Merge pull request #745 from baagaard-usgs/prepare-release-4.1.1

Prepare release 4.1.1

CHANGES.md

@@ -5,6 +5,12 @@ 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 4.1.1 (2024/06/09)
+
+* **Fixed**
+  * Improved setup of variable block Jacobian preconditioner used for elasticity with faults to reduce runtime.
+  * Fix several typos and update a few diagrams in the documentation.
+
 ## Version 4.1.0 (2024/06/05)
 
 * **Changed**
@@ -16,7 +22,7 @@ The version numbers are in the form `MAJOR.MINOR.PATCH`, where major releases in
   * New 2D and 3D crustal strike-slip faults examples based on the 2019 Ridgecrest earthquake.
   * New 2D subduction zone outer-rise faulting example examining poroelastic response to bending stresses.
   * New `pylith_viz` utility for plotting PyLith results.
-  * Updated `examples/strikeslip-2d` and `examples/reverse-2d` to demonstrate use of uniform refinement and higher ordder discretizations to improve resolution of solution.
+  * Updated `examples/strikeslip-2d` and `examples/reverse-2d` to demonstrate use of uniform refinement and higher order discretizations to improve resolution of solution.
   * Documentation
     * Developer Guide: Added description of the process for adding event logging and evaluating performance, including performance logging.
     * Developer Guide: Added checklist for what is needed when contributing examples.

CITATION.cff

@@ -22,7 +22,7 @@ authors:
     orcid: "https://orcid.org/0000-0001-7435-9196"
 identifiers:
   - type: doi
-    value: 10.5281/zenodo.11479383
+    value: 10.5281/zenodo.11534872
 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: 4.1.0
+version: 4.1.1
 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.11479383.svg)](https://doi.org/10.5281/zenodo.11479383)
+[![DOI](https://www.zenodo.org/badge/DOI/10.5281/zenodo.11534872.svg)](https://doi.org/10.5281/zenodo.11534872)
 [![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], [4.1.0], [https://geodynamics.org/resources/pylith])
+AC_INIT([PyLith], [4.1.1], [https://geodynamics.org/resources/pylith])
 AC_CONFIG_AUX_DIR([./aux-config])
 AC_CONFIG_HEADER([portinfo])
 AC_CONFIG_MACRO_DIR([m4])
@@ -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.11479383"], [Define PyLith doi])
+AC_DEFINE_UNQUOTED([PYLITH_DOI], ["10.5281/zenodo.11534872"], [Define PyLith doi])
 
 dnl ENDIANNESS
 AC_C_BIGENDIAN

developer/pdf_to_svg.py

@@ -0,0 +1,16 @@
+#!/usr/bin/env nemesis
+
+import sys
+import pymupdf
+
+if len(sys.argv) != 2:
+    print("usage: pdf_to_svg.py FILENAME")
+    sys.exit(1)
+
+filename_pdf = sys.argv[1]
+doc = pymupdf.open(filename_pdf) # open a document
+page = doc[0]
+
+filename_svg = filename_pdf.replace(".pdf", ".svg")
+with open(filename_svg, "w", encoding="utf-8") as svg_out:
+    svg_out.write(page.get_svg_image())

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 = '4.1.0'
+release = '4.1.1'
 
 
 # -- 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 v4.1.0.* Davis, CA: Computational Infrastructure of Geodynamics. DOI: 10.5281/zenodo.11479383.
+- Aagaard, B., M. Knepley, C. Williams (2024a), *PyLith v4.1.1.* Davis, CA: Computational Infrastructure of Geodynamics. DOI: 10.5281/zenodo.11534872.
 
-- Aagaard, B., M. Knepley, C. Williams (2024b), *PyLith Manual, Version 4.1.0.* Davis, CA: Computational Infrastructure of Geodynamics. https://pylith.readthedocs.io/en/v4.1.0
+- Aagaard, B., M. Knepley, C. Williams (2024b), *PyLith Manual, Version 4.1.1.* Davis, CA: Computational Infrastructure of Geodynamics. https://pylith.readthedocs.io/en/v4.1.1
 
 ## 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 4.1.0 (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 4.1.1 (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/examples/magma-2d/step02-inflation-statevars.md

@@ -93,7 +93,7 @@ ksp_divtol = 1.0e+5
 ---
 caption: Run Step 2 simulation
 ---
-$ pylith step02_inflation.cfg
+$ pylith step02_inflation_statevars.cfg
 
 # The output should look something like the following.
  >> /software/unix/py3.12-venv/pylith-opt/lib/python3.12/site-packages/pylith/apps/PyLithApp.py:77:main

docs/user/install/index.md

@@ -49,10 +49,10 @@ 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-4.1.0-linux-x86_64.tar.gz
+      $ tar -xzf pylith-4.1.1-linux-x86_64.tar.gz
 
       # macOS
-      $ tar -xzf pylith-4.1.0-macOS-10.15-x86_64.tar.gz
+      $ tar -xzf pylith-4.1.1-macOS-10.15-x86_64.tar.gz
       ```
 4. Set environment variables.
 The provided `setup.sh` script only works if you are using bash shell.
@@ -66,20 +66,20 @@ 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.
 
 ```
-curl -L -O https://github.com/geodynamics/pylith/releases/download/v4.1.0/pylith-4.1.0-macOS-10.15-x86_64.tar.gz
+curl -L -O https://github.com/geodynamics/pylith/releases/download/v4.1.1/pylith-4.1.1-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):
 
 ```
 # Show extended attributes
-xattr ./pylith-4.1.0-macOS-10.15-x86_64
+xattr ./pylith-4.1.1-macOS-10.15-x86_64
 
 # Output should be
 com.apple.quarantine
 
 # Remove quarantine attributes
-sudo xattr -r -d com.apple.quarantine ./pylith-4.1.0-macOS-10.15-x86_64
+sudo xattr -r -d com.apple.quarantine ./pylith-4.1.1-macOS-10.15-x86_64
 ```
 :::
 
@@ -142,7 +142,7 @@ For each package this utility downloads the source code, configures it, builds i
 ## Verifying PyLith is Installed Correctly
 
 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-4.1.0/examples` while in the source distribution, they are located in `pylith-4.1.0/examples`.
+In the binary distribution, the examples are located in `src/pylith-4.1.1/examples` while in the source distribution, they are located in `pylith-4.1.1/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`: