Porespy

:wrench: Maintenace

- Removed `nanomesh` from dependencies as it broke our conda-forge builds (because it's pip-only)

:rocket: New features

- Added polydisperse_cylinders function to beta
- Added a `rectangular_pillars` micro-model generator to the `beta` module
- Add `flux` and `tau_from_cmap` to simulations module
- Added `tortuosity_gdd` method to compute tortuosity using domain decomposition
- Added `ramp` to `beta` module for inclusion in `generators` eventually
- Added `local_diff` filter to `beta` module for inclusion in `filters` eventually
- Added `beta` module for introducing new functions which may still need tweaking
- Added `pc_to_seq` function
- Added `pc_map_to_pc_curve` function for much faster generation of pc curves from images

:cake: Enhancements

- Added several micromodels functions to the generators module
- Improved speed of cylinders 5x by using _insert_disk_at_points_parallel method instead of dilating using edt
- Sped up sphere insertions using parallelization
- Readded `tic` and `toc` functions to `tools` module
- Enhanced `satn_profile` function to accept pre-thresholded image
- Enhanced `satn_profile` function to throw an exception if requested saturation cannot be obtained

:wrench: Maintenace

- Migrated from bump2version to hatch for resolving version number
- Refactored and updated Actions
- Deprecated Python 3.8 and 3.9
- Added linter Action: ruff
- Unified project config (pytest.ini, setup.cfg) files in pyproject.toml
- Removed pyfastnoisesimd from dependencies as it no longer works on Python 3.9+
- Migrated from setup.py to pyproject.toml
- Migrated from flat layout to the PyPA recommended src layout
- Enhanced api with type annotations and defaults
- Updated the python version coverage to include 3.11
- Tidyied up after some recent PRs
- Enhanced `satn_profile` function to return a `Results` object with data as attributes

:rocket: New features

- Added function to compute diffusive size factor using dns \new
- Added `zip_to_stack` for converting 2D tiff files in a zip folder into a 3D tiff image \new
- Added `folder_to_stack` for converting 2D tiff files in a folder into a 3D tiff image \new
- Added `random_spheres` as a wrapper to `rsa` for more descriptive name (rsa to be deprecated eventually) \new
- Added `show_panels` function to visualizations module \new
- Added `spheres_from_coords` to generators \new
- Added `find_bbox` to tools \new
- Add better sierpinski foam generator that accepts shape \new

:cake: Enhancements

- Added `mode='drainage/imbibition'` argument to all seq/size/satn functions, to accomodate upcoming imbibition simulations \enh
- Make `Results` object more useful by including name of function that produced it, and time \enh
- Added `seed` argument to all random generators \enh
- Enhanced `spheres_from_coords` to work with negative coordinates \enh \bug
- Improved the speed of `find_bbox` \enh
- Added protrusion argument to `rsa` \enh

:wrench: Maintenace

- adding release.yml to package to assist with automatic changelog generation \maint
- Fixed imageio deprecation warnings in 2 examples \doc, \maint
- using \__all\__ everywhere for imports \maint
- Removed optional dependencies from setup.py \maint

:warning: API changes

- Changed radius to r in `voronoi_edges` \api
- Moved ibip percolation functions to simulations module

:bug: Bugfixes

- Included dtype in np.sum calls throughout to ensure it returns the correct value on large images \bug
- Fixed bug in `find_trapped_regions` when no solid present on outlet face \bug
- Fix parse bug in `_parse_pad_width` used by `snow2` if boundary\_width was a list of lists \bug
- Fix divs bug in `blobs` \bug
- Improved output of Results object when large dicts present \bug
- Enhanced `spheres_from_coords` to work with negative coordinates \enh \bug
- Fixed some bugs pertaining to numpy deprecations becoming reality \bug
- Fixed bugs in rsa when using clearance \bug
- Fixed dynamically changing loglevel \bug
- `tortuosity_fd` should raise Exception if all pores are floating pores \bug

:green\_book: Documentation

- Fixed formatting of the Results table in tortuosity notebook \doc
- Fixed imageio deprecation warnings in 2 examples \doc, \maint
- Added tutorial notebook explaining the use of `spheres_from_coords` on various csv files \doc
- Fix link to installation guide in readme \docs
- Added examples on snow2, regions\_to\_network, and other network extraction related function \docs
- Added examples on often asked questions in the Discussions \doc

Installation
The txt files below contain the specific packages and their versions to install to get a functioning installation for archival purposes using conda. Instructions for installing are in the top of the file.

:cake: Enhancements
- Replaced `loguru` with `rich` for logging
- `tortuosity_fd` now uses PyAMG instead of PyPardiso, which makes it way faster
- `tortuosity_fd` now optionally accepts an OpenPNM solver object for more fine-grained control

:wrench: Maintenace
- Add example notebook on how to create multiscale images
- PoreSpy is now compatible with OpenPNM v3 API

:rocket: New features

- Added `AI_diffusive_size_factor` to `networks` module for predicting diffusive conductance from watershed segmentation using tensorflow

:cake: Enhancements

- Enhanced parallelized operations (such as filters) to not oversubscribe the CPU, hence should run faster
- Enhanced two point correlation function for speed, flexibility and compatibility
- `regions_to_network` is now more flexible and can handle noncontiguous phase labels
- Added a jitted get\_radial\_sum to tpcf, updated parse histogram to incorporate tpcf outputs

:wrench: Maintenace

- Added Python 3.10 to CI workflows
- Unified `requirements.txt` with `install_requires` in `setup.py`
- Fixed version regex in setup.cfg that incorrectly incremented the 4th digit

:bug: Bugfixes

- Fixed `bundle_of_tubes` to work with `scipy` 1.9+

:green\_book: Documentation

- Fixed "diffusive conductance using AI" example notebooks
- Large batch of updates to the examples