Enh/ap 25245 pixi env creator #47

marc-lehner · 2026-01-26T12:38:38Z

Add support for the new python environment provider node and it's pixi port object to the python scripts

AP-25245 ()

…ports AP-25245 ()

AP-25245 ()

…ancelable AP-25245 ()

…knime-conda instead AP-25245 ()

…org.knime.pixi.port.PixiPythonCommand;) AP-25245 ()

Copilot

Pull request overview

This PR adds support for a new Python environment provider node with a Pixi port object, integrating it into the Python scripting nodes ecosystem. The changes enable Python script nodes to receive Python environments through an optional input port instead of only relying on configured preferences.

Changes:

Introduced PythonProcessProvider as a replacement interface for the deprecated PythonCommand to support multiple environment sources
Added optional Python environment port support to Python Script and Python View nodes
Implemented environment port extraction and installation logic with progress reporting

Reviewed changes

Copilot reviewed 41 out of 41 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
org.knime.python3/src/main/java/org/knime/python3/PythonCommand.java	Deprecated PythonCommand interface, now extends PythonProcessProvider for backward compatibility
org.knime.python3/src/main/java/org/knime/python3/SimplePythonCommand.java	Updated documentation to reference PythonProcessProvider
org.knime.python3/src/main/java/org/knime/python3/QueuedPythonGatewayFactory.java	Refactored to use PythonProcessProvider instead of PythonCommand
org.knime.python3/src/main/java/org/knime/python3/PythonGatewayFactory.java	Updated gateway description to work with PythonProcessProvider
org.knime.python3.scripting.nodes/src/main/java/org/knime/python3/scripting/nodes2/script/PythonScriptNodeFactory.java	Added optional Python environment port to Python Script node
org.knime.python3.scripting.nodes/src/main/java/org/knime/python3/scripting/nodes2/view/PythonViewNodeFactory.java	Added optional Python environment port to Python View node
org.knime.python3.scripting.nodes/src/main/java/org/knime/python3/scripting/nodes2/PythonScriptNodeModel.java	Implemented environment port extraction and prioritization over configured Python command
org.knime.python3.scripting.nodes/src/main/java/org/knime/python3/scripting/nodes2/PythonScriptingService.java	Added environment port handling for interactive sessions
org.knime.python3.scripting.nodes/src/main/java/org/knime/python3/scripting/nodes2/PythonScriptingSession.java	Added PythonCommandAdapter to bridge PythonProcessProvider to legacy PythonCommand
org.knime.python3.scripting.nodes/src/main/java/org/knime/python3/scripting/nodes/PortsConfigurationUtils.java	Added utility methods for environment port detection and installation
org.knime.python3.scripting.nodes/src/main/java/org/knime/python3/scripting/nodes2/PythonIOUtils.java	Updated to filter out environment ports from data processing
org.knime.python3.scripting.nodes/src/main/java/org/knime/python3/scripting/nodes2/PythonScriptingInputOutputModelUtils.java	Added logic to skip environment ports in input/output model generation

...pting.nodes/src/main/java/org/knime/python3/scripting/nodes2/view/PythonViewNodeFactory.java

...g.nodes/src/main/java/org/knime/python3/scripting/nodes2/script/PythonScriptNodeFactory.java

...ipting.nodes/src/main/java/org/knime/python3/scripting/nodes/view/PythonViewNodeFactory.java

...ng.nodes/src/main/java/org/knime/python3/scripting/nodes/script/PythonScriptNodeFactory.java

...scripting.nodes/src/main/java/org/knime/python3/scripting/nodes2/PythonScriptingService.java

Copilot · 2026-01-26T12:39:53Z

...g.nodes/src/main/java/org/knime/python3/scripting/nodes2/PythonScriptPortsConfiguration.java

+    @Deprecated(since = "5.10", forRemoval = true)
+    public boolean hasPixiPort() {


The deprecation message should explain what to use instead. Add 'Use {@link #hasEnvironmentPort()} instead' to the @deprecated tag.

wait... you introduce this method, which is deprecated, and introduce the replacement at the same time?? How about getting rid of hasPixiPort?

Copilot · 2026-01-26T12:39:54Z

...g.nodes/src/main/java/org/knime/python3/scripting/nodes2/PythonScriptPortsConfiguration.java

+    @Deprecated(since = "5.10", forRemoval = true)
+    public boolean hasPythonEnvPort() {


The deprecation message should explain what to use instead. Add 'Use {@link #hasEnvironmentPort()} instead' to the @deprecated tag.

Copilot · 2026-01-26T12:39:54Z

org.knime.python3/src/main/java/org/knime/python3/PythonCommand.java

+    @Deprecated
+    @Override
    ProcessBuilder createProcessBuilder();


The @deprecated annotation on interface methods should include forRemoval=true and since parameters for consistency with the interface-level deprecation at line 67.

chaubold · 2026-01-26T17:02:52Z

....nodes/src/main/java/org/knime/python3/scripting/nodes/AbstractPythonScriptingNodeModel.java

    protected PortObjectSpec[] configure(final PortObjectSpec[] inSpecs) throws InvalidSettingsException {
-        for (int i = 0; i < m_inPorts.length; i++) {
+        // The Pixi port (if present) is at the end of the input specs
+        final int numRegularPorts = m_inPorts.length;


I think we should drop the pixi port here, right?

…uld be removed completely? Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

chaubold · 2026-01-26T17:17:18Z

...scripting.nodes/src/main/java/org/knime/python3/scripting/nodes/PortsConfigurationUtils.java

+        try {
+            // Check if any input port is a PythonEnvironmentPortObject
+            for (final PortType inType : inTypes) {
+                if (inType.equals(PythonEnvironmentPortObject.TYPE) || inType.equals(PythonEnvironmentPortObject.TYPE_OPTIONAL)) {


you could simply use the isPixiPort method from below here, then you don't need to write the check twice

chaubold · 2026-01-26T17:20:03Z

...scripting.nodes/src/main/java/org/knime/python3/scripting/nodes/PortsConfigurationUtils.java

+     * @throws IOException if installation fails
+     * @throws CanceledExecutionException if the operation is canceled
+     */
+    public static void installPythonEnvironmentIfPresent(


I'd have expected this method inside the port object, so that the Python node only calls PythonEnvironmentPortObject.installEnvironment(exec) and that does its thing...

chaubold · 2026-01-26T17:23:51Z

...s/src/main/java/org/knime/python3/scripting/nodes2/PythonScriptingInputOutputModelUtils.java

+            LOGGER.debugWithFormat("Checking if port type '%s' is environment port: %s",
+                portType.getName(), isPythonEnvPort);
+            return isPythonEnvPort;
+        } catch (NoClassDefFoundError e) {


you have this check in many places but... don't we have a dependency in the MANIFEST.MF to the package defining the PythonEnvironmentPortObject? How should that ever be missing then?

chaubold · 2026-01-26T17:37:16Z

...scripting.nodes/src/main/java/org/knime/python3/scripting/nodes2/PythonScriptingService.java

+                    if (pythonCommand != null) {
+                        LOGGER.info("Using Python environment from connected Pixi port for interactive session");
+                        // Filter out Pixi port from data ports - it's not a data port for setupIO
+                        dataPortObjects = java.util.Arrays.copyOf(inputData, inputData.length - 1);


import Arrays instead of using the full type here

chaubold · 2026-01-26T17:38:47Z

...scripting.nodes/src/main/java/org/knime/python3/scripting/nodes2/PythonScriptingService.java

+            if (portObject instanceof PythonEnvironmentPortObject) {
+                final PythonEnvironmentPortObject pythonEnvPort = (PythonEnvironmentPortObject)portObject;
+                try {
+                    // PythonEnvironmentPortObject.getPythonCommand() returns org.knime.pixi.port.PythonCommand,


comment is outdated

chaubold · 2026-01-26T17:43:40Z

....scripting.nodes/src/main/java/org/knime/python3/scripting/nodes2/PythonScriptNodeModel.java

