From d4f637386093dfd67c9669cb31d2f322628b3302 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Mon, 19 Sep 2022 21:39:51 +0100
Subject: [PATCH 01/18] shpc install now does a clean reinstallation

---
 shpc/client/__init__.py   |  2 +-
 shpc/main/modules/base.py | 18 ++++++++++++++++++
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/shpc/client/__init__.py b/shpc/client/__init__.py
index 4309ae47e..6fdc01b22 100644
--- a/shpc/client/__init__.py
+++ b/shpc/client/__init__.py
@@ -125,7 +125,7 @@ def get_parser():
         "--force",
         "-f",
         dest="force",
-        help="replace existing symlinks",
+        help="Go through the installation, deleting old files, replacing existing symlinks, etc.",
         default=False,
         action="store_true",
     )
diff --git a/shpc/main/modules/base.py b/shpc/main/modules/base.py
index 30b9b0b39..bf0575a0b 100644
--- a/shpc/main/modules/base.py
+++ b/shpc/main/modules/base.py
@@ -393,6 +393,24 @@ def install(
         # We always load overrides for an install
         module.load_override_file()
 
+        # Check previous installations of this module
+        installed_modules = self._get_module_lookup(
+            self.settings.module_base, self.modulefile, module.name
+        )
+        if (module.name in installed_modules) and (module.config.tag.name in installed_modules[module.name]):
+            if not force:
+                logger.exit(
+                    "%s:%s is already installed. Add --force to proceed with a reinstallation."
+                    % (module.name, module.config.tag.name)
+                )
+            logger.info("%s:%s is already installed. Reinstalling." % (module.name, module.config.tag.name))
+            # Don't explicitly remove the container, since we still need it,
+            # though it may still happen if shpc is configured to store
+            # containers and modules in the same directory
+            self._uninstall(
+                module.module_dir, self.settings.module_base, "$module_base/%s" % module.name
+            )
+
         # Create the module and container directory
         utils.mkdirp([module.module_dir, module.container_dir])
 

From 7d9aa90e0718458c60239c1abf91a50ca711040d Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Mon, 19 Sep 2022 23:21:31 +0100
Subject: [PATCH 02/18] Updated the tests

---
 shpc/tests/test_client.py | 40 +++++++++++++++++++++++++++++++++++++--
 1 file changed, 38 insertions(+), 2 deletions(-)

diff --git a/shpc/tests/test_client.py b/shpc/tests/test_client.py
index c1b3e31e8..27a1f93dd 100644
--- a/shpc/tests/test_client.py
+++ b/shpc/tests/test_client.py
@@ -51,8 +51,6 @@ def test_install_get(tmp_path, module_sys, module_file, container_tech, remote):
 
     assert client.get("python:3.9.2-alpine")
 
-    client.install("python:3.9.2-alpine")
-
 
 @pytest.mark.parametrize(
     "module_sys,module_file,remote",
@@ -377,3 +375,41 @@ def test_add(tmp_path, module_sys, remote):
         client.get("dinosaur/salad:latest")
     client.install("dinosaur/salad:latest")
     assert client.get("dinosaur/salad:latest")
+
+
+@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_reinstall(tmp_path, module_sys, module_file, container_tech, remote):
+    """
+    Test install and reinstall
+    """
+    client = init_client(str(tmp_path), module_sys, container_tech, remote=remote)
+
+    # Install known tag
+    client.install("python:3.9.2-alpine")
+    module_dir = os.path.join(client.settings.module_base, "python", "3.9.2-alpine")
+    env_file = os.path.join(module_dir, client.settings.environment_file)
+    dummy = os.path.join(module_dir, "dummy.sh")
+    # Ensure the content is initially as expected
+    assert os.path.exists(env_file)
+    assert not os.path.exists(dummy)
+    # Modify it
+    os.unlink(env_file)
+    shpc.utils.write_file(module_file, "")
+    assert not os.path.exists(env_file)
+    assert os.path.exists(dummy)
+    # The reinstallation should restore everything
+    client.install("python:3.9.2-alpine", force=True)
+    assert os.path.exists(env_file)
+    assert not os.path.exists(dummy)

From ea7627b230c4a09f02225ded730541e67f0eb918 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Mon, 19 Sep 2022 11:37:36 +0100
Subject: [PATCH 03/18] Function to find all the modules that can be upgraded

---
 shpc/main/modules/base.py | 44 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/shpc/main/modules/base.py b/shpc/main/modules/base.py
index bf0575a0b..8b0fffec8 100644
--- a/shpc/main/modules/base.py
+++ b/shpc/main/modules/base.py
@@ -458,3 +458,47 @@ def view_install(self, view_name, name, force=False, container_image=None):
         # Don't continue if it exists, unless force is True
         view.confirm_install(module.module_dir, force=force)
         view.install(module.module_dir)
+
+    def reinstall_all(self, pattern=False, force=False, **kwargs):
+        """
+        Reinstall (and possibly upgrade) all the current modules, possibly filtered by pattern.
+        """
+        modules = self._get_module_lookup(
+            self.settings.module_base, self.modulefile, pattern
+        )
+
+        # If we don't have modules, exit early
+        if not modules:
+            logger.exit("You don't have any install modules. Try shpc show.", 0)
+
+        unavailable_modules = False
+        for module_name, versions in modules.items():
+            result = self.registry.find(module_name)
+            if result:
+                valid_tags = container.ContainerConfig(result).tags
+                new_versions = set()
+                for version in versions:
+                    if version in valid_tags:
+                        new_versions.add(version)
+                    else:
+                        latest_version = valid_tags.latest.name
+                        if latest_version in versions:
+                            logger.info(
+                                "%s:%s is not available anymore. The latest version, %s, is already installed and will be reinstalled."
+                                % (module_name, version, latest_version)
+                            )
+                        else:
+                            logger.warning(
+                                "%s:%s is not available anymore. The latest version, %s, will be installed instead."
+                                % (module_name, version, valid_tags.latest.name)
+                            )
+                            new_versions.add(valid_tags.latest.name)
+                            unavailable_modules = True
+            else:
+                logger.warning(
+                    "%s is not available anymore and will be skipped" % module_name
+                )
+        if unavailable_modules and not force:
+            logger.exit(
+                "Some modules could not be found. Add --force to go through with the proposed upgrades."
+            )

