#3058 Update linkcheck parameters

.github/linkspector.yml

@@ -1,8 +1,12 @@
 dirs:
   - .
 useGitIgnore: true
+# Ignore URLs that sometimes fail due to timeouts on slow responses or
+# unauthorised accesses
 ignorePatterns:
   - pattern: '^https://mybinder.org/v2/gh/stfc/psyclone'
+  - pattern: '^https://codecov.io/gh/stfc/PSyclone'
+  - pattern: '^https://code.metoffice.gov.uk/svn'
 replacementPatterns:
   - pattern: '^https:\/\/(psyclone.*\.readthedocs\.io\/en)\/stable$'
     replacement: 'https://$1/latest'

.github/workflows/linkcheck.yml

@@ -14,3 +14,5 @@ jobs:
           reporter: github-pr-check
           fail_on_error: true
           config_file: '.github/linkspector.yml'
+          filter_mode: nofilter
+          show_stats: true

README.md

@@ -20,18 +20,18 @@ DSLs following the PSyKAl model developed in the
 [GungHo project](https://www.metoffice.gov.uk/research/foundation/dynamics/next-generation).
 
 PSyclone is currently used to support the [LFRic mixed finite-element PSyKAl
-DSL](https://psyclone.readthedocs.io/en/latest/lfric.html)
+DSL](https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html)
 for the [UK MetOffice's next generation modelling
 system](https://www.metoffice.gov.uk/research/modelling-systems/lfric/) and
 the [GOcean finite-difference PSyKAl
-DSL](https://psyclone.readthedocs.io/en/latest/gocean1p0.html) for a [prototype
+DSL](https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html) for a [prototype
 2D ocean modelling system](https://gtr.ukri.org/projects?ref=NE%2FL01209X%2F1).
 It is also used to [insert GPU offloading
-directives](https://psyclone.readthedocs.io/en/latest/nemo.html) into existing
+directives](https://psyclone.readthedocs.io/en/latest/tutorials_and_examples/nemo_examples.html) into existing
 directly-addressed MPI applications such as the
 [NEMO ocean model](https://www.nemo-ocean.eu/).
 
-For more detailed information see the [PSyclone Documentation](http://psyclone.readthedocs.io).
+For more detailed information see the [PSyclone Documentation](http://psyclone.readthedocs.io/en/latest).
 
 # Installation #
 
@@ -60,8 +60,9 @@ PSyclone is also available in the
 [Spack](https://packages.spack.io/package.html?name=py-psyclone) package
 managers.
 
-For more information about the installation process see
-[this section of the User Guide](https://psyclone.readthedocs.io/en/latest/system_specific_setup.html).
+For more information about the installation process see the
+[Getting Going](https://psyclone.readthedocs.io/en/latest/user_guide/getting_going.html).
+section of the User Guide.
 
 <!---  TODO #2627
 # Try it on Binder #

examples/gocean/eg5/value_range_check/README.md

@@ -29,7 +29,7 @@ invalid numbers (Infinity).
 ## Running
 In order to activate the value range checking, you need to
 specify the value range for variables as outlined here:
-https://psyclone.readthedocs.io/en/latest/psy_data.html#value-range-check
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html#value-range-check
 
 ```
 $ PSYVERIFY__main__init__b_fld=2:3    ./value_range_check

examples/lfric/eg14/README.md

@@ -6,7 +6,8 @@ more detail in the directory
 ``<PSYCLONEHOME>/examples/lfric/eg17/full_example``.
 
 The script ``acc_parallel.py`` applies various OpenACC transformations
-to all kernels. See the PSyclone User Guide for [details](https://psyclone.readthedocs.io/en/stable/examples.html#example-14-openacc).
+to all kernels. See the PSyclone User Guide for [details](
+https://psyclone.readthedocs.io/en/latest/tutorials_and_examples/lfric_examples.html#example-14-openacc).
 
 ## Compilation
 

examples/lfric/eg17/full_example_extract/README.md

@@ -7,14 +7,14 @@ directory ``../full_example``.
 This example applies the PSyData extraction transformations to the
 two invoke statements, the first initialising two fields, the second
 doing some computations.
-See the [PSyKE](https://psyclone.readthedocs.io/en/stable/psyke.html)
+See the [PSyKE](https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html)
 chapter of the PSyclone documentation for details about this transformation.
 
 ## Compilation
 
 A simple makefile is provided to compile the example. It can use one of
 three extraction libraries, as outlined in the
-[PSyKE extraction libraries](https://psyclone.readthedocs.io/en/stable/psyke.html#extraction-libraries) section.
+[PSyKE extraction libraries](https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#extraction-libraries) section.
 
 By default, the stand-alone binary version will be used,
 but you can set the ``TYPE`` environment variable to either ``ascii``

examples/lfric/scripts/KGOs/lfric_psyclone.cfg

@@ -46,7 +46,7 @@ REPRODUCIBLE_REDUCTIONS = false
 # Amount to pad the local summation array when REPRODUCIBLE_REDUCTIONS is true
 REPROD_PAD_SIZE = 8
 PSYIR_ROOT_NAME = psyir_tmp
-VALID_PSY_DATA_PREFIXES = profile, extract, read_only_verify, nan_test
+VALID_PSY_DATA_PREFIXES = profile, extract, read_only_verify, value_range_check
 
 # Specify number of OpenCL devices per node. When combining OpenCL with MPI,
 # the mpirun/mpiexec ranks_per_node parameter must match this number.

examples/lfric/scripts/KGOs/lfric_psyclone_no_annexed.cfg

@@ -46,7 +46,7 @@ REPRODUCIBLE_REDUCTIONS = false
 # Amount to pad the local summation array when REPRODUCIBLE_REDUCTIONS is true
 REPROD_PAD_SIZE = 8
 PSYIR_ROOT_NAME = psyir_tmp
-VALID_PSY_DATA_PREFIXES = profile, extract, read_only_verify, nan_test
+VALID_PSY_DATA_PREFIXES = profile, extract, read_only_verify, value_range_check
 
 # Specify number of OpenCL devices per node. When combining OpenCL with MPI,
 # the mpirun/mpiexec ranks_per_node parameter must match this number.

examples/nemo/README.md

@@ -55,7 +55,7 @@ Contains:
 ## Scripts
 
 Contains the scripts used to process the NEMO code base and to add profiling
-instrumentation (https://psyclone.readthedocs.io/en/stable/profiling.html)
+instrumentation (https://psyclone.readthedocs.io/en/latest/user_guide/profiling.html)
 and OpenACC or OpenMP directives:
 
 1. `process_nemo.py` is a driver script that allows the user to specify

lib/README.md

@@ -1,7 +1,7 @@
 # Wrapper Libraries for Use with PSyclone
 
 This directory contains [PSyData-API-based](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) wrapper libraries.
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) wrapper libraries.
 They enable PSyclone to provide transformations that will insert callbacks
 to an external library at runtime. These callbacks allow third-party libraries
 to access data structures at specified locations in the code for different
@@ -13,11 +13,11 @@ The wrapper libraries for the supported use cases are listed
 
 Wrapper libraries can be accessed from a clone of PSyclone repository
 or a PSyclone [installation](
-https://psyclone.readthedocs.io/en/stable/getting_going.html). In a
+https://psyclone.readthedocs.io/en/latest/user_guide/getting_going.html). In a
 PSyclone installation the libraries may be found in ``share/psyclone/lib``
 under your Python (or PSyclone, depending on the ``pip install`` options)
 installation, see ["Getting Going"](
-https://psyclone.readthedocs.io/en/stable/getting_going.html)
+https://psyclone.readthedocs.io/en/latest/user_guide/getting_going.html)
 for possible locations.
 
 If working with wrapper libraries from a PSyclone installation, it
@@ -32,7 +32,7 @@ dependencies, see [below](#compilation) for more information.
 
 The file ``psy_data_base.jinja`` contains a Jinja template that can be used
 by the [PSyData-API-based](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) wrapper libraries.
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) wrapper libraries.
 Full documentation on using this template is provided in the PSyclone
 [Developer Guide](
 https://psyclone.readthedocs.io/en/latest/developer_guide/psy_data.html#jinja). The
@@ -51,10 +51,10 @@ rely on a file compiled in this directory.
 Contains code for extracting kernel data - i.e. all input and output
 parameters of a kernel invocation.
 
-### [``nan_test``](./nan_test) directory
+### [``value_range_check``](./value_range_check) directory
 
 Contains PSyData-API-based libraries for checking that input and output
-parameters of kernels are valid numbers (i.e. not ``NaN`` or infinity).
+values of kernels are within valid ranges (i.e. not ``NaN`` or infinity).
 
 ### [``profiling``](./profiling) directory
 
@@ -80,23 +80,23 @@ Fortran compiler (``gfortran``), i.e. simply running ``make`` will build a
 wrapper library with the version of ``gfortran`` available in a user's
 environment. The compilation flags vary from one library to another (they
 are usually set to debugging). As for the compilation of the [API examples](
-https://psyclone.readthedocs.io/en/latest/examples.html#compilation), these
+https://psyclone.readthedocs.io/en/latest/tutorials_and_examples/examples_intro.html#compilation), these
 flags can be set to a different compiler. For instance,
 
