4991 Proofread INSTALL file.
#4990 [website] Standardize Documentation index page.
#4989 improve Euler number example

Closed pull requests (not merged)

none

Merged pull requests

#5003 Update sphinx mapping for sklearn and numpy
#5001 Update docstring for random_noise function
#4997 Let tifffile.imread handle additional keyword arguments
#4992 Catch leftover typos in INSTALL file.
#4991 Proofread INSTALL file.
#4989 improve Euler number example
#4984 Add instructions to download the entire dataset
#4913 Replacing data/camera.png due to copyright

Older pull requests with new comments or commits

#4953 Add (interactive) slice explorer in plotly.
#4946 Start example using 3D multichannel image.
#4924 OpenMP support in MSVC
#4851 New: add rolling ball algorithm for background substraction
#4760 Refactor and fix peak_local_max
#4444 WIP: Move RAGs from future to segmentation

new issues

#5007 Is the structural similarity index calculated correctly within skimage?
#5005 (Windows 10) import skimage.io is not work for me
#5004 Expression for speckle noise addition might need correction
#5000 Docstring of the function random_noise requires correction
#4998 Resizing a binary image as a bool array failed to produced the result as expected.
#4996 CI broken on master following tifffile release
#4995 Active Contour does not work properly
#4994 Not able to install scikit-image
#4993 Update documentation to new data.camera()
#4988 Add link to API in website homepage

Older issues updated last week

#4987 Pyinstaller cannot implement scikit-image
#4883 skimage.segmentation.slic crashes when passed NaNs
#4868 More default values for parameters
#4865 Why is morphology.convex_hull_object 2D only?
#4831 Work on structure_tensor: gallery example, row/col notation, port to 3D
#4748 Sphinx gallery issues
#4486 Calendar of community management
#3812 Regionprops for 3D surfaces and perimeters

Closed issues

#5000 Docstring of the function random_noise requires correction
#4998 Resizing a binary image as a bool array failed to produced the result as expected.
#4996 CI broken on master following tifffile release
#4995 Active Contour does not work properly
#4994 Not able to install scikit-image
#4971 Write a piece of documentation on data.download_all() in the install procedure
#4161 Add the iterative Lucas-Kanade (iLK) optical flow method
#3927 camera(man) image must be removed for license issues
#716 Adding a mask parameter to SLIC segmentation

@alexdesiqueira
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2020/10/5 - 2020/10/12

Some movement this week. I'll point to #4898, which will help a lot when we release 0.18. #4739 needs some reviews; please check it out if you can.

new pull requests open last week

#5018 [WIP] Update documentation to new data.camera()
#5017 Fix usage of numpy.pad for old versions of numpy
#5016 Bump numpy versions to match scipy (kinda)
#5015 Updates to setup.py
#5014 Update docstring slic superpixels
#5013 Added README to binary (wheel) distribution
#5012 Add gallery example for structure_tensor... in 3D!
#5010 example with interactive exploration of properties obtained with regionprops

closed pull requests (not merged)

#5013 Added README to binary (wheel) distribution

merged pull requests

#5017 Fix usage of numpy.pad for old versions of numpy
#5010 example with interactive exploration of properties obtained with regionprops
#5002 Make structure_tensor support 3d
#4990 [website] Standardize Documentation index page.

Older pull requests with new comments or commits

#5006 Refactoring: threshold methods with histogram parameters
#4999 Update Hough ellipse
#4898 Changelog back-log
#4760 Refactor and fix peak_local_max
#4739 trainable segmentation (algorithm + gallery example)
#4390 Lddmm registration

new issues

#5019 MemoryError in computing Convex Hull of a large 3D image
#5011 No DLL module _fblas when importing skimage.io
#5009 AttributeError: module 'skimage' has no attribute 'filters' (On Ubuntu 20.04, conda-forge channel installation)
#5008 TypeError: _open() got an unexpected keyword argument 'as_grey'
#5007 Is the structural similarity index calculated correctly within skimage?

older issues updated last week

#4993 Update documentation to new data.camera()
#4883 skimage.segmentation.slic crashes when passed NaNs
#4831 Work on structure_tensor: gallery example, row/col notation, port to 3D
#4486 Calendar of community management
#2591 Divide by Zero Error in exposure.py:465

closed issues

#5011 No DLL module _fblas when importing skimage.io
#5009 AttributeError: module 'skimage' has no attribute 'filters' (On Ubuntu 20.04, conda-forge channel installation)
#5008 TypeError: _open() got an unexpected keyword argument 'as_grey'
#5007 Is the structural similarity index calculated correctly within skimage?
#5005 (Windows 10) import skimage.io is not work for me
#3019 Small bug in skimage.feature.peak_local_max()
#1912 MCP_Geometric generates negative cumulative costs
#1035 Interpolation: fast code path may yield different results

