2021's calendar of community management #5169
Comments
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Thanks for organizing this new issue @alexdesiqueira. I am flexible on dates, so feel free to shuffle me around if others prefer those specific dates. |
2021/1/4 - 2021/1/11One new feature (Normalized Mutual information) and a couple of bugfix PRs were merged. 10 new PRs were opened (2 of which were already merged, but many others have at least 1 review). A couple of these are maintenance PRs related to new New pull requests open last week#5182 Correction to linspace call in hough_line default Closed pull requests (not merged)none Merged pull requests#5175 Resolve stochastic rank filter test failures on CI Older pull requests with new comments or commits#5163 Single out docs-only PRs in review process. new issues#5178 Hausdorff distance to return the pair of points that defines it Older issues updated last week#5169 2021's calendar of community management Closed issues#5176 Marching cubes algorithm on own x,y,z data |
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Hi all, Still a quiet week last week. Also we have no one rostered for this week but I'm feeling generous, I'll take it also. =P The tally: +2 on PRs, +2 on issues. That's not so great — I'll try to make a concerted push to reduce the numbers this week. 2021/1/11 - 2020/1/18New pull requests open last week#5188 Add nD support to several geometric transform classes Closed pull requests (not merged)none Merged pull requests#5184 Added 1/2 pixel bounds to extent of displayed images Older pull requests with new comments or commits#5179 bugfix: prevent integer overflow in EllipseModel new issues#5189 Feature request: implement generalized histogram thresholding Older issues updated last week#5178 Hausdorff distance to return the pair of points that defines it Closed issues#5028 Remove usage of numpy's private functions |
2021/01/25 - 2020/01/31Lots of movement this week. Some low-hanging fruits to merge, but I didn't have the time to analyze too much*; I apologize. new pull requests open last week#5212 update minimum supported Matplotlib, SciPy and Pillow closed pull requests (not merged)none merged pull requests#5210 Backport PR #5197 on branch v0.18.x (Build aarch64 wheels) Older pull requests with new comments or commits#5180 Function for assigning labels to points new issues#5213 regionprops: consistent naming scheme older issues updated last week#5194 Feature request: MS-SSIM calculation support in skimage.metrics closed issues#5203 Small typo in utils.py |
2021/2/1 - 2021/2/8New pull requests open last week#5221 Remove approximation in ransac circle model Closed pull requests (not merged)none Merged pull requests#5212 update minimum supported Matplotlib, SciPy and Pillow Older pull requests with new comments or commits#5207 Add hausdorff points new issues#5225 Problems with some modules Older issues updated last week#5186 CircleModel does not minimize squared distances Closed issues#5211 3.7 minimum requirements test builds are failing |
2021/2/8 - 2021/2/15I opened a new "scikit-image 1.0 API" project a couple of weeks ago (see the Projects tab between "Actions" and "Wiki" in the GitHub UI) . I am trying it out for organizing various issues related to proposed API changes for scikit-image 1.0. These are not strictly PRs that should be merged for 1.0 itself, but may include things we want to merge in 0.19 to give at least 1 release deprecation cycle prior to 1.0. Changing from New pull requests open last week#5238 Fix Laplacian matrix size bug in random_walker Closed pull requests (not merged)none Merged pull requests#5227 See if latest Ubuntu image fixes QEMU CPU detection issue Older pull requests with new comments or commits#5219 single precision support in skimage.restoration module new issues#5237 exposure.equalize_adapthist doesn't work for 3D data, and error with calling cells3d Older issues updated last week#5223 Add new illuminants for color conversion Closed issues#5237 exposure.equalize_adapthist doesn't work for 3D data, and error with calling cells3d |
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Please also review: scikit-image/boilerplate-utils#7 where I modified the report generation script to respect the |
2021/2/15 - 2021/2/22The list of older pull requests with new updates is abnormally large today, just because New pull requests open last week#5246 Tiny spelling correction: witch -> which Closed pull requests (not merged)#5241 run Haar application gallery example in single-threaded mode Merged pull requests#5246 Tiny spelling correction: witch -> which Older pull requests with new comments or commits#5234 Add new illuminants new issues#5244 Problem when building from source on ARM M1 Mac Older issues updated last week#5232 Issue with unordered_map in remap.pyx scikit-image 0.17.2 Closed issues#5244 Problem when building from source on ARM M1 Mac |
