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Merge remote-tracking branch 'origin/master' into 1623_add_training
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@hiker
hiker committed Jan 10, 2025
2 parents 6b93d3c + 4b3662e commit 42eafc2
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2 changes: 1 addition & 1 deletion .github/workflows/compilation.yml
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2020-2024, Science and Technology Facilities Council.
# Copyright (c) 2020-2025, 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 .github/workflows/lfric_test.yml
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2023-2024, Science and Technology Facilities Council.
# Copyright (c) 2023-2025, Science and Technology Facilities Council.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
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3 changes: 2 additions & 1 deletion .github/workflows/linkcheck.yml
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Expand Up @@ -4,7 +4,8 @@ jobs:
check-links:
if: ${{ github.repository != 'stfc/PSyclone-mirror' }}
name: Run linkspector
runs-on: ubuntu-latest
# TODO 2838: linkspector doesn't support ubuntu-latest at the moment.
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v4
- name: Run linkspector
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2 changes: 1 addition & 1 deletion .github/workflows/nemo_tests.yml
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2024, Science and Technology Facilities Council.
# Copyright (c) 2024-2025, 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 .github/workflows/nemo_v5_tests.yml
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2024, Science and Technology Facilities Council.
# Copyright (c) 2024-2025, Science and Technology Facilities Council.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
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6 changes: 4 additions & 2 deletions .github/workflows/python-package.yml
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2020-2024, Science and Technology Facilities Council.
# Copyright (c) 2020-2025, Science and Technology Facilities Council.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
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# Modified by A. J. Voysey, Met Office
# Modified by J. Henrichs, Bureau of Meteorology
# Modified by N. Nobre, STFC Daresbury Lab
# Modified by A. B. G. Chalk, STFC Daresbury Lab

# This workflow will install Python dependencies, run tests and lint with a
# variety of Python versions.
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- run: cd doc/developer_guide; make html; make doctest
build:
if: ${{ github.repository != 'stfc/PSyclone-mirror' }}
runs-on: ubuntu-latest
# TODO 2837: Switch to ubuntu-latest once Python 3.7 support is removed.
runs-on: ubuntu-22.04
strategy:
matrix:
python-version: [3.7, 3.8, 3.13]
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2 changes: 1 addition & 1 deletion .github/workflows/repo-sync.yml
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2023, Science and Technology Facilities Council.
# Copyright (c) 2023-2025, 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 LICENSE
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BSD 3-Clause License

Copyright (c) 2017-2024, Science and Technology Facilities Council.
Copyright (c) 2017-2025, 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 MANIFEST.in
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2017-2022, Science and Technology Facilities Council.
# Copyright (c) 2017-2025, 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 apt.txt
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2019-2020, Science and Technology Facilities Council.
# Copyright (c) 2019-2025, 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 bin/psyad
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2021, Science and Technology Facilities Council
# Copyright (c) 2021-2025, 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 bin/psyclone
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2017, Science and Technology Facilities Council
# Copyright (c) 2017-2025, 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 bin/psyclone-kern
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2017-2022, Science and Technology Facilities Council
# Copyright (c) 2017-2025, Science and Technology Facilities Council
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
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13 changes: 13 additions & 0 deletions changelog
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AST tree. There are two new FortranReader arguments to select the behaviour
for comments and directives (by default they are not parsed).

5) PR #2836 for #2835. Reverts GHA to use Ubuntu 22.04 as python-3.7
not available in ubuntu-latest and linkspector is also broken.

6) PR #2820 for #2773. Adds support for the Vernier timing library.

7) PR #2840 for #2839. Raise error in FortranReader if ignore_directives
is True but ignore_comments is True.

8) PR #2832 for #2831. Reorders the arguments to the parser to meet best
practices.