From 4ceacf59c07bd5f454b003883871f375f899ac7c Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Sat, 1 Oct 2022 22:45:15 +0100
Subject: [PATCH 04/18] Skeleton for the reinstall and upgrade modes

---
 shpc/client/__init__.py   | 30 ++++++++++++++++++++++++++++++
 shpc/client/reinstall.py  | 37 +++++++++++++++++++++++++++++++++++++
 shpc/main/modules/base.py | 28 +++++++++++-----------------
 3 files changed, 78 insertions(+), 17 deletions(-)
 create mode 100644 shpc/client/reinstall.py

diff --git a/shpc/client/__init__.py b/shpc/client/__init__.py
index 6fdc01b22..d95ef4f5e 100644
--- a/shpc/client/__init__.py
+++ b/shpc/client/__init__.py
@@ -130,6 +130,33 @@ def get_parser():
         action="store_true",
     )
 
+    # Reinstall already installed recipes
+    reinstall = subparsers.add_parser(
+        "reinstall",
+        description="reinstall a recipe.",
+        formatter_class=argparse.RawTextHelpFormatter,
+    )
+    reinstall.add_argument(
+        "reinstall_recipe",
+        nargs="?",
+        help="recipe to reinstall\nshpc reinstall python\nshpc reinstall python:3.9.5-alpine",
+        default=None,
+    )
+    reinstall.add_argument(
+        "--all",
+        dest="all",
+        help="reinstall all currently installed modules.",
+        action="store_true",
+    )
+    reinstall.add_argument(
+        "--force",
+        "-f",
+        dest="force",
+        help="Ignore and leave intact the versions that don't exist in the registry anymore.",
+        default=False,
+        action="store_true",
+    )
+
     # List installed modules
     listing = subparsers.add_parser("list", description="list installed modules.")
     listing.add_argument("pattern", help="filter to a pattern", nargs="?")
@@ -372,6 +399,7 @@ def get_parser():
         inspect,
         install,
         listing,
+        reinstall,
         shell,
         test,
         uninstall,
@@ -491,6 +519,8 @@ def help(return_code=0):
         from .get import main
     elif args.command == "install":
         from .install import main
+    elif args.command == "reinstall":
+        from .reinstall import main
     elif args.command == "inspect":
         from .inspect import main
     elif args.command == "list":
diff --git a/shpc/client/reinstall.py b/shpc/client/reinstall.py
new file mode 100644
index 000000000..b9d4a555c
--- /dev/null
+++ b/shpc/client/reinstall.py
@@ -0,0 +1,37 @@
+__author__ = "Vanessa Sochat"
+__copyright__ = "Copyright 2021-2022, 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)
+
+    # It doesn't make sense to give a module name and --all
+    if args.reinstall_recipe and args.all:
+        logger.exit("Conflicting arguments reinstall_recipe and --all, choose one.")
+    # One option must be present
+    if not args.reinstall_recipe and not args.all:
+        logger.exit("Missing arguments: provide reinstall_recipe or --all.")
+
+    # And do the reinstall
+    cli.reinstall(
+        args.reinstall_recipe,
+        upgrade=False,
+        force=args.force,
+    )
diff --git a/shpc/main/modules/base.py b/shpc/main/modules/base.py
index 8b0fffec8..aa4f244d4 100644
--- a/shpc/main/modules/base.py
+++ b/shpc/main/modules/base.py
@@ -459,7 +459,7 @@ def view_install(self, view_name, name, force=False, container_image=None):
         view.confirm_install(module.module_dir, force=force)
         view.install(module.module_dir)
 
