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Merge pull request #669 from baagaard-usgs/increment-version-4.0.0
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Increment version to 4.0.0 in main
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@baagaard-usgs
baagaard-usgs authored Dec 14, 2023
2 parents 5f126c0 + 79a16ee commit be40cc8
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7 changes: 5 additions & 2 deletions CHANGES.md
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Expand Up @@ -20,13 +20,16 @@ The version numbers are in the form `MAJOR.MINOR.PATCH`, where major releases in
* The default solver settings use the PETSc proper orthogonal decomposition (POD) methodology for initial guess of solutions to improve convergence.
* Add demonstration of `pylith_powerlaw_gendb` in Step 8 of `examples/reverse-2d`.
* Add demonstration of using poroelasticity with porosity as a state variable to `examples/magma-2d`.
* Switched from CppUnit to Catch2 as the C++ testing framework.
* Update to PETSc 3.20.2
* Switched from CppUnit to Catch2 for the C++ testing framework.
* Improve integration with VSCode for testing and debugging (see Developer Guide)
* Bug fixes
* Fix errors in KinSrcTimeHistory.py
* Fix creation of PETSc label for edges when importing Gmsh files. This fixes creation of faults with buried edges for 3D meshes imported from Gmsh.
* Add containers for solution fields for poroelasticity with faults.
* Update PETSc to version 3.20.2
* Update Python requirement to version 3.8 or later.
* Update Pyre requirement to version 1.1.0 or later.
* Update SpatialData requirement to version 3.1.0 or later.

## Version 3.0.3

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6 changes: 3 additions & 3 deletions CITATION.cff
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Expand Up @@ -22,7 +22,7 @@ authors:
orcid: "https://orcid.org/0000-0001-7435-9196"
identifiers:
- type: doi
value: 10.5281/zenodo.7072811
value: 10.5281/zenodo.10359667
repository-code: "https://github.com/geodynamics/pylith"
url: "https://geodynamics.org/resources/pylith"
keywords:
Expand All @@ -31,8 +31,8 @@ keywords:
- earthquake
- finite element
license: MIT
version: 3.0.3
date-released: "2022-10-14"
version: 4.0.0
date-released: "2023-12-14"
preferred-citation:
type: article
authors:
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9 changes: 5 additions & 4 deletions DEPENDENCIES
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Expand Up @@ -12,9 +12,10 @@ using the PyLith installer utility for installing PyLith.
Note: Several of these packages (for example, Python, PETSc, proj)
have additional dependencies.

Python
Python (version 3.8 or later)
MPI (mpich, openmpi, etc)
PETSc (knepley/pylith branch)
HDF5 (http://www.hdfgroup.org/HDF5/)
pythia (https://geodynamics.org/resources/pythia)
spatialdata (https://geodynamics.org/resources/spatialdata)
proj (https://trac.osgeo.org/proj/)
Expand All @@ -24,7 +25,7 @@ git (if building from repository)

OPTIONAL DEPENDENCIES

cppunit (http://sourceforge.net/projects/cppunit/)
HDF5 (http://www.hdfgroup.org/HDF5/)
CUBIT (http://cubit.sandia.gov)
Catch2 (https://github.com/catchorg/Catch2)
CUBIT (https://cubit.sandia.gov)
Gmsh (https://gmsh.info)
netcdf (http://www.unidata.ucar.edu/software/netcdf/)
2 changes: 1 addition & 1 deletion LICENSE.md
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## License

Copyright (c) 2010-2022 University of California, Davis
Copyright (c) 2010-2023 University of California, Davis

Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
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21 changes: 7 additions & 14 deletions Makefile.am
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# -*- Makefile -*-
# =================================================================================================
# This code is part of PyLith, developed through the Computational Infrastructure
# for Geodynamics (https://github.com/geodynamics/pylith).
#
# ----------------------------------------------------------------------
# Copyright (c) 2010-2023, University of California, Davis and the PyLith Development Team.
# All rights reserved.
#
# Brad T. Aagaard, U.S. Geological Survey
# Charles A. Williams, GNS Science
# Matthew G. Knepley, University at Buffalo
#
# This code was developed as part of the Computational Infrastructure
# for Geodynamics (http://geodynamics.org).
#
# Copyright (c) 2010-2022 University of California, Davis
#
# See LICENSE.md for license information.
#
# ----------------------------------------------------------------------
# See https://mit-license.org/ and LICENSE.md and for license information.
# =================================================================================================

