Merge pull request #487 from geodynamics/baagaard/update-version-3.0.1

Set version to 3.0.1; update release information

CHANGES.md

@@ -1,5 +1,31 @@
 See <https://github.com/geodynamics/pylith/commits/main> for the complete log of changes made to PyLith.
 
+## Version 3.0.1
+
+This is a bug fix release with no new features or changes to the user interface.
+
+* Bug fixes
+  * Fix lots of small bugs related to running in parallel
+  * Fix several discrepancies among the code, examples, and manual
+* Examples
+  * Added `examples/subduction-3d` steps 1-4 (included in the manual)
+  * Added `examples/troubleshooting-2d` (included in the PyLith v3.0 tutorials but not yet added to the manual)
+* Documentation
+  * Added instructions for how to remove Apple quarantine attributes
+  * Fix LaTeX build of documentation (now available at https://pylith.readthedocs.io)
+  * Improved instructions on how to run ParaView Python scripts when starting ParaView from a shortcut
+  * Added notes indicating steps of examples are not yet updated for v3.0
+  * Fix lots of typos
+
+### Binary packages
+
+* Updated PyLith Parameter Viewer (v2.0.0) for Python 3.
+
+### Known issues
+
+* The default PETSc options provide a computationally expensive preconditioner when solving incompressible elasticity problems in parallel. We expect to have a more optimal preconditioner in the next release.
+* You may still encounter a few bugs when running in parallel; they appear to cases with specific partitioning of the mesh in relation to one or more faults.
+
 ## Version 3.0.0
 
 Version 3.0.0 includes major changes to the underlying finite-element formulation and implementation in order to support a more flexible specification of the governing equations and higher order basis functions.

README.md

@@ -1,6 +1,6 @@
 # PyLith
 
-[![DOI](https://www.zenodo.org/badge/DOI/10.5281/zenodo.6622161.svg)](https://doi.org/10.5281/zenodo.6622161)
+[![DOI](https://www.zenodo.org/badge/DOI/10.5281/zenodo.6667614.svg)](https://doi.org/10.5281/zenodo.6667614)
 [![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

@@ -17,7 +17,7 @@ dnl ----------------------------------------------------------------------
 dnl Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.59)
-AC_INIT([PyLith], [3.0.0], [https://geodynamics.org/resources/pylith])
+AC_INIT([PyLith], [3.0.1], [https://geodynamics.org/resources/pylith])
 AC_CONFIG_AUX_DIR([./aux-config])
 AC_CONFIG_HEADER([portinfo])
 AC_CONFIG_MACRO_DIR([m4])
@@ -179,7 +179,7 @@ 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.6622161"], [Define PyLith doi])
+AC_DEFINE_UNQUOTED([PYLITH_DOI], ["10.5281/zenodo.6667614"], [Define PyLith doi])
 
 dnl ENDIANNESS
 AC_C_BIGENDIAN

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 = '3.0.0'
+release = '3.0.1'
 
 
 # -- General configuration ---------------------------------------------------

docs/intro/conventions.md

@@ -14,7 +14,7 @@ This is a tip, helpful hint, or suggestion.
 
 For features recently added to PyLith, we show the version number when they
 were added.
-*New in v3.0.0dev*
+*New in v3.0.0*
 
 ## Command Line Arguments
 

docs/intro/development-plan.md

@@ -6,9 +6,9 @@ Future implementation of features is guided by several target applications, incl
 * Inversion of geodetic data for slow slip events, fault creep, and long-term fault slip rates.
 * Quasistatic and dynamic modeling of fluids and faulting.
 
-## Version 3.0.1 (June 2022)
+## Version 3.0.2 (July 2022)
 
-Finish updating examples and documentation.
+Updates for examples and documentation along with bugfixes.
 
 ## Version 3.1.0 (October 2022)
 

docs/intro/preface.md

@@ -17,9 +17,9 @@ The following peer-reviewed paper discussed the development of PyLith:
 
 To cite the software and manual, use:
 
-- Aagaard, B., M. Knepley, C. Williams (2022), *PyLith v3.0.0.* Davis, CA: Computational Infrastructure of Geodynamics. DOI: 10.5281/zenodo.6622161.
+- Aagaard, B., M. Knepley, C. Williams (2022), *PyLith v3.0.1.* Davis, CA: Computational Infrastructure of Geodynamics. DOI: 10.5281/zenodo.6667614.
 