@rfezzani
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Last week was in positive balance with 6 new PR VS 6 merged PR and 4 closed issues VS 3 new ones 🎉. I just want to draw your attention to #5020, #5006, #4760 and #4739 for some review, thank you all 😉.

new pull requests open last week

#5024 Fix IndexError when calling hough_line_peaks with too few angles
#5021 bumped plotly requirement for docs
#5020 ENH: Reduce memory use for convex_hull_image by checking hull inequalities in sequence
#5018 [MRG] Update documentation to new data.camera()
#5017 Fix usage of numpy.pad for old versions of numpy
#5016 Bump numpy versions to match scipy (kinda)

merged pull requests

#5021 bumped plotly requirement for docs
#5018 [MRG] Update documentation to new data.camera()
#5017 Fix usage of numpy.pad for old versions of numpy
#5016 Bump numpy versions to match scipy (kinda)
#5014 Update docstring slic superpixels
#4898 Changelog back-log

Older pull requests with new comments or commits

#5015 Updates to setup.py
#5012 Add gallery example for structure_tensor... in 3D!
#5006 Refactoring: threshold methods with histogram parameters
#4951 Add missing datasets to public API
#4828 Fix equalize_adapthist (CLAHE) for clip value 1.0, fix docstrings
#4760 Refactor and fix peak_local_max
#4739 trainable segmentation (algorithm + gallery example)

new issues

#5025 Possible data type issue and unchecked parameter limit with local_binary_pattern
#5022 Store pivchallenge data on gitlab
#5019 MemoryError in computing Convex Hull of a large 3D image

older issues updated last week

#4865 Why is morphology.convex_hull_object 2D only?

closed issues

#4993 Update documentation to new data.camera()
#3019 Small bug in skimage.feature.peak_local_max()
#2591 Divide by Zero Error in exposure.py:465
#1912 MCP_Geometric generates negative cumulative costs

@jni
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jni commented Oct 19, 2020

Thank you @rfezzani! Gotta love paying down that debt! 🎉

I notice another gap in the calendar. I'll take this week. Been wanting to make another push on 0.18! 🤞

@jni
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jni commented Oct 27, 2020

2020/10/19 - 2020/10/26

Hi everyone,

Last week was pretty quiet but we still managed to accrue a negative balance. 😞 I made a push on #4444 (thank you @emmanuelle for the help there) as well as some issues related to 0.18.

As always, I'd like to point everyone to the list of PRs with one approved review, to see if we can merge some of these soon!

New pull requests open last week

#5030 Fixes broken link to CODE_OF_CONDUCT.md
#5029 Fix point_in_polygon
#5027 Code simplification after latest numpy bump
#5026 Deconvolution with Gauss Prior

Closed pull requests (not merged)

none

Merged pull requests

#5030 Fixes broken link to CODE_OF_CONDUCT.md
#5027 Code simplification after latest numpy bump

Older pull requests with new comments or commits

#5020 ENH: Reduce memory use for convex_hull_image by checking hull inequalities in sequence
#5006 Refactoring: threshold methods with histogram parameters
#4999 Update Hough ellipse
#4951 Add missing datasets to public API
#4828 Fix equalize_adapthist (CLAHE) for clip value 1.0, fix docstrings
#4760 Refactor and fix peak_local_max
#4739 trainable segmentation (algorithm + gallery example)
#4444 WIP: Move RAGs from future to segmentation
#4342 Refactor canny edge detector
#3883 move the location of fast_exp to help compilation with strange flags
#3329 Fix #3327: Add functionality for benchmark coverage

new issues

#5036 Discussion: deprecating (most of) skimage.io in favour of imageio
#5035 Idea: additive regionprops
#5034 random_walker segmentation can create incorrect laplacian matrix
#5033 threshold_li could be sped up by using histogram
#5032 Error appeared everytime i ran sckit image
#5031 mark_boundaries documentation needs improvement
#5028 Remove usage of numpy's private functions
#5025 Possible data type issue and unchecked parameter limit with local_binary_pattern

Older issues updated last week

#4883 skimage.segmentation.slic crashes when passed NaNs
#4486 Calendar of community management
#4342 Refactor canny edge detector
#3929 skimage.draw.ellipse_perimeter falls into an endless loop
#3892 some edge points not included in points_in_poly result
#3883 move the location of fast_exp to help compilation with strange flags
#3828 "Dilation" of drawing function outputs
#3329 Fix #3327: Add functionality for benchmark coverage

