vantage6 5.0.0a36__tar.gz → 5.0.0a38__tar.gz

{vantage6-5.0.0a36 → vantage6-5.0.0a38}/.gitignore

@@ -30,4 +30,7 @@ dev/.tasks/
 dev/.db/
 
 # Helm
-charts/**/*.tgz
+charts/**/*.tgz
+
+# MacOS
+.DS_Store

{vantage6-5.0.0a36 → vantage6-5.0.0a38}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vantage6
-Version: 5.0.0a36
+Version: 5.0.0a38
 Summary: vantage6 command line interface
 Author: Vantage6 Team
 Maintainer-email: Frank Martin <f.martin@iknl.nl>, Bart van Beusekom <b.vanbeusekom@iknl.nl>
@@ -14,12 +14,12 @@ Requires-Dist: ipython==8.10.0
 Requires-Dist: jinja2==3.1.6
 Requires-Dist: kubernetes==28.1.0
 Requires-Dist: pandas>=2.2.3
-Requires-Dist: questionary==1.10.0
+Requires-Dist: questionary==2.1.1
 Requires-Dist: rich==13.5.2
 Requires-Dist: schema==0.7.5
 Requires-Dist: sqlalchemy==2.0.37
-Requires-Dist: vantage6-client==5.0.0a36
-Requires-Dist: vantage6-common==5.0.0a36
+Requires-Dist: vantage6-client==5.0.0a38
+Requires-Dist: vantage6-common==5.0.0a38
 Provides-Extra: dev
 Requires-Dist: black; extra == 'dev'
 Requires-Dist: coverage==7.10.2; extra == 'dev'

{vantage6-5.0.0a36 → vantage6-5.0.0a38}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "vantage6"
-version = "5.0.0a36"
+version = "5.0.0a38"
 description = "vantage6 command line interface"
 readme = "README.md"
 license = {text = "MIT"}
@@ -25,12 +25,12 @@ dependencies = [
     "jinja2==3.1.6",
     "kubernetes==28.1.0",
     "pandas>=2.2.3",
-    "questionary==1.10.0",
+    "questionary==2.1.1",
     "rich==13.5.2",
     "schema==0.7.5",
     "sqlalchemy==2.0.37",
-    "vantage6-common==5.0.0a36",
-    "vantage6-client==5.0.0a36",
+    "vantage6-common==5.0.0a38",
+    "vantage6-client==5.0.0a38",
 ]
 
 [project.optional-dependencies]
@@ -54,13 +54,12 @@ where = ["vantage6/cli"]
 
 [tool.setuptools.package-data]
 "vantage6/cli/" = [
-    "rabbimq/rabbitmq.config",
     "template/node_config.j2",
     "template/node_config_nonk8s.j2",
     "template/server_config.j2",
     "template/algo_store_config.j2",
     "template/auth_config.j2",
-    "dev/data/olympic_athletes_2016.csv",
-    "dev/data/km_dataset.csv",
+    "sandbox/data/olympic_athletes_2016.csv",
+    "sandbox/data/km_dataset.csv",
     "prometheus/prometheus.yml",
 ]

{vantage6-5.0.0a36 → vantage6-5.0.0a38}/tests_cli/test_node_cli.py

@@ -9,7 +9,7 @@ from unittest.mock import MagicMock, patch
 from click.testing import CliRunner
 
 from vantage6.common import STRING_ENCODING
-from vantage6.common.globals import Ports
+from vantage6.common.globals import LOCALHOST, Ports
 
 from vantage6.cli.common.utils import print_log_worker
 from vantage6.cli.globals import APPNAME
@@ -84,14 +84,14 @@ class NodeCLITest(unittest.TestCase):
             "-----------------------------------------------------\n",
         )
 
-    @patch("vantage6.cli.node.new.configuration_wizard")
+    @patch("vantage6.cli.node.new.make_configuration")
     @patch("vantage6.cli.node.new.ensure_config_dir_writable")
     @patch("vantage6.cli.node.common.NodeContext")
-    def test_new_config(self, context, permissions, wizard):
+    def test_new_config(self, context, permissions, make_configuration):
         """No error produced when creating new configuration."""
         context.config_exists.return_value = False
         permissions.return_value = True
-        wizard.return_value = "/some/file/path"
+        make_configuration.return_value = "/some/file/path"
 
         runner = CliRunner()
         result = runner.invoke(
@@ -108,8 +108,8 @@ class NodeCLITest(unittest.TestCase):
         # check OK exit code
         self.assertEqual(result.exit_code, 0)
 
-    @patch("vantage6.cli.node.new.configuration_wizard")
-    def test_new_config_replace_whitespace_in_name(self, _):
+    @patch("vantage6.cli.node.new.make_configuration")
+    def test_new_config_replace_whitespace_in_name(self, make_configuration):
         """Whitespaces are replaced in the name."""
 
         runner = CliRunner()
@@ -172,7 +172,7 @@ class NodeCLITest(unittest.TestCase):
 
     @patch("vantage6.cli.node.common.NodeContext")
     @patch("vantage6.cli.node.files.NodeContext")
-    @patch("vantage6.cli.node.common.select_configuration_questionaire")
+    @patch("vantage6.cli.node.common.select_configuration_questionnaire")
     def test_files(self, select_config, context, common_context):
         """No errors produced when retrieving filepaths."""
 
@@ -382,7 +382,7 @@ class NodeCLITest(unittest.TestCase):
     def test_client(self, client, error, debug, info):
         ctx = MagicMock(
             config={
-                "server_url": "localhost",
+                "server_url": LOCALHOST,
                 "port": Ports.DEV_SERVER.value,
                 "api_path": "",
             }

{vantage6-5.0.0a36 → vantage6-5.0.0a38}/tests_cli/test_server_cli.py

@@ -113,15 +113,15 @@ class ServerCLITest(unittest.TestCase):
         self.assertIsNone(result.exception)
         self.assertEqual(result.exit_code, 0)
 
-    @patch("vantage6.cli.server.new.configuration_wizard")
+    @patch("vantage6.cli.server.new.make_configuration")
     @patch("vantage6.cli.server.new.ensure_config_dir_writable")
     @patch("vantage6.cli.server.new.ServerContext")
-    def test_new(self, context, permissions, wizard):
+    def test_new(self, context, permissions, make_configuration):
         """New configuration without errors."""
 
         context.config_exists.return_value = False
         permissions.return_value = True
-        wizard.return_value = "/some/file.yaml"
+        make_configuration.return_value = "/some/file.yaml"
 
         runner = CliRunner()
         result = runner.invoke(cli_server_new, ["--name", "iknl"])

{vantage6-5.0.0a36 → vantage6-5.0.0a38}/tests_cli/test_wizard.py

@@ -4,14 +4,14 @@ from unittest.mock import MagicMock, patch
 
 from vantage6.common.globals import InstanceType, NodePolicy
 
-from vantage6.cli.configuration_wizard import (
-    configuration_wizard,
+from vantage6.cli.configuration_create import (
+    make_configuration,
     node_configuration_questionaire,
-    select_configuration_questionaire,
+    select_configuration_questionnaire,
     server_configuration_questionaire,
 )
 
-module_path = "vantage6.cli.configuration_wizard"
+module_path = "vantage6.cli.configuration_create"
 
 
 class WizardTest(unittest.TestCase):
@@ -29,7 +29,7 @@ class WizardTest(unittest.TestCase):
                     result[name] = None
         return result
 
-    @patch("vantage6.cli.configuration_wizard.NodeClient.authenticate")
+    @patch("vantage6.cli.configuration_create.NodeClient.authenticate")
     def test_node_wizard(self, authenticate):
         """An error is printed when docker is not running"""
         authenticate.return_value = None
@@ -115,19 +115,19 @@ class WizardTest(unittest.TestCase):
     @patch(f"{module_path}.server_configuration_questionaire")
     @patch(f"{module_path}.ServerConfigurationManager")
     @patch(f"{module_path}.NodeConfigurationManager")
-    @patch("vantage6.cli.configuration_wizard.AppContext")
-    def test_configuration_wizard_interface(
+    @patch("vantage6.cli.configuration_create.AppContext")
+    def test_configuration_create_interface(
         self, context, node_m, server_m, server_q, node_q
     ):
         context.instance_folders.return_value = {"config": "/some/path/"}
 
-        file_ = configuration_wizard(InstanceType.NODE, "vtg6", False)
+        file_ = make_configuration(InstanceType.NODE, "vtg6", False)
         self.assertEqual(Path("/some/path/vtg6.yaml"), file_)
 
-        file_ = configuration_wizard(InstanceType.SERVER, "vtg6", True)
+        file_ = make_configuration(InstanceType.SERVER, "vtg6", True)
         self.assertEqual(Path("/some/path/vtg6.yaml"), file_)
 
-    @patch("vantage6.cli.configuration_wizard.AppContext.available_configurations")
+    @patch("vantage6.cli.configuration_create.AppContext.available_configurations")
     def test_select_configuration(self, available_configurations):
         config = MagicMock()
         config.name = "vtg6"
@@ -136,6 +136,6 @@ class WizardTest(unittest.TestCase):
 
         with patch(f"{module_path}.q") as q:
             q.select.return_value.unsafe_ask.return_value = "vtg6"
-            name = select_configuration_questionaire(InstanceType.NODE, True)
+            name = select_configuration_questionnaire(InstanceType.NODE, True)
 
         self.assertEqual(name, "vtg6")

{vantage6-5.0.0a36 → vantage6-5.0.0a38}/vantage6/cli/algorithm/generate_algorithm_json.py

@@ -215,7 +215,6 @@ class Function:
                 "display_name": self._pretty_print_name(name),
                 "description": self._extract_parameter_description(name),
                 "type": type_.value if type_ else None,
-                "required": param.default == inspect.Parameter.empty,
                 "has_default_value": param.default != inspect.Parameter.empty,
                 "is_frontend_only": False,
             }

vantage6-5.0.0a38/vantage6/cli/algostore/attach.py

@@ -0,0 +1,39 @@
+import click
+
+from vantage6.common import info
+
+from vantage6.cli.common.attach import attach_logs
+from vantage6.cli.context import InstanceType
+from vantage6.cli.globals import InfraComponentName
+
+
+@click.command()
+@click.option("-n", "--name", default=None, help="Name of the configuration")
+@click.option("--system", "system_folders", flag_value=True, help="Use system folders")
+@click.option("--user", "system_folders", flag_value=False, help="Use user folders")
+@click.option("--context", default=None, help="Kubernetes context to use")
+@click.option("--namespace", default=None, help="Kubernetes namespace to use")
+@click.option(
+    "--sandbox", "is_sandbox", flag_value=True, help="Attach to a sandbox environment"
+)
+def cli_algo_store_attach(
+    name: str | None,
+    system_folders: bool,
+    context: str,
+    namespace: str,
+    is_sandbox: bool,
+) -> None:
+    """
+    Show the store logs in the current console.
+    """
+    info("Attaching to store logs...")
+    attach_logs(
+        name,
+        instance_type=InstanceType.ALGORITHM_STORE,
+        infra_component=InfraComponentName.ALGORITHM_STORE,
+        system_folders=system_folders,
+        context=context,
+        namespace=namespace,
+        is_sandbox=is_sandbox,
+        additional_labels="component=store-server",
+    )

{vantage6-5.0.0a36 → vantage6-5.0.0a38}/vantage6/cli/algostore/list.py

@@ -2,7 +2,7 @@ import click
 
 from vantage6.common.globals import InstanceType
 
-from vantage6.cli.common.utils import get_server_configuration_list
+from vantage6.cli.common.list import get_configuration_list
 
 
 @click.command()
@@ -10,4 +10,4 @@ def cli_algo_store_configuration_list() -> None:
     """
     Print the available server configurations.
     """
-    get_server_configuration_list(InstanceType.ALGORITHM_STORE)
+    get_configuration_list(InstanceType.ALGORITHM_STORE)

{vantage6-5.0.0a36 → vantage6-5.0.0a38}/vantage6/cli/algostore/new.py

@@ -8,7 +8,7 @@ from vantage6.common.globals import (
 )
 
 from vantage6.cli.common.new import new
-from vantage6.cli.configuration_wizard import add_common_server_config
+from vantage6.cli.configuration_create import add_common_server_config
 from vantage6.cli.globals import DEFAULT_SERVER_SYSTEM_FOLDERS
 
 
@@ -43,7 +43,8 @@ def cli_algo_store_new(
     """
 
     new(
-        questionnaire_function=algo_store_configuration_questionaire,
+        config_producing_func=algo_store_configuration_questionaire,
+        config_producing_func_args=(name,),
         name=name,
         system_folders=system_folders,
         namespace=namespace,

{vantage6-5.0.0a36 → vantage6-5.0.0a38}/vantage6/cli/algostore/start.py

@@ -6,6 +6,7 @@ from vantage6.common.globals import (
     Ports,
 )
 
+from vantage6.cli.common.attach import attach_logs
 from vantage6.cli.common.decorator import click_insert_context
 from vantage6.cli.common.start import (
     helm_install,
@@ -13,11 +14,11 @@ from vantage6.cli.common.start import (
     start_port_forward,
 )
 from vantage6.cli.common.utils import (
-    attach_logs,
     create_directory_if_not_exists,
+    select_context_and_namespace,
 )
 from vantage6.cli.context.algorithm_store import AlgorithmStoreContext
-from vantage6.cli.globals import ChartName
+from vantage6.cli.globals import ChartName, InfraComponentName
 
 
 @click.command()
@@ -30,8 +31,13 @@ from vantage6.cli.globals import ChartName
     default=False,
     help="Print server logs to the console after start",
 )
+@click.option("--local-chart-dir", default=None, help="Local chart directory to use")
+@click.option("--sandbox/--no-sandbox", "sandbox", default=False)
 @click_insert_context(
-    InstanceType.ALGORITHM_STORE, include_name=True, include_system_folders=True
+    InstanceType.ALGORITHM_STORE,
+    include_name=True,
+    include_system_folders=True,
+    sandbox_param="sandbox",
 )
 def cli_algo_store_start(
     ctx: AlgorithmStoreContext,
@@ -42,14 +48,18 @@ def cli_algo_store_start(
     ip: str,
     port: int,
     attach: bool,
+    local_chart_dir: str,
 ) -> None:
     """
     Start the algorithm store.
     """
     info("Starting algorithm store...")
 
-    prestart_checks(
-        ctx, InstanceType.ALGORITHM_STORE, name, system_folders, context, namespace
+    prestart_checks(ctx, InstanceType.ALGORITHM_STORE, name, system_folders)
+
+    context, namespace = select_context_and_namespace(
+        context=context,
+        namespace=namespace,
     )
 
     create_directory_if_not_exists(ctx.log_dir)
@@ -60,6 +70,7 @@ def cli_algo_store_start(
         values_file=ctx.config_file,
         context=context,
         namespace=namespace,
+        local_chart_dir=local_chart_dir,
     )
 
     info("Port forwarding for algorithm store")
@@ -73,4 +84,12 @@ def cli_algo_store_start(
     )
 
     if attach:
-        attach_logs("app=store", "component=store-server")
+        attach_logs(
+            name,
+            instance_type=InstanceType.ALGORITHM_STORE,
+            infra_component=InfraComponentName.ALGORITHM_STORE,
+            system_folders=system_folders,
+            context=context,
+            namespace=namespace,
+            is_sandbox=ctx.is_sandbox,
+        )

{vantage6-5.0.0a36 → vantage6-5.0.0a38}/vantage6/cli/algostore/stop.py

@@ -25,6 +25,7 @@ from vantage6.cli.globals import DEFAULT_SERVER_SYSTEM_FOLDERS, InfraComponentNa
     flag_value=False,
     help="Search for configuration in the user folders instead of system folders.",
 )
+@click.option("--sandbox/--no-sandbox", "sandbox", default=False)
 @click.option("--all", "all_stores", flag_value=True, help="Stop all algorithm stores")
 def cli_algo_store_stop(
     name: str,
@@ -32,6 +33,7 @@ def cli_algo_store_stop(
     namespace: str,
     system_folders: bool,
     all_stores: bool,
+    sandbox: bool,
 ):
     """
     Stop one or all running algorithm store(s).
@@ -45,6 +47,7 @@ def cli_algo_store_stop(
         namespace=namespace,
         context=context,
         system_folders=system_folders,
+        is_sandbox=sandbox,
     )
 
 

vantage6-5.0.0a38/vantage6/cli/algostore/version.py

@@ -0,0 +1,62 @@
+import click
+import requests
+
+from vantage6.common import error, info
+from vantage6.common.globals import (
+    DEFAULT_API_PATH,
+    HTTP_LOCALHOST,
+    InstanceType,
+    Ports,
+)
+
+from vantage6.cli import __version__
+from vantage6.cli.common.version import get_and_select_ctx
+from vantage6.cli.globals import DEFAULT_SERVER_SYSTEM_FOLDERS
+
+
+@click.command()
+@click.option("-n", "--name", default=None, help="Configuration name")
+@click.option("--system", "system_folders", flag_value=True)
+@click.option(
+    "--user", "system_folders", flag_value=False, default=DEFAULT_SERVER_SYSTEM_FOLDERS
+)
+@click.option("--context", default=None, help="Kubernetes context to use")
+@click.option("--namespace", default=None, help="Kubernetes namespace to use")
+@click.option(
+    "--sandbox", "is_sandbox", flag_value=True, help="Is this a sandbox environment?"
+)
+def cli_algo_store_version(
+    name: str, system_folders: bool, context: str, namespace: str, is_sandbox: bool
+) -> None:
+    """
+    Print the version of the vantage6 algorithm store.
+    """
+
+    ctx = get_and_select_ctx(
+        InstanceType.ALGORITHM_STORE,
+        name,
+        system_folders,
+        context,
+        namespace,
+        is_sandbox,
+    )
+    store_config = ctx.config.get("store", {})
+
+    port = store_config.get("port", Ports.DEV_ALGO_STORE.value)
+    api_path = store_config.get("api_path", DEFAULT_API_PATH)
+    if not port:
+        error("No port found in algorithm store configuration.")
+        return
+    if not api_path:
+        error("No API path found in algorithm store configuration.")
+        return
+
+    response = requests.get(f"{HTTP_LOCALHOST}:{port}{api_path}/version")
+    if response.status_code != 200:
+        error("Failed to get algorithm store version.")
+        return
+    algorithm_store_version = response.json().get("version", "")
+
+    info("")
+    info(f"Algorithm store version: {algorithm_store_version}")
+    info(f"CLI version: {__version__}")

{vantage6-5.0.0a36 → vantage6-5.0.0a38}/vantage6/cli/auth/attach.py

@@ -3,8 +3,8 @@ import click
 from vantage6.common import error, info
 from vantage6.common.globals import InstanceType
 
+from vantage6.cli.common.attach import attach_logs
 from vantage6.cli.common.utils import (
-    attach_logs,
     find_running_service_names,
     select_context_and_namespace,
     select_running_service,

{vantage6-5.0.0a36 → vantage6-5.0.0a38}/vantage6/cli/auth/list.py

@@ -2,7 +2,7 @@ import click
 
 from vantage6.common.globals import InstanceType
 
-from vantage6.cli.common.utils import get_server_configuration_list
+from vantage6.cli.common.list import get_configuration_list
 
 
 @click.command()
@@ -10,4 +10,4 @@ def cli_auth_configuration_list() -> None:
     """
     Print the available auth configurations.
     """
-    get_server_configuration_list(InstanceType.AUTH)
+    get_configuration_list(InstanceType.AUTH)

