v2.0.0

[jgostick]

🚀 New features

• Added optional parallelization to many functions using dask
• Added image-based invasion percolation algorithm (ibip) to filters
• GPU-accelerated the image-based invasion percolation (IBIP) algorithm
• Added nl_means_layered function for parallelized noise removal #new
• Added boxcount to metrics #new
• Added random_cantor_dust and sierpinski_foam to generators #new
• Added borders and faces to generators #new
• Added pseudo_electrostatic_packing to generators #new
• Added pseudo_gravity_packing of spheres to generators #new
• Added wrapper to generic ImageJ functions #new
• Added a lightweight wrapper for the classic MaximalBall algorithm #new
• Added settings to top level of package to control behavior like hidding progress bars and messages #new
• Added unpad function to tools module #new
• New IO method to_stl for exporting an image to STL mesh #new
• Added cylinder_plug function to generators, used in extract_cylinder function for improved speed #new
• Added ps_round function to tools to produce disk and ball strels programmtically #new
• Added ps_rect function to tools for programatically generating 2D or 3D rectilinear strels #new
• Added io function to save an image as a Paraview state file and open directly in Paraview #new
• Added function to export a sphere pack image to COMSOL #new

🍰 Enhancements

• Exposed sigma and r_max in snow_2 #enh
• Better support for 2D images #enh
• Added option to trim_nearby_peak to apply a threshold for distance check #enh
• Added ability to set loglevel by number as well as name #enh
• Unified various snow extraction algorithms under new snow2 function #enh
• Added more robust inference of Python environment (terminal vs. notebook) #enh
• Migrated to "loguru" from Python's stdlib "logging" for logger messages #enh
• Improved various metrics and the bar chart function in the visualization module to work together better #enh
• Added spacing to show_planes #enh
• Extended RSA api with clearance and return_spheres arguments, and now accepts im or shape #enh
• Cylinders generator now also accepts porosity (previously only number of cylinders) #enh
• Refactored make_contiguous to use less memory and by 5x faster #enh

🔧 Maintenance

• Fix a bug in examples CI where if no tests were collected, CI reported as failed #maint
• Replaced array_split dependency with custom-made function #maint
• Parallelized examples' CI, and switched to Mambaforge #maint
• Fixed codecov to include numba-jitted methods in coverage report #maint
• Removed Dask progress bars and minor refactoring #maint
• Included ParaView unit tests in the macOS build #maint
• Update Actions to accommodate the native support of "ci skip" by GitHub + minor tweaks #maint
• Migrate from pip to conda for CI #maint

⚠️ API changes

• Replaced namedtuples with custom Results container #api
• Replaced perlin_noise with fractal_noise in the generators module based on fastnoisesimd (and pyfastnoisesimd) packages #api
• Moved several functions between submodules, deleted others, and renamed files #api
• Altered phase_fractions to accept alias and return dict, e.g. {'void': 0.44, 'solid':0.56} #api
• Switched radius argument to just r throughout package #api
• Switched to maxiter throughout, instead of max_iter or max_iters or iter_max #api
• Radial density distribution now only accepts distance transform #api
• Reduced the number of arguments in the snow family of functions #api
• Enhanced add_boundary_regions function to accept pad_width instead of face names #api
• Updated lattice_spheres to be much more flexible, renamed and added args #api
• Remove to_openpnm function from io module #api
• Renamed some metrics to be more consistent with each other #api
• Fixed up regionprops_3d to behave equivalently to scikits-image, including delayed evaluation #api

🐛 Bugfixes

• Fixed tqdm progress bar bug that always defaulted to text-based #bug
• Fixed edge case bugs on RSA and insert_cylinders #bug
• Rewrote trim_saddle_points to avoid hitting max_iters as oftern #bug
• Fixed tiny bug in L value used in dns.tortuosity (L -> (L -1)) that was prevent tau =1 in open space #bug
• Fixed bug in find_outer_region #bug
• Fixed missing type check in hold_peaks #bug
• Added check to ensure filter output size matches input in chunked_func #bug
• Fixed bug in trim_percolation_paths #bug
• Fixed snow_dual to handle unsegmented solid regions #bug
• Fixed a bug in add_boundary_regions that occasionally led to some unlabeled pores #bug

📗 Documentation

• Large overhaul of docstrings, consistent argument naming between functions #doc
• Added many new example notebooks and revamped documentation site #docs
• Moved documentation from readthedocs to GitHub Pages + major enhancements #doc

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This discussion was created from the release v2.0.0.

[vasudevanv]

Is there a more detailed guide for the functions that were moved/renamed/removed? I have a package that was built on top of porespy. Trying to migrate from v1.3 to v2.0 now.

[jgostick]

Wow, I'm sorry for that! I hadn't really considered that possibility when doing the re-organization. I was picturing mostly people have to update a few notebooks or scripts. Anyway, I'm sorry but there is not a guide anywhere, although the list of 'api changes' in the above changelog seems to be a pretty good summary according to my recollection.

I can assure you that there will not be any api breaking changes in porespy for a long time. It's pretty tidy now. We'll be adding functionality, but not breaking things.

[vasudevanv]

No worries. I was able to sort out almost all of the renames/moves by going through the list and commit history. Only a couple of deprecations remain and that too mostly because I forgot why I was using them in the first place 🤔

Thanks!