1.8.3

Summary

• Removed all old 2to3 code
• Removed pytables dependency so only h5py is needed
• Moved tests from proteus package to standalone test directory in repo
• Discontinued support for hashdist-based builds and removed stack submodule
• Added directions and scripts for PETSc build system
• Various updates in response to API changes in dependencies (petsc, chrono, scorec)
• FCT support for Richards equation and ADR (in development ) @abarua-ce
• Local adaptive mesh refinement for topbathy (in development) @linojr

Full Changelog: 1.8.2...1.8.3

1.8.2

• remove air-water-vv and proteus_tutorial submodules. Not because those are being deprecated but because the main reason for having them as submodules was automated testing, and I think it's better to run the tests on those submodules separately. We might add them back using a test matrix or some other way to allow longer runtimes.
• remove conda os x test because it exceeds the time limit (could re-enable if we can get multiple cpu's)
• numerous updates to tests to ensure they work on linux and mac os x (despite not running on mac for travis)
• multiple changes to Makefile, setup.py, etc. to address changes in python packaging infrastructure
• changes to address Cython package updates. Mainly I switched to use language_level=3 (e.g. strict Python3) uniformly.
• fix deprecated np.int. Should just be int
• updates to PETSc options (naming)
• updates due to Chrono API changes
• FCT support in Richards model
• Some updates to CutFEM support for solid/air/water models

@cekees @abarua-ce and @jhcollins

1.8.1

Summary

• updated calls to chrono API (#1258) (@cekees @minrk)
• updated calls to scorec API (@jhcollins @zhang-alvin )
• removed dependence on recordtype by using built-in dataclasses (@cekees @jan-janssen)
• updated hashdist and conda stacks (@jhcollins @cekees)
• SWFlow, SWE, and SGN, multiple improvements on methods and testing (@ejtovar )
• WaveTools improvements, custom spectrum, etc. (@adimako )
• changed submodule git protocol from git: to https:
• updated travis build environments
• removed nose and tables dependencies

What's Changed

• Dev1.8.0 by @cekees in #1252
• update stack (expat) by @cekees in #1253
• switch from git to https for submodules by @cekees in #1255
• Changes to SWFlow solvers by @ejtovar in #1254
• Adding custom spectrum function for random waves by @adimako in #1256
• Update CONTRIBUTORS.md by @adimako in #1257
• Replace recordtype using standard dataclasses module by @cekees in #1260
• update conda package versions; update chrono ANCF headers by @cekees in #1261
• Mesh adapt fix by @cekees in #1263
• Set up 1.8.1 release by @cekees in #1264

Full Changelog: 1.8.0...1.8.1

1.8.0

• Improved behavior with arguments_dict @JohanMabille
• Refactored automated meshing @zhang-alvin
• DSWE/SWE model improvements and fixes @ejtovar
• Support for CutFEM and Equivalent Polynomais @cekees, @jhcollins, @zhang-alvin

1.7.5

• Added accurate spatially-variable bathymetry/topography for Dispersive Shallow Water Equations @ejtovar
• Added embedded solid obstacles in 2D and 3D Twophase RANS using CutFEM and equivalent polynomials @cekees, @jhcollins
• Fixed regression on ghost boundaries so that boundaries with non-positive tags are skipped as in prior releases @cekees
• Updated HPCMP custom configs for centennial, mustang, @cekees
• Fixes issues with mesh motion, old issues on higher-order FEM, unreliable solver tests, code coverage, etc. @zhang-alvin, @jhcollins, @ejtovar, @cekees

1.7.4

• Use logEvent instead of std::cout in MeshAdaptPUMI. @zhang-alvin
• SWFlow update for solvers and tests. @ejtovar
• Fix some problems with rans3p with new pybind11/ArgumentsDict. @cekees
• Add and update HPCMP configurations. @cekees
• Use Docker containers from erdc/stack. @cekees
• Add cutfem 2d and 3d (development). @cekees
• Updated to stack to use petsc 3.13.1, numpy, scipy, chrono, etc. @cekees, @tridelat, @zhang-alvin
• Fix update of node/element diameters after mesh motion. @zhang-alvin
• Pytest changes to enable testing on macOS. @ejtovar
• Create directory for Dockerfiles, organized by build settings @zhang-alvin
• Add ArgumentsDict support and simplify interfaces to c++ models mprans. @JohanMabille, @davidbrochart
• Added missing dependencies in setup.py. @zhang-alvin
• Multi-body dynamics (MBD): Add setters/getters and fix mooring lines viz. @tridelat
• Fix AutoFenton error message. @adimako
• Decouple compilation of 2D and 3D mprans extension classes. @cekees
• Re-enable air-water-vv tests. @zhang-alvin
• Fix sed classes. @cekees
• Fix parallel python build of proteus to use only N cores. @cekees
• Add Conda-based Dockerfile @zhang-alvin
• Improvements to adapt workflow with TwoPhaseFlow, made clsvof compatible. @zhang-alvin
• Remove hard-wired 'r-true' for petsc and reorder init. @cekees
• Update PR template to include contributors @zhang-alvin
• Make post-processing of velocity into BDM1 the default for Two-Phase app. @cekees
• Fix conservation with porosity and added sloshing tests. @jhcollins
• Fix LFS pointers error with *.geo files. @tridelat
• Fix MoveMesh for 3D cases + add 3D FSI test. @tridelat
• Fixed porosity scaling in mass correction. @cekees
• Making MeshAdaptPUMI more flexible with models. @zhang-alvin
• Log chrono link-lock joint residuals. @dloney
• Update MBD from chrono 4.0.0 to 5.0.0. @tridelat
• Isolate MeshAdaptPUMI from NumericalSolution. @zhang-alvin
• Add TPF + FSI test. @tridelat
• Add .gitattributes that were not initially included. @zhang-alvin
• Pin conda dependencies. @davidbrochart

1.7.3

• made Coefficients class directly accessible @tridelat
• additional test fixes for SWFlow and gmsh tests @zhang-alvin
• added logging to chrono @dloney
• spatial tools update with stl documentation @BranocRichards
• migrated documentation to external repo and couple generation/deployment with Travis-CI @tridelat
• fixed flcbdfwrappers for OSX @ejtovar
• removal of large files in history to downsize repo @zhang-alvin
• added adaptation logic updates @zhang-alvin
• git submodules have absolute paths to avoid issues when forking @tridelat
• fix conda package issues by removing file references in setup.py @zhang-alvin
• migrated mprans to use xtensor structures @JohanMabille , @davidbrochart

1.7.2

• Conda install finalization @davidbrochart
• Fixes for Green-Naghdi equations @ejtovar
• Enable coupling between MBD/Chrono and IBM with SDF @tridelat
• Overhaul of tests, use pre-generated mesh files, reduce size of test files @zhang-alvin
• BC: boundary normals as argument; Relaxation zones: vertical axis passed explicitly @adimako
• Overhaul of documentation @tridelat
• Fixes for compiler warnings of mprans modules @JohanMabille

1.7.1

• Python 2 to 3 fixes for conda-forge

1.6.2

This version is to allow for bug fixes in 1.6.1