Merge pull request #78 from baagaard-usgs/prepare-release-4.1.3

baagaard-usgs · web-flow · commit 966f14acd554 · 2024-07-26T11:26:49.000-06:00
Prepare release 4.1.3
diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@ This installer builds the current PyLith release and its dependencies from sourc
 ## Documentation
 
 * [Development version](https://pylith-installer.readthedocs.io/en/latest/)
-* [Stable version](heeps://pylith-installer.readthedocs.io/en/v4.1.2-0)
+* [Stable version](heeps://pylith-installer.readthedocs.io/en/v4.1.3-0)
 * See the corresponding version of the PyLith manual for v2.2.2 and earlier
 
 ## Author
diff --git a/configure.ac b/configure.ac
@@ -10,7 +10,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.59)
-AC_INIT([PyLith Installer], [4.1.2-0], [https://community.geodynamics.org/c/pylith/])
+AC_INIT([PyLith Installer], [4.1.3-0], [https://community.geodynamics.org/c/pylith/])
 AC_CONFIG_AUX_DIR([./aux-config])
 AC_CONFIG_MACRO_DIR([m4])
 AM_INIT_AUTOMAKE([foreign tar-pax])
diff --git a/developer/release-announcement.md b/developer/release-announcement.md
@@ -1,4 +1,4 @@
-We are pleased to announce release of PyLith Installer version 4.1.2-0.
+We are pleased to announce release of PyLith Installer version 4.1.3-0.
 
 Please submit bug reports via GitHub issues:
     https://github.com/geodynamics/pylith_installer/issues
@@ -10,4 +10,4 @@ from source on Unix flavored operating systems.
 
 You can download the installer from https://geodynamics.org/resources/pylith.
 
-Instructions are online at https://pylith-installer.readthedocs.io/en/v4.1.2-0.
+Instructions are online at https://pylith-installer.readthedocs.io/en/v4.1.3-0.
diff --git a/docs/conf.py b/docs/conf.py
@@ -21,7 +21,7 @@
 author = 'Brad T. Aagaard'
 
 # The full version, including alpha/beta/rc tags
-release = 'v4.1.2-0'
+release = 'v4.1.3-0'
 
 
 # -- General configuration ---------------------------------------------------
diff --git a/docs/configs/centos.md b/docs/configs/centos.md
@@ -44,7 +44,7 @@ export HDF5_INCDIR=${PREFIX_DIR}/dependencies/include
 ### Configure
 
 ```bash
-$HOME/src/pylith/pylith-installer-4.1.2-0/configure \
+$HOME/src/pylith/pylith-installer-4.1.3-0/configure \
     --prefix=$PREFIX_DIR \
     --with-fetch=curl \
     --with-fortran=no \
@@ -117,7 +117,7 @@ export HDF5_INCDIR=${PREFIX_DIR}/dependencies/include
 ### Configure
 
 ```bash
-$HOME/src/pylith/pylith-installer-4.1.2-0/configure \
+$HOME/src/pylith/pylith-installer-4.1.3-0/configure \
     --prefix=$PREFIX_DIR \
     --with-fetch=curl \
     --with-fortran=no \
@@ -183,7 +183,7 @@ export HDF5_INCDIR=${PREFIX_DIR}/dependencies/include
 ### Configure
 
 ```bash
-$HOME/src/pylith/pylith-installer-4.1.2-0/configure \
+$HOME/src/pylith/pylith-installer-4.1.3-0/configure \
     --prefix=$PREFIX_DIR \
     --with-fetch=curl \
     --with-fortran=no \
diff --git a/docs/configs/clusters.md b/docs/configs/clusters.md
@@ -18,5 +18,5 @@ We assume that Python was not built with the same compiler suite as MPI. The `--
 If Python was built with the same compilers used to build MPI, then then you do not need the `--enable-python` option.
 
 ```bash
-$HOME/src/pylith/pylith-installer-4.1.2-0/configure --enable-python --with-make-threads=8 --prefix=$HOME/pylith
+$HOME/src/pylith/pylith-installer-4.1.3-0/configure --enable-python --with-make-threads=8 --prefix=$HOME/pylith
 ```
diff --git a/docs/configs/debian.md b/docs/configs/debian.md
@@ -52,7 +52,7 @@ HDF5_LIBDIR=/usr/lib/x86_64-linux-gnu/hdf5/mpich
 ### Configure
 
