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2 changes: 1 addition & 1 deletion .github/workflows/lfric_test.yml
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Expand Up @@ -84,7 +84,7 @@ jobs:
export CXX="g++"
export FPP="cpp -traditional-cpp"
export LDMPI="mpif90"
export FFLAGS="-I$(spack location -e lfric-gnu)/.spack-env/view/include"
export FFLAGS="-Wall -Werror=conversion -Werror=unused-variable -Werror=character-truncation -Werror=unused-value -Werror=tabs -I$(spack location -e lfric-gnu)/.spack-env/view/include"
export LDFLAGS="-L$(spack location -e lfric-gnu)/.spack-env/view/lib"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$(spack location -e lfric-gnu)/.spack-env/view/lib"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$(spack location -e lfric-gnu)/.spack-env/view/lib64"
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17 changes: 17 additions & 0 deletions changelog
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Expand Up @@ -113,6 +113,23 @@

42) PR #2240 for #2132. Update Integration test software stack.

43) PR #2454 for #2418. Fix OMPTaskTrans attempts to inline IntrinsicCalls.

44) PR #2459 for #2458. Fix broken documentation links.

45) PR #2472 for #2471. Update all copyright dates to include 2024 and
add utils/update_copyright.sh script to do this task.

46) PR #2443 for #2442. Fix bug for PSy-layer generation involving CMA
operators in the LFRic API.

47) PR #2481 for #1192. Unpin jsonschema version.

48) PR #2470 for #2468 and towards #237. Fixes Sphinx link-check errors
for links to anchors in User Guide and also updates the name of the
dl_esm_inf library and updates associated links (remove references to
puma).

release 2.4.0 29th of September 2023

1) PR #1758 for #1741. Splits the PSyData read functionality into a
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2 changes: 1 addition & 1 deletion doc/_ext/apilinks.py
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2022, Science and Technology Facilities Council.
# Copyright (c) 2022-2024, Science and Technology Facilities Council.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/developer_guide/APIs.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2019-2023, Science and Technology Facilities Council.
.. Copyright (c) 2019-2024, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/developer_guide/code_snippets/newnode.py
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2020-2021, Science and Technology Facilities Council
# Copyright (c) 2020-2024, Science and Technology Facilities Council
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/developer_guide/dependency.rst
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.. -----------------------------------------------------------------------------
BSD 3-Clause License
Copyright (c) 2021-2023, Science and Technology Facilities Council.
Copyright (c) 2021-2024, Science and Technology Facilities Council.
All rights reserved.
Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/developer_guide/index.rst
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.. -----------------------------------------------------------------------------
BSD 3-Clause License
Copyright (c) 2017-2021, Science and Technology Facilities Council.
Copyright (c) 2017-2024, Science and Technology Facilities Council.
All rights reserved.
Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/developer_guide/modules.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2019-2023, Science and Technology Facilities Council.
.. Copyright (c) 2019-2024, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/developer_guide/parsing.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2019-2023, Science and Technology Facilities Council.
.. Copyright (c) 2019-2024, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/developer_guide/psy_data.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2019-2023, Science and Technology Facilities Council.
.. Copyright (c) 2019-2024, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/developer_guide/psyir.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2019-2023, Science and Technology Facilities Council.
.. Copyright (c) 2019-2024, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/developer_guide/psyir_backends.rst
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.. -----------------------------------------------------------------------------
BSD 3-Clause License
Copyright (c) 2017-2023, Science and Technology Facilities Council.
Copyright (c) 2017-2024, Science and Technology Facilities Council.
All rights reserved.
Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/developer_guide/psyir_symbols.rst
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.. -----------------------------------------------------------------------------
BSD 3-Clause License
Copyright (c) 2020-2023, Science and Technology Facilities Council.
Copyright (c) 2020-2024, Science and Technology Facilities Council.
All rights reserved.
Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/developer_guide/sympy.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2021-2023, Science and Technology Facilities Council.
.. Copyright (c) 2021-2024, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/developer_guide/transformations.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2019-2023, Science and Technology Facilities Council.
.. Copyright (c) 2019-2024, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/developer_guide/working_practises.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2019-2023, Science and Technology Facilities Council.
.. Copyright (c) 2019-2024, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/psyad/user_guide/implementation.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2021-2023, Science and Technology Facilities Council.
.. Copyright (c) 2021-2024, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/psyad/user_guide/index.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2021-2022, Science and Technology Facilities Council.
.. Copyright (c) 2021-2024, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/psyad/user_guide/introduction.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2021-2022, Science and Technology Facilities Council.
.. Copyright (c) 2021-2024, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/psyad/user_guide/psyad_command.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2021-2023, Science and Technology Facilities Council.
.. Copyright (c) 2021-2024, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/user_guide/built_ins.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2017-2023, Science and Technology Facilities Council
.. Copyright (c) 2017-2024, Science and Technology Facilities Council
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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8 changes: 4 additions & 4 deletions doc/user_guide/conf.py
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Expand Up @@ -372,11 +372,11 @@
linkcheck_anchors_ignore = ['user-content-netcdf-library-lfric-examples']

# MyBinder fails on a very regular basis so we skip those links.
# The puma site no longer exists but the GOcean documentation needs to be
# updated (TODO #237).
# Despite its name 'collab.metoffice.../twiki' requires authenticated access.
linkcheck_ignore = [r'^https://mybinder.org/v2/gh/stfc/psyclone',
r'https://puma.nerc.ac.uk/trac/GOcean',
# Shpinx has problems wiht Github anchors, so we skip the links to anchors to
# the main README
r'^https://github.com/stfc/PSyclone#',
# Requires authentication
r'code.metoffice.gov.uk/trac/lfric/attachment/wiki/'
r'LFRicDocumentationPapers/lfric_documentation.pdf']

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2 changes: 1 addition & 1 deletion doc/user_guide/configuration.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2018-2023, Science and Technology Facilities Council
.. Copyright (c) 2018-2024, Science and Technology Facilities Council
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/user_guide/dynamo0p3.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2017-2023, Science and Technology Facilities Council
.. Copyright (c) 2017-2024, Science and Technology Facilities Council
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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4 changes: 2 additions & 2 deletions doc/user_guide/examples.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2018-2023, Science and Technology Facilities Council.
.. Copyright (c) 2018-2024, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
Expand Down Expand Up @@ -56,7 +56,7 @@ what each example does and how to run each example please see the
Alternatively, some of the examples have associated Jupyter notebooks
that may be launched with Binder on `MyBinder <https://mybinder.org/>`_.
This is most easily done by following the links from the top-level
`README <https://github.com/stfc/PSyclone#user-content-try-it-on-binder>`_.
`README <https://github.com/stfc/PSyclone#try-it-on-binder>`_.

For the purposes of correctness checking, the whole suite of examples
may be executed using Gnu ``make`` (this functionality is used by GitHub
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8 changes: 4 additions & 4 deletions doc/user_guide/getting_going.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2017-2022, Science and Technology Facilities Council.
.. Copyright (c) 2017-2024, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
Expand Down Expand Up @@ -219,7 +219,7 @@ support Python 2.7 was version 2.1.0.)
PSyclone immediately relies on four external Python packages; ``configparser``,
``fparser``, ``sympy``, and ``pyparsing``. The easiest way to satisfy the
Python dependencies is to use the
`PyPI installation <https://packaging.python.org/installing>`_
`PyPI installation <https://packaging.python.org/tutorials/installing-packages/>`_
and ``pip``.

If everything is working correctly then using ``pip`` to install PSyclone::
Expand Down Expand Up @@ -260,7 +260,7 @@ parser originally developed as a part of the `f2py project

``fparser`` is available from the Python Package
Index and thus may be installed using ``pip``
(https://packaging.python.org/installing/#requirements-for-installing-packages):
(https://packaging.python.org/tutorials/installing-packages/#requirements-for-installing-packages):
::

> pip install fparser
Expand Down Expand Up @@ -523,4 +523,4 @@ Take a look at the ``print_psyir_trans.py`` script for more information. *Hint*;
you can insert a single line in that script in order to break into the Python
interpreter during execution: ``import pdb; pdb.set_trace()``. This then enables
interactive exploration of the PSyIR if you are interested. Alternatively,
you can play with some interactive examples on `Binder <https://github.com/stfc/PSyclone#user-content-try-it-on-binder>`_.
you can play with some interactive examples on `Binder <https://github.com/stfc/PSyclone#try-it-on-binder>`_.
26 changes: 13 additions & 13 deletions doc/user_guide/gocean1p0.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2017-2019, Science and Technology Facilities Council
.. Copyright (c) 2017-2024, Science and Technology Facilities Council
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
Expand Down Expand Up @@ -59,22 +59,22 @@ describe the functionality provided by the GOcean Library.

