adding uninstall all and fixing bug with depot install (#626)

* adding uninstall all and fixing bug with depot install
* ensure path is abspath

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)
+ - Support for uninstall and fixing bug in biocontainers install (0.1.18)
  - GitHub action to update a registry from a cache or listing (0.1.17)
    - Support for "remove" command to more easily remove / uninstall entries
  - Fix bugs uninstalling all tags of a module (0.1.16)

docs/getting_started/user-guide.rst

@@ -1608,7 +1608,15 @@ You can also uninstall an entire family  of modules:
     $ shpc uninstall python
 
 The uninstall will go up to the top level module folder but not remove it
-in the case that you've added it to your ``MODULEPATH``.
+in the case that you've added it to your ``MODULEPATH``. As of version 0.1.18,
+you can also ask to uninstall all:
+
+
+.. code-block:: console
+
+    $ shpc uninstall --all --force
+
+
 
 .. _getting_started-commands-pull:
 

example/biocontainer-match.py

@@ -24,6 +24,7 @@
 
 from shpc.logger import logger
 from shpc.main import get_client
+from shpc.main.container import ContainerConfig
 
 
 def get_parser():
@@ -84,9 +85,10 @@ def main():
         tagged = f"{container}:{tag}"
 
         match = cli.registry.find(tagged)
+
+        # We don't have an exact match but can share aliases
         if not match:
-            tagged = container
-            match = cli.registry.find(tagged)
+            match = cli.registry.find(container)
 
         if not match:
             logger.warning(f"Warning: no match for {path}")
@@ -97,10 +99,28 @@ def main():
             seen.add(repo)
             continue
 
-        print(f"Installing {path} to {tagged}")
+        # Note we need to install the correct version but using aliases
+        # from the one we have (and they should be comparable)
+        print(f"Installing {path} to {tagged} with aliases from {match.module}")
+
+        # Make sure we use the full container path
+        path = os.path.join(depot, path)
+
+        # Create a new module, force the tag since the digest could be unknown
+        module = cli.new_module(tagged)
+        module.config = ContainerConfig(match)
+        module.config.set_tag(tag, force=True)
+        module.load_config(module.config, tagged)
+        module.add_local_container(path, keep_path=True)
 
         # We found a match! Install it (forcing keep path to not copy the container)
-        cli.install(tagged, force=args.force, container_image=path, keep_path=True)
+        cli.install(
+            tagged,
+            force=args.force,
+            module=module,
+            container_image=path,
+            keep_path=True,
+        )
         seen.add(repo)
 
 

shpc/client/__init__.py

@@ -310,7 +310,15 @@ def get_parser():
         action="store_true",
     )
     uninstall.add_argument(
-        "uninstall_recipe", help="module to uninstall (module/version)"
+        "uninstall_recipe", help="module to uninstall (module/version)", nargs="?"
+    )
+    uninstall.add_argument(
+        "--all",
+        "-a",
+        dest="uninstall_all",
+        help="uninstall all recipes",
+        default=False,
+        action="store_true",
     )
 
     # Update gets latest tags from OCI registries

shpc/client/uninstall.py

@@ -3,6 +3,7 @@
 __license__ = "MPL 2.0"
 
 import shpc.utils
+from shpc.logger import logger
 
 
 def main(args, parser, extra, subparser):
@@ -20,4 +21,14 @@ def main(args, parser, extra, subparser):
 
     # Update config settings on the fly
     cli.settings.update_params(args.config_params)
-    cli.uninstall(args.uninstall_recipe, force=args.force)
+    if args.uninstall_all:
+        if not args.force:
+            if not shpc.utils.confirm_uninstall("all modules?"):
+                return
+        for module_name in cli.list(return_modules=True):
+            cli.uninstall(module_name, force=True)
+
+    else:
+        if not args.uninstall_recipe:
+            logger.exit("Please provide a recipe to uninstall or select --all")
+        cli.uninstall(args.uninstall_recipe, force=args.force)

shpc/main/container/config.py

@@ -213,14 +213,18 @@ def set(self, key, value):
     def add_tag(self, key, value):
         self.entry._config["tags"][key] = value
 
-    def set_tag(self, tag):
+    def set_tag(self, tag, force=False):
         """
         Set a tag to be the config default (defaults to latest otherwise)
         """
         # If a tag isn't provided, default to latest
         if not tag:
             self.tag = self.tags.latest
 
+        # Force means we are explicitly adding a container knowing we won't check the tag
+        elif force:
+            self.tag = Tag(tag, "unknown")
+
         # This way, if the user explicitly asks for a tag that does not exist
         # this value will be none (and we can raise an error)
         else:

shpc/main/modules/base.py

@@ -258,17 +258,25 @@ def get(self, module_name, env_file=False):
             return self.container.get_environment_file(module_name)
         return self.container.get(module_name)
 
-    def list(self, pattern=None, names_only=False, out=None, short=False):
+    def list(
+        self,
+        pattern=None,
+        names_only=False,
+        out=None,
+        short=False,
+        return_modules=False,
+    ):
         """
         List installed modules.
         """
-        self._list_modules(
+        return self._list_modules(
             self.settings.module_base,
             self.modulefile,
             pattern,
             names_only,
             out,
             short=short,
+            return_modules=return_modules,
         )
 
     def docgen(self, module_name, registry=None, out=None, branch="main"):
@@ -328,14 +336,25 @@ def inspect(self, module_name):
         return self.container.inspect(image)
 
     def _list_modules(
-        self, base, filename, pattern=None, names_only=False, out=None, short=False
+        self,
+        base,
+        filename,
+        pattern=None,
+        names_only=False,
+        out=None,
+        short=False,
+        return_modules=False,
     ):
         """
         A shared function to list modules or registry entries.
         """
         out = out or sys.stdout
         modules = self._get_module_lookup(base, filename, pattern)
 
+        # Return names
+        if return_modules:
+            return modules
+
         # If we don't have modules, exit early
         if not modules:
             logger.exit("You don't have any install modules. Try shpc show.", 0)
@@ -424,7 +443,7 @@ def install(
         "force" is currently not used.
         """
         # Create a new module
-        module = self.get_module(
+        module = kwargs.get("module") or self.get_module(
             name, container_image=container_image, keep_path=keep_path
         )
 

shpc/version.py

@@ -2,7 +2,7 @@
 __copyright__ = "Copyright 2021-2023, Vanessa Sochat"
 __license__ = "MPL 2.0"
 
-__version__ = "0.1.17"
+__version__ = "0.1.18"
 AUTHOR = "Vanessa Sochat"
 EMAIL = "[email protected]"
 NAME = "singularity-hpc"