Todo/ap 25545 update deps #26

AtR1an · 2026-01-26T00:36:55Z

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Copilot

Pull request overview

This PR updates multiple dependencies in the project, particularly transitioning from older LangChain packages to newer versions and package structures.

Changes:

Migration from langchain to langchain-classic for legacy agent and chain components
Switch from langchain-google-vertexai to langchain-google-genai for Google model integrations
Update to Python 3.13 and comprehensive dependency version updates in pixi.toml

Reviewed changes

Copilot reviewed 11 out of 12 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/tools/vectorstore.py	Updates imports to use `langchain_classic` for retrieval chains
src/models/google/_port_types.py	Switches from Vertex AI to Google Generative AI SDK with updated parameter names
src/models/_adapter.py	Changes LLM invocation method from direct call to `.invoke()`
src/indexes/chroma.py	Simplifies Chroma vectorstore handling logic
src/eval/giskard/giskard_patch.py	Adds monkey-patch for scipy compatibility with Giskard
src/eval/giskard/init.py	Imports the new giskard_patch module
src/agents/openai.py	Updates import to use `langchain_classic`
src/agents/base_deprecated.py	Moves imports to local scope and adds ToolNode usage
src/agents/base.py	Updates agent execution to use `langchain_classic.agents.AgentExecutor` and adds ToolNode
src/agents/_tool.py	Switches from `langchain.tools` to `langchain_core.tools`
pixi.toml	Major dependency reorganization with Python 3.13 upgrade and version updates

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Copilot · 2026-01-26T00:37:37Z

src/agents/base_deprecated.py

+        validate_ai_message,
+        LANGGRAPH_RECURSION_MESSAGE,


Inconsistent indentation in the import statement. The closing parenthesis should align with the opening line or the imported items should be consistently indented.

Suggested change

validate_ai_message,

LANGGRAPH_RECURSION_MESSAGE,

validate_ai_message,

LANGGRAPH_RECURSION_MESSAGE,

Copilot · 2026-01-26T00:37:37Z

pixi.toml


 [pypi-options]
-no-build = true
+# no-build = true


Commented-out configuration should either be removed or include a comment explaining why it's disabled and under what circumstances it should be re-enabled.

Suggested change

# no-build = true

# no-build = true # Disabled to allow building packages from source during local development; re-enable in CI for reproducible binary-only builds.

Copilot · 2026-01-26T00:37:37Z

pixi.toml

+python = "3.13.*" # Runtime: Python 3.13
+knime-extension = "5.8.*" # Framework: KNIME Python integration
+knime-python-base = "*" # Framework: KNIME base libraries
+# knime-python-versions = "5.8.*"


Commented-out dependency should either be removed or include a comment explaining why it's disabled and when it should be re-enabled.

Suggested change

# knime-python-versions = "5.8.*"

# knime-python-versions = "5.8.*" # Disabled: only needed for multi-runtime KNIME setups; re-enable if/when multiple Python versions must be supported

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Pull request overview

Copilot reviewed 11 out of 12 changed files in this pull request and generated 1 comment.

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Copilot · 2026-01-26T16:19:53Z

src/models/google/_port_types.py

            max_retries=2,  # default is 6, instead we just try twice before failing
            base_url=self.custom_base_api_url or self.base_api_url,
            credentials=google_credentials,
+            task_type="RETRIEVAL_QUERY", # for backwards compatibility with old VertexAIEmbeddings


Missing space after '#' in comment.

Suggested change

task_type="RETRIEVAL_QUERY", # for backwards compatibility with old VertexAIEmbeddings

task_type="RETRIEVAL_QUERY", # for backwards compatibility with old VertexAIEmbeddings

Copilot

Pull request overview

Copilot reviewed 11 out of 12 changed files in this pull request and generated no new comments.

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Which now provides a unified API for Google AI Studio and Vertex AI

For backwards compatibility

Because chroma no longer provides the information where the vectorstore is persisted.

Tested locally on Windows.

AP-25545 (Update to latest langchain 1.x version)

Copilot

Pull request overview

Copilot reviewed 11 out of 12 changed files in this pull request and generated no new comments.

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AP-25545 (Update to latest langchain 1.x version)

Copilot

Pull request overview

Copilot reviewed 11 out of 12 changed files in this pull request and generated 3 comments.

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Copilot · 2026-02-06T09:51:35Z

src/models/google/_port_types.py

            max_retries=2,  # default is 6, instead we just try twice before failing
            base_url=self.custom_base_api_url or self.base_api_url,
            credentials=google_credentials,
+            task_type="RETRIEVAL_QUERY", # for backwards compatibility with old VertexAIEmbeddings


Missing space after '#' in comment. Should be '# for backwards compatibility'.

Copilot · 2026-02-06T09:51:35Z

src/eval/giskard/giskard_patch.py

+# AP-25545: Monkey-patch scipy.stats.stats to fix Giskard import error with newer scipy versions
+# The error is: ImportError: cannot import name 'Ks_2sampResult' from 'scipy.stats.stats'


Consider adding documentation about when this patch can be removed (e.g., 'Remove when Giskard updates to support scipy >= X.Y.Z' or a link to the upstream issue).

