Merge branch 'add/symlink-install' into add/symlink-install-cli-arg

.gitignore

@@ -17,3 +17,4 @@ __pycache__
 *.img
 .eggs
 modules
+symlinks

docs/getting_started/user-guide.rst

@@ -181,7 +181,7 @@ variable replacement. A summary table of variables is included below, and then f
      - singularity
    * - symlink_base
      - If set, where you want to install a simplified module tree to using ``--symlink-tree``
-     - unset
+     - $root_dir/symlinks
    * - symlink_tree
      - If set to true, ALWAYS generate a symlink tree given that a symlink base is defined regardless of ``--symlink-tree`` flag
      - false
@@ -385,8 +385,9 @@ By default, your modules are installed to your ``module_base`` described above w
 namespace, meaning the container registry from where they arise. We do this so that the namespace
 is consistent and there are no conflicts. However, if you want a simplified tree to install from,
 meaning the module full names are _just_ the final container name, you can set the ``symlink_base``
-in your settings to a different root. For example, let's say we want to install a set of modules,
-after seting our symlink base to ``tmp-modules``. We could do:
+in your settings to a different root. For example, let's say we want to install a set of modules.
+We can use the default ``symlink_base`` of ``$root_dir/symlinks`` or set our own ``symlink_base``
+in the settings.yaml. We could do:
 
 .. code-block:: console
 
@@ -398,7 +399,7 @@ available!
 
 .. code-block:: console
 
-    $ module use ./tmp-modules
+    $ module use ./symlinks
     $ module load clingo/5.5.1/module
 
 This is much more efficient compared to the install that uses the full paths:

shpc/main/modules/__init__.py

@@ -212,14 +212,12 @@ def check_symlink(self, module_dir, symlink=False):
         Given an install command, if --symblink is provided make sure we have
         a symlink_base defined in settings and the directory exists.
         """
-
         if not symlink:
             return
-        if symlink and not self.settings.symlink_base:
-            logger.exit('To request symlink you must set symlink_base in settings.yml: shpc config set symlink_base:/path/desired')
 
-        elif symlink and not os.path.exists(self.settings.symlink_base):
-            logger.exit('%s does not exist, create before trying to use it!' % self.settings.symlink_base)
+        # Create the symlink base for the user if it does not exist
+        if symlink and not os.path.exists(self.settings.symlink_base):
+            utils.mkdirp([self.settings.symlink_base])
 
         # Get the symlink path - does it exist?
         symlink_path = self.get_symlink_path(module_dir)
@@ -381,7 +379,8 @@ def install(self, name, tag=None, symlink=False, **kwargs):
 
         # Global override to arg
         symlink = self.settings.symlink_tree is True or symlink
-        # Cut out early if symlink desired but no home
+
+        # Cut out early if symlink desired or already exists
         self.check_symlink(module_dir, symlink)
         shpc.utils.mkdirp([module_dir, container_dir])
 

shpc/settings.yml

@@ -36,7 +36,7 @@ container_base: $root_dir/containers
 
 # If defined, create a simplified "symlink install" that shortens module names
 # to be just the container, e.g., ghcr.io/autamus/samtools -> module load samtools
-symlink_base: null
+symlink_base: $root_dir/symlinks
 
 # Always generate a symlink, even without the command line argument
 symlink_tree: false
@@ -76,7 +76,7 @@ wrapper_scripts:
   podman: docker.sh
 
   # use for singularity aliases (set to null to disable)
-  singularity: singularity.sh 
+  singularity: singularity.sh
 
   # Add an extra custom template directory (searched first)
   templates: null