bugfix for singularity pull (repeated output) and wrapper scripts template (#506)

* bugfix for singularity pull (repeated output) and wrapper scripts template check
Signed-off-by: vsoch <[email protected]>

Author: vsoch

CHANGELOG.md

@@ -14,6 +14,7 @@ and **Merged pull requests**. Critical items to know are:
 The versions coincide with releases on pip. Only major versions will be released as tags on Github.
 
 ## [0.0.x](https://github.com/singularityhub/singularity-hpc/tree/main) (0.0.x)
+ - fixing but with stream command repeating output (0.0.46)
  - Adding support for wrapper scripts for global and container.yaml (0.0.45)
  - Lua and tcl module file bug fixes for shell functions and aliases (0.0.44)
   - restoring -B for Singularity bindpaths over using envar

shpc/main/container/singularity.py

@@ -310,7 +310,12 @@ def _pull_regular(self, uri, dest):
         """
         pull_folder = os.path.dirname(dest)
         name = os.path.basename(dest)
-        return self.client.pull(uri, name=name, pull_folder=pull_folder)
+        image, lines = self.client.pull(
+            uri, name=name, pull_folder=pull_folder, stream=True
+        )
+        for line in lines:
+            print(line, end="")
+        return image
 
     def inspect(self, image):
         """

shpc/main/settings.py

@@ -195,6 +195,10 @@ def parse_null(self, value):
         """
         if isinstance(value, str) and value.lower() in ["none", "null"]:
             return None
+
+        # Ensure we strip strings
+        if isinstance(value, str):
+            value = value.strip()
         return value
 
     def set(self, key, value):

shpc/main/wrappers/base.py

@@ -91,7 +91,7 @@ def load_template(self):
         template_paths = [os.path.dirname(template_file), templates]
 
         # Do we have a custom template path directory?
-        if "templates" in self.settings.wrapper_scripts:
+        if self.settings.wrapper_scripts.get("templates"):
             path = self.settings.wrapper_scripts["templates"]
             if not os.path.exists(path):
                 logger.exit(

shpc/settings.yml

@@ -69,14 +69,14 @@ 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
 
 # the module namespace you want to install from. E.g., if you have ghcr.io/autamus/clingo
 # and you set the namespace to ghcr.io/autamus, you can just do: shpc install clingo.
-namespace:
+namespace: null
 
 # THe name of the environment file to bind to the container.
 # This determines order of load

shpc/version.py

@@ -2,7 +2,7 @@
 __copyright__ = "Copyright 2021-2022, Vanessa Sochat"
 __license__ = "MPL 2.0"
 
-__version__ = "0.0.45"
+__version__ = "0.0.46"
 AUTHOR = "Vanessa Sochat"
 NAME = "singularity-hpc"
 PACKAGE_URL = "https://github.com/singularityhub/singularity-hpc"