2021/02/23 – 2020/03/01Some new infrastructure issues worth considering this week. Had a low bandwidth, could not keep up; sorry about that. new pull requests open last week#5254 Introduce a conistent naming scheme for measure.regionprops closed pull requests (not merged)#5251 Dim generalization merged pull requests#5249 Ensure that README.txt has write permissions for subsequent imports. Older pull requests with new comments or commits#5245 updated regionprops_table test for iterable properties new issues#5253 Set upper limits on our dependencies older issues updated last week#5242 imread loads some images with wrong shape closed issues#5250 binary_blobs fails with io.imshow |
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Hi @jni, it looks like we were responsible for the last two weeks. I can just run the script for both of them today and upload here, but please take a look if you want to add any additional summary/info. |
2021/3/1 - 2021/3/8New pull requests open last week#5257 Improve salt and pepper noise performance Closed pull requests (not merged)none Merged pull requests#5256 Fix rescale using small scale factor Older pull requests with new comments or commits#4946 Start example using 3D multichannel image. new issues#5259 PolynomialTransform.estimate() potentially uses more memory than it needs to Older issues updated last week#5213 regionprops: consistent naming scheme Closed issues#5252 skimage.transform.rescale fails for scale < 0.2 |
2021/3/8 - 2021/3/15One highlight this week was merging of nD support for geometric transforms (thanks @jni). My initial PR related to the New pull requests open last week#5271 Watershed connectivity bug: considering connectivity to calculate markers. Closed pull requests (not merged)none Merged pull requests#5265 Deprecate input kwarg in label Older pull requests with new comments or commits#5257 Improve salt and pepper noise performance new issues#5273 Proposal: add 'medoid' to regionprops Older issues updated last week#5259 PolynomialTransform.estimate() potentially uses more memory than it needs to Closed issues#5260 label() segfault with arrays of shape (n,0,m) on linux + anaconda |
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Hmmm. Looks like something is still a bit off in the boilerplate script. At least the 3/1 to 3/8 summary includes some things newer than 3/8. I manually removed some overlapping ones here, but will take a look at the script again to fix it going forward. |
nevermind, I was just using an outdated version of the script (I hadn't updated for the master->main branch rename for that repository) |
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Thanks @grlee77 for picking up my slack... I must say I'm a little overwhelmed with notifications and I have not been a good community manager. Thanks all for keeping things running smoothly! 🙏 |
2021/3/15 - 2021/3/22This past week was dominated by small fixes for bugs and inconsistencies (still ongoing). Nothing to report at the high level. New pull requests open last week#5282 Stick with usual convention for 3D spatial coords Closed pull requests (not merged)none Merged pull requests#5271 Watershed: consider connectivity when calculating markers. Older pull requests with new comments or commits#5269 Mention possible filters in radon_transform -> filtered-back-projection new issues#5279 Watershed does not segment my array Older issues updated last week#5272 Are there any plans for adding GPU/CUDA support for some functions? Closed issues#5279 Watershed does not segment my array |
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Hi @alexdesiqueira, can you add the summary for last week? Thanks |
2021/3/23 — 2021/3/31Sorry about that @grlee77; it's my week off and I forgot to deliver that before leaving 🙂 new pull requests open last week#5308 Add new illuminants to data registry. closed pull requests (not merged)none merged pull requests#5307 DOC: Specify the release note version instead of the misleading Older pull requests with new comments or commits#5281 Improved gaussian filter and convert_to_float(#5195) new issues#5302 Are we ready for manylinux2010 older issues updated last week#5266 test_thresholding fails with last dask version (2021.3.0) closed issues#5278 Error in documentation for watershed |
