Merge pull request #768 from baagaard-usgs/prepare-release-4.1.3

Prepare release 4.1.3

Author: baagaard-usgs

CHANGES.md

@@ -5,7 +5,7 @@ Starting with v3.0.0, we strictly follow the [semantic versioning guidelines](ht
 The version numbers are in the form `MAJOR.MINOR.PATCH`, where major releases indicate changes to the public API (parameters), minor releases indicate new functionality that is backward compatible, and patch releases indicate backward compatible bug fixes.
 :::
 
-## Version 4.1.3 (2024/07/XX)
+## Version 4.1.3 (2024/07/31)
 
 * **Added**
   * Expanded the section of the manual discussing mesh generation with Cubit and Gmsh. Added a list of useful functions in the Cubit and Gmsh Python interfaces.
@@ -23,6 +23,14 @@ The version numbers are in the form `MAJOR.MINOR.PATCH`, where major releases in
 * **Fixed**
   * Fix inconsistency in normal direction on fault surfaces. Orientation was correct but direction was flipped at some locations. This affected local slip direction and the resulting deformation close to the fault.
 
+### Contributors
+
+* Brad Aagaard ![ORCID iD](/_static/images/ORCIDiD_icon32x32.png){w=16px}[0000-0002-8795-9833](https://orcid.org/0000-0002-8795-9833)
+* Matthew Knepley ![ORCID iD](/_static/images/ORCIDiD_icon32x32.png){w=16px}[0000-0002-2292-0735](https://orcid.org/0000-0002-2292-0735)
+* Charles Williams ![ORCID iD](/_static/images/ORCIDiD_icon32x32.png){w=16px}[0000-0001-7435-9196](https://orcid.org/0000-0001-7435-9196)
+* Grant Block ![ORCID iD](/_static/images/ORCIDiD_icon32x32.png){w=16px}[0009-0003-3402-0923](https://orcid.org/0009-0003-3402-0923)
+
+
 ## Version 4.1.1 (2024/06/09)
 
 * **Fixed**

CITATION.cff

@@ -22,7 +22,7 @@ authors:
     orcid: "https://orcid.org/0000-0001-7435-9196"
 identifiers:
   - type: doi
-    value: 10.5281/zenodo.11624232
+    value: 10.5281/zenodo.13134616
 repository-code: "https://github.com/geodynamics/pylith"
 url: "https://geodynamics.org/resources/pylith"
 keywords:
@@ -31,7 +31,7 @@ keywords:
   - earthquake
   - finite element
 license: MIT
-version: 4.1.2
+version: 4.1.3
 date-released: "2024-06-05"
 preferred-citation:
   type: article

README.md

@@ -1,6 +1,6 @@
 # PyLith
 
-[![DOI](https://www.zenodo.org/badge/DOI/10.5281/zenodo.11624232.svg)](https://doi.org/10.5281/zenodo.11624232)
+[![DOI](https://www.zenodo.org/badge/DOI/10.5281/zenodo.13134616.svg)](https://doi.org/10.5281/zenodo.13134616)
 [![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)

configure.ac

@@ -10,7 +10,7 @@ dnl ============================================================================
 dnl Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.59)
-AC_INIT([PyLith], [4.1.2], [https://geodynamics.org/resources/pylith])
+AC_INIT([PyLith], [4.1.3], [https://geodynamics.org/resources/pylith])
 AC_CONFIG_AUX_DIR([./aux-config])
 AC_CONFIG_HEADER([portinfo])
 AC_CONFIG_MACRO_DIR([m4])
@@ -102,7 +102,7 @@ AC_CHECK_HEADER([mpi.h], [], [AC_MSG_ERROR([header 'mpi.h' not found])])
 
 dnl PETSC
 AC_LANG(C)
-CIT_PATH_PETSC([3.21.2])
+CIT_PATH_PETSC([3.21.3])
 CIT_HEADER_PETSC
 CIT_CHECK_LIB_PETSC
 
@@ -173,7 +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.11624232"], [Define PyLith doi])
+AC_DEFINE_UNQUOTED([PYLITH_DOI], ["10.5281/zenodo.13134616"], [Define PyLith doi])
 
