Merge pull request #638 from douglasjacobsen/update-docs-urls

Update URLs in rst docs

lib/ramble/docs/configuration_files.rst

@@ -18,7 +18,7 @@ This document describes each config section and its purpose. This document
 does not cover the :ref:`workspace configuration file<workspace-config>`, which has its own document.
 
 Ramble's configuration logic closely follows
-`Spack's configuration logic <https://spack.readthedocs.io/en/latest/configuration.html>`.
+`Spack's configuration logic <https://spack.readthedocs.io/en/latest/configuration.html>`_.
 
 -----------------------
 Configuration Sections:
@@ -98,7 +98,7 @@ this command with an active workspace will include configuration sections
 defined within a workspace scope.
 
 Ramble's merging logic closely follows `Spack's configuration scope logic
-<https://spack.readthedocs.io/en/latest/configuration.html#configuration-scopes>`.
+<https://spack.readthedocs.io/en/latest/configuration.html#configuration-scopes>`_.
 
 .. _application-config:
 

lib/ramble/docs/package_managers.rst

@@ -68,7 +68,7 @@ Environment Modules Package Manager
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Setting the package manager config option to ``environment-modules`` enables
-the use of `Environment Modules <https://modules.readthedocs.io/en/latest/>`
+the use of `Environment Modules <https://modules.readthedocs.io/en/latest/>`_
 within the resulting experiments. Ramble will inject ``module load`` commands
 into each experiment, to prepare the execution environment.
 
@@ -78,14 +78,14 @@ determine what modules to load within the resulting environment.
 The use of this package manager requires an installation of
 ``environment-modules`` outside of Ramble. This is handled by system
 administrators on several clusters, but for more information see
-`environment-modules's documentation <https://modules.readthedocs.io/en/latest/INSTALL.html>`.
+`environment-modules's documentation <https://modules.readthedocs.io/en/latest/INSTALL.html>`_.
 
 ^^^^^^^^^^^^^^^^^^^^^
 EESSI Package Manager
 ^^^^^^^^^^^^^^^^^^^^^
 
 Setting the package manager config option to ``eessi`` enables the use of
-`the European Environment for Scientific Software Installations (EESSI) <https://www.eessi.io/docs/>`
+`the European Environment for Scientific Software Installations (EESSI) <https://www.eessi.io/docs/>`_
 for each experiment. Ramble will then inject commands to initialize the use of
 EESSI, and load the correct module files for the execution environment.
 
@@ -94,7 +94,7 @@ determine what modules to load within the resulting environment.
 
 The use of this package manager requires an installation of EESSI outside of
 Ramble. For more information, see
-`EESSI's documentation <https://www.eessi.io/docs/getting_access/native_installation/>`.
+`EESSI's documentation <https://www.eessi.io/docs/getting_access/native_installation/>`_.
 
 ^^^^^^^^^^^^^^^^^^^
 Pip Package Manager
@@ -113,14 +113,14 @@ determine what packages to install within the resulting virtual environment.
 The use of this package manager requires ``pip`` to be installed outside of
 Ramble. This happens automatically in several Python installations. For more
 information see
-`pip's documentation<https://pip.pypa.io/en/stable/installation/>`.
+`pip's documentation<https://pip.pypa.io/en/stable/installation/>`_.
 
 ^^^^^^^^^^^^^^^^^^^^^
 Spack Package Manager
 ^^^^^^^^^^^^^^^^^^^^^
 
 Setting the package manager config option to ``spack`` enables the use of
-`Spack <https://spack.io/>` for each experiment. During the ``setup`` pipeline,
+`Spack <https://spack.io/>`_ for each experiment. During the ``setup`` pipeline,
 Ramble will construct Spack environments and install the requested software.
 The experiments using Spack will automatically load the environment to prepare
 the experiment for execution.
@@ -134,15 +134,15 @@ mirror software source.
 
 The use of this package manager requires an external installation of Spack. For
 instructions on installing Spack, see
-`Spack's documentation <https://github.com/spack/spack#-spack>`.
+`Spack's documentation <https://github.com/spack/spack#-spack>`_.
 
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Spack Lightweight Package Manager
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Setting the package manager config option to ``spack-lightweight`` enables the
-use of a lightweight version of `Spack <https://spack.io/>` for each
+use of a lightweight version of `Spack <https://spack.io/>`_ for each
 experiment. During the ``setup`` pipeline, Ramble will construct Spack
 environments, however installation is deferred. This allows experiments to
 install their own software, enabling parallel installation, rather than
@@ -157,4 +157,4 @@ mirror software source.
 
 The use of this package manager requires an external installation of Spack. For
 instructions on installing Spack, see
-`Spack's documentation <https://github.com/spack/spack#-spack>`.
+`Spack's documentation <https://github.com/spack/spack#-spack>`_.

lib/ramble/docs/success_criteria.rst

@@ -116,7 +116,7 @@ The above example shows the full interface for defining success criteria with
 * ``fom_context``: (Optional) The context ``fom_name`` should exist in. Defaults to ``null``.
 
 Both ``fom_name`` and ``fom_context`` support
-`python style globbing<https://docs.python.org/3/library/fnmatch.html>`.
+`python style globbing<https://docs.python.org/3/library/fnmatch.html>`_.
 
 When using the globbing functionality, all contexts that match the
 ``fom_context`` argument are searched. Within each context, all FOMs that match

lib/ramble/docs/tutorials/EESSI_package_manager.rst

@@ -16,7 +16,7 @@ In this tutorial, you will set up and run a benchmark simulation using
 `GROMACS <https://www.gromacs.org/>`_, a free and open-source application
 for molecular dynamics. The execution environment will be created and managed
 using the
-`European Environment for Scientific Software Installations (EESSI) package manager <https://www.eessi.io/docs/>`.
+`European Environment for Scientific Software Installations (EESSI) package manager <https://www.eessi.io/docs/>`_.
 
 This tutorial builds off of concepts introduced in previous tutorials. Please
 make sure you review those before starting with this tutorial's content,
@@ -256,7 +256,7 @@ contents of ``$RAMBLE_ROOT/examples/eessi_gromacs_config.yaml``:
 
 **NOTE**: This workspace utilizes the ``eessi`` package manager. As a result, it
 requires ``eessi`` is installed following
-`EESSI installation instructions <https://www.eessi.io/docs/getting_access/native_installation/>`.
+`EESSI installation instructions <https://www.eessi.io/docs/getting_access/native_installation/>`_.
 Modifications to the ``package_manager`` variant will change this behavior.
 
 .. literalinclude:: ../../../../examples/gromacs_eessi_config.yaml

lib/ramble/docs/workspace.rst

@@ -398,7 +398,7 @@ the installation and generate software environments for each experiment.
 
 As an example, if the applications and workspace configuration file provide a
 configuration for Spack, Ramble will generate
-`Spack environments<https://spack.readthedocs.io/en/latest/environments.html>`.
+`Spack environments<https://spack.readthedocs.io/en/latest/environments.html>`_.
 
 By default, Ramble uses the following format for creating a spack environment file:
 

lib/ramble/docs/workspace_config.rst

@@ -1248,7 +1248,7 @@ In the above example, the chained experiment would have a namespace of:
 ``hostname.serial.test_exp2.chain.0.hostname.serial.test_exp1``
 
 The ``name`` attribute can use `globbing
-syntax<https://docs.python.org/3/library/fnmatch.html#module-fnmatch>` to chain
+syntax<https://docs.python.org/3/library/fnmatch.html#module-fnmatch>`_ to chain
 multiple experiments at once.
 
 The ``order`` keyword is optional. Valid options include: