Update documentation links and fix minor typos across multiple files (MetOffice#467)

Correct various documentation links to reflect the proper repository
name and fix minor typographical errors throughout the codebase.

Addresses some of issues in MetOffice#329

Author: yaswant

Documentation/Design/GraphObject.puml

@@ -137,4 +137,4 @@ object fileSink02 {
 }
 link02 -> fileSink02
 
-@end uml
+@enduml

Documentation/source/advanced_config.rst

@@ -23,14 +23,14 @@ could be helpful to factor out the commonality into a shared module. Remember,
 your build configuration is just a Python script at the end of the day.
 
 In Fab's
-`example configurations <https://github.com/metomi/fab/tree/master/run_configs>`_,
+`example configurations <https://github.com/MetOffice/fab/tree/main/run_configs>`_,
 we have two build scripts to compile GCOM. Much of the configuration for these
 two scripts is identical. We extracted the common steps into
-`gcom_build_steps.py <https://github.com/metomi/fab/blob/master/run_configs/gcom/gcom_build_steps.py>`_
+`gcom_build_steps.py <https://github.com/MetOffice/fab/blob/main/run_configs/gcom/gcom_build_steps.py>`_
 and used them in
-`build_gcom_ar.py <https://github.com/metomi/fab/blob/master/run_configs/gcom/build_gcom_ar.py>`_
+`build_gcom_ar.py <https://github.com/MetOffice/fab/blob/main/run_configs/gcom/build_gcom_ar.py>`_
 and
-`build_gcom_so.py <https://github.com/metomi/fab/blob/master/run_configs/gcom/build_gcom_so.py>`_.
+`build_gcom_so.py <https://github.com/MetOffice/fab/blob/main/run_configs/gcom/build_gcom_so.py>`_.
 
 
 Separate grab and build scripts
@@ -289,7 +289,7 @@ will be affected consistently.
 
 
 Tool arguments
-============== 
+==============
 
 Sometimes it is necessary to pass additional arguments when we call a software
 tool.
@@ -398,13 +398,13 @@ We can currently only *add* flags for a path.
     This can require some understanding of where and when files are placed in
     the *build_output* folder: It will generally match the structure you've
     created in ``*<project workspace>/source*``, with your grab steps.
-    
+
     Early steps like preprocessors generally read files from ``*source*`` and
     write to ``*build_output*``.
-    
+
     Later steps like compilers generally read files which are already in
     ``*build_output*``.
-    
+
     For more information on where files end up see :ref:`Directory Structure`.
 
 
@@ -608,7 +608,7 @@ Custom Step
 An alternative approach for some problems is to write a custom step to modify
 the source so that the language parser can process it. Here's a simple example,
 based on a
-`real workaround <https://github.com/metomi/fab/blob/216e00253ede22bfbcc2ee9b2e490d8c40421e5d/run_configs/um/build_um.py#L42-L65>`_
+`real workaround <https://github.com/MetOffice/fab/blob/216e00253ede22bfbcc2ee9b2e490d8c40421e5d/run_configs/um/build_um.py#L42-L65>`_
 where the parser gets confused by a variable called `NameListFile`.
 
 .. code-block::

Documentation/source/conf.py

@@ -12,7 +12,9 @@
 #
 import os
 import sys
+
 from fab import __version__ as fab_version
+
 sys.path.insert(0, os.path.abspath('../../source'))
 
 
@@ -73,7 +75,7 @@
     "icon_links": [
         {
             "name": "GitHub",
-            "url": "https://github.com/metomi/fab",
+            "url": "https://github.com/MetOffice/fab",
             "icon": "fa-brands fa-github"
         }
     ],

Documentation/source/development.rst

@@ -19,7 +19,7 @@ This lets you edit the code without needing to reinstall fab after every change.
 
 .. code-block:: console
 
-    $ git clone https://github.com/metomi/fab.git <fab-folder>
+    $ git clone https://github.com/MetOffice/fab.git <fab-folder>
     $ pip install -e <fab-folder>
 
 
@@ -138,7 +138,7 @@ Build these docs
 
 The github action to build the docs is defined in
 ``.github/workflows/build_docs.yml``. It is manually triggered and can be run
-from any branch in the metomi repo.
+from any branch in the MetOffice repo.
 
 You can also run it on your fork to produce a separate build, for viewing work
 in progress.

Documentation/source/environment.rst

@@ -41,7 +41,7 @@ preferable to use one of the managed packages.
 Packages are made available through `PyPI`_ and `Conda forge`_ and are installed
 in the usual way for these services. Some examples follow.
 
-.. _source: https://github.com/metomi/fab
+.. _source: https://github.com/MetOffice/fab
 .. _PyPI: https://pypi.org/project/sci-fab/
 .. _Conda forge: https://anaconda.org/conda-forge/sci-fab
 
@@ -74,8 +74,8 @@ If you want to compile C you will need to add the prerequisites for that:
 
     $ pip install python-clang
 
-Note that this requires a suitible `libclang` to be installed on your system
-which may require system administrator internvention.
+Note that this requires a suitable `libclang` to be installed on your system
+which may require system administrator intervention.
 
 Finally, to get plots from the metrics you will need:
 
@@ -90,7 +90,7 @@ Using Anaconda
 --------------
 
 Anaconda can be used in a similar way to the built in Python virtual
-environemnt but can also handle your C needs:
+environment but can also handle your C needs:
 
 .. code-block:: console
 
@@ -118,7 +118,7 @@ And again, if you want to plot the build metrics:
 Using Containers
 ----------------
 
-The dockerfile in `envs/docker`_ can be used to create a suitible container for
+The dockerfile in `envs/docker`_ can be used to create a suitable container for
 running Fab:
 
 .. code-block:: console
@@ -129,4 +129,4 @@ running Fab:
 This was tested on Windows, running Ubuntu in WSL but is not regularly tested
 so can not be guaranteed.
 
-.. _envs/docker: https://github.com/metomi/fab/tree/master/envs/docker
+.. _envs/docker: https://github.com/MetOffice/fab/tree/main/envs/docker

Documentation/source/features.rst

@@ -82,7 +82,7 @@ Limitations
 ===========
 
 Known problems at the time of writing. For further issues see the
-`issue tracker <https://github.com/metomi/fab/issues>`_.
+`issue tracker <https://github.com/MetOffice/fab/issues>`_.
 
 Fortran single-line IF calls
 ----------------------------
@@ -98,7 +98,7 @@ Name Clash
 
 Fab currently assumes there are no name clashes in your project by the time we reach certain build steps:
 
-- C and Fortran symbols go into one symbol table so there can be no duplicate 
+- C and Fortran symbols go into one symbol table so there can be no duplicate
   symbol names by the time we reach the analysis stage.
 - Fortran mod files are created in a flat folder, so Fortran module names must
   be unique by the time we reach the compile stage.
@@ -122,4 +122,4 @@ override). It will *not* notice if a Fortran `*.mod` changes in an include
 folder elsewhere.
 
 An example is the UM build which uses GCom's mpl.mod. This issue is raised in
-`#192 <https://github.com/metomi/fab/issues/192>`_.
+`#192 <https://github.com/MetOffice/fab/issues/192>`_.

Documentation/source/index.rst

@@ -61,9 +61,9 @@ Config files
 
 See also
 ========
-* `Project wiki <https://github.com/metomi/fab/wiki>`_
+* `Project wiki <https://github.com/MetOffice/fab/wiki>`_
 * `Fab on PyPI <https://pypi.org/project/sci-fab/>`_
-* `Fab on Github <https://github.com/metomi/fab>`_
+* `Fab on Github <https://github.com/MetOffice/fab>`_
 * :ref:`Developers guide<Development>`
 
 

Documentation/source/metoffice.rst

@@ -47,7 +47,7 @@ Singularity Container
 
 You can run Fab in a singularity container as follows::
 
-    singularity run oras://$URL/metomi/fab/MyImage:latest
+    singularity run oras://$URL/MetOffice/fab/MyImage:latest
 
 The necessary URL is that normally used with singularity. Ask Science I.T. for
 details.
@@ -115,12 +115,12 @@ so that changes you make are immediately available through the environment.
     $ pip install --editable $FAB_WORKING_COPY
 
 
-Mixing Conda and Environemnt Modules
+Mixing Conda and Environment Modules
 ------------------------------------
 
 In order to have both an environment capable of building C files and modern
 Fortran compilers and the LFRic library stack you will need an awkward
-amalgemation of conda environment and environment modules.
+amalgamation of conda environment and environment modules.
 
 The conda environment is created as follows:
 
@@ -165,7 +165,7 @@ to be that in the conda environment.
 Rose
 ----
 Various configs for building projects using Rose on SPICE can be found in
-`run_configs <https://github.com/metomi/fab/tree/master/run_configs>`_.
+`run_configs <https://github.com/MetOffice/fab/tree/main/run_configs>`_.
 
 
 .. _MetOfficeDevelopment:
@@ -192,12 +192,12 @@ The config file in envs/picasso defines the contents of a Singularity image
 which is built by the experimental Picasso app. We can build this image using a
 GitHub action, defined in ``.github/workflows/picasso_build.yml``.
 
-This action is manually triggered. You have to push a branch to the metomi repo,
+This action is manually triggered. You have to push a branch to the MetOffice repo,
 not a fork, then you can trigger the action from your branch. Please remember
 to clean up the branch when you're finished.
 
 You can see the image in artefactory
-`here <https://metoffice.jfrog.io/ui/repos/tree/General/docker-local/picasso/metomi/fab/MyImage>`_.
+`here <https://metoffice.jfrog.io/ui/repos/tree/General/docker-local/picasso/MetOffice/fab/MyImage>`_.
 
 
 See also

Documentation/source/site-specific-config.rst

@@ -37,7 +37,7 @@ the user explicitly puts a tool into the ToolBox).
           compile, or a hard-coded set of criteria) which compiler to use.
 
 Category
-==========
+========
 All possible categories are defined in
 :class:`~fab.tool.category.Category`. If additional categories
 should be required, they can be added.
@@ -218,4 +218,4 @@ instance in the Tool Repository
 Also, a lot of content in this chapter is not actually about site-specific
 configuration. This should likely be renamed or split (once we
 have details about the using site-specific configuration, which might be
-once the Baf base script is added to Fab).
+once the Baf base script is added to Fab).

Documentation/source/writing_config.rst

@@ -141,11 +141,11 @@ before you run the :func:`~fab.steps.analyse.analyse` step below.
 * For :func:`~fab.steps.psyclone.psyclone`:
             You can pass in:
 
-            * kernel file roots to `kernel_roots`, 
-            * a function to get transformation script to `transformation_script` 
+            * kernel file roots to `kernel_roots`,
+            * a function to get transformation script to `transformation_script`
               (see examples in ``~fab.run_configs.lfric.gungho.py`` and ``~fab.run_configs.lfric.atm.py``),
             * command-line arguments to `cli_args`,
-            * override for input files to `source_getter`, 
+            * override for input files to `source_getter`,
             * folders containing override files to `overrides_folder`.
 
 
@@ -271,7 +271,7 @@ ArtefactStore
 =============
 Each build configuration contains an artefact store, containing various
 sets of artefacts. The artefact sets used by Fab are defined in the
-enum :class:`~fab.artefacts.ArtefactSet`. The most important sets are ``FORTRAN_BUILD_FILES``, 
+enum :class:`~fab.artefacts.ArtefactSet`. The most important sets are ``FORTRAN_BUILD_FILES``,
 ``C_BUILD_FILES``, which will always contain all known source files that
 will need to be analysed for dependencies, compiled, and linked. All existing
 steps in Fab will make sure to maintain these artefact sets consistently,
@@ -333,4 +333,4 @@ More advanced configuration topics are discussed in
 :ref:`Advanced Config`.
 
 You can see more complicated configurations in the
-`developer testing directory <https://github.com/metomi/fab/tree/master/run_configs>`_.
+`developer testing directory <https://github.com/MetOffice/fab/tree/main/run_configs>`_.