 dnl ENDIANNESS
 AC_C_BIGENDIAN

docs/Makefile.am

@@ -100,6 +100,7 @@ dist_noinst_DATA = \
 	user/components/materials/AuxSubfieldsIsotropicPowerLaw.md \
 	user/components/materials/AuxSubfieldsPoroelasticity.md \
 	user/components/materials/DerivedSubfieldsElasticity.md \
+	user/components/materials/DerivedSubfieldsPoroelasticity.md \
 	user/components/materials/Elasticity.md \
 	user/components/materials/Homogeneous.md \
 	user/components/materials/IncompressibleElasticity.md \
@@ -150,6 +151,8 @@ dist_noinst_DATA = \
 	user/components/problems/SolnDispPresLagrange.md \
 	user/components/problems/SolnDispPresTracStrain.md \
 	user/components/problems/SolnDispPresTracStrainVelPdotTdot.md \
+	user/components/problems/SolnDispPresTracStrainLagrange.md \
+	user/components/problems/SolnDispPresTracStrainVelPdotTdotLagrange.md \
 	user/components/problems/SolnDispPresVel.md \
 	user/components/problems/SolnDispVel.md \
 	user/components/problems/SolnDispVelLagrange.md \
@@ -323,6 +326,7 @@ dist_noinst_DATA = \
 	user/examples/magma-2d/figs/geometry-cubit.pdf \
 	user/examples/magma-2d/figs/geometry-gmsh.svg \
 	user/examples/magma-2d/figs/geometry-gmsh.pdf \
+	user/examples/magma-2d/figs/gmsh-tri.png \
 	user/examples/magma-2d/figs/cubit-quad.png \
 	user/examples/magma-2d/figs/cubit-tri.png \
 	user/examples/magma-2d/figs/step01-diagram.pdf \

docs/conf.py

@@ -22,7 +22,7 @@
 author = 'Brad T. Aagaard, Matthew G. Knepley, Charles A. Williams'
 
 # The full version, including alpha/beta/rc tags
-release = '4.1.2'
+release = '4.1.3'
 
 
 # -- General configuration ---------------------------------------------------

docs/intro/preface.md

@@ -17,9 +17,9 @@ The following peer-reviewed paper discusses the development of PyLith:
 
 To cite the software and manual, use:
 
-- Aagaard, B., M. Knepley, C. Williams (2024a), *PyLith v4.1.2.* Davis, CA: Computational Infrastructure of Geodynamics. DOI: 10.5281/zenodo.11624232.
+- Aagaard, B., M. Knepley, C. Williams (2024a), *PyLith v4.1.3.* Davis, CA: Computational Infrastructure of Geodynamics. DOI: 10.5281/zenodo.13134616.
 
-- Aagaard, B., M. Knepley, C. Williams (2024b), *PyLith Manual, Version 4.1.2.* Davis, CA: Computational Infrastructure of Geodynamics. https://pylith.readthedocs.io/en/v4.1.2
+- Aagaard, B., M. Knepley, C. Williams (2024b), *PyLith Manual, Version 4.1.3.* Davis, CA: Computational Infrastructure of Geodynamics. https://pylith.readthedocs.io/en/v4.1.3
 
 ## Publishing Models
 
@@ -43,7 +43,7 @@ Common output files include the solution fields and state variables as `.h5`, `.
 
 The configuration files, parameters of the simulation, and solution field for the models in this study are available at DOI (Authors X, Y, Z) under CC BY-NC-SA 4.0.
 
-PyLith version 4.1.2 (Aagaard et al., 2013; Aagaard et al., 2023a; Aagaard et al., 2023b) used in these models is freely available under the MIT license for download through its software landing page https://geodynamics.org/resources/pylith or Zenodo (10.5281/zenodo.11479383).
+PyLith version 4.1.3 (Aagaard et al., 2013; Aagaard et al., 2023a; Aagaard et al., 2023b) used in these models is freely available under the MIT license for download through its software landing page https://geodynamics.org/resources/pylith or Zenodo (10.5281/zenodo.11479383).
 The project is being actively developed on GitHub and can be accessed via https://github.com/geodynamics/pylith.
 
