v5.13.1 release

Author: rjleveque

ClawPlotAxes.html

@@ -10,9 +10,9 @@
     <link rel="stylesheet" href="_static/layout.css" type="text/css" />
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="_static/flasky.css?v=59fe8e2d" />
-    <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=4ae1632d" />
+    <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
     <script src="_static/documentation_options.js?v=7bb99aaf"></script>
-    <script src="_static/doctools.js?v=9bcbadda"></script>
+    <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="icon" href="_static/clawicon.ico"/>
     <link rel="author" title="About these documents" href="about.html" />
@@ -93,7 +93,7 @@ <h3>Navigation</h3>
 </div>
 <dl class="py class">
 <dt class="sig sig-object py" id="ClawPlotAxes">
-<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ClawPlotAxes</span></span><a class="headerlink" href="#ClawPlotAxes" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ClawPlotAxes</span></span><a class="headerlink" href="#ClawPlotAxes" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <section id="attributes">

ClawPlotData.html

@@ -10,9 +10,9 @@
     <link rel="stylesheet" href="_static/layout.css" type="text/css" />
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="_static/flasky.css?v=59fe8e2d" />
-    <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=4ae1632d" />
+    <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
     <script src="_static/documentation_options.js?v=7bb99aaf"></script>
-    <script src="_static/doctools.js?v=9bcbadda"></script>
+    <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="icon" href="_static/clawicon.ico"/>
     <link rel="author" title="About these documents" href="about.html" />
@@ -87,7 +87,7 @@ <h3>Navigation</h3>
 <p>For usage see <a class="reference internal" href="plotting.html#plotting"><span class="std std-ref">Plotting with Visclaw</span></a>, <a class="reference internal" href="setplot.html#setplot"><span class="std std-ref">Using setplot.py to specify the desired plots</span></a>, and <a class="reference internal" href="plotexamples.html#plotexamples"><span class="std std-ref">Plotting examples</span></a>.</p>
 <dl class="py class">
 <dt class="sig sig-object py" id="ClawPlotData">
-<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ClawPlotData</span></span><a class="headerlink" href="#ClawPlotData" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ClawPlotData</span></span><a class="headerlink" href="#ClawPlotData" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <section id="attributes">

ClawPlotFigure.html

@@ -10,9 +10,9 @@
     <link rel="stylesheet" href="_static/layout.css" type="text/css" />
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="_static/flasky.css?v=59fe8e2d" />
-    <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=4ae1632d" />
+    <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
     <script src="_static/documentation_options.js?v=7bb99aaf"></script>
-    <script src="_static/doctools.js?v=9bcbadda"></script>
+    <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="icon" href="_static/clawicon.ico"/>
     <link rel="author" title="About these documents" href="about.html" />
@@ -89,7 +89,7 @@ <h3>Navigation</h3>
 <a class="reference internal" href="ClawPlotData.html#clawplotdata"><span class="std std-ref">ClawPlotData</span></a> object.</p>
 <dl class="py class">
 <dt class="sig sig-object py" id="ClawPlotFigure">
-<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ClawPlotFigure</span></span><a class="headerlink" href="#ClawPlotFigure" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ClawPlotFigure</span></span><a class="headerlink" href="#ClawPlotFigure" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <section id="attributes">

ClawPlotItem.html

@@ -10,9 +10,9 @@
     <link rel="stylesheet" href="_static/layout.css" type="text/css" />
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="_static/flasky.css?v=59fe8e2d" />
-    <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=4ae1632d" />
+    <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
     <script src="_static/documentation_options.js?v=7bb99aaf"></script>
-    <script src="_static/doctools.js?v=9bcbadda"></script>
+    <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="icon" href="_static/clawicon.ico"/>
     <link rel="author" title="About these documents" href="about.html" />
@@ -99,7 +99,7 @@ <h3>Navigation</h3>
 </div>
 <dl class="py class">
 <dt class="sig sig-object py" id="ClawPlotItem">
-<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ClawPlotItem</span></span><a class="headerlink" href="#ClawPlotItem" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ClawPlotItem</span></span><a class="headerlink" href="#ClawPlotItem" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <section id="attributes">

