From be22d50b1b10be76b8edb394a35ad0b09b234020 Mon Sep 17 00:00:00 2001
From: Ausbeth <chiemekaaguguo@gmail.com>
Date: Wed, 23 Oct 2024 12:12:40 +0100
Subject: [PATCH] Cleaning up (removing previous code on upgrade)

---
 shpc/client/__init__.py   |  34 +---
 shpc/client/help.py       |  33 ----
 shpc/client/upgrade.py    | 190 ----------------------
 shpc/main/client.py       |  10 --
 shpc/tests/test_client.py | 325 --------------------------------------
 shpc/tests/test_client.sh |  11 --
 6 files changed, 1 insertion(+), 602 deletions(-)
 delete mode 100644 shpc/client/upgrade.py

diff --git a/shpc/client/__init__.py b/shpc/client/__init__.py
index 890f98c02..c7186862d 100644
--- a/shpc/client/__init__.py
+++ b/shpc/client/__init__.py
@@ -332,35 +332,6 @@ def get_parser():
         action="store_true",
     )
 
-    # Upgrade a software to its latest version
-    upgrade = subparsers.add_parser(
-        "upgrade",
-        description=help.upgrade_description,
-        formatter_class=argparse.RawTextHelpFormatter,
-    )
-    upgrade.add_argument(
-        "upgrade_recipe",
-        help="software to upgrade",
-        nargs="?",
-    )
-
-    upgrade.add_argument(
-        "--all",
-        "-a",
-        help="upgrade all installed software.",
-        dest="upgrade_all",
-        action="store_true",
-    )
-
-    upgrade.add_argument(
-        "--force",
-        "-f",
-        dest="force",
-        help="force upgrade without prompting for confirmation to uninstall current version(s) or install latest version to view(s).",
-        default=False,
-        action="store_true",
-    )
-
     # Update gets latest tags from OCI registries
     update = subparsers.add_parser(
         "update",
@@ -414,7 +385,7 @@ def get_parser():
         action="store_true",
     )
 
-    for command in update, upgrade, install, sync:
+    for command in update, install, sync:
         command.add_argument(
             "--dry-run",
             "-d",
@@ -437,7 +408,6 @@ def get_parser():
         shell,
         test,
         uninstall,
-        upgrade,
         view,
     ]:
         command.add_argument(
@@ -585,8 +555,6 @@ def help(return_code=0):
         from .uninstall import main
     elif args.command == "update":
         from .update import main
-    elif args.command == "upgrade":
-        from .upgrade import main
     elif args.command == "sync-registry":
         from .sync import sync_registry as main
 