 ## Support

docs/user/install/index.md

@@ -48,10 +48,10 @@ On macOS systems you can check the operating system version by clicking on the A
 3. Unpack the tarball.
     ```{code-block} bash
       # Linux 64-bit
-      tar -xzf pylith-4.1.2-linux-x86_64.tar.gz
+      tar -xzf pylith-4.1.3-linux-x86_64.tar.gz
 
       # macOS
-      tar -xzf pylith-4.1.2-macOS-10.15-x86_64.tar.gz
+      tar -xzf pylith-4.1.3-macOS-10.15-x86_64.tar.gz
       ```
 4. Set environment variables.
 The provided `setup.sh` script only works if you are using bash shell.
@@ -65,20 +65,20 @@ Ready to run PyLith.
 To bypass macOS quarantine restrictions, simply use command line program `curl` to download the tarball from within a terminal rather than using a web browser.
 
 ```{code-block} console
-curl -L -O https://github.com/geodynamics/pylith/releases/download/v4.1.2/pylith-4.1.2-macOS-10.15-x86_64.tar.gz
+curl -L -O https://github.com/geodynamics/pylith/releases/download/v4.1.3/pylith-4.1.3-macOS-10.15-x86_64.tar.gz
 ```
 
 Alternatively, if you do download the tarball using a web browser, after you unpack the tarball you can remove the macOS quarantine flags using the following commands (requires Administrator access):
 
 ```{code-block} bash
 # Show extended attributes
-xattr ./pylith-4.1.2-macOS-10.15-x86_64
+xattr ./pylith-4.1.3-macOS-10.15-x86_64
 
 # Output should be
 com.apple.quarantine
 
 # Remove quarantine attributes
-sudo xattr -r -d com.apple.quarantine ./pylith-4.1.2-macOS-10.15-x86_64
+sudo xattr -r -d com.apple.quarantine ./pylith-4.1.3-macOS-10.15-x86_64
 ```
 :::
 
@@ -176,7 +176,7 @@ For each package this utility downloads the source code, configures it, builds i
 ## Verifying PyLith Installation
 
 The easiest way to verify that PyLith has been installed correctly is to run one or more of the examples supplied with the binary and source code.
-In the binary distribution, the examples are located in `src/pylith-4.1.2/examples` while in the source distribution, they are located in `pylith-4.1.2/examples`.
+In the binary distribution, the examples are located in `src/pylith-4.1.3/examples` while in the source distribution, they are located in `pylith-4.1.3/examples`.
 {ref}`sec-examples` discusses how to run and visualize the results for the examples.
 To run the example discussed in Section {ref}`sec-examples-box-2d`:
 

pylith/__init__.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env nemesis
 # =================================================================================================
 # This code is part of PyLith, developed through the Computational Infrastructure
 # for Geodynamics (https://github.com/geodynamics/pylith).
@@ -8,11 +7,8 @@
 #
 # See https://mit-license.org/ and LICENSE.md and for license information. 
 # =================================================================================================
-# @file pylith/__init__.py
 
-# @brief Python top-level PyLith module initialization
-
-__version__ = "2.2.1"
+__version__ = "4.1.3"
 
 __all__ = ['apps',
            'bc',
@@ -22,9 +18,10 @@
            'meshio',
            'mpi',
            'problems',
+           'testing',
            'topology',
            'utils',
-           'tests',
+           'viz',
            ]
 
 

release-notes/Makefile.am

@@ -45,7 +45,8 @@ EXTRA_DIST = \
 	announce_v4.0.0.md \
 	announce_v4.1.0.md \
 	announce_v4.1.1.md \
-	announce_v4.1.2.md
+	announce_v4.1.2.md \
+	announce_v4.1.3.md
 
 
 # End of file