-    def reinstall_all(self, pattern=False, force=False, **kwargs):
+    def reinstall(self, pattern, upgrade=False, force=False, **kwargs):
         """
         Reinstall (and possibly upgrade) all the current modules, possibly filtered by pattern.
         """
@@ -477,28 +477,22 @@ def reinstall_all(self, pattern=False, force=False, **kwargs):
             if result:
                 valid_tags = container.ContainerConfig(result).tags
                 new_versions = set()
-                for version in versions:
-                    if version in valid_tags:
-                        new_versions.add(version)
-                    else:
-                        latest_version = valid_tags.latest.name
-                        if latest_version in versions:
-                            logger.info(
-                                "%s:%s is not available anymore. The latest version, %s, is already installed and will be reinstalled."
-                                % (module_name, version, latest_version)
-                            )
+                if upgrade:
+                    new_versions.add(valid_tags.latest.name)
+                else:
+                    for version in versions:
+                        if version in valid_tags:
+                            new_versions.add(version)
                         else:
                             logger.warning(
-                                "%s:%s is not available anymore. The latest version, %s, will be installed instead."
-                                % (module_name, version, valid_tags.latest.name)
+                                "%s:%s is not available anymore and will be skipped"
+                                % (module_name, version)
                             )
-                            new_versions.add(valid_tags.latest.name)
                             unavailable_modules = True
             else:
                 logger.warning(
                     "%s is not available anymore and will be skipped" % module_name
                 )
+                unavailable_modules = True
         if unavailable_modules and not force:
-            logger.exit(
-                "Some modules could not be found. Add --force to go through with the proposed upgrades."
-            )
+            logger.exit("Some modules could not be found. Add --force to proceed.")

From ae97aebf0b0044e2cbd22c60c009de3987b2b1c6 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Sat, 1 Oct 2022 23:33:10 +0100
Subject: [PATCH 05/18] First working version

---
 shpc/main/modules/base.py | 92 ++++++++++++++++++++++++++-------------
 1 file changed, 61 insertions(+), 31 deletions(-)

diff --git a/shpc/main/modules/base.py b/shpc/main/modules/base.py
index aa4f244d4..b21dc35a5 100644
--- a/shpc/main/modules/base.py
+++ b/shpc/main/modules/base.py
@@ -459,40 +459,70 @@ def view_install(self, view_name, name, force=False, container_image=None):
         view.confirm_install(module.module_dir, force=force)
         view.install(module.module_dir)
 
-    def reinstall(self, pattern, upgrade=False, force=False, **kwargs):
+    def reinstall(self, module_name, upgrade=False, force=False):
         """
         Reinstall (and possibly upgrade) all the current modules, possibly filtered by pattern.
         """
-        modules = self._get_module_lookup(
-            self.settings.module_base, self.modulefile, pattern
-        )
+        if module_name:
+            tag = None
+            if ":" in module_name:
+                module_name, tag = module_name.split(":", 1)
+            modules = self._get_module_lookup(
+                self.settings.module_base, self.modulefile, module_name
+            )
+            assert module_name in modules
+            self._reinstall(module_name, [tag] if tag else modules[module_name], upgrade=upgrade, force=force)
+        else:
+            modules = self._get_module_lookup(self.settings.module_base, self.modulefile)
+            for module_name, versions in modules.items():
+                self._reinstall(module_name, versions, upgrade=upgrade, force=force)
 
-        # If we don't have modules, exit early
-        if not modules:
-            logger.exit("You don't have any install modules. Try shpc show.", 0)
+    def _reinstall(self, module_name, versions, upgrade=False, force=False):
+        """
+        Reinstall (and possibly upgrade) all the current modules, possibly filtered by pattern.
+        """
+        result = self.registry.find(module_name)
+        if result:
+
+
+            valid_tags = container.ContainerConfig(result).tags
+            if upgrade:
+
+                views_with_module = set()
+                for version in versions:
+                    module_dir = os.path.join(self.settings.module_base, module_name, version)
+                    for view_name, entry in self.views.items():
+                        if entry.exists(module_dir):
+                            views_with_module.add(view_name)
+
+                latest = valid_tags.latest.name
+                self.install(module_name, tag=latest, view=None, force=True)
+                for view in views_with_module:
+                    self.views[view].install(module_dir)
+
+                for version in versions:
+                    if version != latest:
+                        self.uninstall(module_name + ":" + version, force=True)
 
-        unavailable_modules = False
-        for module_name, versions in modules.items():
-            result = self.registry.find(module_name)
-            if result:
-                valid_tags = container.ContainerConfig(result).tags
-                new_versions = set()
-                if upgrade:
-                    new_versions.add(valid_tags.latest.name)
-                else:
-                    for version in versions:
-                        if version in valid_tags:
-                            new_versions.add(version)
-                        else:
-                            logger.warning(
-                                "%s:%s is not available anymore and will be skipped"
-                                % (module_name, version)
-                            )
-                            unavailable_modules = True
             else:
-                logger.warning(
-                    "%s is not available anymore and will be skipped" % module_name
-                )
-                unavailable_modules = True
-        if unavailable_modules and not force:
-            logger.exit("Some modules could not be found. Add --force to proceed.")
+                for version in versions:
+                    if version in valid_tags:
+                        module_dir = os.path.join(self.settings.module_base, module_name, version)
+                        these_views = []
+                        # TODO: switch to .values()
+                        for view_name, entry in self.views.items():
+                            if entry.exists(module_dir):
+                                these_views.append(entry)
+                        self.install(module_name, tag=version, view=None, force=True)
+                        for view in these_views:
+                            view.install(module_dir)
+
+                    else:
+                        logger.warning(
+                            "%s:%s is not available anymore and will be skipped"
+                            % (module_name, version)
+                        )
+        else:
+            logger.warning(
+                "%s is not available anymore and will be skipped" % module_name
+            )

From 197c6d57c7d34a4c6ad4ede17001d2c365d4e6f2 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Sun, 16 Oct 2022 03:48:24 +0100
Subject: [PATCH 06/18] Restore initial explanation

---
 shpc/client/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/shpc/client/__init__.py b/shpc/client/__init__.py
index d95ef4f5e..2626dde2e 100644
--- a/shpc/client/__init__.py
+++ b/shpc/client/__init__.py
@@ -125,7 +125,7 @@ def get_parser():
         "--force",
         "-f",
         dest="force",
-        help="Go through the installation, deleting old files, replacing existing symlinks, etc.",
+        help="replace existing symlinks",
         default=False,
         action="store_true",
     )

From 7e90d75169911a348deee007f02be5ccb9457cfb Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Sun, 16 Oct 2022 03:49:06 +0100
Subject: [PATCH 07/18] The --force argument is not used for core installations

---
 shpc/client/install.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/shpc/client/install.py b/shpc/client/install.py
index 57aca791f..d2d3de563 100644
--- a/shpc/client/install.py
+++ b/shpc/client/install.py
@@ -27,7 +27,6 @@ def main(args, parser, extra, subparser):
     # And do the install
     cli.install(
         args.install_recipe,
-        force=args.force,
         container_image=args.container_image,
         keep_path=args.keep_path,
     )

From 11a44936e92b506b50e74b5cd26c0e98c1dc3f90 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Sun, 16 Oct 2022 03:50:39 +0100
Subject: [PATCH 08/18] Much simpler implementation

---
 shpc/main/modules/base.py | 17 +++++------------
 1 file changed, 5 insertions(+), 12 deletions(-)

diff --git a/shpc/main/modules/base.py b/shpc/main/modules/base.py
index b21dc35a5..ab69792f6 100644
--- a/shpc/main/modules/base.py
+++ b/shpc/main/modules/base.py
@@ -375,7 +375,7 @@ def get_module(self, name, container_image=None, keep_path=False):
         return module
 
     def install(
-        self, name, force=False, container_image=None, keep_path=False, **kwargs
+        self, name, allow_reinstall=False, container_image=None, keep_path=False, **kwargs
     ):
         """
         Given a unique resource identifier, install a recipe.
@@ -383,7 +383,6 @@ def install(
         For lmod, this means creating a subfolder in modules, pulling the
         container to it, and writing a module file there. We've already
         grabbed the name from docker (which is currently the only supported).
-        "force" is currently not used.
         """
         # Create a new module
         module = self.get_module(
@@ -394,16 +393,10 @@ def install(
         module.load_override_file()
 
         # Check previous installations of this module
-        installed_modules = self._get_module_lookup(
-            self.settings.module_base, self.modulefile, module.name
-        )
-        if (module.name in installed_modules) and (module.config.tag.name in installed_modules[module.name]):
-            if not force:
-                logger.exit(
-                    "%s:%s is already installed. Add --force to proceed with a reinstallation."
-                    % (module.name, module.config.tag.name)
-                )
-            logger.info("%s:%s is already installed. Reinstalling." % (module.name, module.config.tag.name))
+        if os.path.exists(module.module_dir):
+            if not allow_reinstall:
+                logger.exit("%s is already installed. Do `shpc reinstall` to proceed with a reinstallation." % module.tagged_name)
+            logger.info("%s is already installed. Reinstalling." % module.tagged_name)
             # Don't explicitly remove the container, since we still need it,
             # though it may still happen if shpc is configured to store
             # containers and modules in the same directory

From aa93eedfe5fa75aceeae53c208f1e11a5e257eff Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Sun, 16 Oct 2022 03:52:09 +0100
Subject: [PATCH 09/18] Call install

---
 shpc/main/modules/base.py | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/shpc/main/modules/base.py b/shpc/main/modules/base.py
index ab69792f6..b9448b109 100644
--- a/shpc/main/modules/base.py
+++ b/shpc/main/modules/base.py
@@ -452,23 +452,27 @@ def view_install(self, view_name, name, force=False, container_image=None):
         view.confirm_install(module.module_dir, force=force)
         view.install(module.module_dir)
 
-    def reinstall(self, module_name, upgrade=False, force=False):
+    def reinstall(self, module_name, force=False):
         """
-        Reinstall (and possibly upgrade) all the current modules, possibly filtered by pattern.
+        Reinstall the module, or all modules
         """
         if module_name:
-            tag = None
             if ":" in module_name:
                 module_name, tag = module_name.split(":", 1)
-            modules = self._get_module_lookup(
-                self.settings.module_base, self.modulefile, module_name
-            )
-            assert module_name in modules
-            self._reinstall(module_name, [tag] if tag else modules[module_name], upgrade=upgrade, force=force)
+                self.install(module_name, tag=tag, allow_reinstall=True, force=force)
+            else:
+                modules = self._get_module_lookup(
+                    self.settings.module_base, self.modulefile, module_name
+                )
+                if module_name not in modules:
+                    logger.exit("%s is not installed. Nothing to reinstall." % module_name)
+                for version in modules[module_name]:
+                    self.install(module_name, tag=version, allow_reinstall=True, force=force)
         else:
             modules = self._get_module_lookup(self.settings.module_base, self.modulefile)
             for module_name, versions in modules.items():
-                self._reinstall(module_name, versions, upgrade=upgrade, force=force)
+                for version in versions:
+                    self.install(module_name, tag=version, allow_reinstall=True, force=force)
 
     def _reinstall(self, module_name, versions, upgrade=False, force=False):
         """

From d1cf57d676fab4a0c2bf016573e785aa81028ff3 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Sun, 6 Nov 2022 22:49:23 +0000
Subject: [PATCH 10/18] Upgrade the code to the latest pre-commit requirements

---
 shpc/main/modules/base.py | 42 +++++++++++++++++++++++++++++----------
 1 file changed, 32 insertions(+), 10 deletions(-)

diff --git a/shpc/main/modules/base.py b/shpc/main/modules/base.py
index b9448b109..bb9ad2dc4 100644
--- a/shpc/main/modules/base.py
+++ b/shpc/main/modules/base.py
@@ -375,7 +375,12 @@ def get_module(self, name, container_image=None, keep_path=False):
         return module
 
     def install(
-        self, name, allow_reinstall=False, container_image=None, keep_path=False, **kwargs
+        self,
+        name,
+        allow_reinstall=False,
+        container_image=None,
+        keep_path=False,
+        **kwargs
     ):
         """
         Given a unique resource identifier, install a recipe.
@@ -395,13 +400,18 @@ def install(
         # Check previous installations of this module
         if os.path.exists(module.module_dir):
             if not allow_reinstall:
-                logger.exit("%s is already installed. Do `shpc reinstall` to proceed with a reinstallation." % module.tagged_name)
+                logger.exit(
+                    "%s is already installed. Do `shpc reinstall` to proceed with a reinstallation."
+                    % module.tagged_name
+                )
             logger.info("%s is already installed. Reinstalling." % module.tagged_name)
             # Don't explicitly remove the container, since we still need it,
             # though it may still happen if shpc is configured to store
             # containers and modules in the same directory
             self._uninstall(
-                module.module_dir, self.settings.module_base, "$module_base/%s" % module.name
+                module.module_dir,
+                self.settings.module_base,
+                "$module_base/%s" % module.name,
             )
 
         # Create the module and container directory
@@ -465,14 +475,22 @@ def reinstall(self, module_name, force=False):
                     self.settings.module_base, self.modulefile, module_name
                 )
                 if module_name not in modules:
-                    logger.exit("%s is not installed. Nothing to reinstall." % module_name)
+                    logger.exit(
+                        "%s is not installed. Nothing to reinstall." % module_name
+                    )
                 for version in modules[module_name]:
-                    self.install(module_name, tag=version, allow_reinstall=True, force=force)
+                    self.install(
+                        module_name, tag=version, allow_reinstall=True, force=force
+                    )
         else:
-            modules = self._get_module_lookup(self.settings.module_base, self.modulefile)
+            modules = self._get_module_lookup(
+                self.settings.module_base, self.modulefile
+            )
             for module_name, versions in modules.items():
                 for version in versions:
-                    self.install(module_name, tag=version, allow_reinstall=True, force=force)
+                    self.install(
+                        module_name, tag=version, allow_reinstall=True, force=force
+                    )
 
     def _reinstall(self, module_name, versions, upgrade=False, force=False):
         """
@@ -481,13 +499,14 @@ def _reinstall(self, module_name, versions, upgrade=False, force=False):
         result = self.registry.find(module_name)
         if result:
 
-
             valid_tags = container.ContainerConfig(result).tags
             if upgrade:
 
                 views_with_module = set()
                 for version in versions:
-                    module_dir = os.path.join(self.settings.module_base, module_name, version)
+                    module_dir = os.path.join(
+                        self.settings.module_base, module_name, version
+                    )
                     for view_name, entry in self.views.items():
                         if entry.exists(module_dir):
                             views_with_module.add(view_name)
@@ -504,7 +523,9 @@ def _reinstall(self, module_name, versions, upgrade=False, force=False):
             else:
                 for version in versions:
                     if version in valid_tags:
-                        module_dir = os.path.join(self.settings.module_base, module_name, version)
+                        module_dir = os.path.join(
+                            self.settings.module_base, module_name, version
+                        )
                         these_views = []
                         # TODO: switch to .values()
                         for view_name, entry in self.views.items():
@@ -519,6 +540,7 @@ def _reinstall(self, module_name, versions, upgrade=False, force=False):
                             "%s:%s is not available anymore and will be skipped"
                             % (module_name, version)
                         )
+
         else:
             logger.warning(
                 "%s is not available anymore and will be skipped" % module_name

From b936038189172f6572827007df85a3d44f15f23e Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Sun, 6 Nov 2022 22:52:32 +0000
Subject: [PATCH 11/18] Synchronised with the latest version of install

---
 shpc/main/modules/base.py | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

diff --git a/shpc/main/modules/base.py b/shpc/main/modules/base.py
index bb9ad2dc4..6891deb5a 100644
--- a/shpc/main/modules/base.py
+++ b/shpc/main/modules/base.py
@@ -468,8 +468,7 @@ def reinstall(self, module_name, force=False):
         """
         if module_name:
             if ":" in module_name:
-                module_name, tag = module_name.split(":", 1)
-                self.install(module_name, tag=tag, allow_reinstall=True, force=force)
+                self.install(module_name, allow_reinstall=True)
             else:
                 modules = self._get_module_lookup(
                     self.settings.module_base, self.modulefile, module_name
@@ -479,18 +478,14 @@ def reinstall(self, module_name, force=False):
                         "%s is not installed. Nothing to reinstall." % module_name
                     )
                 for version in modules[module_name]:
-                    self.install(
-                        module_name, tag=version, allow_reinstall=True, force=force
-                    )
+                    self.install(module_name + ":" + version, allow_reinstall=True)
         else:
             modules = self._get_module_lookup(
                 self.settings.module_base, self.modulefile
             )
             for module_name, versions in modules.items():
                 for version in versions:
-                    self.install(
-                        module_name, tag=version, allow_reinstall=True, force=force
-                    )
+                    self.install(module_name + ":" + version, allow_reinstall=True)
 
     def _reinstall(self, module_name, versions, upgrade=False, force=False):
         """
@@ -511,13 +506,12 @@ def _reinstall(self, module_name, versions, upgrade=False, force=False):
                         if entry.exists(module_dir):
                             views_with_module.add(view_name)
 