+     * @return the Python command, or null if the port is not connected or doesn't contain a valid Python executable
+     * @throws InvalidSettingsException if the Python executable path from the environment doesn't exist
+     */
+    private static PythonProcessProvider extractPythonCommandFromPixiPort(final PortObject portObject)


again: this is a copy, and it shouldn't live here but in the PortObject

chaubold · 2026-01-26T17:44:08Z

...g.nodes/src/main/java/org/knime/python3/scripting/nodes2/PythonScriptPortsConfiguration.java

        // Count the number of the different ports (skip the flow var port)
        var numInTables = 0;
        var numInObjects = 0;
+        var hasEnvironmentPort = false;


aha, see, here it's called hasEnvironmentPort :)

chaubold · 2026-01-26T17:46:05Z

...g.nodes/src/main/java/org/knime/python3/scripting/nodes2/PythonScriptPortsConfiguration.java

            } else {
+                // Check if it's a Python environment port
+                try {
+                    if (PythonEnvironmentPortObject.TYPE.equals(portType)


this check already exists somewhere else. Maybe even put the check for isPythonEnvironmentPortObject into the port object itself?

chaubold · 2026-01-26T17:47:07Z

...g.nodes/src/main/java/org/knime/python3/scripting/nodes2/PythonScriptPortsConfiguration.java

+    @Deprecated(since = "5.10", forRemoval = true)
+    public boolean hasPixiPort() {


wait... you introduce this method, which is deprecated, and introduce the replacement at the same time?? How about getting rid of hasPixiPort?

chaubold · 2026-01-26T17:54:05Z

org.knime.python3.nodes/META-INF/MANIFEST.MF

 Eclipse-RegisterBuddy: org.knime.ext.py4j
 Eclipse-BundleShape: dir
 Bundle-Activator: org.knime.python3.nodes.Activator
+Import-Package: org.knime.python3.processprovider


why do we do it like this, and don't add a dependency to the plugin org.knime.python3.processprovider? Then we can also get rid of all the NoClassDefFound checks

Copilot

Pull request overview

Copilot reviewed 41 out of 41 changed files in this pull request and generated 3 comments.

Comments suppressed due to low confidence (2)

org.knime.python3.scripting.nodes/src/main/java/org/knime/python3/scripting/nodes2/script/PythonScriptNodeFactory.java:1

The variable pythonEnvClass is declared but never used on line 130 and 139. This appears to be a leftover from development and should be removed to reduce code clutter.

/*

org.knime.python3.scripting.nodes/src/main/java/org/knime/python3/scripting/nodes2/view/PythonViewNodeFactory.java:1

The variable pythonEnvClass is declared on line 91 in the view factory but never used. This appears to be a leftover from development and should be removed to reduce code clutter.

/*

Copilot · 2026-01-26T17:56:00Z

...pting.nodes/src/main/java/org/knime/python3/scripting/nodes2/view/PythonViewNodeFactory.java

+        try {
+            final Class<?> pythonEnvClass = PythonEnvironmentPortObject.class;
+            b.addOptionalInputPortGroup(PORTGR_ID_PYTHON_ENV, PythonEnvironmentPortObject.TYPE_OPTIONAL);
+            LOGGER.debug("Successfully added Python environment port");
+        } catch (NoClassDefFoundError e) {
+            LOGGER.debug("PythonEnvironmentPortObject not available: " + e.getMessage());
+        }


The variable pythonEnvClass is declared but never used. This appears to be a leftover from development and should be removed to reduce code clutter.

Copilot · 2026-01-26T17:56:00Z

...g.nodes/src/main/java/org/knime/python3/scripting/nodes2/script/PythonScriptNodeFactory.java

+        try {
+            final Class<?> pythonEnvClass = PythonEnvironmentPortObject.class;
+            b.addOptionalInputPortGroup(PORTGR_ID_PYTHON_ENV, PythonEnvironmentPortObject.TYPE_OPTIONAL);
+            LOGGER.debug("Successfully added Python environment port");
+        } catch (NoClassDefFoundError e) {
+            LOGGER.debug("PythonEnvironmentPortObject not available: " + e.getMessage());
+        }


The variable pythonEnvClass is declared but never used. This appears to be a leftover from development and should be removed to reduce code clutter.