diff --git a/shpc/client/help.py b/shpc/client/help.py
index ceb451a5c..34405d2b3 100644
--- a/shpc/client/help.py
+++ b/shpc/client/help.py
@@ -253,36 +253,3 @@
   # Filter all modules to those with "python"
   $ shpc show --filter python
 """
-
-upgrade_description = """Upgrade software to the latest version.
-
-  # Upgrade a software to its latest version and give option to uninstall older versions or not.
-  # Do not include the version in the command
-  $ shpc upgrade quay.io/biocontainers/samtools
-
-  # Upgrade all software
-  $ shpc upgrade --all
-      OR
-  $ shpc upgrade -a
-
-  # Valid arguement combinations:
-  # Perform dry-run on a software to check if the latest is installed or not without upgrading it.
-  $ shpc upgrade quay.io/biocontainers/samtools --dry-run
-      OR
-  $ shpc upgrade quay.io/biocontainers/samtools -d
-
-  # Perform dry-run to show version details of all installed software, to check if the latest version is installed or not without upgrading them.
-  $ shpc upgrade --all --dry-run
-      OR
-  $ shpc upgrade -a -d
-
-  # Invalid arguement combinations:
-  $ shpc upgrade quay.io/biocontainers/samtools --all
-      OR
-  $ shpc upgrade quay.io/biocontainers/samtools -a
-
-  $ shpc upgrade quay.io/biocontainers/samtools --all --dry-run
-      OR
-  $ shpc upgrade quay.io/biocontainers/samtools -a -d
-
-"""
diff --git a/shpc/client/upgrade.py b/shpc/client/upgrade.py
deleted file mode 100644
index 78df6b3f1..000000000
--- a/shpc/client/upgrade.py
+++ /dev/null
@@ -1,190 +0,0 @@
-__author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2021-2024, Vanessa Sochat"
-__license__ = "MPL 2.0"
-
-import shpc.utils as utils
-from shpc.logger import logger
-
-
-def main(args, parser, extra, subparser):
-    from shpc.main import get_client
-
-    utils.ensure_no_extra(extra)
-
-    cli = get_client(quiet=args.quiet, settings_file=args.settings_file)
-
-    # Update config settings on the fly
-    cli.settings.update_params(args.config_params)
-
-    # Check if user entered an incomplete command
-    if not args.upgrade_recipe and not args.upgrade_all:
-        subparser.error(
-            "Incomplete command. The following arguments are required: upgrade_recipe, --all, or -h for more details"
-        )
-
-    # Get the list of installed software
-    installed_software = cli.list(return_modules=True)
-
-    # Ensure the user has software installed before carrying out upgrade
-    if not installed_software:
-        logger.exit(
-            "Cannot perform shpc upgrade because you currently do not have any software installed.",
-            0,
-        )
-
-    # Upgrade a specific installed software
-    if args.upgrade_recipe:
-        # Check if the provided recipe is known in any registry
-        try:
-            cli._load_container(args.upgrade_recipe)
-        except SystemExit:
-            # Give additional messages relating to shpc upgrade, to the original exit message in _load_container function
-            logger.exit(
-                "This means it cannot be upgraded 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 user typed an invalid argument combination
-        if args.upgrade_all:
-            logger.exit(
-                "Cannot use '--all' with a specific recipe. Please choose one option."
-            )
-        # Check if the user specified a version
-        if ":" in args.upgrade_recipe:
-            logger.exit("Please use 'shpc upgrade recipe' without including a version.")
-        # Check if the specific software is installed
-        if args.upgrade_recipe not in installed_software:
-            logger.exit(
-                f"You currently do not have {args.upgrade_recipe} installed.\nYou can install it with this command: shpc install {args.upgrade_recipe}",
-                0,
-            )
-
-        # Does the user just want a dry-run of the specific software?
-        if args.dryrun:
-            version_info = upgrade(
-                args.upgrade_recipe, cli, args, dryrun=True
-            )  # This returns the latest version if its available, else returns None
-            if version_info:
-                logger.info(
-                    f"You do not have the latest version installed.\nLatest version avaiable is {version_info}"
-                )
-            else:
-                logger.info(
-                    f"You have the latest version of {args.upgrade_recipe} installed."
-                )
-
-        # Upgade the software
-        else:
-            upgrade(args.upgrade_recipe, cli, args, dryrun=False, force=args.force)
-
-    # Upgrade all installed software
-    elif args.upgrade_all:
-        # Store the number of all outdated software
