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

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

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

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

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

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

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

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

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

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

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

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.

/*

...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

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

Copilot

Pull request overview

Copilot reviewed 41 out of 41 changed files in this pull request and generated 13 comments.

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

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

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

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

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

sonarqubecloud · 2026-02-10T16:12:53Z

Quality Gate failed

Failed conditions
18.5% Coverage on New Code (required ≥ 85%)
13.2% Duplication on New Code (required ≤ 1%)

See analysis details on SonarQube Cloud

Copilot

Pull request overview

Copilot reviewed 41 out of 41 changed files in this pull request and generated 9 comments.

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

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

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

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

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

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

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

Copilot

Pull request overview

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

Copilot · 2026-02-11T10:44:26Z

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

+        final PortObject[] filtered = new PortObject[inObjects.length - 1];
+        int filteredIndex = 0;
+        for (int i = 0; i < inTypes.length && i < inObjects.length; i++) {
+            if (!isPythonEnvironmentPort(inTypes[i])) {
+                filtered[filteredIndex++] = inObjects[i];
+            }
+        }


filterEnvironmentPort assumes exactly one environment port and blindly allocates inObjects.length - 1. If the configuration ever contains 0 or >1 environment ports (e.g., future changes, misconfiguration, or different port typing), this can either drop a data port or return an array containing trailing nulls (risking downstream NPEs). Allocate the filtered array by counting non-environment ports (based on inTypes) and fill it accordingly, or build a dynamic list and convert to array to guarantee correct sizing.

Suggested change

final PortObject[] filtered = new PortObject[inObjects.length - 1];

int filteredIndex = 0;

for (int i = 0; i < inTypes.length && i < inObjects.length; i++) {

if (!isPythonEnvironmentPort(inTypes[i])) {

filtered[filteredIndex++] = inObjects[i];

}

}

final int max = Math.min(inTypes.length, inObjects.length);

// First pass: count non-environment ports within the overlapping range

int nonEnvCount = 0;

for (int i = 0; i < max; i++) {

if (!isPythonEnvironmentPort(inTypes[i])) {

nonEnvCount++;

}

}

// Any remaining PortObjects beyond the typed range are treated as non-environment ports

if (inObjects.length > max) {

nonEnvCount += inObjects.length - max;

}

final PortObject[] filtered = new PortObject[nonEnvCount];

int filteredIndex = 0;

// Second pass: copy non-environment ports from the overlapping range

for (int i = 0; i < max; i++) {

if (!isPythonEnvironmentPort(inTypes[i])) {

filtered[filteredIndex++] = inObjects[i];

}

}

// Third pass: copy any remaining ports beyond the typed range

for (int i = max; i < inObjects.length; i++) {

filtered[filteredIndex++] = inObjects[i];

}

Copilot · 2026-02-11T10:44:26Z

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

+    public static PythonEnvironmentPortObject extractPythonEnvironmentPort(
+            final PortsConfiguration config, final PortObject[] inObjects) {
+        final PortType[] inTypes = config.getInputPorts();
+        for (int i = 0; i < inTypes.length; i++) {
+            if (isPythonEnvironmentPort(inTypes[i]) && PythonEnvironmentPortObject.isPythonEnvironmentPortObject(inObjects[i])) {
+                return (PythonEnvironmentPortObject) inObjects[i];
+            }
+        }
+        return null;
+    }


This utility method hard-links to PythonEnvironmentPortObject in its signature and body even though org.knime.pixi.port is declared optional. In OSGi, such direct type references can still trigger NoClassDefFoundError at class load/link time (not just at execution), which would prevent the scripting nodes bundle from loading when the optional bundle isn’t available. To keep the dependency truly optional, avoid exposing Pixi types in public method signatures and isolate direct references behind reflection or a separate fragment/bundle that is only resolved when org.knime.pixi.port is present.

Copilot · 2026-02-11T10:44:27Z

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

+        if (m_ports.hasPythonEnvironmentPort()) {
+            PortsConfigurationUtils.installPythonEnvironmentIfPresent(getPortsConfiguration(), inObjects, exec);
+        }
+
+        // Extract Python command from environment port if connected, otherwise use configured command
+        final PythonProcessProvider pythonCommand;
+        final PythonProcessProvider pythonCommandFromEnv = PythonEnvironmentPortObject.extractPythonCommand(
+            PortsConfigurationUtils.extractPythonEnvironmentPort(getPortsConfiguration(), inObjects));
+        if (pythonCommandFromEnv != null) {
+            LOGGER.debug("Using Python from environment port");
+            pythonCommand = pythonCommandFromEnv;


New behavior is introduced for (1) early environment installation and (2) precedence of the environment-port-provided Python over the configured executable. Please add tests that cover: env port connected vs. not connected; extraction failure fallback to executable selection; and ensuring the environment port is not forwarded as a data input to the session (i.e., input port filtering). This helps prevent regressions given the multiple new paths and optional-dependency behavior.