-- Aagaard, B., M. Knepley, C. Williams (2022), *PyLith Manual, Version 3.0.0.* Davis, CA: Computational Infrastructure of Geodynamics. https://pylith.readthedocs.io/en/v3.0.0
+- Aagaard, B., M. Knepley, C. Williams (2022), *PyLith Manual, Version 3.0.1.* Davis, CA: Computational Infrastructure of Geodynamics. https://pylith.readthedocs.io/en/v3.0.1
 
 ## Support
 

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-3.0.0-linux-x86_64.tar.gz
+      $ tar -xzf pylith-3.0.1-linux-x86_64.tar.gz
 
       # macOS
-      $ tar -xzf pylith-3.0.0-macOS-11.6.6-x86_64.tar.gz
+      $ tar -xzf pylith-3.0.1-macOS-11.6.6-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/v3.0.0/pylith-3.0.0-macOS-11.6.6-x86_64.tar.gz
+curl -L -O https://github.com/geodynamics/pylith/releases/download/v3.0.1/pylith-3.0.1-macOS-11.6.6-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-3.0.0-macOS-11.6.6-x86_64
+xattr ./pylith-3.0.1-macOS-11.6.6-x86_64
 
 # Output should be
 com.apple.quarantine
 
 # Remove quarantine attributes
-sudo xattr -r -d com.apple.quarantine ./pylith-3.0.0-macOS-11.6.6-x86_64
+sudo xattr -r -d com.apple.quarantine ./pylith-3.0.1-macOS-11.6.6-x86_64
 ```
 :::
 
@@ -143,7 +143,7 @@ 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-3.0.0/examples` while in the source distribution, they are located in `pylith-3.0.0/examples`.
+In the binary distribution, the examples are located in `src/pylith-3.0.1/examples` while in the source distribution, they are located in `pylith-3.0.1/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`:
 

examples/subduction-3d/input/README.md

@@ -6,6 +6,7 @@ Follow the instructions below the download the necessary files.
 ## Cubit Mesh
 
 ```
-curl -L -O https://github.com/geodynamics/pylith/releases/download/v3.0.1/mesh_tet.exo.gz 
+curl -L -O https://github.com/geodynamics/pylith/releases/download/v3.0.1/examples-subduction-3d-mesh_tet.exo.gz
+mv examples-subduction-3d-mesh_tet.exo.gz mesh_tet.exo.gz 
 gunzip mesh_tet.exo.gz 
 ```

release-notes/Makefile.am

@@ -45,7 +45,8 @@ EXTRA_DIST = \
 	announce_v2.1.4.txt \
 	announce_v2.2.0.txt \
 	announce_v2.2.1.txt \
-	announce_v3.0.0.txt
+	announce_v3.0.0.txt \
+	announce_v3.0.1.txt
 
 
 # End of file 

release-notes/announce_v3.0.1.txt

@@ -0,0 +1,41 @@
+# PyLith v3.0.1 now available
+
+I am pleased to announce the release of PyLith 3.0.1, a finite-element code designed to solve dynamic elastic problems and quasistatic viscoelastic problems in tectonic deformation.
+
+You can download the source code and binaries from
+  <https://geodynamics.org/resources/pylith>
+
+Documentation
+  <https://pylith.readthedocs.org/en/v3.0.1>
+
+## Release Notes
+
+This is a bug fix release with no new features or changes to the user interface.
+
+* Bug fixes
+  * Fix lots of small bugs related to running in parallel
+  * Fix several discrepancies among the code, examples, and manual
+* Examples
+  * Added `examples/subduction-3d` steps 1-4 (included in the manual)
+  * Added `examples/troubleshooting-2d` (included in the PyLith v3.0 tutorials but not yet added to the manual)
+* Documentation
+  * Added instructions for how to remove Apple quarantine attributes
+  * Fix LaTeX build of documentation (now available at https://pylith.readthedocs.io)
+  * Improved instructions on how to run ParaView Python scripts when starting ParaView from a shortcut
+  * Added notes indicating steps of examples are not yet updated for v3.0
+  * Fix lots of typos
+
+## Binary packages
+
+* Updated PyLith Parameter Viewer (v2.0.0) for Python 3.
+
+## Known issues
+
+* The default PETSc options provide a computationally expensive preconditioner when solving incompressible elasticity problems in parallel. We expect to have a more optimal preconditioner in the next release.
+* You may still encounter a few bugs when running in parallel; they appear to cases with specific partitioning of the mesh in relation to one or more faults.
+
+## Contributors
+
+* Brad Aagaard
+* Matthew Knepley
+* Charles Williams

setup.cfg

@@ -4,7 +4,7 @@ tag_date = 0
 
 [metadata]
 name = pylith
-version = 3.0.0
+version = 3.0.1
 author = Brad Aagaard, Matthew Knepley, Charles Williams
 author_email = [email protected], [email protected], [email protected]
 description = Finite-element software for modeling crustal deformation with an emphasis on earthquake faulting.