ACLOCAL_AMFLAGS = -I m4

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4 changes: 2 additions & 2 deletions NEWS
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@@ -1,2 +1,2 @@
Please report bugs at <https://github.com/geodynamics/pylith/issues>.
Send questions to cig-short@geodynamics.org.
Please report bugs at https://github.com/geodynamics/pylith/issues.
Post questions at https://community.geodynamics.org/c/pylith/.
13 changes: 4 additions & 9 deletions README.md
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# PyLith

[![DOI](https://www.zenodo.org/badge/DOI/10.5281/zenodo.7072811.svg)](https://doi.org/10.5281/zenodo.7072811)
[![DOI](https://www.zenodo.org/badge/DOI/10.5281/zenodo.10359667.svg)](https://doi.org/10.5281/zenodo.10359667)
[![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/geodynamics/pylith/blob/main/LICENSE.md)
[![Build Status](https://dev.azure.com/baagaard-usgs/pylith/_apis/build/status/geodynamics.pylith?branchName=main)](https://dev.azure.com/baagaard-usgs/pylith/_build/latest?definitionId=2&branchName=main)
[![codecov](https://codecov.io/gh/geodynamics/pylith/branch/master/graph/badge.svg?token=JiwLVB64EF)](https://codecov.io/gh/geodynamics/pylith)
Expand All @@ -12,18 +12,13 @@ quasi-static simulations of crustal deformation, primarily earthquakes
and volcanoes.

* Main page: [https://geodynamics.org/resources/pylith](https://geodynamics.org/resources/pylith)
* [User Guide](https://pylith.readthedocs.io/en/latest/user/index.html)
* [Documentation](https://pylith.readthedocs.io/en/latest/)
* Binary packages
* Utility to build PyLith and all of its dependencies from source
*
[PyLith parameter viewer](https://geodynamics.github.io/pylith_parameters/) for viewing `.json` parameter files.
* PyLith Wiki: [https://wiki.geodynamics.org/software:pylith:start](https://wiki.geodynamics.org/software:pylith:start)
* Archive of online tutorials
* Hints, tips, tricks, etc
* [PyLith development plan](https://github.com/geodynamics/pylith/wiki/Development-Plans)
* Submit bug reports via [GitHub issues](https://github.com/geodynamics/pylith/issues).
* Post all questions to the [PyLith category](https://community.geodynamics.org/c/pylith/29) on the [CIG Community Forum](https://community.geodynamics.org).

* Post all questions to the [PyLith category](https://community.geodynamics.org/c/pylith/) on the [CIG Community Forum](https://community.geodynamics.org).

## Features

Expand Down Expand Up @@ -57,5 +52,5 @@ PyLith is continually being improved by a growing, collaborative, and inclusive

A complete and growing list of the authors that have contributed over the years can be found at [GitHub contributors](https://github.com/geodynamics/pylith/graphs/contributors).

Please see the User Guide for complete and [acknowledgement and citation](https://pylith.readthedocs.io/en/latest/intro/preface.html#citation) information.
Please see the User Guide for [acknowledgement and citation](https://pylith.readthedocs.io/en/latest/intro/preface.html#citation) information.

19 changes: 7 additions & 12 deletions applications/pylith
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#!/usr/bin/env nemesis
# ----------------------------------------------------------------------
# =================================================================================================
# This code is part of PyLith, developed through the Computational Infrastructure
# for Geodynamics (https://github.com/geodynamics/pylith).
#
# Brad T. Aagaard, U.S. Geological Survey
# Charles A. Williams, GNS Science
# Matthew G. Knepley, University at Buffalo
# Copyright (c) 2010-2023, University of California, Davis and the PyLith Development Team.
# All rights reserved.
#
# This code was developed as part of the Computational Infrastructure
# for Geodynamics (http://geodynamics.org).
#
# Copyright (c) 2010-2022 University of California, Davis
#
# See LICENSE.md for license information.
#
# ----------------------------------------------------------------------
# See https://mit-license.org/ and LICENSE.md and for license information.
# =================================================================================================

if __name__ == "__main__":

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19 changes: 7 additions & 12 deletions applications/pylith_dumpparameters
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#!/usr/bin/env nemesis
# ======================================================================
#
# Brad T. Aagaard, U.S. Geological Survey
# Charles A. Williams, GNS Science
# Matthew G. Knepley, University of Chicago
#
# This code was developed as part of the Computational Infrastructure
# for Geodynamics (http://geodynamics.org).
# =================================================================================================
# This code is part of PyLith, developed through the Computational Infrastructure
# for Geodynamics (https://github.com/geodynamics/pylith).
#
# Copyright (c) 2010-2022 University of California, Davis
# Copyright (c) 2010-2023, University of California, Davis and the PyLith Development Team.
# All rights reserved.
#
# See LICENSE.md for license information.
#
# ======================================================================
# See https://mit-license.org/ and LICENSE.md and for license information.
# =================================================================================================
"""
This script dumps all PyLith parameters (defaults plus those
specified by the user to a text file. The default name of the output
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21 changes: 7 additions & 14 deletions applications/pylith_eqinfo
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@@ -1,20 +1,13 @@
#!/usr/bin/env nemesis
# -*- Python -*-
# =================================================================================================
# This code is part of PyLith, developed through the Computational Infrastructure
# for Geodynamics (https://github.com/geodynamics/pylith).
#
# ======================================================================
# Copyright (c) 2010-2023, University of California, Davis and the PyLith Development Team.
# All rights reserved.
#
# Brad T. Aagaard, U.S. Geological Survey
# Charles A. Williams, GNS Science
# Matthew G. Knepley, University at Buffalo
#
# This code was developed as part of the Computational Infrastructure
# for Geodynamics (http://geodynamics.org).
#
# Copyright (c) 2010-2022 University of California, Davis
#
# See LICENSE.md for license information.
#
# ======================================================================
# See https://mit-license.org/ and LICENSE.md and for license information.
# =================================================================================================
"""
This script creates a Python file with earthquake rupture information computed
from PyLith output. The rupture information includes:
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19 changes: 7 additions & 12 deletions applications/pylith_genxdmf
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@@ -1,18 +1,13 @@
#!/usr/bin/env nemesis
# ======================================================================
#
# Brad T. Aagaard, U.S. Geological Survey
# Charles A. Williams, GNS Science
# Matthew G. Knepley, University at Buffalo
#
# This code was developed as part of the Computational Infrastructure
# for Geodynamics (http://geodynamics.org).
# =================================================================================================
# This code is part of PyLith, developed through the Computational Infrastructure
# for Geodynamics (https://github.com/geodynamics/pylith).
#
# Copyright (c) 2010-2022 University of California, Davis
# Copyright (c) 2010-2023, University of California, Davis and the PyLith Development Team.
# All rights reserved.
#
# See LICENSE.md for license information.
#
# ======================================================================
# See https://mit-license.org/ and LICENSE.md and for license information.
# =================================================================================================
"""
This script creates a metadata file (.xmf) from an HDF5 file written by
PyLith permitting the data to be viewed in VTK visualization software,
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19 changes: 7 additions & 12 deletions applications/pylith_powerlaw_gendb
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@@ -1,18 +1,13 @@
#!/usr/bin/env nemesis
# ----------------------------------------------------------------------
#
# Brad T. Aagaard, U.S. Geological Survey
# Charles A. Williams, GNS Science
# Matthew G. Knepley, University at Buffalo
#
# This code was developed as part of the Computational Infrastructure
# for Geodynamics (http://geodynamics.org).
# =================================================================================================
# This code is part of PyLith, developed through the Computational Infrastructure
# for Geodynamics (https://github.com/geodynamics/pylith).
#
# Copyright (c) 2010-2022 University of California, Davis
# Copyright (c) 2010-2023, University of California, Davis and the PyLith Development Team.
# All rights reserved.
#
# See LICENSE.md for license information.
#
# ----------------------------------------------------------------------
# See https://mit-license.org/ and LICENSE.md and for license information.
# =================================================================================================
"""
Pyre application to compute power-law parameters used by PyLith, given
spatial databases describing the temperature and laboratory-derived
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8 changes: 5 additions & 3 deletions azure-pipelines.yml
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Expand Up @@ -4,7 +4,7 @@ trigger:
- main

pool:
vmImage: "ubuntu-20.04"
vmImage: "ubuntu-22.04"

variables:
IMAGE_REGISTRY: "ghcr.io/geodynamics/pylith_installer"
Expand Down Expand Up @@ -55,10 +55,12 @@ stages:
BASE_IMAGE: "testenv-ubuntu-22.04"
ubuntu_23.04:
BASE_IMAGE: "testenv-ubuntu-23.04"
fedora_37:
BASE_IMAGE: "testenv-fedora-37"
ubuntu_23.10:
BASE_IMAGE: "testenv-ubuntu-23.10"
fedora_38:
BASE_IMAGE: "testenv-fedora-38"
fedora_39:
BASE_IMAGE: "testenv-fedora-39"
centos_7:
BASE_IMAGE: "testenv-centos-7"
rockylinux_8:
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33 changes: 13 additions & 20 deletions configure.ac
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dnl -*- autoconf -*-
dnl ================================================================================================
dnl This code is part of PyLith, developed through the Computational Infrastructure
dnl for Geodynamics (https://github.com/geodynamics/pylith).
dnl
dnl ----------------------------------------------------------------------
dnl
dnl Brad T. Aagaard, U.S. Geological Survey
dnl Charles A. Williams, GNS Science
dnl Matthew G. Knepley, University at Buffalo
dnl
dnl This code was developed as part of the Computational Infrastructure
dnl for Geodynamics (http://geodynamics.org).
dnl Copyright (c) 2010-2023, University of California, Davis and the PyLith Development Team.
dnl All rights reserved.
dnl
dnl Copyright (c) 2010-2022 University of California, Davis
dnl
dnl See LICENSE.md for license information.
dnl
dnl ----------------------------------------------------------------------
dnl See https://mit-license.org/ and LICENSE.md and for license information.
dnl ================================================================================================
dnl Process this file with autoconf to produce a configure script.

AC_PREREQ(2.59)
AC_INIT([PyLith], [3.0.3], [https://geodynamics.org/resources/pylith])
AC_INIT([PyLith], [4.0.0], [https://geodynamics.org/resources/pylith])
AC_CONFIG_AUX_DIR([./aux-config])
AC_CONFIG_HEADER([portinfo])
AC_CONFIG_MACRO_DIR([m4])
Expand Down Expand Up @@ -96,11 +89,11 @@ AX_CXX_COMPILE_STDCXX(14)

dnl PYTHON/PYTHIA (nemesis must be set before python)
CIT_PATH_NEMESIS
AM_PATH_PYTHON([3.6])
AM_PATH_PYTHON([3.8])
CIT_PYTHON_SYSCONFIG
CIT_CHECK_PYTHON_HEADER
CIT_CHECK_PYTHON_SHARED
CIT_PYTHON_MODULE([pythia],[1.0.0])
CIT_PYTHON_MODULE([pythia],[1.1.0])

dnl MPI
AC_LANG(C++)
Expand Down Expand Up @@ -159,7 +152,7 @@ AC_REQUIRE_CPP
AC_LANG(C++)
CIT_SPATIALDATA_HEADER
CIT_SPATIALDATA_LIB
CIT_PYTHON_MODULE([spatialdata],[3.0.0])
CIT_PYTHON_MODULE([spatialdata],[3.1.0])

dnl TEST COVERAGE
AM_CONDITIONAL([ENABLE_TEST_COVERAGE], [test "$enable_test_coverage" = yes])
Expand All @@ -180,7 +173,7 @@ CIT_FUNCTIONSTRING
dnl VERSION
CIG_PKG_GIT(PYLITH)
AC_DEFINE_UNQUOTED([PYLITH_VERSION], ["$PACKAGE_VERSION"], [Define PyLith version])
AC_DEFINE_UNQUOTED([PYLITH_DOI], ["10.5281/zenodo.7072811"], [Define PyLith doi])
AC_DEFINE_UNQUOTED([PYLITH_DOI], ["10.5281/zenodo.10359667"], [Define PyLith doi])

dnl ENDIANNESS
AC_C_BIGENDIAN
Expand All @@ -199,8 +192,8 @@ AC_CONFIG_FILES([Makefile
libsrc/pylith/meshio/Makefile
libsrc/pylith/problems/Makefile
libsrc/pylith/topology/Makefile
libsrc/pylith/testing/Makefile
libsrc/pylith/utils/Makefile
libsrc/pylith/testing/Makefile
modulesrc/Makefile
modulesrc/include/Makefile
modulesrc/bc/Makefile
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21 changes: 7 additions & 14 deletions developer/Makefile.am
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# -*- Makefile -*-
# =================================================================================================
# This code is part of PyLith, developed through the Computational Infrastructure
# for Geodynamics (https://github.com/geodynamics/pylith).
#
# ----------------------------------------------------------------------
# Copyright (c) 2010-2023, University of California, Davis and the PyLith Development Team.
# All rights reserved.
#
# Brad T. Aagaard, U.S. Geological Survey
# Charles A. Williams, GNS Science
# Matthew G. Knepley, University at Buffalo
#
# This code was developed as part of the Computational Infrastructure
# for Geodynamics (http://geodynamics.org).
#
# Copyright (c) 2010-2022 University of California, Davis
#
# See LICENSE.md for license information.
#
# ----------------------------------------------------------------------
# See https://mit-license.org/ and LICENSE.md and for license information.
# =================================================================================================

dist_noinst_PYTHON = \
downloads.py \
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