9) PR #2842 for #2841. Update all copyright date ranges for 2025.

release 3.0.0 6th of December 2024

1) PR #2477 for #2463. Add support for Fortran Namelist statements.
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2 changes: 1 addition & 1 deletion config/psyclone.cfg
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2017-2024, Science and Technology Facilities Council
# Copyright (c) 2017-2025, 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/_ext/apilinks.py
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2022-2024, Science and Technology Facilities Council.
# Copyright (c) 2022-2025, 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/.readthedocs.yaml
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2023, Science and Technology Facilities Council.
# Copyright (c) 2023-2025, 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) 2019-2024, Science and Technology Facilities Council.
.. Copyright (c) 2019-2025, 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) 2020-2024, Science and Technology Facilities Council
# Copyright (c) 2020-2025, 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/conf.py
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# General information about the project.
project = "PSyclone Developer Guide"
project_copyright = '2017-2024, STFC Daresbury Laboratory'
project_copyright = '2017-2025, STFC Daresbury Laboratory'

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
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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) 2021-2024, Science and Technology Facilities Council.
Copyright (c) 2021-2025, 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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Expand Up @@ -6,7 +6,7 @@
.. -----------------------------------------------------------------------------
BSD 3-Clause License
Copyright (c) 2017-2024, Science and Technology Facilities Council.
Copyright (c) 2017-2025, 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/module_manager.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2019-2024, Science and Technology Facilities Council.
.. Copyright (c) 2019-2025, 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) 2019-2024, Science and Technology Facilities Council.
.. Copyright (c) 2019-2025, 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/pip_requirements.txt
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2018-2023, Science and Technology Facilities Council.
# Copyright (c) 2018-2025, Science and Technology Facilities Council.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
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10 changes: 5 additions & 5 deletions doc/developer_guide/psy_data.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2019-2024, Science and Technology Facilities Council.
.. Copyright (c) 2019-2025, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
Expand Down Expand Up @@ -72,8 +72,8 @@ the same time as checking that read-only values are indeed not modified,
different module names and data types must be used.

PSyData divides its application into different classes. For example,
the class "profile" is used for all profiling tools (e.g. TAU, DrHook or the
NVIDIA profiling tools). This class name is used as a prefix for
the class "profile" is used for all profiling tools (e.g. TAU, Vernier,
DrHook, or the NVIDIA profiling tools). This class name is used as a prefix for
the module name, the ``PSyDataType`` and functions. So if a profiling application
is linked the above code will actually look like this::

Expand Down Expand Up @@ -101,7 +101,7 @@ The class prefixes supported at the moment are:
Class Prefix Description
======================= =======================================================
profile All libraries related to profiling tools like TAU,
DrHook, NVIDIA's profiling tools etc. See
DrHook, NVIDIA's profiling tools, Vernier etc. See
:ref:`user_guide:profiling` for details.
extract For libraries used for kernel data extraction. See
:ref:`user_guide:psyke` for details.
Expand Down Expand Up @@ -970,7 +970,7 @@ by storing pointers to the profiling data to be able to
print all results in a ProfileFinalise() subroutine.
Some of the wrapper libraries use the PSyData base class (e.g. dl_timer,
simple_timing, template), others do not (e.g. NVIDIA profiling, TAU,
DrHook wrapper).
Vernier, DrHook wrapper).

.. _psyke:

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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) 2019-2024, Science and Technology Facilities Council.
.. Copyright (c) 2019-2025, 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) 2017-2024, Science and Technology Facilities Council.
Copyright (c) 2017-2025, 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) 2020-2024, Science and Technology Facilities Council.
Copyright (c) 2020-2025, 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/psykal.rst
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.. -----------------------------------------------------------------------------
.. BSD 3-Clause License
..
.. Copyright (c) 2018-2024, Science and Technology Facilities Council.
.. Copyright (c) 2018-2025, 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) 2021-2024, Science and Technology Facilities Council.
.. Copyright (c) 2021-2025, 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) 2019-2024, Science and Technology Facilities Council.
.. Copyright (c) 2019-2025, 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) 2019-2024, Science and Technology Facilities Council.
.. Copyright (c) 2019-2025, 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/.readthedocs.yaml
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2023, Science and Technology Facilities Council.
# Copyright (c) 2023-2025, 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/conf.py
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# -- Project information -----------------------------------------------------

project = 'PSyAD'
copyright = '2021-2023, Rupert Ford and Andrew Porter'
copyright = '2021-2025, Rupert Ford and Andrew Porter'
author = 'Rupert Ford and Andrew Porter'

# The full version, including alpha/beta/rc tags
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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) 2021-2024, Science and Technology Facilities Council.
.. Copyright (c) 2021-2025, 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) 2021-2024, Science and Technology Facilities Council.
.. Copyright (c) 2021-2025, 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) 2021-2024, Science and Technology Facilities Council.
.. Copyright (c) 2021-2025, Science and Technology Facilities Council.
.. All rights reserved.
..
.. Redistribution and use in source and binary forms, with or without
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