Autogenerated - All Package Index

The All Packages Index is autogenerated using this repository .

The autogenerated files can serve as a foundation to enhance more detailed documentation in the first four sections of Software on Stanage .

We can use the autogenerated imports to ensure for example, module list versions are up to date:

.. include:: /referenceinfo/imports/stanage/packages/software-name-ml-el7-icelake-znver-stanage.rst

The most useful autogenerated imports are:

.. include:: /referenceinfo/imports/stanage/packages/software-name-sdbr-el7-icelake-znver-stanage.rst                   # sidebar
.. include:: /referenceinfo/imports/stanage/packages/software-name-dscr-el7-icelake-znver-stanage.rst                   # description
.. include:: /referenceinfo/imports/stanage/packages/software-name-ml-el7-icelake-znver-stanage.rst                     # module load (versions)
.. include:: /referenceinfo/imports/stanage/packages/software-name-inst-el7-icelake-znver-stanage.rst                   # installation notes
.. include:: /referenceinfo/imports/stanage/packages/software-name-dpnd-el7-icelake-znver-stanage.rst                   # dependencies of latest version

Using API ReST Files as Templates for Software Pages

If we want to add a fully documented page which does not currently exist for a software that is already installed on Stanage to, for example, stanage/software/apps within sheffield_hpc, then we would do the following:

cd stanage/software/apps
cp ../stacks/el7-icelake-znver-stanage/Bio/<package-name>.rst .

Here Bio is the module class of the package, The module class of a package can be found in it’s easyconfig.

Alternatively, find module class and also remove lines not needed:

cd stanage/software/apps
module_class=$(grep -r <package-name> ../stacks/el7-icelake-znver-stanage/All/index.rst | sed -E 's/-/\n/g' | tail -n 5 | head -n 1 | sed 's/./\U&/')
awk '/packages_note| -cust-/{getline; next} {print}' ../stacks/el7-icelake-znver-stanage/${module_class}/<package-name>.rst > ./<package-name>.rst

Now we can edit the template which looks like the following:

.. _software-name-bio-el7-icelake-znver-stanage:                                                                         # Edit this line to avoid conflicts

software-name
=============

.. include:: /referenceinfo/imports/stanage/packages/software-name-sdbr-el7-icelake-znver-stanage.rst

.. include:: /referenceinfo/imports/stanage/packages/software-name-dscr-el7-icelake-znver-stanage.rst

.. include:: /referenceinfo/imports/stanage/packages/packages_note.rst                                                   # Delete this line as not needed

.. include:: /referenceinfo/imports/scheduler/SLURM/common_commands/srun_start_interactive_session_import_stanage.rst

A version of software-name can then be made available with *one* of the following:

.. include:: /referenceinfo/imports/stanage/packages/software-name-ml-el7-icelake-znver-stanage.rst

.. include:: /referenceinfo/imports/stanage/packages/custom/software-name-cust-el7-icelake-znver-stanage.rst             # Delete this line as not needed

Notes
-----

.. include:: /referenceinfo/imports/stanage/packages/software-name-inst-el7-icelake-znver-stanage.rst

.. include:: /referenceinfo/imports/stanage/packages/software-name-dpnd-el7-icelake-znver-stanage.rst

.. _software-name-bio-el7-icelake-znver-stanage:                                                                         # Edit this line to avoid conflicts

software-name
=============

.. include:: /referenceinfo/imports/stanage/packages/software-name-sdbr-el7-icelake-znver-stanage.rst

.. include:: /referenceinfo/imports/stanage/packages/software-name-dscr-el7-icelake-znver-stanage.rst

.. include:: /referenceinfo/imports/scheduler/SLURM/common_commands/srun_start_interactive_session_import_stanage.rst

A version of software-name can then be made available with *one* of the following:

.. include:: /referenceinfo/imports/stanage/packages/software-name-ml-el7-icelake-znver-stanage.rst

Notes
-----

.. include:: /referenceinfo/imports/stanage/packages/software-name-inst-el7-icelake-znver-stanage.rst

.. include:: /referenceinfo/imports/stanage/packages/software-name-dpnd-el7-icelake-znver-stanage.rst

Note

In this example, the internal page reference _software-name-bio-el7-icelake-znver-stanage:, should be updated to _softwarename_stanage: for consitency with fully documented software page references.