-        num_outdated = 0
-
-        # Does the user just want a dry-run of all software?
-        if args.dryrun:
-            print("Performing a dry-run on all your software...")
-            for software in installed_software.keys():
-                version_info = upgrade(software, cli, args, dryrun=True)
-                if version_info:
-                    logger.info(
-                        f"{software} is outdated. Latest version available is {version_info}"
-                    )
-                    num_outdated += 1
-                else:
-                    logger.info(f"{software} is up to date.")
-            # Provide a report on the dry-run
-            if num_outdated == 0:
-                logger.info("All your software are currently up to date.")
-            else:
-                logger.info(f"You have a total of {num_outdated} outdated software.")
-
-        # Upgrade all software
-        else:
-            print("Checking your list to upgrade outdated software...")
-            for software in installed_software.keys():
-                # Attempt upgrade on each software
-                upgrade_info = upgrade(
-                    software, cli, args, dryrun=False, force=args.force
-                )
-                # Count actual upgrades
-                if upgrade_info:
-                    num_outdated += 1
-            if num_outdated == 0:
-                logger.info("No upgrade needed. All your software are up to date.")
-            else:
-                logger.info(
-                    f"Updated {num_outdated} outdated software from your list\nAll your software are now up to date."
-                )
-
-
-def upgrade(name, cli, args, dryrun=False, force=False):
-    """
-    Upgrade a software to its latest version. Or preview available upgrades from the user's software list
-    """
-    # Add namespace
-    name = cli.add_namespace(name)
-
-    # Load the container configuration for the specified recipe
-    config = cli._load_container(name)
-
-    # Store the installed versions and the latest version tag
-    installed_versions = cli.list(pattern=name, return_modules=True)
-    latest_version_tag = get_latest_version(name, config)
-
-    # Compare the latest version with the user's installed version
-    if any(latest_version_tag in versions for versions in installed_versions.values()):
-        if not dryrun:
-            logger.info("You have the latest version of " + name + " installed already")
-        return None  # No upgrade necessary
-
-    else:
-        if dryrun:
-            return (
-                latest_version_tag  # Return the latest version for upgrade information
-            )
-        print(
-            "Upgrading "
-            + name
-            + " to its latest version. Version "
-            + latest_version_tag
-        )
-
-        # Get the list of views the software was in
-        views_with_module = set()
-        view_dir = cli.new_module(name).module_dir
-        for view_name, entry in cli.views.items():
-            if entry.exists(view_dir):
-                views_with_module.add(view_name)
-
-        # Ask if the user wants to unintall old versions
-        if not cli.uninstall(name, force=force):
-            logger.info("Old versions of " + name + " were preserved")
-
-        # Install the latest version
-        cli.install(name)
-
-        # Install the latest version to views where the outdated version was found
-        if views_with_module:
-            msg = f"Do you also want to install the latest version of {name} to the view(s) of the previous version(s)?"
-            if utils.confirm_action(msg, force=force):
-                for view_name in views_with_module:
-                    cli.view_install(view_name, name)
-                    logger.info(
-                        f"Installed the latest version of {name} to view: {view_name}"
-                    )
-
-        return latest_version_tag  # Upgrade occured
-
-
-def get_latest_version(name, config):
-    """
-    Given an added namespace of a recipe and a loaded container configuration of that namespace,
-    Retrieve the latest version tag.
-    """
-    latest_version_info = config.get("latest")
-    if not latest_version_info:
-        logger.exit(f"No latest version found for {name}")
-
-    # Extract the latest version tag
-    latest_version_tag = list(latest_version_info.keys())[0]
-    return latest_version_tag
diff --git a/shpc/main/client.py b/shpc/main/client.py
index a221d93f8..7ef602b92 100644
--- a/shpc/main/client.py
+++ b/shpc/main/client.py
@@ -62,16 +62,6 @@ def install(self, name, tag=None, **kwargs):
         """
         raise NotImplementedError
 