Closed issues

@alexdesiqueira
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2020/11/02 – 2020/11/09

Please keep an eye on #5053 y'all; we're dropping support to py3.6 and improving machinery for py3.8.

new pull requests open last week

#5057 [WIP] Use nep29 to help with the Python 3.6 -> 3.9 transition
#5056 Clarify disk documentation inconsistency regarding 'shape'
#5055 debug travis build
#5054 fix Azure Pipelines, pytest config, and trove classifiers for Python 3.8
#5052 update trove classifiers and tests for Python 3.9 + fix pytest config
#5050 [ENH] Changing threshold_li using histogram for integer images
#5046 [WIP] Drop python 3.6 from the build matrix
#5045 [WIP] Automate release process

closed pull requests (not merged)

#5055 debug travis build
#5046 [WIP] Drop python 3.6 from the build matrix

merged pull requests

#5054 fix Azure Pipelines, pytest config, and trove classifiers for Python 3.8
#5006 Refactoring: threshold methods with histogram parameters
#4760 Refactor and fix peak_local_max

Older pull requests with new comments or commits

#4342 Refactor canny edge detector

new issues

#5053 dropping 3.6 and a few other things
#5051 pip install error: implicit declaration of function 'unwrap2D' is invalid in C99
#5049 Missing documentation for ordering of labels in skimage.measure.label
#5048 when missing intensity_image, regionprop_table fails with less explicit error message than regionprop
#5047 feature.peak_local_max changes labels

older issues updated last week

#5038 disk Inconsistency between shape=None and shape=actual_shape
#5036 Discussion: deprecating (most of) skimage.io in favour of imageio
#5033 threshold_li could be sped up by using histogram
#5028 Remove usage of numpy's private functions
#4766 Missing attribute 'offsets' in skimage.graph.MCP_Geometric
#4342 Refactor canny edge detector

closed issues

#5047 feature.peak_local_max changes labels
#4756 Peaks may not be detected in peak_local_max when label is provided
#4743 Wrong MSE computation in the SSIM code example
#3990 Trivial image check for peak_local_max
#2592 peak_local_max fails to enforce min_distance

@mkcor
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mkcor commented Nov 16, 2020

2020/11/9 - 2020/11/16

Hello! Since they don't appear below, maybe I should draw our attention to PRs #2815 and #3070 ? Both are in for 0.18 and have one approval at the moment.

New pull requests open last week

#5067 reduce OSX build time so that Travis is happy
#5062 Optimize ensure_spacing
#5059 MAINT Build fix for pyodide

Closed pull requests (not merged)

none

Merged pull requests

#5067 reduce OSX build time so that Travis is happy
#5006 Refactoring: threshold methods with histogram parameters

Older pull requests with new comments or commits

#5057 [WIP] Use nep29 to help with the Python 3.6 -> 3.9 transition
#5056 Clarify disk documentation inconsistency regarding 'shape'
#5052 update trove classifiers and tests for Python 3.9 + fix pytest config
#5050 [ENH] Changing threshold_li using histogram for integer images
#4342 Refactor canny edge detector

new issues

#5066 OSX build in Travis is taking too long
#5065 poetry add scikit-image fails with WinError 123
#5064 enable scipy grid-constant boundary handling
#5063 pip install scikit-image fails for python3.9 freshly installed with brew
#5061 ensure_spacing function may be slow
#5060 pip install fails under Python 3.9 if numpy isn't already installed
#5058 Frangi/Hessian for Anisotropic Voxel

Older issues updated last week

#5053 dropping 3.6 and a few other things
#5051 pip install error: implicit declaration of function 'unwrap2D' is invalid in C99
#4486 Calendar of community management
#4342 Refactor canny edge detector

Closed issues

#5063 pip install scikit-image fails for python3.9 freshly installed with brew
#1585 Inconsistent 2D vs 3D interpolation behavior for mode 'reflect'

@rfezzani
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rfezzani commented Dec 2, 2020

Oups! I am so sorry, I just realized that it was my turn last week 😞

@NinjaAtWork
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Oups! I am so sorry, I just realized that it was my turn last week 😞

you will change that emoji to something glad if you realize that your effort will happy a kid in paint by python app and or continue to rescue a father from cancer die by scikit scientific image recognition :)

@grlee77
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grlee77 commented Dec 7, 2020

2020/11/30 - 2020/12/7

The last week has mostly been work related to preparing the 0.18 release. In the last few weeks, CI and wheel building jobs were moved off of Travis-CI now that free credits are much more limited. We may keep ARM wheel builds on Travis, but all x86 jobs have been moved elsewhere.