2021/3/29 - 2021/4/5New pull requests open last week#5311 remove misleading comment in example code Closed pull requests (not merged)#5304 WIP: Backport of: Use manylinux2010 for python 3.9+ #5303 onto v0.18.x Merged pull requests#5311 remove misleading comment in example code Older pull requests with new comments or commits#5289 multichannel to channel_axis (6 of 6): segmentation new issues#5309 call unclear in documentation Older issues updated last week#5290 Changes not reported in the doc for 0.17 and 0.18 Closed issues#5300 MrMeeseeks and main |
2021/4/5 - 2021/4/12Most issues/PRs closed this week were fixes to documentation builds and CI. New pull requests open last week#5326 Update pyproject.toml to ensure pypy compatibility and aarch compatibility Closed pull requests (not merged)none Merged pull requests#5325 DOC: add empty line before section for proper parsing. Older pull requests with new comments or commits#5308 Add new illuminants to data registry. new issues#5324 Older issues updated last week#5299 Version 0.18.2 -- aarch64 wheels Closed issues#5318 sphinx: role 'arxiv' is already registered |
2021/4/12 - 2021/4/19Hi, over the past week, most active issues/PRs related to maintenance. Note that a new feature ( New pull requests open last week#5336 Test setup and teardown Closed pull requests (not merged)none Merged pull requests#5335 Backport PR #5319 on branch v0.18.x (Fix sphinx: role already being registered) Older pull requests with new comments or commits#5323 Lddmm registration new issues#5337 warnings from skimage.io module in test suite Older issues updated last week#5272 Are there any plans for adding GPU/CUDA support for some functions? Closed issues#5324 |
2021/04/27 — 2021/05/03Last week's summary. Took advantage to merge some @grlee77 stuff (thanks Greg!); we updated minimal numpy and Pillow versions as well. new pull requests open last week#5374 add numpy version specification on aarch for cpython 3.8 closed pull requests (not merged)#5371 [WIP] change numpy version in pyproject.toml merged pull requests#5370 increase cibuildwheel verbosity Older pull requests with new comments or commits#5357 MAINT/ENH: refactor np.random.x to use np.random.Generator new issues#5369 Reading FLIF Images Throws Error older issues updated last week#5342 ENH/DOC: remove references to np.random.RandomState in favour of np.random.Generator closed issues#5361 profile_line's reduce_func parameter should be np.nanmean by default |
2021/5/3 - 2021/5/10Most PRs merged this week were related to the upcoming v0.18.2 with aarch64 support. A recent PR on Fisher vectors was updated and looks ready for a final review/merge. We also received a new contributor PR involving Butterworth filtering in the Fourier domain (#5382). The code in that PR should be fairly easily adaptable to other Fourier domain filters as well. I would like to solicit reviewers for recent PRs related to the New pull requests open last week#5383 Backport PR #5175 on branch v0.18.x (Resolve stochastic rank filter test failures on CI) Closed pull requests (not merged)#5371 [WIP] change numpy version in pyproject.toml Merged pull requests#5383 Backport PR #5175 on branch v0.18.x (Resolve stochastic rank filter test failures on CI) Older pull requests with new comments or commits#5365 Add stitching gallery example new issues#5384 Feature Request: Considering 'Knight's move' in find_cost/route_through_array Older issues updated last week#5339 Unable to install binary or build from master on ARM64 Ubuntu 20.04.2 LTS Closed issues#5377 Double requirements clash with development environment setup in installation guide |
2021/5/10 - 2021/5/17Hi, I think the highlight of last week is that we welcomed several first-time contributors: @felipegb94, @hiren-2911, @klaussfreire, and @lilisako, if I'm not mistaken! I'm sorry I haven't been as responsive to them as I expected. Otherwise, on the road to scikit-image 1.0, we have started the deprecation cycle to move to 'gray' spelling (away from 'grey') in the API: thanks, @grlee77! Also, Greg's call was heard and the New pull requests open last week#5399 Allow rank filters to work with nogil Closed pull requests (not merged)none Merged pull requests#5394 Speed up find_local_max when given a finite num_peaks Older pull requests with new comments or commits#5382 Added 2D butterworth filter new issues#5398 imshow does not work on binary images Older issues updated last week#5384 Feature Request: Considering 'Knight's move' in find_cost/route_through_array Closed issues#5396 The RANSAC example uses the ransac function in an inappropriate way |