-                latest = valid_tags.latest.name
-                self.install(module_name, tag=latest, view=None, force=True)
+                self.install(module_name, allow_reinstall=True)
                 for view in views_with_module:
                     self.views[view].install(module_dir)
 
                 for version in versions:
-                    if version != latest:
+                    if version != valid_tags.latest.name:
                         self.uninstall(module_name + ":" + version, force=True)
 
             else:
@@ -531,7 +525,7 @@ def _reinstall(self, module_name, versions, upgrade=False, force=False):
                         for view_name, entry in self.views.items():
                             if entry.exists(module_dir):
                                 these_views.append(entry)
-                        self.install(module_name, tag=version, view=None, force=True)
+                        self.install(module_name + ":" + version, allow_reinstall=True)
                         for view in these_views:
                             view.install(module_dir)
 

From 6173ee66288a30d6e18d29369ede89ba0efb8579 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Sun, 6 Nov 2022 23:18:39 +0000
Subject: [PATCH 12/18] Currently not in use

---
 shpc/client/reinstall.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/shpc/client/reinstall.py b/shpc/client/reinstall.py
index b9d4a555c..cae9fcb57 100644
--- a/shpc/client/reinstall.py
+++ b/shpc/client/reinstall.py
@@ -32,6 +32,5 @@ def main(args, parser, extra, subparser):
     # And do the reinstall
     cli.reinstall(
         args.reinstall_recipe,
-        upgrade=False,
         force=args.force,
     )

From 562bb5f45a561dd7c153862fdb3f6036fe110f57 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Sun, 6 Nov 2022 23:18:51 +0000
Subject: [PATCH 13/18] More comments

---
 shpc/main/modules/base.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/shpc/main/modules/base.py b/shpc/main/modules/base.py
index 6891deb5a..b909f22c9 100644
--- a/shpc/main/modules/base.py
+++ b/shpc/main/modules/base.py
@@ -468,8 +468,10 @@ def reinstall(self, module_name, force=False):
         """
         if module_name:
             if ":" in module_name:
+                # Reinstall this one version
                 self.install(module_name, allow_reinstall=True)
             else:
+                # Find all the versions currently installed
                 modules = self._get_module_lookup(
                     self.settings.module_base, self.modulefile, module_name
                 )
@@ -477,9 +479,11 @@ def reinstall(self, module_name, force=False):
                     logger.exit(
                         "%s is not installed. Nothing to reinstall." % module_name
                     )
+                # Reinstall them one by one
                 for version in modules[module_name]:
                     self.install(module_name + ":" + version, allow_reinstall=True)
         else:
+            # Reinstall everything that is currently installed
             modules = self._get_module_lookup(
                 self.settings.module_base, self.modulefile
             )

From 8d637f49abdc856f86bb41d67b949fea3c78535c Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Sun, 6 Nov 2022 23:34:27 +0000
Subject: [PATCH 14/18] Completed the bulk of reinstall

---
 shpc/main/modules/base.py | 36 +++++++++++++++++-------------------
 1 file changed, 17 insertions(+), 19 deletions(-)

diff --git a/shpc/main/modules/base.py b/shpc/main/modules/base.py
index b909f22c9..78de5bf5d 100644
--- a/shpc/main/modules/base.py
+++ b/shpc/main/modules/base.py
@@ -462,32 +462,30 @@ def view_install(self, view_name, name, force=False, container_image=None):
         view.confirm_install(module.module_dir, force=force)
         view.install(module.module_dir)
 
-    def reinstall(self, module_name, force=False):
+    def reinstall(self, module, force=False):
         """
         Reinstall the module, or all modules
         """
-        if module_name:
-            if ":" in module_name:
-                # Reinstall this one version
-                self.install(module_name, allow_reinstall=True)
-            else:
-                # Find all the versions currently installed
-                modules = self._get_module_lookup(
-                    self.settings.module_base, self.modulefile, module_name
-                )
-                if module_name not in modules:
-                    logger.exit(
-                        "%s is not installed. Nothing to reinstall." % module_name
-                    )
-                # Reinstall them one by one
-                for version in modules[module_name]:
-                    self.install(module_name + ":" + version, allow_reinstall=True)
+        if module:
+            module_name, _, version = module.partition(":")
+            # Find all the versions currently installed
+            installed_modules = self._get_module_lookup(
+                self.settings.module_base, self.modulefile, module_name
+            )
+            if (module_name not in installed_modules) or (
+                version and version not in installed_modules[module_name]
+            ):
+                logger.exit("%s is not installed. Nothing to reinstall." % module)
+            versions = [version] if version else installed_modules[module_name]
+            # Reinstall the required version(s) one by one
+            for version in versions:
+                self.install(module_name + ":" + version, allow_reinstall=True)
         else:
             # Reinstall everything that is currently installed
-            modules = self._get_module_lookup(
+            installed_modules = self._get_module_lookup(
                 self.settings.module_base, self.modulefile
             )
-            for module_name, versions in modules.items():
+            for module_name, versions in installed_modules.items():
                 for version in versions:
                     self.install(module_name + ":" + version, allow_reinstall=True)
 