A new proposed feature is installing scikit-image[data] instead of just scikit-image to get an install with the optional pooch dependency included. The lazy importing proposed in #5101 looks like a nice convenience.

Also, there is a request for comments on imagio API imageio/imageio#569 (related to IO offloading issue #5036)

New pull requests open last week

#5111 Recent backports from skimage master
#5110 Backport PR #5104 on branch v0.18.x (Use v{} for version tags with pooch)
#5109 revert bool back to np.bool_ for np.issubdtype calls
#5108 Backport PR #5103 on branch v0.18.x (Replace np.bool, np.int, np.float with bool, int, float)
#5107 Fix compilation error in XCode 12
#5106 Add 0.18 release notes (#5085)
#5105 Add data optional reqs to allow pip install scikit-image[data]
#5104 Use v{} for version tags with pooch
#5103 Replace np.bool, np.int, np.float with bool, int, float
#5101 Implement lazy submodule importing
#5099 disable Travis-CI builds
#5098 Add builds for aarch64
#5097 Improvements to CircleCI build: no parallelization and caching
#5096 Backport PR #5094 on branch v0.18.x (added link to imagesc forum in example pages)
#5094 added link to imagesc forum in example pages
#5090 BUG: random_walker: fix import path for umfpack

Closed pull requests (not merged)

none

Merged pull requests

#5109 revert bool back to np.bool_ for np.issubdtype calls
#5108 Backport PR #5103 on branch v0.18.x (Replace np.bool, np.int, np.float with bool, int, float)
#5107 Fix compilation error in XCode 12
#5105 Add data optional reqs to allow pip install scikit-image[data]
#5104 Use v{} for version tags with pooch
#5103 Replace np.bool, np.int, np.float with bool, int, float
#5099 disable Travis-CI builds
#5097 Improvements to CircleCI build: no parallelization and caching
#5096 Backport PR #5094 on branch v0.18.x (added link to imagesc forum in example pages)
#5094 added link to imagesc forum in example pages
#5090 BUG: random_walker: fix import path for umfpack
#4924 OpenMP support in MSVC

Older pull requests with new comments or commits

#4762 [WIP] wip on viz libraries

new issues

#5112 Feature request: add voxel spacing to skimage.measure.regionprops
#5102 feret_diameter_max not available
#5100 skimage.measure.label is not working correctly for non binary 3d array
#5095 Image License correction
#5093 SLIC does not work for grayscale images, or RGB with convert2lab = False
#5092 issue: centroid property of skimage.measure.regionprops is outside of regions
#5091 Building from source on master fails on Windows 10.0.19041

Older issues updated last week

#5087 Feature request: points to labels
#5036 Discussion: deprecating (most of) skimage.io in favour of imageio
#4537 Feature request: mesh decimation algorithm
#4507 Automatic color generation in the label2rgb function
#4486 Calendar of community management

Closed issues

#5100 skimage.measure.label is not working correctly for non binary 3d array
#5093 SLIC does not work for grayscale images, or RGB with convert2lab = False
#5066 OSX build in Travis is taking too long
#5051 pip install error: implicit declaration of function 'unwrap2D' is invalid in C99
#4890 Sporadic pooch failures in CI
#4488 Add a link to forum at the bottom of gallery examples

@alexdesiqueira
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2020/12/07 - 2020/12/15

Lots of movement this week as we (as in @jni 🙂) prepare our 0.18 release! Thank you all for your hard work!

new pull requests open last week

#5137 Update release notes with latest backports
#5136 Backport PR #5126 on branch v0.18.x (Proofread gallery example for rank filters.)
#5135 Backport PR #5062 on branch v0.18.x (Optimize ensure_spacing)
#5134 Improve error message when installing from source and cython isn't installed.
#5133 Backport PR #5131 on branch v0.18.x (consistent zoom boundary behavior across SciPy versions)
#5132 Backport PR #2815 on branch v0.18.x (Restandardize handling of Multi-Image files)
#5131 consistent zoom boundary behavior across SciPy versions
#5129 Backport PR #5128 on branch v0.18.x (Add farid filters in all, to populate the documentation)
#5128 Add farid filters in all, to populate the documentation
#5126 Proofread gallery example for rank filters.
#5125 Backport PR #5117 on branch v0.18.x (Remove Python 3.6 support)
#5123 Backport PR #5115 on branch v0.18.x (change plausible script to track outbound links)
#5120 example to show the 3d dataset
#5119 Backport PR #5097 on branch v0.18.x (Improvements to CircleCI build: no parallelization and caching)
#5118 Backport PR #5116 on branch v0.18.x (added missing datasets to gallery examples)
#5117 Remove Python 3.6 support
#5116 added missing datasets to gallery examples
#5115 change plausible script to track outbound links
#5114 Deprecate high_threshold and low_threshold in canny
#5113 Update release notes with latest backported changes from master
#5111 Recent backports from skimage master
#5110 Backport PR #5104 on branch v0.18.x (Use v{} for version tags with pooch)

closed pull requests (not merged)