AP-25245 ()

…ports AP-25245 ()

AP-25245 ()

…ancelable AP-25245 ()

…knime-conda instead AP-25245 ()

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

Co-authored-by: Copilot <[email protected]>

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

....nodes/src/main/java/org/knime/python3/scripting/nodes/AbstractPythonScriptingNodeModel.java Show resolved Hide resolved

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

marc-lehner force-pushed the enh/AP-25245-pixi-env-creator branch 2 times, most recently from 5297ab6 to a396f21 Compare February 10, 2026 14:29

Copilot AI review requested due to automatic review settings February 10, 2026 15:28

Copilot AI reviewed Feb 10, 2026

View reviewed changes

Copilot AI review requested due to automatic review settings February 11, 2026 08:35

Copilot AI reviewed Feb 11, 2026

View reviewed changes

marc-lehner force-pushed the enh/AP-25245-pixi-env-creator branch from 732d9ac to 15d85da Compare February 11, 2026 09:37

Copilot AI review requested due to automatic review settings February 11, 2026 10:39

marc-lehner force-pushed the enh/AP-25245-pixi-env-creator branch from 15d85da to 3e4affb Compare February 11, 2026 10:39

Copilot AI reviewed Feb 11, 2026

View reviewed changes

marc-lehner force-pushed the enh/AP-25245-pixi-env-creator branch from 3e4affb to 68c0942 Compare February 11, 2026 14:20

marc-lehner added 9 commits February 11, 2026 16:04

AP-25245: add pixi port to python scripting node

ce416a1

AP-25245 ()

AP-25245: move ports to dedicated plugin

ecb8f80

AP-25245 ()

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

566f3c8

…ports AP-25245 ()

AP-25245: add pixi port to python view

9682bbf

AP-25245 ()

AP-25245: add pixi port to interactive execution

65cbd5e

AP-25245 ()

AP-25245: replace pixi port with python port

5644fcb

AP-25245 ()

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

42072d1

…ancelable AP-25245 ()

AP-25245: deprecate PythonCommand and use PythonProcessProvider from …

a840697

…knime-conda instead AP-25245 ()

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

dce5538

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

chaubold and others added 4 commits February 11, 2026 16:05

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

c8b6f16

Co-authored-by: Copilot <[email protected]>

AP-25245: update all plugins to 5.11

0691a21

AP-25245 ()

AP-25245: move pixi code to python port

54aa7b5

AP-25245 ()

AP-25245: consistent nameing of python environment port and methods

d461935

AP-25245 ()

marc-lehner force-pushed the enh/AP-25245-pixi-env-creator branch from 68c0942 to d461935 Compare February 11, 2026 15:05

-        final PortObject[] filtered = new PortObject[inObjects.length - 1];
-        int filteredIndex = 0;
-        for (int i = 0; i < inTypes.length && i < inObjects.length; i++) {
-            if (!isPythonEnvironmentPort(inTypes[i])) {
-                filtered[filteredIndex++] = inObjects[i];
-            }
-        }
+        final int max = Math.min(inTypes.length, inObjects.length);
+        // First pass: count non-environment ports within the overlapping range
+        int nonEnvCount = 0;
+        for (int i = 0; i < max; i++) {
+            if (!isPythonEnvironmentPort(inTypes[i])) {
+                nonEnvCount++;
+            }
+        }
+        // Any remaining PortObjects beyond the typed range are treated as non-environment ports
+        if (inObjects.length > max) {
+            nonEnvCount += inObjects.length - max;
+        }
+        final PortObject[] filtered = new PortObject[nonEnvCount];
+        int filteredIndex = 0;
+        // Second pass: copy non-environment ports from the overlapping range
+        for (int i = 0; i < max; i++) {
+            if (!isPythonEnvironmentPort(inTypes[i])) {
+                filtered[filteredIndex++] = inObjects[i];
+            }
+        }
+        // Third pass: copy any remaining ports beyond the typed range
+        for (int i = max; i < inObjects.length; i++) {
+            filtered[filteredIndex++] = inObjects[i];
+        }

Enh/ap 25245 pixi env creator #47

Are you sure you want to change the base?

Enh/ap 25245 pixi env creator #47

Conversation

marc-lehner commented Jan 26, 2026

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

sonarqubecloud bot commented Feb 10, 2026

Quality Gate failed

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Uh oh!

Copilot AI Feb 11, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Feb 11, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Feb 11, 2026

Choose a reason for hiding this comment

Uh oh!