update shpc show output stream and support --limit (#647)

Signed-off-by: vsoch <[email protected]>
Co-authored-by: vsoch <[email protected]>

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)
+ - Do not write directly to output with shpc show (0.1.22)
  - Podman template bug (0.1.21)
  - Improvement to shpc help command output (0.1.2)
  - Support for remote registries on self-hosted Gitlab instances (0.1.19)

docs/getting_started/user-guide.rst

@@ -1100,6 +1100,12 @@ To filter down the result set, use ``--filter``:
     biocontainers/bedtools
     biocontainers/tpp
 
+Set a limit of results with `--limit`:
+
+.. code-block:: console
+
+    $ shpc show --filter bio --limit 5
+
 
 To get details about a package, you would then add it's name to show:
 

shpc/client/__init__.py

@@ -446,6 +446,13 @@ def get_parser():
         default=None,
         dest="filter_string",
     )
+    show.add_argument(
+        "-l",
+        "--limit",
+        help="set a limit for the number to show",
+        default=None,
+        type=int,
+    )
 
     for command in docgen, show, add, remove, sync:
         command.add_argument(

shpc/client/show.py

@@ -19,4 +19,9 @@ def main(args, parser, extra, subparser):
     if args.registry:
         cli.settings.registry = [args.registry]
         cli.reload_registry()
-    cli.show(args.name, names_only=not args.versions, filter_string=args.filter_string)
+    cli.show(
+        args.name,
+        names_only=not args.versions,
+        filter_string=args.filter_string,
+        limit=args.limit,
+    )

shpc/main/client.py

@@ -5,7 +5,6 @@
 
 import os
 import shutil
-import sys
 
 import shpc.main.container as container
 import shpc.main.registry as registry
@@ -228,7 +227,7 @@ def docgen(self, module_name, registry=None):
         """
         raise NotImplementedError
 
-    def show(self, name, names_only=False, out=None, filter_string=None):
+    def show(self, name, names_only=False, out=None, filter_string=None, limit=None):
         """
         Show available packages
         """
@@ -237,13 +236,27 @@ def show(self, name, names_only=False, out=None, filter_string=None):
             config = self._load_container(name)
             config.dump(out)
         else:
-            out = out or sys.stdout
+            # Assemble the list of contents to write
+            modules = []
+            for i, entry in enumerate(
+                self.registry.iter_registry(filter_string=filter_string)
+            ):
+                # Break after the limit
+                if limit and i > limit:
+                    break
 
-            # List the known registry modules
-            for entry in self.registry.iter_registry(filter_string=filter_string):
                 config = container.ContainerConfig(entry)
                 if names_only:
-                    out.write("%s\n" % config.name)
+                    if out is None:
+                        print(config.name)
+                    modules.append(config.name)
                 else:
                     for version in config.tags.keys():
-                        out.write("%s:%s\n" % (config.name, version))
+                        module = "%s:%s" % (config.name, version)
+                        if out is None:
+                            print(module)
+                        modules.append(module)
+
+            # Write output to file or print to terminal
+            if out is not None:
+                utils.write_file(out, "\n".join(modules))

shpc/version.py

@@ -2,7 +2,7 @@
 __copyright__ = "Copyright 2021-2023, Vanessa Sochat"
 __license__ = "MPL 2.0"
 
-__version__ = "0.1.21"
+__version__ = "0.1.22"
 AUTHOR = "Vanessa Sochat"
 EMAIL = "[email protected]"
 NAME = "singularity-hpc"