2021/5/17 - 2021/5/24New pull requests open last weekThis was a pretty quiet week. A couple of PRs improved interoperability with multithreading (e.g. via Dask) by releasing the GIL for rank filters and skimage.restoration functions. #5407 [WIP] Improving parallelization user guide Closed pull requests (not merged)#5405 [WIP] Improving parallelization user guide Merged pull requests#5400 release the GIL in denoise_tv_bregman and denoise_bilateral Older pull requests with new comments or commits#5332 Threshold generalized histogram new issues#5408 watershed labels some foreground pixels as 0 when using mask argument Older issues updated last week#4780 Getting "ImportError: DLL load failed: The specified module could not be found." Closed issues#5406 MacOS PyInstaller - No module named 'skimage.filters.rank.core_cy_3d' |
2021/5/24 - 2021/5/31New pull requests open last weeknone Closed pull requests (not merged)none Merged pull requestsnone Older pull requests with new comments or commits#5407 [WIP] Improving parallelization user guide new issues#5411 Lucy Richardson output mostly white lines Older issues updated last week#5398 imshow does not work on binary images Closed issues#5270 ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject |
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Thank you for updating, @grlee77! |
2021/5/31 - 2021/6/6New pull requests open last week#5412 Extended rolling ball example with ECG data (1D) Closed pull requests (not merged)none Merged pull requests#5392 Integral_image: promote floating point inputs to double by default Older pull requests with new comments or commits#5402 Use sparse svd from scipy to save memory usage new issues#5414 Incorrect link for Older issues updated last week#5411 Lucy Richardson output mostly white lines Closed issues#5408 watershed labels some foreground pixels as 0 when using mask argument |
2021/6/7 - 2021/6/14Our first substantial PR under the DevOps CZI work was merged (#5397). A new PR related to checking the benchmarks on CI was also opened this week and would welcome feedback (#5424). Another PR that was updated this week and should be nearly ready to merge is lazy submodule loading (#5101). Oddly, I do not see it in the summary below, despite new commits being added on the 11th. A somewhat large PR related to use of New pull requests open last week#5427 residual multichannel->channel_axis fixes Closed pull requests (not merged)#5417 DOC: add fallback intersphinx file for matplotlib Merged pull requests#5426 Benchmarks: fix ResizeLocalMeanSuite.time_resize_local_mean signature Older pull requests with new comments or commits#5407 [WIP] Improving parallelization user guide new issues#5423 CI has been updated to build on tags; RELEASE.txt needs to be updated Older issues updated last week#5389 Speeding up _remap.pyx Closed issues#5418 |
2021/6/14 - 2021/6/22Hi, sorry about the 8-day-long interval this time (2021/6/14 - 2021/6/22); since the start date is inclusive and the end date exclusive, I had to start with 2021/6/14 because the previous report ended with 2021/6/14, and I ended with 2021/6/22 to include today's action. Indeed, the long-standing discussion in #5281 (about changing the default value of Over the past week, we used the one-approval-only policy to merge a few PRs for docs and CI hotfixes. One substantial PR we merged is the nD Butterworth filter implementation (#5382). Let me please draw your attention to the three New pull requests open last week#5437 avoid warnings about use of deprecated Closed pull requests (not merged)#5435 Revert "Improved gaussian filter and convert_to_float(#5195)" Merged pull requests#5437 avoid warnings about use of deprecated Older pull requests with new comments or commits#5424 Add benchmark checks to CI new issues#5432 'subpixel' boundaries at the edges of an image Older issues updated last week#5423 CI has been updated to build on tags; RELEASE.txt needs to be updated Closed issues#5414 Incorrect link for |
2021/6/28 - 2021/7/5No one was assigned this week and it was overall pretty quiet. New pull requests open last week#5456 Pin pillow to !=8.3.0 Closed pull requests (not merged)none Merged pull requests#5452 Fix 'blog_dog' typo in gaussian docs Older pull requests with new comments or commits#4482 fixed DoG function for correct scaling new issues#5455 New pillow release has broken array coercion Older issues updated last week#5032 Error appeared everytime i ran sckit image Closed issues#5449 haar_like_feature generates Nan's |