#5114 Deprecate high_threshold and low_threshold in canny

merged pull requests

#5137 Update release notes with latest backports
#5136 Backport PR #5126 on branch v0.18.x (Proofread gallery example for rank filters.)
#5135 Backport PR #5062 on branch v0.18.x (Optimize ensure_spacing)
#5134 Improve error message when installing from source and cython isn't installed.
#5133 Backport PR #5131 on branch v0.18.x (consistent zoom boundary behavior across SciPy versions)
#5132 Backport PR #2815 on branch v0.18.x (Restandardize handling of Multi-Image files)
#5131 consistent zoom boundary behavior across SciPy versions
#5129 Backport PR #5128 on branch v0.18.x (Add farid filters in all, to populate the documentation)
#5128 Add farid filters in all, to populate the documentation
#5126 Proofread gallery example for rank filters.
#5125 Backport PR #5117 on branch v0.18.x (Remove Python 3.6 support)
#5123 Backport PR #5115 on branch v0.18.x (change plausible script to track outbound links)
#5119 Backport PR #5097 on branch v0.18.x (Improvements to CircleCI build: no parallelization and caching)
#5118 Backport PR #5116 on branch v0.18.x (added missing datasets to gallery examples)
#5117 Remove Python 3.6 support
#5116 added missing datasets to gallery examples
#5115 change plausible script to track outbound links
#5113 Update release notes with latest backported changes from master
#5111 Recent backports from skimage master
#5110 Backport PR #5104 on branch v0.18.x (Use v{} for version tags with pooch)
#5108 Backport PR #5103 on branch v0.18.x (Replace np.bool, np.int, np.float with bool, int, float)
#5107 Fix compilation error in XCode 12
#5106 Add 0.18 release notes (#5085)
#5105 Add data optional reqs to allow pip install scikit-image[data]
#5104 Use v{} for version tags with pooch
#5062 Optimize ensure_spacing

Older pull requests with new comments or commits

#4953 Add (interactive) slice explorer in plotly.
#4201 Add rescale_local_mean

new issues

#5140 upgrade from 0.16.2 to 0.17.2 destroys skimage.external
#5139 Potential optimisation need in new 3D warps code
#5138 phase_cross_correlation returns only 1 argument in the masked case
#5130 pre builds broken by scipy 1.6.0rc1
#5127 Confusing error message when Cython is not installed
#5124 Possible bug in label connected regions in large volume crushes all kernel
#5122 Feature request: Draw line with specific width
#5121 Pip3 install of scikit-image fails for Python 3.9 on macOS 10.15 (Catalina)
#5112 Feature request: add voxel spacing to skimage.measure.regionprops

older issues updated last week

#5095 Image License correction
#5065 poetry add scikit-image fails with WinError 123
#4544 Simplify the release process
#4507 Automatic color generation in the label2rgb function
#4486 Calendar of community management
#4201 Add rescale_local_mean
#3070 Allow passing callable for high and low threshold of Canny

closed issues

#5130 pre builds broken by scipy 1.6.0rc1
#5127 Confusing error message when Cython is not installed
#5121 Pip3 install of scikit-image fails for Python 3.9 on macOS 10.15 (Catalina)
#5102 feret_diameter_max not available
#5100 skimage.measure.label is not working correctly for non binary 3d array
#5088 filters.farid missing from skimage.filters documentation
#5061 ensure_spacing function may be slow
#5053 dropping 3.6 and a few other things
#5051 pip install error: implicit declaration of function 'unwrap2D' is invalid in C99
#4890 Sporadic pooch failures in CI
#2815 Restandardize handling of Multi-Image files

@alexdesiqueira alexdesiqueira changed the title Calendar of community management 2020's calendar of community management Jan 2, 2021
@alexdesiqueira alexdesiqueira unpinned this issue Jan 2, 2021
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Thank you everyone for your hard work! We appreciate your help throughout the year.

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🤔 Planning 🔧 type: Maintenance Refactoring and maintenance of internals
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