_sources/changes_to_master.rst.txt

@@ -3,12 +3,12 @@
 .. _changes_to_master:
 
 ===============================
-Changes to master since v5.13.0
+Changes to master since v5.13.1
 ===============================
 
 
 Follow the links to see changes that have been made to the master branch of
-each repository since the last release (v5.13.0) on August 23, 2025.
+each repository since the last release (v5.13.1) on Sept. 12, 2025.
 
 These changes should appear in the next release.  If you need them now,
 see :ref:`developers` for instructions on cloning and installing from the
@@ -31,48 +31,48 @@ Changes to classic
 
 
 See `classic diffs
-<https://github.com/clawpack/classic/compare/v5.13.0...master>`_
+<https://github.com/clawpack/classic/compare/v5.13.1...master>`_
 
 Changes to clawutil
 -------------------
 
 
 See `clawutil diffs
-<https://github.com/clawpack/clawutil/compare/v5.13.0...master>`_
+<https://github.com/clawpack/clawutil/compare/v5.13.1...master>`_
 
 Changes to visclaw
 ------------------
 
 
 See `visclaw diffs
-<https://github.com/clawpack/visclaw/compare/v5.13.0...master>`_
+<https://github.com/clawpack/visclaw/compare/v5.13.1...master>`_
 
 Changes to riemann
 ------------------
 
 
 See `riemann diffs
-<https://github.com/clawpack/riemann/compare/v5.13.0...master>`_
+<https://github.com/clawpack/riemann/compare/v5.13.1...master>`_
 
 Changes to amrclaw
 ------------------
 
 
 See `amrclaw diffs
-<https://github.com/clawpack/amrclaw/compare/v5.13.0...master>`_
+<https://github.com/clawpack/amrclaw/compare/v5.13.1...master>`_
 
 Changes to geoclaw
 ------------------
 
 
-See `geoclaw diffs <https://github.com/clawpack/geoclaw/compare/v5.13.0...master>`_
+See `geoclaw diffs <https://github.com/clawpack/geoclaw/compare/v5.13.1...master>`_
 
 
 Changes to PyClaw
 ------------------
 
 
-See `pyclaw diffs <https://github.com/clawpack/pyclaw/compare/v5.13.0...master>`_
+See `pyclaw diffs <https://github.com/clawpack/pyclaw/compare/v5.13.1...master>`_
 
 ===========================
 Other Clawpack Repositories
@@ -82,10 +82,10 @@ The repositories below are not included in the Clawpack tarfile or pip
 install, but changes to these repositories may also be of interest.
 
 - `apps diffs
-  <https://github.com/clawpack/apps/compare/v5.13.0...master>`_
+  <https://github.com/clawpack/apps/compare/v5.13.1...master>`_
 
 - `doc diffs
   <https://github.com/clawpack/doc/compare/v5.13.x...dev>`_
 
 - `docker-files diffs
-  <https://github.com/clawpack/docker-files/compare/v5.13.0...master>`_
+  <https://github.com/clawpack/docker-files/compare/v5.13.1...master>`_

_sources/howto_release.rst.txt

@@ -137,6 +137,8 @@ simply build from a clean clone and upload::
     git submodule update
     python -m build
 
+For the last step to work you may need to pip install build.
+
 To upload to Pypi you need an account there and you must be listed as a
 maintainer of Clawpack.  Then you can update using
 `twine <https://pypi.org/project/twine/>`__.