 ```shell
 F90=ifort F90FLAGS="-g -check bounds" make
 ```
 
 Similar to compilation of the [examples](
-https://psyclone.readthedocs.io/en/latest/examples.html#compilation), the
+https://psyclone.readthedocs.io/en/latest/tutorials_and_examples/examples_intro.html#compilation), the
 compiled library can be removed by running ``make clean``. There is also
 the ``allclean`` target that removes the compiled wrapper library as well
 as the compiled infrastructure library that the wrapper may
 [depend on](#dependencies).
 
 The compilation of wrapper libraries was tested with the Gnu and Intel
 Fortran compilers, see [here](
-https://psyclone.readthedocs.io/en/latest/examples.html#supported-compilers)
+https://psyclone.readthedocs.io/en/latest/tutorials_and_examples/examples_intro.html#supported-compilers)
 for the full list. Please let the PSyclone developers know if you have
 problems using a compiler that has been tested or if you are working
 with a different compiler.
@@ -112,13 +112,13 @@ is by default set to the relative path to the top-level `lib` directory.
 libraries are compiled in a clone of PSyclone repository or in a PSyclone
 [installation](#installation).
 
-Compilation of ``extract``, ``nan_test``, ``read_only`` and some of the
+Compilation of ``extract``, ``values_ragne_check``, ``read_only`` and some of the
 profiling wrapper libraries depends on infrastructure libraries relevant
 to the API they are used for. [GOcean API](
-https://psyclone.readthedocs.io/en/stable/gocean1p0.html) uses the
+https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html) uses the
 [``dl_esm_inf`` library](https://github.com/stfc/dl_esm_inf) and
 [LFRic API](
-https://psyclone.readthedocs.io/en/latest/lfric.html)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html)
 uses the LFRic infrastructure (see the linked documentation on how to
 access and use the LFRic code). The locations of the respective
 infrastructure libraries can be configured with the variables

lib/extract/README.md

@@ -1,7 +1,7 @@
 # Kernel Extraction Library
 
 This directory contains files related to [writing (extracting)](
-https://psyclone.readthedocs.io/en/stable/psyke.html) input and output
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html) input and output
 parameters of instrumented code regions.
 
 For now the parameter extraction is only implemented to write out the

lib/extract/ascii/dl_esm_inf/README.md

@@ -1,9 +1,9 @@
 # Stand-alone ASCII Kernel Extraction Library for GOcean
 
 This wrapper library is used to [write (extract)](
-https://psyclone.readthedocs.io/en/stable/psyke.html)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html)
 input and output parameters of instrumented code regions to an [ASCII file](
-https://psyclone.readthedocs.io/en/stable/psyke.html#extraction_libraries)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#extraction_libraries)
 using the [``dl_esm_inf`` library](https://github.com/stfc/dl_esm_inf).
 A stand-alone driver can then be used to rerun this specific code region and
 verify the results (or compare performance). This version of the extraction
@@ -19,7 +19,7 @@ https://github.com/stfc/PSyclone/tree/master/examples/gocean/eg5/extract).
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - The [GOcean](https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html)

lib/extract/ascii/generic/README.md

@@ -1,20 +1,20 @@
 # Stand-alone Kernel Extraction Library for generic Fortran code
 
 This wrapper library is used to [write (extract)](
-https://psyclone.readthedocs.io/en/stable/psyke.html)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html)
 input and output parameters of instrumented code regions to an [ASCII file](
-https://psyclone.readthedocs.io/en/stable/psyke.html#extraction_libraries).
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#extraction_libraries).
 A stand-alone driver can then be used to rerun this specific code region and
 verify the results (or compare performance).
 
 A full, stand-alone and runnable example can be found in
-[``examples/nemo/eg7/``](
-https://github.com/stfc/PSyclone/tree/master/examples/nemo/eg7).
+[``examples/nemo/eg5/``](
+https://github.com/stfc/PSyclone/tree/master/examples/nemo/eg5).
 
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - The ExtractAsciiBase (``extract_ascii_base.jinja``)

lib/extract/ascii/lfric/README.md

@@ -1,17 +1,17 @@
 # Kernel Extraction Library for LFRic
 
 This wrapper library [writes (extracts)](
-https://psyclone.readthedocs.io/en/stable/psyke.html) input and output
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html) input and output
 parameters of instrumented code regions to a stand-alone
-[binary file](https://psyclone.readthedocs.io/en/stable/psyke.html#extraction_libraries)
+[binary file](https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#extraction_libraries)
 using the LFRic infrastructure library. A stand-alone driver can then be