-    def upgrade(self, name, dryrun=False, force=False):
-        """
-        Upgrade an outdated software
-        """
-        from shpc.client.upgrade import upgrade
-
-        cli = self
-        args = {}
-        upgrade(name, cli, args, dryrun=dryrun, force=force)
-
     def uninstall(self, name, tag=None):
         """
         Uninstall must also implemented by the subclass (e.g., lmod)
diff --git a/shpc/tests/test_client.py b/shpc/tests/test_client.py
index c2315862c..6cdfc85cf 100644
--- a/shpc/tests/test_client.py
+++ b/shpc/tests/test_client.py
@@ -9,14 +9,11 @@
 import io
 import os
 import shutil
-from unittest import mock
 
 import pytest
 
-import shpc.main.modules.views as views
 import shpc.main.registry as registry
 import shpc.utils
-from shpc.client.upgrade import get_latest_version as glv
 
 from .helpers import here, init_client
 
@@ -413,325 +410,3 @@ def test_remove(tmp_path):
     # Remove the module (with force)
     client.remove(module, force=True)
     assert client.registry.exists(module) is None
-
-
-@pytest.mark.parametrize(
-    "module_sys, module_file, container_tech, remote, dryrun",
-    [
-        ("lmod", "module.lua", "singularity", False, False),
-        ("lmod", "module.lua", "podman", False, False),
-        ("tcl", "module.tcl", "singularity", False, False),
-        ("tcl", "module.tcl", "podman", False, False),
-        ("lmod", "module.lua", "singularity", True, False),
-        ("lmod", "module.lua", "podman", True, False),
-        ("tcl", "module.tcl", "singularity", True, False),
-        ("tcl", "module.tcl", "podman", True, False),
-        ("lmod", "module.lua", "singularity", False, True),
-        ("lmod", "module.lua", "podman", False, True),
-        ("tcl", "module.tcl", "singularity", False, True),
-        ("tcl", "module.tcl", "podman", False, True),
-        ("lmod", "module.lua", "singularity", True, True),
-        ("lmod", "module.lua", "podman", True, True),
-        ("tcl", "module.tcl", "singularity", True, True),
-        ("tcl", "module.tcl", "podman", True, True),
-    ],
-)
-def test_upgrade_software_with_force(
-    tmp_path, module_sys, module_file, container_tech, remote, dryrun
-):
-    """
-    Test upgrading a software where uninstalling older versions and installing latest version to view is also done.
-    """
-    client = init_client(str(tmp_path), module_sys, container_tech, remote=remote)
-
-    # Install an outdated version of a software
-    client.install("quay.io/biocontainers/samtools:1.18--h50ea8bc_1")
-
-    # Create the default view if it doesn't exist
-    view_handler = views.ViewsHandler(
-        settings_file=client.settings.settings_file, module_sys=module_sys
-    )
-    assert "mpi" not in client.views
-    view_handler.create("mpi")
-    client.detect_views()
-    assert "mpi" in client.views
-    view = client.views["mpi"]
-    assert view.path == os.path.join(tmp_path, "views", "mpi") and os.path.exists(
-        view.path
-    )
-    assert os.path.exists(view.config_path)
-    assert view._config["view"]["name"] == "mpi"
-    assert not view._config["view"]["modules"]
-    assert not view._config["view"]["system_modules"]
-
-    # Install the software to the view
-    client.view_install("mpi", "quay.io/biocontainers/samtools:1.18--h50ea8bc_1")
-
-    # Upgrade the software to its latest version
-    client.upgrade("quay.io/biocontainers/samtools", dryrun=dryrun, force=True)
-
-    # Load the container configuration for the software and get its latest version tag
-    name = client.add_namespace("quay.io/biocontainers/samtools")
-    config = client._load_container(name)
-    latest_version = glv(name, config)
-
-    # Verify if the latest version of the software was installed
-    if not dryrun:
-        # Verify the module's directory exists and module files were installed
-        module_dir = os.path.join(
-            client.settings.module_base,
-            "quay.io/biocontainers/samtools",
-            latest_version,
-        )
-        assert os.path.exists(module_dir), "Latest version directiory should exist."
-        module_file_path = os.path.join(module_dir, module_file)
-        assert os.path.exists(
-            module_file_path
-        ), "Latest version's module files should be installed."
-
-        # Check if the older version's module directory was removed and if its module files were uninstalled
-        module_dir_old = os.path.join(
-            client.settings.module_base,
-            "quay.io/biocontainers/samtools",
-            "1.18--h50ea8bc_1",
-        )
-        assert not os.path.exists(module_dir_old), "Older version should be uninstalled"
-        module_file_path = os.path.join(module_dir_old, module_file)
-        assert not os.path.exists(
-            module_file_path
-        ), "Older version's module files should be uninstalled."
-
-        # Ensure the latest version was added to the view
-        assert client.views["mpi"].exists(
-            module_dir
-        ), "Upgraded software should be added to the view 'mpi'"
-
-    # Verify that the latest version of the software was not installed if dry-run is TRUE
-    else:
-        module_dir = os.path.join(
-            client.settings.module_base,
-            "quay.io/biocontainers/samtools",
-            latest_version,
-        )
-        assert not os.path.exists(module_dir), "Latest version should not be installed."