Suggested change

# AP-25545: Monkey-patch scipy.stats.stats to fix Giskard import error with newer scipy versions

# The error is: ImportError: cannot import name 'Ks_2sampResult' from 'scipy.stats.stats'

# AP-25545: Monkey-patch scipy.stats.stats to fix Giskard import error with newer scipy versions.

# The error is: ImportError: cannot import name 'Ks_2sampResult' from 'scipy.stats.stats'.

# TODO: Remove this patch when Giskard no longer imports Ks_2sampResult from scipy.stats.stats,

# or when we depend on a Giskard version that supports newer SciPy versions without this workaround.

Copilot · 2026-02-06T09:51:36Z

pixi.toml

+
+# --- Vector Stores & Indexes ---
+faiss-cpu = "*" # Direct: used in indexes/faiss.py
+langchain-chroma = "==1.1.0" # Direct: used in indexes/chroma.py installed via pypi because conda packages don't support python 3.13


The comment runs over multiple concepts without proper separation. Consider splitting into: 'Direct: used in indexes/chroma.py. Installed via PyPI because conda packages don't support Python 3.13'.

Suggested change

langchain-chroma = "==1.1.0" # Direct: used in indexes/chroma.py installed via pypi because conda packages don't support python 3.13

langchain-chroma = "==1.1.0" # Direct: used in indexes/chroma.py. Installed via PyPI because conda packages don't support Python 3.13

Copilot AI review requested due to automatic review settings January 26, 2026 00:36

AtR1an requested a review from a team as a code owner January 26, 2026 00:36

AtR1an requested review from knime-ghub-bot and removed request for a team January 26, 2026 00:36

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AtR1an force-pushed the todo/AP-25545-update-deps branch from 2b561f7 to 9520191 Compare January 26, 2026 00:47

Copilot AI review requested due to automatic review settings January 26, 2026 16:19

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Copilot AI review requested due to automatic review settings January 27, 2026 09:36

marc-lehner force-pushed the todo/AP-25545-update-deps branch from 4cf2a2d to 6a4a163 Compare January 27, 2026 09:36

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AtR1an and others added 12 commits January 27, 2026 10:43

AP-25545: Defer expensive imports

34a7cc0

AP-25545: Update StructuredTool import

adb04a6

AP-25545: Migrate Vertex nodes to langchain_google_genai

5b8d530

Which now provides a unified API for Google AI Studio and Vertex AI

AP-25545: Use RETRIEVAL_QUERY task type in Vertex AI Embeddings

968191a

For backwards compatibility

AP-25545: Always copy chroma vector store

ddf9a21

Because chroma no longer provides the information where the vectorstore is persisted.

AP-25545: Change imports of deprecated agent nodes to langchain_classic

c538339

AP-25545: Restore tool error behavior

fa90c7a

AP-25545: Update dependencies

6b56e2e

AP-25545: Adapt LLMChatModelAdapter to langchain 1.x API

d78fd72

AP-25545: Monkey-patch giskard to support newer scipy

c3e9889

AP-25545: Update and document dependencies

03f7d6b

Tested locally on Windows.

AP-25545: update to extension bundling 5.10 (includes pixi 0.63.2)

d341769

AP-25545 (Update to latest langchain 1.x version)

marc-lehner force-pushed the todo/AP-25545-update-deps branch from 6a4a163 to e216fa0 Compare January 27, 2026 09:50

Copilot AI review requested due to automatic review settings January 27, 2026 13:22

marc-lehner force-pushed the todo/AP-25545-update-deps branch from e216fa0 to 8f521fb Compare January 27, 2026 13:22

Copilot AI reviewed Jan 27, 2026

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AP-25545: add knime-python-versions 5.10 and knime-extension 5.10

11b6898

AP-25545 (Update to latest langchain 1.x version)

marc-lehner force-pushed the todo/AP-25545-update-deps branch from 8f521fb to 11b6898 Compare January 27, 2026 13:26

chaubold approved these changes Jan 27, 2026

View reviewed changes

AP-25545: update to 5.11

47dc00c

AP-25545 (Update to latest langchain 1.x version)

Copilot AI review requested due to automatic review settings February 6, 2026 09:50

Copilot AI reviewed Feb 6, 2026

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Todo/ap 25545 update deps #26

Todo/ap 25545 update deps #26

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	# no-build = true
	# no-build = true # Disabled to allow building packages from source during local development; re-enable in CI for reproducible binary-only builds.

	# knime-python-versions = "5.8.*"
	# knime-python-versions = "5.8.*" # Disabled: only needed for multi-runtime KNIME setups; re-enable if/when multiple Python versions must be supported

	task_type="RETRIEVAL_QUERY", # for backwards compatibility with old VertexAIEmbeddings
	task_type="RETRIEVAL_QUERY", # for backwards compatibility with old VertexAIEmbeddings

		# AP-25545: Monkey-patch scipy.stats.stats to fix Giskard import error with newer scipy versions
		# The error is: ImportError: cannot import name 'Ks_2sampResult' from 'scipy.stats.stats'

-# AP-25545: Monkey-patch scipy.stats.stats to fix Giskard import error with newer scipy versions
-# The error is: ImportError: cannot import name 'Ks_2sampResult' from 'scipy.stats.stats'
+# AP-25545: Monkey-patch scipy.stats.stats to fix Giskard import error with newer scipy versions.
+# The error is: ImportError: cannot import name 'Ks_2sampResult' from 'scipy.stats.stats'.
+# TODO: Remove this patch when Giskard no longer imports Ks_2sampResult from scipy.stats.stats,
+#       or when we depend on a Giskard version that supports newer SciPy versions without this workaround.

	langchain-chroma = "==1.1.0" # Direct: used in indexes/chroma.py installed via pypi because conda packages don't support python 3.13
	langchain-chroma = "==1.1.0" # Direct: used in indexes/chroma.py. Installed via PyPI because conda packages don't support Python 3.13

Todo/ap 25545 update deps #26

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