Ausbeth reinstall

shpc/client/__init__.py

@@ -126,6 +126,34 @@ def get_parser():
         action="store_true",
     )
 
+    # Reinstall an installed software
+    reinstall = subparsers.add_parser(
+        "reinstall",
+        description=help.reinstall_description,
+        formatter_class=argparse.RawTextHelpFormatter,
+    )
+    reinstall.add_argument(
+        "reinstall_recipe",
+        help="recipe to reinstall",
+        nargs="?",
+    )
+
+    reinstall.add_argument(
+        "--update-containers",
+        "-u",
+        dest="update_containers",
+        help="Also reinstall the containers (by default, containers are preserved)",
+        default=False,
+        action="store_true",
+    )
+
+    reinstall.add_argument(
+        "--all",
+        "-a",
+        help="reinstall all installed software",
+        action="store_true",
+    )
+
     # List installed modules
     listing = subparsers.add_parser(
         "list",
@@ -397,6 +425,7 @@ def get_parser():
         install,
         listing,
         remove,
+        reinstall,
         shell,
         test,
         uninstall,
@@ -535,6 +564,8 @@ def help(return_code=0):
         from .pull import main
     elif args.command == "remove":
         from .remove import main
+    elif args.command == "reinstall":
+        from .reinstall import main
     elif args.command == "shell":
         from .shell import main
     elif args.command == "show":

shpc/client/help.py

@@ -39,6 +39,45 @@
   $ shpc install python:3.9.5-alpine
 """
 
+reinstall_description = """Reinstall a software. Containers are kept by default
+
+  # Reinstall a specific version of a software
+  $ shpc reinstall quay.io/biocontainers/samtools:1.20--h50ea8bc_1
+
+  # Reinstall all versions of a software
+  $ shpc reinstall quay.io/biocontainers/samtools
+
+  # Reinstall all installed software
+  $ shpc reinstall --all
+    OR
+  $ shpc reinstall -a
+
+  # Completely reinstall a specific version of a software without keeping the container
+  $ shpc reinstall quay.io/biocontainers/samtools:1.20--h50ea8bc_1 --update_container
+    OR
+  $ shpc reinstall quay.io/biocontainers/samtools:1.20--h50ea8bc_1 -u
+
+  # Completely reinstall all versions of a software without keeping the container
+  $ shpc reinstall quay.io/biocontainers/samtools --update_container
+    OR
+  $ shpc reinstall quay.io/biocontainers/samtools -u
+
+  # Completely reinstall all software without keeping the container
+  $ shpc reinstall --all --update_container
+    OR
+  $ shpc reinstall -a -u
+
+  # Invalid arguement combinations:
+  $ shpc reinstall quay.io/biocontainers/samtools:1.20--h50ea8bc_1 --all
+      OR
+  $ shpc reinstall quay.io/biocontainers/samtools:1.20--h50ea8bc_1 -a
+
+  $ shpc reinstall quay.io/biocontainers/samtools --all
+      OR
+  $ shpc reinstall quay.io/biocontainers/samtools -a
+"""
+
+
 listing_description = """List installed modules.
 
