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updates to install directions and for v5.8.1, doc@90790be
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rjleveque committed Oct 20, 2021
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1 change: 1 addition & 0 deletions _sources/about.rst.txt
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Expand Up @@ -133,6 +133,7 @@ Here's the bibtex::
Please fill in the version number that you used, and its year, with the
appropriate DOI from `Zenodo <https://zenodo.org>`_, if available.
See :ref:`releases`.

It is best to refer to the particular release used to obtain your results,
but if you need to refer to multiple past releases,
or to cite Clawpack more generally, you can also use the DOI
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29 changes: 16 additions & 13 deletions _sources/changes_to_master.rst.txt
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Expand Up @@ -3,12 +3,12 @@
.. _changes_to_master:

===============================
Changes to master since v5.8.0
Changes to master since v5.8.1
===============================


Follow the links to see changes that have been made to the master branch of
each repository since the last release (v5.8.0) on February 4, 2021.
each repository since the last release (v5.8.1) on October 19, 2021.

These changes should appear in the next release. If you need them now,
see :ref:`developers` for instructions on cloning and installing from the
Expand All @@ -31,40 +31,41 @@ Changes to classic


See `classic diffs
<https://github.com/clawpack/classic/compare/v5.8.0...master>`_
<https://github.com/clawpack/classic/compare/v5.8.1...master>`_

Changes to clawutil
-------------------


See `clawutil diffs
<https://github.com/clawpack/clawutil/compare/v5.8.0...master>`_
<https://github.com/clawpack/clawutil/compare/v5.8.1...master>`_

Changes to visclaw
------------------


See `visclaw diffs
<https://github.com/clawpack/visclaw/compare/v5.8.0...master>`_
<https://github.com/clawpack/visclaw/compare/v5.8.1...master>`_

Changes to riemann
------------------


See `riemann diffs
<https://github.com/clawpack/riemann/compare/v5.8.0...master>`_
<https://github.com/clawpack/riemann/compare/v5.8.1...master>`_

Changes to amrclaw
------------------


See `amrclaw diffs
<https://github.com/clawpack/amrclaw/compare/v5.8.0...master>`_
<https://github.com/clawpack/amrclaw/compare/v5.8.1...master>`_

Changes to geoclaw
------------------


See `geoclaw diffs
<https://github.com/clawpack/geoclaw/compare/v5.8.0...master>`_

See `geoclaw diffs <https://github.com/clawpack/geoclaw/compare/v5.6.1...master>`_


Changes to PyClaw
Expand All @@ -75,7 +76,7 @@ For changes in PyClaw, see the `PyClaw changelog
<https://github.com/clawpack/pyclaw/blob/master/CHANGES.md>`_.

See `pyclaw diffs
<https://github.com/clawpack/pyclaw/compare/v5.8.0...master>`_
<https://github.com/clawpack/pyclaw/compare/v5.8.1...master>`_

===========================
Other Clawpack Repositories
Expand All @@ -85,11 +86,13 @@ 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/v5.8.0...master>`_
<https://github.com/clawpack/apps/compare/v5.8.1...master>`_

- `doc diffs
<https://github.com/clawpack/doc/compare/v5.8.x...dev>`_
shows changes in the `dev` branch not yet in the posted version of the
documentation.

- `docker-files diffs
<https://github.com/clawpack/docker-files/compare/v5.8.0...master>`_
<https://github.com/clawpack/docker-files/compare/v5.8.1...master>`_

7 changes: 5 additions & 2 deletions _sources/contents.rst.txt
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Expand Up @@ -10,7 +10,7 @@ the Clawpack open source software project.
Full Table of Contents
====================================================

This is the documentation for **Clawpack Version 5.8.0.**
This is the documentation for **Clawpack Version 5.8.1.**
For documentation corresponding to older versions see the list of
past releases in the menu to the left. The *future* version refers
to new documentation for features that have been merged into the
Expand All @@ -35,7 +35,7 @@ Overview and Getting Started
packages
installing
installing_pip
installing_more_options
installing_fortcodes
setenv
first_run
clawpack_components
Expand All @@ -58,11 +58,14 @@ Examples and Applications
:maxdepth: 1

apps
galleries
fvmbook
contribute_apps
testing
sphinxdoc

.. _contents_fortcodes:

Classic, AMRClaw, and GeoClaw
==============================

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4 changes: 2 additions & 2 deletions _sources/docker_image.rst.txt
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Expand Up @@ -9,8 +9,8 @@ you have `Docker <https://www.docker.com/>`_ installed then you can now use a
docker image from the `DockerHub Clawpack repositories
<https://hub.docker.com/u/clawpack/dashboard/>`_.