2021/7/5 - 2021/7/12The team had recent meetings related to API changes summarized in #5439 with notes available at https://github.com/scikit-image/meeting-notes/blob/main/2021/july-api-meetings.md. The channel_axis suggestion for the color module was implemented in #5462. Please also review #5463 which implements the remaining deprecations from our TODO list for the 0.19 release. New pull requests open last week#5469 fix #5448 : Release wheels before source Closed pull requests (not merged)#5247 Added support for binary images in is_low_contrast to fix imshow of binary images Merged pull requests#5466 readd gallery testing condition Older pull requests with new comments or commits#5402 Use sparse svd from scipy to save memory usage new issues#5470 Discretization of disk footprints (also ellipse, ball) Older issues updated last week#5439 Meta-issue: pending API changes for 1.0 Closed issues#5464 skeletonize_3d does not seem to do anything on my 3d input array |
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Also, there are currently 5 issues just needing a second review ( |
2021/7/12 - 2021/7/19Hi, the highlights of last week were that:
PS: There are now 6 (oh, 5, thanks @rfezzani) issues just needing a second review (label New pull requests open last week#5480 Fix wrong syntax for the string argument to ValueError Closed pull requests (not merged)#5453 Add a draw_poly_on_array function to skimage.draw Merged pull requests#5480 Fix wrong syntax for the string argument to ValueError Older pull requests with new comments or commits#5463 Remove deprecated functions and arguments for the 0.19 release new issues#5481 Allow local maxima and local minima to ignore plateaus Older issues updated last week#5468 Does medial axis skeletonization work for 3D input arrays ? Closed issues#5451 Handling really large polygons with draw.polygon |
2021/7/19 - 2021/7/26New pull requests open last week#5490 Update thresholding.py with Singh function Closed pull requests (not merged)none Merged pull requests#5485 remove _fast_pad utility (now that we require NumPy >= 1.17) Older pull requests with new comments or commits#5477 Adds towncrier functionality to help improve automation of release note aggregation. new issues#5484 AttributeError: module 'skimage' has no attribute 'measure' Older issues updated last week#5470 Discretization of disk footprints (also ellipse, ball) Closed issues#5484 AttributeError: module 'skimage' has no attribute 'measure' |
2021/7/26 - 2021/8/2New pull requests open last week#5495 Update codecov config Closed pull requests (not merged)none Merged pull requests#5493 [minor docs fix] Fix reference to multiscale_basic_features in TrainableSegmenter Older pull requests with new comments or commits#5454 Add default values for denoise_tv_bregman / block_reduce / threshold_local method new issues#5494 issue with rgb2hed and hed2rgb Older issues updated last week#5481 Allow local maxima and local minima to ignore plateaus Closed issuesnone |
2021/8/2 - 2021/8/9I think the PR with the large number of of 0.19 TODO items has been reviewed and remaining comments were just addressed (thanks @mkcor and @rfezzani!). I would like to restore the doctests (#5505) and get a small revision to a recently merged Let me know what you think. New pull requests open last week#5506 WIP: enable Ccache during GitHub Actions tests Closed pull requests (not merged)#5506 WIP: enable Ccache during GitHub Actions tests Merged pull requests#5497 Fixed NaN issue in threshold_otsu Older pull requests with new comments or commits#5487 simplify blob_log using vectorized linspace and logspace new issues#5502 Broken doctests (doctests not being run on CI) Older issues updated last week#5169 2021's calendar of community management Closed issues#5500 peak_local_max should raise error when given >2D array |
2021/8/9 - 2021/8/16Hi, keeping the focus on the 0.19 milestone, wrt last week:
New pull requests open last week#5510 .format() coverted to f-strings in registration & restoration subpackage Closed pull requests (not merged)none Merged pull requests#5509 Slight Older pull requests with new comments or commits#5504 Mention commit messages in the contribution guidelines. new issuesnone Older issues updated last week#5474 Closed issues#5413 uint8 overflow in exposure.adjust_gamma |
2021/08/31 - 2021/09/06new pull requests open last week#5560 Add hyperlinks to referenced documentation places. closed pull requests (not merged)none merged pull requests#5560 Add hyperlinks to referenced documentation places. Older pull requests with new comments or commits#5550 Support nD images and labels in label2rgb new issues#5561 Meijering scaling issue older issues updated last week#5538 SSIM result is different from pytorch-msssim.ssim closed issues#5558 AttributeError: '<class 'skimage.measure._regionprops.RegionProperties'>' object has no attribute 'axis_major_length' |