 ```bash
-$HOME/src/pylith/pylith-installer-4.1.2-0/configure \
+$HOME/src/pylith/pylith-installer-4.1.3-0/configure \
     --prefix=$PREFIX_DIR \
     --with-fetch=curl \
     --with-fortran=no \
@@ -119,7 +119,7 @@ HDF5_LIBDIR=/usr/lib/x86_64-linux-gnu/hdf5/openmpi
 ### Configure
 
 ```bash
-$HOME/src/pylith/pylith-installer-4.1.2-0/configure \
+$HOME/src/pylith/pylith-installer-4.1.3-0/configure \
     --prefix=$PREFIX_DIR \
     --with-fetch=curl \
     --with-fortran=no \
diff --git a/docs/configs/fedora.md b/docs/configs/fedora.md
@@ -59,7 +59,7 @@ PATH=$PATH:/usr/lib64/mpich/bin
 ### Configure
 
 ```bash
-$HOME/src/pylith/pylith-installer-4.1.2-0/configure \
+$HOME/src/pylith/pylith-installer-4.1.3-0/configure \
     --prefix=$PREFIX_DIR \
     --with-fetch=curl \
     --with-fortran=no \
@@ -136,7 +136,7 @@ PATH=$PATH:/usr/lib64/openmpi/bin
 ### Configure
 
 ```bash
-$HOME/src/pylith/pylith-installer-4.1.2-0/configure \
+$HOME/src/pylith/pylith-installer-4.1.3-0/configure \
     --prefix=$PREFIX_DIR \
     --with-fetch=curl \
     --with-fortran=no \
diff --git a/docs/configs/macos.md b/docs/configs/macos.md
@@ -25,7 +25,7 @@ PREFIX=$HOME/pylith
 # Define PETSc options
 petsc_options="--download-chaco=1 --download-ml --download-f2cblaslapack --with-fc=0 --with-hwloc=0 --with-ssl=0 --with-x=0 --with-c2html=0 --with-lgrind=0"
 #
-${HOME}/src/pylith/pylith_installer-4.1.2-0/configure  \
+${HOME}/src/pylith/pylith_installer-4.1.3-0/configure  \
     --prefix=${PREFIX} \
     --enable-force-install \
     --with-fetch=curl \
diff --git a/docs/configs/ubuntu.md b/docs/configs/ubuntu.md
@@ -52,7 +52,7 @@ PREFIX_DIR=$HOME/pylith
 ### Configure
 
 ```bash
-$HOME/src/pylith/pylith-installer-4.1.2-0/configure \
+$HOME/src/pylith/pylith-installer-4.1.3-0/configure \
     --prefix=$PREFIX_DIR \
     --with-fetch=curl \
     --with-fortran=no \
@@ -119,7 +119,7 @@ PREFIX_DIR=$HOME/pylith
 ### Configure
 
 ```bash
-$HOME/src/pylith/pylith-installer-4.1.2-0/configure \
+$HOME/src/pylith/pylith-installer-4.1.3-0/configure \
     --prefix=$PREFIX_DIR \
     --with-fetch=curl \
     --with-fortran=no \
@@ -187,7 +187,7 @@ PREFIX_DIR=$HOME/pylith
 ### Configure
 
 ```bash
-$HOME/src/pylith/pylith-installer-4.1.2-0/configure \
+$HOME/src/pylith/pylith-installer-4.1.3-0/configure \
     --prefix=$PREFIX_DIR \
     --with-fetch=curl \
     --with-fortran=no \
@@ -255,7 +255,7 @@ PREFIX_DIR=$HOME/pylith
 ### Configure
 
 ```bash
-$HOME/src/pylith/pylith-installer-4.1.2-0/configure \
+$HOME/src/pylith/pylith-installer-4.1.3-0/configure \
     --prefix=$PREFIX_DIR \
     --with-fetch=curl \
     --with-fortran=no \
diff --git a/docs/devenv/configs.md b/docs/devenv/configs.md
@@ -52,7 +52,7 @@ We use the following directory structure:
 
 ```{code-block} console
 pylith-developer/
-├── pylith_installer-4.1.2-0 # source code for the installer
+├── pylith_installer-4.1.3-0 # source code for the installer
 ├── build-debug # top-level directory for building with debugging
 └── pylith-debug # directory where PyLith and other CIG code is installed by installer
 ```
@@ -96,7 +96,7 @@ mkdir -p $PYLITH_DIR
 cd $PYLITH_DIR
 
 # Place the installer source code tarball in $PYLITH_DIR and then unpack the tarball.
-tar -xf pylith_installer-4.1.2-0.tar.gz
+tar -xf pylith_installer-4.1.3-0.tar.gz
 ```
 