Copilot · 2026-01-26T17:56:00Z

...nodes/src/main/java/org/knime/python3/scripting/nodes/prefs/Python3ScriptingPreferences.java

     */
    public static BundledPythonCommand getBundledPythonCommand() {
-        return getBundledCondaEnvironmentConfig().getPythonCommand();
+        return (BundledPythonCommand)getBundledCondaEnvironmentConfig().getPythonCommand();


This unchecked cast from PythonProcessProvider to BundledPythonCommand is unsafe and could throw ClassCastException at runtime. Consider adding type validation or changing the method signature of getBundledCondaEnvironmentConfig().getPythonCommand() to return the specific type.

Suggested change

return (BundledPythonCommand)getBundledCondaEnvironmentConfig().getPythonCommand();

final var pythonCommand = getBundledCondaEnvironmentConfig().getPythonCommand();

if (!(pythonCommand instanceof BundledPythonCommand)) {

throw new IllegalStateException(

"Bundled Python environment '" + BUNDLED_PYTHON_ENV_ID

+ "' does not provide a BundledPythonCommand (got: "

+ (pythonCommand == null ? "null" : pythonCommand.getClass().getName()) + ")");

}

return (BundledPythonCommand)pythonCommand;

marc-lehner added 9 commits January 21, 2026 14:57

AP-25245: add pixi port to python scripting node

0b2e88f

AP-25245 ()

AP-25245: move ports to dedicated plugin

cf05f86

AP-25245 ()

AP-25245: use pixi run in pixiPythonCommand for all pixi environment …

366d73f

…ports AP-25245 ()

AP-25245: add pixi port to python view

bbe5ab0

AP-25245 ()

AP-25245: add pixi port to interactive execution

2cc6dfc

AP-25245 ()

AP-25245: replace pixi port with python port

8b0dbff

AP-25245 ()

AP-25245: add progress for the python port installation and make it c…

23b735b

…ancelable AP-25245 ()

AP-25245: deprecate PythonCommand and use PythonProcessProvider from …

18c1007

…knime-conda instead AP-25245 ()

AP-25245: only use import PixiPythonCommand from knime-conda (import …

9d64458

…org.knime.pixi.port.PixiPythonCommand;) AP-25245 ()

marc-lehner requested a review from a team as a code owner January 26, 2026 12:38

marc-lehner requested review from Copilot and knime-ghub-bot and removed request for a team January 26, 2026 12:38

Copilot AI reviewed Jan 26, 2026

View reviewed changes

chaubold reviewed Jan 26, 2026

View reviewed changes

AP-25245: WIP: use debug instead of info log for trivial messages. Co…

3ae27b1

…uld be removed completely? Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot AI review requested due to automatic review settings January 26, 2026 17:54

chaubold requested changes Jan 26, 2026

View reviewed changes

Copilot AI reviewed Jan 26, 2026

View reviewed changes

		@Deprecated(since = "5.10", forRemoval = true)
		public boolean hasPixiPort() {

		@Deprecated(since = "5.10", forRemoval = true)
		public boolean hasPythonEnvPort() {

-        return (BundledPythonCommand)getBundledCondaEnvironmentConfig().getPythonCommand();
+        final var pythonCommand = getBundledCondaEnvironmentConfig().getPythonCommand();
+        if (!(pythonCommand instanceof BundledPythonCommand)) {
+            throw new IllegalStateException(
+                "Bundled Python environment '" + BUNDLED_PYTHON_ENV_ID
+                    + "' does not provide a BundledPythonCommand (got: "
+                    + (pythonCommand == null ? "null" : pythonCommand.getClass().getName()) + ")");
+        }
+        return (BundledPythonCommand)pythonCommand;

Enh/ap 25245 pixi env creator #47

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Enh/ap 25245 pixi env creator #47

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