   # Show installed modules

shpc/client/reinstall.py

@@ -0,0 +1,129 @@
+__author__ = "Vanessa Sochat"
+__copyright__ = "Copyright 2021-2024, Vanessa Sochat"
+__license__ = "MPL 2.0"
+
+import shpc.utils
+from shpc.logger import logger
+
+
+def main(args, parser, extra, subparser):
+    from shpc.main import get_client
+
+    shpc.utils.ensure_no_extra(extra)
+
+    cli = get_client(
+        quiet=args.quiet,
+        settings_file=args.settings_file,
+        module_sys=args.module_sys,
+        container_tech=args.container_tech,
+    )
+
+    # Update config settings on the fly
+    cli.settings.update_params(args.config_params)
+
+    # Check if user entered an incomplete command
+    if not args.reinstall_recipe and not args.all:
+        subparser.error(
+            "You must specify a recipe to reinstall or use --all to reinstall all installed software."
+        )
+
+    # Reinstall all software
+    if args.all:
+        # Check if the user typed an invalid argument combination
+        if args.reinstall_recipe:
+            logger.exit(
+                "You cannot specify a recipe with --all. Use shpc reinstall --all to reinstall all installed software."
+            )
+
+        # Check if the user has any software installed
+        installed_software = cli.list(return_modules=True)
+        if not installed_software:
+            logger.exit("You currently don't have any installed software to reinstall.")
+
+        # Reinstall all installed software
+        print("Reinstalling all installed software...")
+        for software in installed_software.keys():
+            reinstall(software, cli, args, update_containers=args.update_containers)
+        logger.info("All software reinstalled.")
+
+    # Reinstall a specific software
+    else:
+        # Add namespace
+        name = cli.add_namespace(args.reinstall_recipe)
+
+        # Reinstall the software
+        reinstall(name, cli, args, update_containers=args.update_containers)
+
+
+def reinstall(name, cli, args, update_containers=False):
+    """
+    Reinstall a specific version or all versions of a software.
+    """
+    # Check if the provided recipe is known in any registry
+    try:
+        cli._load_container(name)
+    except SystemExit:
+        # Give additional messages relating to shpc reinstall, to the original exit message in _load_container function
+        logger.exit(
+            "This means it cannot be reinstalled because it is not installed, and cannot be installed because it is not known in any registry.\nPlease check the name or try a different recipe."
+        )
+
+    # Check if the software or version is installed
+    installed_versions = cli.list(return_modules=True).get(name.split(":")[0], [])
+    if not installed_versions:
+        logger.exit(
+            f"You currently don't have '{name}' installed.\nTry: shpc install", 0
+        )
+
+    # Determine if a specific version is requested
+    specific_version = ":" in name
+    if specific_version and name.split(":")[1] not in installed_versions:
+        logger.exit(
+            f"You currently don't have '{name}' installed.\nTry: shpc install", 0
+        )
+
+    # Handle reinstallation logic
+    if specific_version:
+        print(f"Reinstalling {name}...")
+        reinstall_version(name, cli, args, update_containers)
+        logger.info(f"Successfully reinstalled {name}.")
+    else:
+        print(f"Reinstalling all versions of {name}...")
+        for version in installed_versions:
+            version_name = f"{name}:{version}"
+            reinstall_version(version_name, cli, args, update_containers)
+        logger.info(f"Successfully reinstalled all versions of {name}.")
+
+
+def reinstall_version(name, cli, args, update_containers):
+    """
+    Sub-function to handle the actual reinstallation
+    """
+    # Get the list of views the software was in
+    views_with_module = set()
+    views_dir = cli.new_module(name).module_dir
+    for view_name, entry in cli.views.items():
+        if entry.exists(views_dir):
+            views_with_module.add(view_name)
+
+    # Uninstallation process. By default, uninstall without prompting the user and keep the container except the user wants a complete reinstall
+    cli.uninstall(name, force=True, keep_container=not update_containers)
+
+    # Display a helpful message to the user about the state of the container during reinstall process
+    if not update_containers:
+        print(
+            "Container was successfully preserved, module files and wrapper scripts will be overwritten..."
+        )
+    else:
+        print("No container was preserved, all files will be overwritten...")
+
+    # Installation process
+    cli.install(name)
+
+    # Restore the software to the captured views
+    print(
+        f"Restoring {name} to the views it was uninstalled from during reinstallation"
+    )
+    for view_name in views_with_module:
+        cli.view_install(view_name, name)
+        logger.info(f"Restored {name} to view: {view_name}")

shpc/main/client.py

@@ -62,6 +62,16 @@ def install(self, name, tag=None, **kwargs):
         """
         raise NotImplementedError
 
+    def reinstall(self, name, update_containers=False):
+        """
+        Reinstall an installed software
+        """
+        from shpc.client.reinstall import reinstall
+
+        cli = self
+        args = {}
+        reinstall(name, cli, args, update_containers=update_containers)
+
     def uninstall(self, name, tag=None):
         """
         Uninstall must also implemented by the subclass (e.g., lmod)

shpc/main/modules/base.py

@@ -85,7 +85,7 @@ def view_uninstall(self, view, name, force=False):
             logger.exit("View %s does not exist, cannot uninstall." % view)
         return self.views[view].uninstall(module.module_dir)
 
-    def uninstall(self, name, force=False):
+    def uninstall(self, name, force=False, keep_container=False):
         """
         Given a unique resource identifier, uninstall a module.
         Set "force" to True to bypass the confirmation prompt.
@@ -100,7 +100,7 @@ def uninstall(self, name, force=False):
 
         # Ask before deleting anything!
         if not force:
-            msg = name + "?"
+            msg = "Do you wish to uninstall " + name + "?"
             if views_with_module:
                 msg += (
                     "\nThis will uninstall the module from views:\n  %s\nAre you sure?"
@@ -110,14 +110,17 @@ def uninstall(self, name, force=False):
                 return
 
         # Podman needs image deletion
-        self.container.delete(module.name)
+        if not keep_container:  # For reinstall
+            self.container.delete(module.name)
 
         if module.container_dir != module.module_dir:
-            self._uninstall(
-                module.container_dir,
-                self.container_base,
-                "$container_base/%s" % module.name,
-            )
+            if not keep_container:
+                self._uninstall(
+                    module.container_dir,
+                    self.container_base,
+                    "$container_base/%s" % module.name,
+                )
+
             self._uninstall(
                 module.module_dir,
                 self.settings.module_base,