 ## Linux
@@ -126,7 +126,7 @@ Configure the installer.
 ```{code-block} bash
 mkdir $PYLITH_DIR/build-debug
 cd $PYLITH_DIR/build-debug
-$PYLITH_DIR/pylith_installer-4.1.2-0/configure \
+$PYLITH_DIR/pylith_installer-4.1.3-0/configure \
     --enable-developer \
     --with-debugging \
     --with-pylith-git=$PYLITH_BRANCH \
@@ -182,7 +182,7 @@ Configure the installer.
 ```{code-block} bash
 mkdir $PYLITH_DIR/build-debug
 cd $PYLITH_DIR/build-debug
-${HOME}/src/pylith/pylith_installer-4.1.2-0/configure  \
+${HOME}/src/pylith/pylith_installer-4.1.3-0/configure  \
     --enable-developer \
     --with-debugging \
     --with-pylith-git=$PYLITH_BRANCH \
diff --git a/docs/devenv/docker/update.md b/docs/devenv/docker/update.md
@@ -15,4 +15,4 @@ Pulling the PyLith development environment Docker image does not update Pythia,
 
 ## Updating PETSc or PyLith
 
-See [Rebuilding PETSc and PyLith in the PyLith Developer Guide](https://pylith.readthedocs.io/en/v4.1.2/developer/contributing/rebuilding.html) for how to update PETSc and PyLith.
+See [Rebuilding PETSc and PyLith in the PyLith Developer Guide](https://pylith.readthedocs.io/en/v4.1.3/developer/contributing/rebuilding.html) for how to update PETSc and PyLith.
diff --git a/docs/install/configure.md b/docs/install/configure.md
@@ -22,7 +22,7 @@ The default configure options assume you have:
 In this case, you simply specify the number of threads and the destination directory:
 ```bash
 mkdir -p $HOME/build/pylith
-$HOME/src/pylith/pylith-installer-4.1.2-0/configure --with-make-threads=2 --prefix=$HOME/pylith
+$HOME/src/pylith/pylith-installer-4.1.3-0/configure --with-make-threads=2 --prefix=$HOME/pylith
 ```
 
 ## Configure options
diff --git a/docs/install/download.md b/docs/install/download.md
@@ -4,13 +4,13 @@
 
   <https://geodynamics.org/resources/pylith>
 
-  We assume the tarball `pylith-installer-4.1.2-0.tgz` is downloaded to `$HOME/Downloads`. We will place the installer source code in the directory `$HOME/src/pylith`.
+  We assume the tarball `pylith-installer-4.1.3-0.tgz` is downloaded to `$HOME/Downloads`. We will place the installer source code in the directory `$HOME/src/pylith`.
 
 ## Unpack the installer source code:
 
 ```bash
 mkdir -p $HOME/src/pylith
 cd $HOME/src/pylith
-mv $HOME/Downloads/pylith-installer-4.1.2-0.tgz $HOME/src/pylith/
-tar -xf pylith-installer-4.1.2-0.tgz
+mv $HOME/Downloads/pylith-installer-4.1.3-0.tgz $HOME/src/pylith/
+tar -xf pylith-installer-4.1.3-0.tgz
 ```
diff --git a/packages.am b/packages.am
@@ -48,7 +48,7 @@ SQLITE_VER=3410200
 TIFF_VER=4.5.0
 PROJ_VER=9.2.0
 
-HDF5_VER=1.14.0
+HDF5_VER=1.14.4-3
 
 NETCDF_VER=4.9.2
 NETCDFPY_VER=1.5.7
@@ -59,13 +59,13 @@ PYTHIA_VER=main
 SPATIALDATA_VER=main
 PYLITH_VER=$(pylith_git)
 if PETSC_TARBALL
-PETSC_VER=4.1.2
+PETSC_VER=4.1.3
 endif
 else
 PYTHIA_VER=1.1.0
-SPATIALDATA_VER=3.1.1
-PYLITH_VER=4.1.2
-PETSC_VER=4.1.2
+SPATIALDATA_VER=3.1.2
+PYLITH_VER=4.1.3
+PETSC_VER=4.1.3
 endif
 
 PARAMETERSGUI_VER=2.0.1

Original file line number	Diff line number	Diff line change
`@@ -25,7 +25,7 @@ PREFIX=$HOME/pylith`
`25`	`25`	`# Define PETSc options`
`26`	`26`	`petsc_options="--download-chaco=1 --download-ml --download-f2cblaslapack --with-fc=0 --with-hwloc=0 --with-ssl=0 --with-x=0 --with-c2html=0 --with-lgrind=0"`
`27`	`27`	`#`
`28`		`-${HOME}/src/pylith/pylith_installer-4.1.2-0/configure \`
	`28`	`+${HOME}/src/pylith/pylith_installer-4.1.3-0/configure \`
`29`	`29`	`--prefix=${PREFIX} \`
`30`	`30`	`--enable-force-install \`
`31`	`31`	`--with-fetch=curl \`