-        module_file_path = os.path.join(module_dir, module_file)
-        assert not os.path.exists(
-            module_file_path
-        ), "Latest version's module files should not be installed."
-
-
-@pytest.mark.parametrize(
-    "module_sys,module_file,container_tech,remote",
-    [
-        ("lmod", "module.lua", "singularity", False),
-        ("lmod", "module.lua", "podman", False),
-        ("tcl", "module.tcl", "singularity", False),
-        ("tcl", "module.tcl", "podman", False),
-        ("lmod", "module.lua", "singularity", True),
-        ("lmod", "module.lua", "podman", True),
-        ("tcl", "module.tcl", "singularity", True),
-        ("tcl", "module.tcl", "podman", True),
-    ],
-)
-@mock.patch("shpc.utils.confirm_action")
-def test_upgrade_software_without_force(
-    mock_confirm_action, tmp_path, module_sys, module_file, container_tech, remote
-):
-    """
-    Test upgrading a software where uninstalling older versions and installing latest version to view is not done.
-    """
-    client = init_client(str(tmp_path), module_sys, container_tech, remote=remote)
-
-    # Install an outdated version of a software
-    client.install("quay.io/biocontainers/samtools:1.18--h50ea8bc_1")
-
-    # Create the default view if it doesn't exist
-    view_handler = views.ViewsHandler(
-        settings_file=client.settings.settings_file, module_sys=module_sys
-    )
-    assert "mpi" not in client.views
-    view_handler.create("mpi")
-    client.detect_views()
-    assert "mpi" in client.views
-    view = client.views["mpi"]
-    assert view.path == os.path.join(tmp_path, "views", "mpi") and os.path.exists(
-        view.path
-    )
-    assert os.path.exists(view.config_path)
-    assert view._config["view"]["name"] == "mpi"
-    assert not view._config["view"]["modules"]
-    assert not view._config["view"]["system_modules"]
-
-    # Install the software to the view
-    client.view_install("mpi", "quay.io/biocontainers/samtools:1.18--h50ea8bc_1")
-
-    # Simulate user's choice for uninstalling older versions and installing latest version to the views of the older versions
-    mock_confirm_action.return_value = False
-
-    # Upgrade the software to its latest version
-    client.upgrade("quay.io/biocontainers/samtools", dryrun=False, force=False)
-
-    # Load the container configuration for the software and get its latest version tag
-    name = client.add_namespace("quay.io/biocontainers/samtools")
-    config = client._load_container(name)
-    latest_version = glv(name, config)
-
-    # Verify the module's directory exists and module files were installed
-    module_dir = os.path.join(
-        client.settings.module_base, "quay.io/biocontainers/samtools", latest_version
-    )
-    assert os.path.exists(module_dir), "Latest version directiory should exist."
-    module_file_path = os.path.join(module_dir, module_file)
-    assert os.path.exists(
-        module_file_path
-    ), "Latest version's module files should be installed."
-
-    # Ensure the older version's module directory still exists and its module files were not uninstalled
-    module_dir_old = os.path.join(
-        client.settings.module_base,
-        "quay.io/biocontainers/samtools",
-        "1.18--h50ea8bc_1",
-    )
-    assert os.path.exists(module_dir_old), "Old version should not be uninstalled"
-    module_file_path = os.path.join(module_dir_old, module_file)
-    assert os.path.exists(
-        module_file_path
-    ), "Older version's module files should not be uninstalled."
-
-    # Ensure the latest version was not added to the view
-    assert not client.views["mpi"].exists(
-        module_dir
-    ), "Upgraded software should not added to the view 'mpi'"
-
-
-@pytest.mark.parametrize(
-    "module_sys,module_file,container_tech,remote",
-    [
-        ("lmod", "module.lua", "singularity", False),
-        ("lmod", "module.lua", "podman", False),
-        ("tcl", "module.tcl", "singularity", False),
-        ("tcl", "module.tcl", "podman", False),
-        ("lmod", "module.lua", "singularity", True),
-        ("lmod", "module.lua", "podman", True),
-        ("tcl", "module.tcl", "singularity", True),
-        ("tcl", "module.tcl", "podman", True),
-    ],
-)
-def test_upgrade_with_latest_already_installed(
-    tmp_path, module_sys, module_file, container_tech, remote
-):
-    client = init_client(str(tmp_path), module_sys, container_tech, remote=remote)
-
-    # Load the container configuration for the software and get is latest version
-    name = client.add_namespace("quay.io/biocontainers/samtools")
-    config = client._load_container(name)
-    latest_version = glv(name, config)
-
-    # Install an outdated and the latest version of a software
-    client.install(f"quay.io/biocontainers/samtools:{latest_version}")
-    client.install("quay.io/biocontainers/samtools:1.18--h50ea8bc_1")
-
-    # Verify the latest version's module directory exists and module files were installed
-    module_dir = os.path.join(
-        client.settings.module_base, "quay.io/biocontainers/samtools", latest_version
-    )
-    assert os.path.exists(module_dir), "Latest version directiory should exist."
-    module_file_path = os.path.join(module_dir, module_file)
-    assert os.path.exists(module_file_path), "Latest version module files should exist."
-
-    # Capture the time the directory was created
-    module_dir_mtime_before = os.path.getmtime(module_dir)