{vantage6-5.0.0a36 → vantage6-5.0.0a38}/vantage6/cli/auth/new.py

@@ -44,7 +44,8 @@ def cli_auth_new(
     Create a new server configuration.
     """
     new(
-        questionnaire_function=auth_configuration_questionaire,
+        config_producing_func=auth_configuration_questionaire,
+        config_producing_func_args=tuple(),
         name=name,
         system_folders=system_folders,
         namespace=namespace,
@@ -53,7 +54,7 @@ def cli_auth_new(
     )
 
 
-def auth_configuration_questionaire(instance_name: str) -> dict[str, Any]:
+def auth_configuration_questionaire() -> dict[str, Any]:
     """
     Kubernetes-specific questionnaire to generate Helm values for the Keycloak helm
     chart.

vantage6-5.0.0a38/vantage6/cli/auth/remove.py

@@ -0,0 +1,89 @@
+import click
+
+from vantage6.common import info, warning
+from vantage6.common.globals import InstanceType
+
+from vantage6.cli.common.decorator import click_insert_context
+from vantage6.cli.common.remove import execute_remove
+from vantage6.cli.context.auth import AuthContext
+from vantage6.cli.globals import InfraComponentName
+from vantage6.cli.utils_kubernetes import get_core_api_with_ssl_handling
+
+
+@click.command()
+@click_insert_context(
+    type_=InstanceType.AUTH, include_name=True, include_system_folders=True
+)
+@click.option("-f", "--force", "force", flag_value=True)
+def cli_auth_remove(
+    ctx: AuthContext, name: str, system_folders: bool, force: bool
+) -> None:
+    """
+    Function to remove a server.
+
+    Parameters
+    ----------
+    ctx : ServerContext
+        Server context object
+    name : str
+        Name of the auth server
+    system_folders : bool
+        Whether to use system folders or user folders
+    force : bool
+        Whether to ask for confirmation before removing or not
+    """
+    auth_remove(ctx, name, system_folders, force)
+
+
+# this new function is just here so that it can be called from the sandbox remove
+# command
+def auth_remove(ctx: AuthContext, name: str, system_folders: bool, force: bool) -> None:
+    # Best-effort cleanup of Keycloak PVCs and their bound PVs after uninstall
+    try:
+        _cleanup_auth_volumes(ctx)
+    except Exception as e:
+        # Cleanup is best-effort; do not fail the remove command if cleanup fails
+        warning(f"Failed to cleanup auth volumes: {e}")
+
+    execute_remove(
+        ctx, InstanceType.AUTH, InfraComponentName.AUTH, name, system_folders, force
+    )
+
+
+def _cleanup_auth_volumes(ctx: AuthContext) -> None:
+    core_api = get_core_api_with_ssl_handling()
+
+    # Label used by the auth chart to tag its resources
+    label_selector = f"app.kubernetes.io/instance={ctx.helm_release_name}"
+
+    # Collect PVCs across all namespaces that belong to this release
+    pvcs = core_api.list_persistent_volume_claim_for_all_namespaces(
+        label_selector=label_selector
+    ).items
+
+    # Track PV names bound to these PVCs
+    pv_names = {
+        pvc.spec.volume_name for pvc in pvcs if pvc.spec and pvc.spec.volume_name
+    }
+
+    # Delete PVCs first (namespaced)
+    for pvc in pvcs:
+        ns = pvc.metadata.namespace
+        name_ = pvc.metadata.name
+        try:
+            info(f"Deleting persistent volume claim {name_} in namespace {ns}")
+            core_api.delete_namespaced_persistent_volume_claim(name=name_, namespace=ns)
+        except Exception as e:
+            # Ignore failures; continue attempting other deletions
+            warning(
+                f"Failed to delete persistent volume claim {name_} in namespace {ns}: "
+                f"{e}"
+            )
+
+    # Delete PVs that were bound to those PVCs (cluster-scoped)
+    for pv_name in pv_names:
+        try:
+            info(f"Deleting persistent volume: {pv_name}")
+            core_api.delete_persistent_volume(name=pv_name)
+        except Exception as e:
+            warning(f"Failed to delete persistent volume {pv_name}: {e}")