From 0048c1783624d1795d0b8af0604eecbd8ba1dfc9 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Mon, 7 Nov 2022 00:00:01 +0000
Subject: [PATCH 15/18] Not used

---
 shpc/client/install.py    | 1 -
 shpc/main/modules/base.py | 4 ++--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/shpc/client/install.py b/shpc/client/install.py
index d2d3de563..fd0e65d6d 100644
--- a/shpc/client/install.py
+++ b/shpc/client/install.py
@@ -35,5 +35,4 @@ def main(args, parser, extra, subparser):
             cli.settings.default_view,
             args.install_recipe,
             force=args.force,
-            container_image=args.container_image,
         )
diff --git a/shpc/main/modules/base.py b/shpc/main/modules/base.py
index 78de5bf5d..c534c92d9 100644
--- a/shpc/main/modules/base.py
+++ b/shpc/main/modules/base.py
@@ -442,12 +442,12 @@ def install(
         logger.info("Module %s was created." % module.tagged_name)
         return module.container_path
 
-    def view_install(self, view_name, name, force=False, container_image=None):
+    def view_install(self, view_name, name, force=False):
         """
         Install a module in a view. The module must already be installed.
         Set "force" to True to allow overwriting existing symlinks.
         """
-        module = self.get_module(name, container_image=container_image)
+        module = self.get_module(name)
 
         # A view is a symlink under views_base/$view/$module
         if view_name not in self.views:

From c70eb850160e1be94c03438aa0274f1f0c990641 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Mon, 7 Nov 2022 00:22:46 +0000
Subject: [PATCH 16/18] Implemented --ignore-missing and --uninstall-missing

---
 shpc/client/__init__.py   | 14 +++++++++++---
 shpc/client/reinstall.py  | 12 +++++++++++-
 shpc/main/modules/base.py | 28 +++++++++++++++++++++-------
 3 files changed, 43 insertions(+), 11 deletions(-)

diff --git a/shpc/client/__init__.py b/shpc/client/__init__.py
index 2626dde2e..6844ea3dc 100644
--- a/shpc/client/__init__.py
+++ b/shpc/client/__init__.py
@@ -149,13 +149,21 @@ def get_parser():
         action="store_true",
     )
     reinstall.add_argument(
-        "--force",
-        "-f",
-        dest="force",
+        "--ignore-missing",
+        "-i",
+        dest="ignore_missing",
         help="Ignore and leave intact the versions that don't exist in the registry anymore.",
         default=False,
         action="store_true",
     )
+    reinstall.add_argument(
+        "--uninstall-missing",
+        "-u",
+        dest="uninstall_missing",
+        help="Uninstall the versions that don't exist in the registry anymore.",
+        default=False,
+        action="store_true",
+    )
 
     # List installed modules
     listing = subparsers.add_parser("list", description="list installed modules.")
diff --git a/shpc/client/reinstall.py b/shpc/client/reinstall.py
index cae9fcb57..d0187ecfa 100644
--- a/shpc/client/reinstall.py
+++ b/shpc/client/reinstall.py
@@ -28,9 +28,19 @@ def main(args, parser, extra, subparser):
     # One option must be present
     if not args.reinstall_recipe and not args.all:
         logger.exit("Missing arguments: provide reinstall_recipe or --all.")
+    if args.ignore_missing and args.uninstall_missing:
+        logger.exit(
+            "Conflicting arguments --ignore-missing and --uninstall-missing, choose one."
+        )
 
     # And do the reinstall
     cli.reinstall(
         args.reinstall_recipe,
-        force=args.force,
+        when_missing=(
+            "ignore"
+            if args.ignore_missing
+            else "uninstall"
+            if args.uninstall_missing
+            else None
+        ),
     )
diff --git a/shpc/main/modules/base.py b/shpc/main/modules/base.py
index c534c92d9..44fd95d56 100644
--- a/shpc/main/modules/base.py
+++ b/shpc/main/modules/base.py
@@ -462,12 +462,12 @@ def view_install(self, view_name, name, force=False):
         view.confirm_install(module.module_dir, force=force)
         view.install(module.module_dir)
 
-    def reinstall(self, module, force=False):
+    def reinstall(self, name, when_missing=None):
         """
         Reinstall the module, or all modules
         """
-        if module:
-            module_name, _, version = module.partition(":")
+        if name:
+            module_name, _, version = name.partition(":")
             # Find all the versions currently installed
             installed_modules = self._get_module_lookup(
                 self.settings.module_base, self.modulefile, module_name
@@ -475,11 +475,11 @@ def reinstall(self, module, force=False):
             if (module_name not in installed_modules) or (
                 version and version not in installed_modules[module_name]
             ):
-                logger.exit("%s is not installed. Nothing to reinstall." % module)
+                logger.exit("%s is not installed. Nothing to reinstall." % name)
             versions = [version] if version else installed_modules[module_name]
             # Reinstall the required version(s) one by one
             for version in versions:
-                self.install(module_name + ":" + version, allow_reinstall=True)
+                self._reinstall(module_name, version, when_missing)
         else:
             # Reinstall everything that is currently installed
             installed_modules = self._get_module_lookup(
@@ -487,12 +487,26 @@ def reinstall(self, module, force=False):
             )
             for module_name, versions in installed_modules.items():
                 for version in versions:
-                    self.install(module_name + ":" + version, allow_reinstall=True)
+                    self._reinstall(module_name, version, when_missing)
 