_sources/installing_fortcodes.rst.txt

@@ -36,9 +36,9 @@ Download a tar file from one of these sources:
 
 After downloading a tar file you can do, e.g. ::
 
-    tar -xzf clawpack-v5.13.0.tar.gz
-    cd clawpack-v5.13.0
-    export CLAW=/full/path/to/clawpack-v5.13.0  # in bash
+    tar -xzf clawpack-v5.13.1.tar.gz
+    cd clawpack-v5.13.1
+    export CLAW=/full/path/to/clawpack-v5.13.1  # in bash
     
 The last command sets an environment variable when using the bash shell.
 The syntax may be different in other shells.  Replace `/full/path/to`
@@ -60,7 +60,7 @@ See :ref:`developers` for more details, but the basic commands are::
 
     git clone https://github.com/clawpack/clawpack.git
     cd clawpack
-    git checkout v5.13.0     # or an older version; `git tag -l` to list options
+    git checkout v5.13.1     # or an older version; `git tag -l` to list options
     git submodule init      # for repositories pyclaw, clawutil, visclaw, etc.
     git submodule update    # clones all the submodule repositories
     export CLAW=/full/path/to/clawpack    # in bash

_sources/installing_pip.rst.txt

@@ -32,7 +32,7 @@ Clawpack is via::
 
 or, more specifically, ::
 
-    pip install --user clawpack==v5.13.0
+    pip install --user clawpack==v5.13.1
 
 or you can choose a previous version from the `PyPi history <https://pypi.org/project/clawpack/#history>`__.
 
@@ -56,7 +56,7 @@ following command
 want to change anything in this command)**::  
 
     pip install --src=$HOME/clawpack_src --user --no-build-isolation -e \
-        git+https://github.com/clawpack/[email protected].0#egg=clawpack
+        git+https://github.com/clawpack/[email protected].1#egg=clawpack
 
 
 **Notes:** 
@@ -71,7 +71,7 @@ want to change anything in this command)**::
   :ref:`installing_options` if you want more control.
 
 - This will download Clawpack (via a git clone) into the directory
-  `$HOME/clawpack_src/clawpack-v5.13.0`.  The top 
+  `$HOME/clawpack_src/clawpack-v5.13.1`.  The top 
   installation directory can be changed by modifying the ``--src`` target 
   (or omit this part to put it in your current working directory).
   If you have already downloaded Clawpack via a different mechanism then
@@ -92,11 +92,11 @@ want to change anything in this command)**::
 
 - In order to use the Fortran codes within Clawpack (`classic`,
   `amrclaw`, or `geoclaw`), you should then set the environment
-  variable `CLAW` to point to the `clawpack-v5.13.0` directory within
+  variable `CLAW` to point to the `clawpack-v5.13.1` directory within
   the installation directory `$HOME/clawpack_src`, and `FC` to point
   to the desired Fortran compiler, e.g. in the bash shell::
   
-        export CLAW=$HOME/clawpack_src/clawpack-v5.13.0
+        export CLAW=$HOME/clawpack_src/clawpack-v5.13.1
         export FC=gfortran
 
 