Using Version 5.8.0
-------------------
Using Version 5.8.0 or above
----------------------------

We are currently having problems creating a new Docker image for v5.8.0.
However, you can follow the instructions below for v5.7.1 and then within a
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5 changes: 3 additions & 2 deletions _sources/first_run_fortran.rst.txt
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Expand Up @@ -7,7 +7,7 @@ This assumes that you have downloaded the Fortran components of Clawpack,
see :ref:`install_fortran`.

First ensure that you have :ref:`setenv`
and that you have the :ref:`install_prerequisites`.
and that you have the :ref:`prereqs`.

As a first test of the Fortran code, try the following::

Expand Down Expand Up @@ -37,7 +37,8 @@ There are similar `tests` subdirectories of `$CLAW/amrclaw` and
Running an example
------------------

Many examples of Clawpack simulations can be seen in the :ref:`galleries`.
Many examples of Clawpack simulations can be seen in the
`gallery <http://www.clawpack.org/gallery/index.html>`__.


Classic
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2 changes: 2 additions & 0 deletions _sources/first_run_pyclaw.rst.txt
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Expand Up @@ -3,6 +3,8 @@
Testing a PyClaw installation and running an example
=====================================================

First ensure that you have :ref:`setenv` and that you have the :ref:`prereqs`.

If you downloaded Clawpack manually, you can test your :ref:`pyclaw`
installation as follows (starting from your `clawpack` directory)::

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28 changes: 25 additions & 3 deletions _sources/galleries.rst.txt
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Expand Up @@ -2,8 +2,30 @@

.. _galleries:

The Clawpack Gallery is available only for the latest release of Clawpack.
==================
Clawpack Gallery
==================

The `Clawpack Gallery <http://www.clawpack.org/gallery/index.html>`__
is available only for the latest release of Clawpack.

The Gallery shows results obtained by running many of the examples that are
included with Clawpack, from the directories

- `$CLAW/pyclaw/examples`
- `$CLAW/classic/examples`
- `$CLAW/amrclaw/examples`
- `$CLAW/geoclaw/examples`

and also from

- `$CLAW/apps`

which must be obtained separately from the main installation of Clawpack,
see :ref:`apps`.
The directory `$CLAW/apps/notebooks` contains a number of Jupyter
notebooks that illustrate various aspects of Clawpack.
Many of these are also visible in rendered html form in the
`Gallery of Notebooks <http://www.clawpack.org/gallery/notebooks.html>`__.

Please see
`<http://www.clawpack.org/gallery/index.html>`_.

12 changes: 10 additions & 2 deletions _sources/howto_release.rst.txt
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Expand Up @@ -176,6 +176,13 @@ on release since that would only archive a zip file of the main `clawpack`
repository. Instead we want to archive the tar file containing all
subrepositories too.

Open Science Framework (OSF)
----------------------------

Go to https://osf.io/kmw6h/files/ and upload the latest tarfile to the set
of versions that can be accessed with the single DOI
`10.17605/osf.io/kmw6h <https://doi.org/10.17605/osf.io/kmw6h>`__.

.. _howto_release_doc:

Updating the documentation
Expand Down Expand Up @@ -213,11 +220,12 @@ When making changes for a new release, the following pages in the directory
Also update the bibtex and recommended citation in `about.rst`.

- Modify several other files to point to the new version number, in particular
`installing.rst` , `installing_pip.rst`, `installing_more_options.rst`,
`installing_pip.rst`, `installing_fortcodes.rst`,
`contents.rst`, `docker_image.rst`.

- Modify the main landing page `_templates/index.html` to cite the
proper version number and DOI.
proper version number and DOI.
(No longer necessary -- This page has been changed to be more generic.)