.. _gocean1.0-library:

The GOcean Library
------------------
The GOcean Infrastructure Library - dl_esm_inf
----------------------------------------------

The use of PSyclone and the GOcean 1.0 API implies the use of a
standard set of data types and associated infrastructure. This is
provided by version 1.0 of the GOcean Library (GOLib v.1.0).
Currently this library is distributed separately from PSyclone and is
available from https://puma.nerc.ac.uk/trac/GOcean.
provided by the GOcean infrastructure library - dl_esm_inf.
Currently this library is distributed separately from PSyclone and
is available from https://github.com/stfc/dl_esm_inf.

.. _gocean1.0-grid:

Grid
++++

The GOLib contains a ``grid_mod`` module which defines a ``grid_type``
and associated constructor::
The dl_esm_inf library contains a ``grid_mod`` module which defines a
``grid_type`` and associated constructor::

use grid_mod
...
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Fields
++++++

Once a model has a grid defined it will require one or more
fields. The GOLib contains a ``field_mod`` module which defines an
Once a model has a grid defined it will require one or more fields.
The dl_esm_inf library contains a ``field_mod`` module which defines an
``r2d_field`` type (real, 2-dimensional field) and associated
constructor::

Expand Down Expand Up @@ -200,7 +200,7 @@ GOcean Library. See ``<PSYCLONEHOME>/examples/gocean/shallow_alg.f90``. In what
follows we will walk through a slightly cut-down example for a
different program.

The following code illustrates the use of the GOLib in constructing an
The following code illustrates the use of dl_esm_inf for constructing an
application::

program gocean2d
Expand Down Expand Up @@ -284,8 +284,8 @@ reading a namelist file. An example might look something like::

end subroutine model_init

Here, only ``grid_type`` and the ``grid_init`` routine come from the
GOLib. The remaining code is all application specific.
Here, only ``grid_type`` and the ``grid_init`` routine come from dl_esm_inf.
The remaining code is all application specific.

Once the grid object is fully configured and all fields have been
constructed, a simulation will proceed by performing calculations with
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7 changes: 4 additions & 3 deletions doc/user_guide/index.rst
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.. -----------------------------------------------------------------------------
BSD 3-Clause License
Copyright (c) 2017-2022, Science and Technology Facilities Council.
Copyright (c) 2017-2024, Science and Technology Facilities Council.
All rights reserved.
Redistribution and use in source and binary forms, with or without
Expand Down Expand Up @@ -51,8 +51,9 @@ PSyclone User Guide
languages (DSLs) for finite element, finite volume and finite difference
codes. Notably, it is used in the
`LFRic Project <https://www.metoffice.gov.uk/research/modelling-systems/
lfric/>`_, and it also supports the `GOcean <https://puma.nerc.ac.uk/trac
/GOcean>`_ (2D, finite difference) DSL. In addition it is being extended
lfric/>`_, and it also supports the
`GOcean <https://gtr.ukri.org/projects?ref=NE%2FL01209X%2F1>`_
(2D, finite difference) DSL. In addition it is being extended
to support the processing of existing finite difference codes such as the
`NEMO <https://www.nemo-ocean.eu/>`_ ocean model.
Find more information in the
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2 changes: 1 addition & 1 deletion doc/user_guide/introduction.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2018-2021, Science and Technology Facilities Council.
.. Copyright (c) 2018-2024, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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2 changes: 1 addition & 1 deletion doc/user_guide/kernel_layer.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2017-2021, Science and Technology Facilities Council
.. Copyright (c) 2017-2024, Science and Technology Facilities Council
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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