_sources/release_5_13_1.rst.txt

@@ -0,0 +1,131 @@
+:orphan:
+
+.. _release_5_13_1:
+
+===============================
+v5.13.1 release notes
+===============================
+
+Clawpack 5.13.1 was released on Sept. 12, 2025. See :ref:`installing`.
+
+Permanent DOI: https://doi.org/10.5281/zenodo.17107527
+
+
+Changes relative to Clawpack 5.13.0 (August 23, 2025) are shown below.
+
+To see more recent changes that are in the the master branch but not yet
+released, see :ref:`changes_to_master`.
+
+
+Changes that are not backward compatible
+----------------------------------------
+
+- None
+
+General changes
+---------------
+
+A couple bugs prevented most GeoClaw code from running and these have
+now been fixed.
+
+Unit testing and continuous integration on Github is now working for
+`amrclaw`, still a work in progress for other repositories.
+We are working on modifying tests to use `pytest` (rather than `nose`) and
+Github CI (rather than travis).
+
+
+Changes to classic
+------------------
+
+- None
+
+See `classic diffs
+<https://github.com/clawpack/classic/compare/v5.13.0...v5.13.1>`_
+
+Changes to clawutil
+-------------------
+
+- A utility `clawutil.util.fullpath_import` was added to make it easier to
+  do imports from arbitrary paths that are not part of any package.
+  See `#186 <https://github.com/clawpack/clawutil/pull/186>`_.
+
+- minor bug fixes
+
+See `clawutil diffs
+<https://github.com/clawpack/clawutil/compare/v5.13.0...v5.13.1>`_
+
+Changes to visclaw
+------------------
+
+- None.
+
+See `visclaw diffs
+<https://github.com/clawpack/visclaw/compare/v5.13.0...v5.13.1>`_
+
+Changes to riemann
+------------------
+
+- None
+
+See `riemann diffs
+<https://github.com/clawpack/riemann/compare/v5.13.0...v5.13.1>`_
+
+Changes to amrclaw
+------------------
+
+- Several changes needed to get pytest working.
+
+See `amrclaw diffs
+<https://github.com/clawpack/amrclaw/compare/v5.13.0...v5.13.1>`_
+
+Changes to geoclaw
+------------------
+
+- The 1D code was failing because the new `override_topo_order` parameter
+  introduced in v5.13.0 in 2D was also written to the `topo.data` files in
+  1D, but was not being read in by the Fortran.  This was fixed in
+  `#669 <https://github.com/clawpack/geoclaw/pull/669>`__.
+  (Only one topofile is currently allowed in 1D, so the value of this
+  flag is moot.)
+
+- A bug introduced in the 2D code resulted in a call to `b4step2` having
+  the wrong number of parameters. This was fixed in
+  `#670 <https://github.com/clawpack/geoclaw/pull/670>`__.
+
+- In `gauges.data` files, the desired `file_format` is converted from a
+  string such as `binary32` or `binary64` to an integer for reading into
+  GeoClaw.  These integers used to be 3 and 2 respectively for these two
+  binary formats and now are 2 and 3 to match the convention used e.g. for
+  `fgout` files.  This should not matter to users as long as `make data`
+  and `make output` are performed with the same version of GeoClaw.
+
+- A utility module `center_points.py` was added to adjust gauges or other
+  points to lie at the center of computational cells on a desired resolution.
+
+- Several other more minor bug fixes and enhancements.
+
+See `geoclaw diffs <https://github.com/clawpack/geoclaw/compare/v5.13.0...v5.13.1>`_
+
+
+Changes to PyClaw
+------------------
+
+- Better command line interface for gauge comparisons.
+
+See `pyclaw diffs <https://github.com/clawpack/pyclaw/compare/v5.13.0...v5.13.1>`_
+
+===========================
+Other Clawpack Repositories
+===========================
+
+The repositories below are not included in the Clawpack tarfile or pip
+install, but changes to these repositories may also be of interest.
+
+- `apps diffs
+  <https://github.com/clawpack/apps/compare/v5.13.0...v5.13.1>`_
+
+- `doc diffs
+  <https://github.com/clawpack/doc/compare/v5.12.x...dev>`_
+
+- `docker-files diffs
+  <https://github.com/clawpack/docker-files/compare/v5.13.0...v5.13.1>`_

_sources/releases.rst.txt

@@ -37,6 +37,8 @@ can also be referenced with the single DOI
 `10.17605/osf.io/kmw6h <https://doi.org/10.17605/osf.io/kmw6h>`__.
 See :ref:`citing` for more information on how best to cite Clawpack.
 
+* :ref:`release_5_13_1`  -- September 12, 2025
+  `[DOI 10.5281/zenodo.17107527] <https://doi.org/10.5281/zenodo.17107527>`_
 * :ref:`release_5_13_0`  -- August 23, 2025
   `[DOI 10.5281/zenodo.16933803] <https://doi.org/10.5281/zenodo.16933803>`_
 * :ref:`release_5_12_0`  -- May 5, 2025