- Update `conf.py` to the new version number, and also
`$CLAW/doc/gallery/conf.py` (For a major release.)
Expand Down
130 changes: 32 additions & 98 deletions _sources/installing.rst.txt
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Expand Up @@ -8,112 +8,44 @@ Installing Clawpack

See also:

* :ref:`clawpack_packages`
* :ref:`releases`
* :ref:`trouble_installation`
- :ref:`releases`
- :ref:`docker_image` as an alternative to installing

**Prerequisites:** Before installing, check that you have the :ref:`prereqs`.


.. _installing_pipintro:

pip install
-----------

The recommended approach is to use `pip install`.
It is also possible to have multiple versions of Clawpack installed and
switch between them (i.e., modify your Python path) using `pip`.
(see :ref:`installing_pip`)
If you plan to do this, or if you also wish to directly use the Fortran
variants of Clawpack (classic, AMRClaw, and/or GeoClaw), then we recommend
using the following version of the `pip install` command
**(you might want to first read the notes below to see if you
want to change anything in this command)**::

pip install --src=$HOME/clawpack_src --user -e \
git+https://github.com/clawpack/[email protected]#egg=clawpack-v5.8.0

This will download Clawpack (via a git clone) into the directory
`$HOME/clawpack_src/clawpack-v5.8.0`. 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
see :ref:`pip_switch_version` rather than using the above command.


See :ref:`clawpack_components` for a list of what's included in this top
level directory.

**Note:** Using pip to install will also check some python
:ref:`prereqs` and may update these on your system, and will use f2py to
convert Fortran Riemann solvers to Python versions. See
:ref:`installing_options` if you want more control.

The ``--user`` flag is necessary if you are installing on a shared computer
where you do not have root access. If you do have root access and want it
to be available to all users, you can omit this flag.
**Register:** Please `register <http://depts.washington.edu/clawpack/register/index.html>`_
if you have not already done so. This is very useful in helping
us track the extent of usage, and important to the :ref:`funding` agencies
who support this work.

The ``-e`` flag makes it an "editable" install, leaving the source code in
place and allowing you to modify it if desired.
(Otherwise, by default, pip would move the python code to some
`site-packages` directory and delete everything else.)

In order to use the Fortran codes within Clawpack,
you should then set the environment
variable `CLAW` to point to the `clawpack-v5.8.0` 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-v5.8.0
export FC=gfortran

See :ref:`setenv` for more information.

For more discussion of `pip` installation, and troubleshooting hints, see
:ref:`installing_pip`.


.. _installing_options:

Other Installation Options
=====================================

In general, *installing* Clawpack requires downloading some version
and then setting
paths so that Python import statements (and possibly Fortran Makefiles) find
the desired version. Switching between versions already on your computer
simply requires resetting paths. For hints and troubleshooting, see:
**Prerequisites:** Before installing, check that you have the :ref:`prereqs`.

**Please see**

- :ref:`setenv`
- :ref:`python_path`
- :ref:`installing_pip`
- :ref:`clawpack_packages`

Rather than using `pip`, there are several other options for using
Clawpack that may be useful depending on your needs. These are summarized
in :ref:`installing_more_options`, including:
before installing, particularly if you are not sure whether you will
be using the Fortran versions of the PDE solvers
(:ref:`contents_fortcodes`) or the :ref:`pyclaw` version of the PDE solvers.

- :ref:`installing_tarfile`
- :ref:`install_dev`
- :ref:`installing_conda`
- :ref:`installing_docker`
- :ref:`installing_aws`
- :ref:`install_pyclaw_parallel`
**Then choose the best installation option** for your needs from this list:

**Python path:**
If you download a tarfile or use `git clone` to download a version, you can
still use `pip install` to set the Python path appropriately.
See :ref:`installing_pip` for details.
- If you **only** plan to use PyClaw to solve the PDEs and Visclaw for plotting,
we suggest

- :ref:`install_quick_pyclaw`.

- If you **only** plan to use the Fortran variants of Clawpack
(:ref:`contents_fortcodes`) for solving the PDEs, together with
Visclaw for plotting and other Python tools (e.g. from geoclaw or clawutil),
then we suggest

- :ref:`installing_fortcodes`.

- If you are a power user who plans to use both PyClaw and the Fortran variants
for solving PDEs, we recommend

- :ref:`install_quick_all`.

If you are *not* using `pip` to set paths, then you will need to set
the `PYTHONPATH`
environment variable to point to a particular version of Clawpack,
but this is `not recommended <https://orbifold.xyz/pythonpath.html>`_.
See :ref:`python_path` for more details and tips on sorting out your path.

**Components:**
See :ref:`clawpack_components` for a list of what is generally included
under the top level `clawpack` directory when using any of the approaches below.
(And what is not included, e.g. the :ref:`apps`.)


Next steps:
Expand All @@ -124,4 +56,6 @@ started:

- :ref:`first_run_pyclaw`
- :ref:`first_run_fortran`
- :ref:`trouble_installation`


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