-    def _reinstall(self, module_name, versions, upgrade=False, force=False):
+    def _reinstall(self, module_name, version, when_missing):
         """
         Reinstall (and possibly upgrade) all the current modules, possibly filtered by pattern.
         """
+        config = self.load_registry_config(module_name)
+        if version in config.tags:
+            self.install(module_name + ":" + version, allow_reinstall=True)
+        elif when_missing == "ignore":
+            pass
+        elif when_missing == "uninstall":
+            self.uninstall(module_name + ":" + version, force=True)
+        else:
+            logger.exit(
+                "%s is not in the Registry any more. Add --uninstall-missing or --ignore-missing."
+                % module_name
+            )
+
+    def _upgrade(self, module_name, versions, upgrade=False, force=False):
         result = self.registry.find(module_name)
         if result:
 

From a82ff27a2bc0a436cae5e1e6249af047cd9b4699 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Mon, 7 Nov 2022 01:08:55 +0000
Subject: [PATCH 17/18] Do the checks at the tool level as well

---
 shpc/main/modules/base.py | 27 +++++++++++++++++++--------
 1 file changed, 19 insertions(+), 8 deletions(-)

diff --git a/shpc/main/modules/base.py b/shpc/main/modules/base.py
index 44fd95d56..817de3e78 100644
--- a/shpc/main/modules/base.py
+++ b/shpc/main/modules/base.py
@@ -493,17 +493,28 @@ def _reinstall(self, module_name, version, when_missing):
         """
         Reinstall (and possibly upgrade) all the current modules, possibly filtered by pattern.
         """
-        config = self.load_registry_config(module_name)
-        if version in config.tags:
-            self.install(module_name + ":" + version, allow_reinstall=True)
-        elif when_missing == "ignore":
-            pass
-        elif when_missing == "uninstall":
-            self.uninstall(module_name + ":" + version, force=True)
+        result = self.registry.find(module_name)
+        if result:
+            config = container.ContainerConfig(result)
+            if version in config.tags:
+                return self.install(module_name + ":" + version, allow_reinstall=True)
+            else:
+                missing = module_name + ":" + version
+        else:
+            missing = module_name
+
+        if when_missing:
+            if when_missing == "ignore":
+                logger.info(
+                    "%s is not in the Registry any more. Ignoring as instructed."
+                    % missing
+                )
+            elif when_missing == "uninstall":
+                self.uninstall(module_name + ":" + version, force=True)
         else:
             logger.exit(
                 "%s is not in the Registry any more. Add --uninstall-missing or --ignore-missing."
-                % module_name
+                % missing
             )
 
     def _upgrade(self, module_name, versions, upgrade=False, force=False):

From 04b5b3154a511953ab95742af3f6166c1207f625 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Wed, 9 Nov 2022 04:28:10 +0000
Subject: [PATCH 18/18] Not needed anymore

---
 shpc/main/modules/base.py | 50 ---------------------------------------
 1 file changed, 50 deletions(-)

diff --git a/shpc/main/modules/base.py b/shpc/main/modules/base.py
index 817de3e78..a468799a8 100644
--- a/shpc/main/modules/base.py
+++ b/shpc/main/modules/base.py
@@ -516,53 +516,3 @@ def _reinstall(self, module_name, version, when_missing):
                 "%s is not in the Registry any more. Add --uninstall-missing or --ignore-missing."
                 % missing
             )
-
-    def _upgrade(self, module_name, versions, upgrade=False, force=False):
-        result = self.registry.find(module_name)
-        if result:
-
-            valid_tags = container.ContainerConfig(result).tags
-            if upgrade:
-
-                views_with_module = set()
-                for version in versions:
-                    module_dir = os.path.join(
-                        self.settings.module_base, module_name, version
-                    )
-                    for view_name, entry in self.views.items():
-                        if entry.exists(module_dir):
-                            views_with_module.add(view_name)
-
-                self.install(module_name, allow_reinstall=True)
-                for view in views_with_module:
-                    self.views[view].install(module_dir)
-
-                for version in versions:
-                    if version != valid_tags.latest.name:
-                        self.uninstall(module_name + ":" + version, force=True)
-
-            else:
-                for version in versions:
-                    if version in valid_tags:
-                        module_dir = os.path.join(
-                            self.settings.module_base, module_name, version
-                        )
-                        these_views = []
-                        # TODO: switch to .values()
-                        for view_name, entry in self.views.items():
-                            if entry.exists(module_dir):
-                                these_views.append(entry)
-                        self.install(module_name + ":" + version, allow_reinstall=True)
-                        for view in these_views:
-                            view.install(module_dir)
-
-                    else:
-                        logger.warning(
-                            "%s:%s is not available anymore and will be skipped"
-                            % (module_name, version)
-                        )
-
-        else:
-            logger.warning(
-                "%s is not available anymore and will be skipped" % module_name
-            )