-
-    # Perform upgrade
-    client.upgrade("quay.io/biocontainers/samtools", dryrun=False, force=True)
-
-    # Capture the time of the directory after upgrade was done
-    module_dir_mtime_after = os.path.getmtime(module_dir)
-
-    # Ensure the directory did not change, to signify upgrade was not performed when the latest was already installed
-    assert (
-        module_dir_mtime_after == module_dir_mtime_before
-    ), "Upgrade should not occur if latest is installed already."
-
-
-@pytest.mark.parametrize(
-    "module_sys,module_file,container_tech,remote",
-    [
-        ("lmod", "module.lua", "singularity", False),
-        ("lmod", "module.lua", "podman", False),
-        ("tcl", "module.tcl", "singularity", False),
-        ("tcl", "module.tcl", "podman", False),
-        ("lmod", "module.lua", "singularity", True),
-        ("lmod", "module.lua", "podman", True),
-        ("tcl", "module.tcl", "singularity", True),
-        ("tcl", "module.tcl", "podman", True),
-    ],
-)
-def test_upgrade_all_software(
-    tmp_path, module_sys, module_file, container_tech, remote
-):
-    """
-    Test upgrading a software where uninstalling older versions and installing latest version to view is also done.
-    """
-    client = init_client(str(tmp_path), module_sys, container_tech, remote=remote)
-
-    # Install two different outdated software
-    client.install("quay.io/biocontainers/samtools:1.18--h50ea8bc_1")
-    client.install("quay.io/biocontainers/bwa:0.7.18--he4a0461_0")
-
-    # Create the default view if it doesn't exist
-    view_handler = views.ViewsHandler(
-        settings_file=client.settings.settings_file, module_sys=module_sys
-    )
-    assert "mpi" not in client.views
-    view_handler.create("mpi")
-    client.detect_views()
-    assert "mpi" in client.views
-    view = client.views["mpi"]
-    assert view.path == os.path.join(tmp_path, "views", "mpi") and os.path.exists(
-        view.path
-    )
-    assert os.path.exists(view.config_path)
-    assert view._config["view"]["name"] == "mpi"
-    assert not view._config["view"]["modules"]
-    assert not view._config["view"]["system_modules"]
-
-    # Install the software to the view
-    client.view_install("mpi", "quay.io/biocontainers/samtools:1.18--h50ea8bc_1")
-    client.view_install("mpi", "quay.io/biocontainers/bwa:0.7.18--he4a0461_0")
-
-    # Upgrade all software to thei latest version
-    installed_software = client.list(return_modules=True)
-    for software, versions in installed_software.items():
-        client.upgrade(software, dryrun=False, force=True)
-
-        # Load the container configuration for the software and get their latest version tag
-        name = client.add_namespace(software)
-        config = client._load_container(name)
-        latest_version = glv(name, config)
-
-        # Verify the module's directory exists and module files were installed
-        module_dir = os.path.join(client.settings.module_base, software, latest_version)
-        assert os.path.exists(module_dir), "Latest version directiory should exist."
-        module_file_path = os.path.join(module_dir, module_file)
-        assert os.path.exists(
-            module_file_path
-        ), "Latest version's module files should be installed."
-
-        for older_version in versions:
-            # Check if the older version's module directory was removed and if its module files were uninstalled
-            module_dir_old = os.path.join(
-                client.settings.module_base, software, older_version
-            )
-            assert not os.path.exists(
-                module_dir_old
-            ), "Older version should be uninstalled"
-            module_file_path = os.path.join(module_dir_old, module_file)
-            assert not os.path.exists(
-                module_file_path
-            ), "Older version's module files should be uninstalled."
-
-        # Ensure the latest versions were added to the view
-        assert client.views["mpi"].exists(
-            module_dir
-        ), "Upgraded software should be added to the view 'mpi'"
diff --git a/shpc/tests/test_client.sh b/shpc/tests/test_client.sh
index 761745c73..c7db9ece2 100755
--- a/shpc/tests/test_client.sh
+++ b/shpc/tests/test_client.sh
@@ -67,17 +67,6 @@ runTest 0 $output shpc --settings-file $settings install python:3.9.2-slim
 runTest 0 $output shpc --settings-file $settings install vanessa/salad:latest
 runTest 0 $output shpc --settings-file $settings install --container_tech podman python
 
-echo
-echo "#### Testing upgrade "
-runTest 0 $output shpc --settings-file $settings upgrade --help
-runTest 0 $output shpc --settings-file $settings install quay.io/biocontainers/samtools:1.20--h50ea8bc_0
-runTest 0 $output shpc --settings-file $settings install quay.io/biocontainers/bioconductor-bags:2.40.0--r43ha9d7317_0
-runTest 0 $output shpc --settings-file $settings install quay.io/biocontainers/bwa:0.7.18--he4a0461_1
-runTest 0 $output shpc --settings-file $settings upgrade quay.io/biocontainers/samtools --dry-run
-runTest 0 $output shpc --settings-file $settings upgrade quay.io/biocontainers/samtools --force
-runTest 0 $output shpc --settings-file $settings upgrade --all --dry-run
-runTest 0 $output shpc --settings-file $settings upgrade --all --force
-
 echo
 echo "#### Testing get "
 runTest 0 $output shpc --settings-file $settings get --help