 used to rerun this specific code region and verify the results (or
 compare performance).
 
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - The LFRic infrastructure library. A pared-down version of LFRic
@@ -20,7 +20,7 @@ the application. The following dependencies must be available:
   https://github.com/stfc/PSyclone/tree/master/examples/lfric/eg17), however
   it is not included in the PSyclone [installation](
   ./../../../README.md#installation). See the [LFRic API](
-  https://psyclone.readthedocs.io/en/stable/dynamo0p3.html) documentation
+  https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html) documentation
   for information on how to obtain access to the LFRic code.
 
 - The ExtractAsciiBase (``extract_ascii_base.jinja``) and PSyData

lib/extract/binary/dl_esm_inf/README.md

@@ -1,9 +1,9 @@
 # Stand-alone Kernel Extraction Library for GOcean
 
 This wrapper library is used to [write (extract)](
-https://psyclone.readthedocs.io/en/stable/psyke.html)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html)
 input and output parameters of instrumented code regions to a [binary file](
-https://psyclone.readthedocs.io/en/stable/psyke.html#extraction_libraries)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#extraction_libraries)
 using the [``dl_esm_inf`` library](https://github.com/stfc/dl_esm_inf).
 A stand-alone driver can then be used to rerun this specific code region and
 verify the results (or compare performance).
@@ -15,7 +15,7 @@ https://github.com/stfc/PSyclone/tree/master/examples/gocean/eg5/extract).
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - The [GOcean](https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html)

lib/extract/binary/generic/README.md

@@ -1,9 +1,9 @@
 # Stand-alone Kernel Extraction Library for generic Fortran code
 
 This wrapper library is used to [write (extract)](
-https://psyclone.readthedocs.io/en/stable/psyke.html)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html)
 input and output parameters of instrumented code regions to a [binary file](
-https://psyclone.readthedocs.io/en/stable/psyke.html#extraction_libraries).
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#extraction_libraries).
 A stand-alone driver can then be used to rerun this specific code region and
 verify the results (or compare performance).
 
@@ -14,7 +14,7 @@ https://github.com/stfc/PSyclone/tree/master/examples/nemo/eg5).
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - The ExtractBinary (``extract_binary_base.jinja``) and PSyData

lib/extract/binary/lfric/README.md

@@ -1,9 +1,9 @@
 # Kernel Extraction Library for LFRic
 
 This wrapper library [writes (extracts)](
-https://psyclone.readthedocs.io/en/stable/psyke.html) input and output
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html) input and output
 parameters of instrumented code regions to a stand-alone
-[binary file](https://psyclone.readthedocs.io/en/stable/psyke.html#extraction_libraries)
+[binary file](https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#extraction_libraries)
 using the LFRic infrastructure library. A stand-alone driver can then be
 used to rerun this specific code region and verify the results (or
 compare performance).
@@ -14,7 +14,7 @@ compilation tests.
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - The LFRic infrastructure library. A pared-down version of LFRic
@@ -23,7 +23,7 @@ the application. The following dependencies must be available:
   https://github.com/stfc/PSyclone/tree/master/examples/lfric/eg17), however
   it is not included in the PSyclone [installation](
   ./../../../README.md#installation). See the [LFRic API](
-  https://psyclone.readthedocs.io/en/latest/lfric.html) documentation
+  https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html) documentation
   for information on how to obtain access to the LFRic code.
 
 - The ExtractBinary (``extract_binary_base.jinja``) and PSyData

lib/extract/netcdf/README.md

@@ -1,9 +1,9 @@
 # Kernel Extraction Library Using NetCDF
 
 This directory contains files related to [writing (extracting)](
-https://psyclone.readthedocs.io/en/stable/psyke.html) input and output
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html) input and output
 parameters of instrumented code regions to a [NetCDF file](
-https://psyclone.readthedocs.io/en/stable/psyke.html#netcdf-extraction-example).
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#netcdf-extraction-example).
 There is a [PSyData base class](
 https://psyclone.readthedocs.io/en/latest/developer_guide/psy_data.html#psydata-base-class)
 as a Jinja template that can be used to simplify the creation of API-specific
@@ -40,7 +40,7 @@ Contains the NetCDF-extract, PSyData-API-based, wrapper library for the
 
 Contains the NetCDF-extract, PSyData-API-based, wrapper library for the
 [LFRic API](
-https://psyclone.readthedocs.io/en/latest/lfric.html).
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html).
 
 <!--
 ## Licence