comments moved over from Discussion2021/10/18 - 2021/10/25 (mkcor)Hi, last week was very active. Many fixes were submitted and some are already merged (thanks @grlee77 and @rfezzani). On the highlight side of things, we welcomed new contributor @rk-exxec and @jni contributed a new feature to work with images (or regions thereof) as graphs of pixels. Although they are definitely not all low-hanging fruits, I'd like to draw your attention to the open PRs which already have one approving review: https://github.com/scikit-image/scikit-image/pulls?q=is%3Apr+is%3Aopen+review%3Aapproved Just this once, I'll spare you the last section (Closed issues) because of #5588 and #5950: Issues actually closed would be drowned in an ocean of issues turned discussions. New pull requests open last week#5982 Fix benchmark suite (watershed function was moved) Closed pull requests (not merged)none Merged pull requests#5978 Update docstring for dilation, which is now nD. Older pull requests with new comments or commits#5601 Weighted estimation of geometric transform matrices New issues#5979 Colorspace conversions are wrong for anything other than uint8 Older issues updated last week#5586 Example image deconvolution "Original Data" image is actually a blurred image |
2021/10/25 - 2021/11/1 (@grlee77)The lazy loading PR was merged last week and should improve the user experience for scikit-image. There is a follow up to this to make loading of My apologies for missing the last couple of updates here. Thanks @mkcor for getting this back on track! New pull requests open last week#5996 Lazily load data_dir into the top-level namespace Closed pull requests (not merged)none Merged pull requests#5996 Lazily load data_dir into the top-level namespace Older pull requests with new comments or commits#5980 Allow color.ycbcr2rgb to work with uint8 input new issues#5997 Increase the usage of augmented assignment statements Older issues updated last week#5598 peak_local_max attribute 'min_distance' issue Closed issues#5984 Gallery example about pixel graphs and geodesic centers should use last plot as thumbnail. |
2021/11/8 - 2021/11/15 (@grlee77)The majority of effort of the past week was on maintenance and updates to the wheel building and continuous integration workflows to add Python 3.10 support. With these updates in place we are in a good position to get a 0.19 release out this week. The handful of remaining 0.19 milestones can be found here. New pull requests open last week#6033 Add example of creating tools using HoloViz Panel and HoloViews Closed pull requests (not merged)#6014 Test Pythran support rebased on main Merged pull requests#6032 Avoid matplotlib import overhead during 'import skimage' Older pull requests with new comments or commits#6005 uint8 histogram equalization new issues#6030 Sphinx 4.3.0 broke documentation generation; unpin when resolved Older issues updated last week#6011 feature.greycomatrix angles clockwise or counterclockwise? Closed issues#6001 Part of metadata file is deprecated |
2021/11/15 - 2021/11/22 (@mkcor)Hi, last week @grlee77 has led the effort to release scikit-image v0.19: See announcement of the first release candidate 0.19.0rc0 on the developer forum! 🎉 New pull requests open last week#6046 Transplant the change of scikit-learn into scikit-image for RANSAC Closed pull requests (not merged)none Merged pull requests#6044 remove all use of the deprecated distutils package Older pull requests with new comments or commits#6033 Add example of creating tools using HoloViz Panel and HoloViews New issues#6047 skimage.transform.resize Older issues updated last week#6028 Performance regression in mean filter (v0.18.0 onwards) Closed issues#6043 DeprecationWarning raised under Python 3.10 |
2021/12/13 - 2021/12/20 (@mkcor)Hi, last week wasn't very active but we released v0.19.1! There are currently a few docs-centric PRs to review: #6033, #6087, #6133, #6134. Merry Christmas! New pull requests open last week#6134 clarify the meaning of the weights term for TV denoising functions Closed pull requests (not merged)none Merged pull requests#6131 Backport PR #6130 on branch v0.19.x (bump deprecated Azure windows environment) Older pull requests with new comments or commits#6077 Cross correlation refactor New issues#6126 Example of bag of visual words (BoVW) using SIFT and a RandomForestClassifier Older issues updated last week#6119 skimage.viewer: incompatibility with Matplotlib 3.5 Closed issues#6122 Feature suggestion: Function that places a structuring element in an array around a given index. |
This is our 2021's calendar of community management.
Here we 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.
Last year's calendar of community management is given at #4486.
jan/2021
feb/2021
mar/2021
apr/2021
may/2021
jun/2021
jul/2021
aug/2021
sep/2021
oct/2021
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