Merge remote-tracking branch 'public/main' into darabos-open-source-merge

.github/workflows/docs.yaml

@@ -0,0 +1,28 @@
+name: docs
+
+on:
+  push:
+    branches: [main]
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+      - uses: actions/cache@v4
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - run: pip install mkdocs-material mkdocstrings-python mkdocs-autorefs
+      - run: mkdocs gh-deploy --force

.github/workflows/release-lynxkite-app.yaml

@@ -0,0 +1,18 @@
+name: release-lynxkite-app
+on:
+  workflow_dispatch:
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+      - name: Build
+        working-directory: lynxkite-app
+        run: uv build
+      - name: Publish
+        working-directory: lynxkite-app
+        run: uv publish

.github/workflows/release-lynxkite-core.yaml

@@ -0,0 +1,18 @@
+name: release-lynxkite-core
+on:
+  workflow_dispatch:
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+      - name: Build
+        working-directory: lynxkite-core
+        run: uv build
+      - name: Publish
+        working-directory: lynxkite-core
+        run: uv publish

.github/workflows/release-lynxkite-graph-analytics.yaml

@@ -0,0 +1,18 @@
+name: release-lynxkite-graph-analytics
+on:
+  workflow_dispatch:
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+      - name: Build
+        working-directory: lynxkite-graph-analytics
+        run: uv build
+      - name: Publish
+        working-directory: lynxkite-graph-analytics
+        run: uv publish

.github/workflows/test.yaml

@@ -2,8 +2,6 @@ name: test
 
 on:
   pull_request:
-  push:
-    branches: [main]
 
 jobs:
   test:

README.md

@@ -7,14 +7,22 @@ sdk: docker
 app_port: 7860
 ---
 
-# LynxKite 2024
+# LynxKite 2000:MM Enterprise
 
-This is an experimental rewrite of [LynxKite](https://github.com/lynxkite/lynxkite). It is not compatible with the
-original LynxKite. The primary goals of this rewrite are:
+LynxKite 2000:MM is a GPU-accelerated data science platform and a general tool for collaboratively edited workflows.
 
-- Target GPU clusters instead of Hadoop clusters. We use Python instead of Scala, RAPIDS instead of Apache Spark.
-- More extensible backend. Make it easy to add new LynxKite boxes. Make it easy to use our frontend for other purposes,
-  configuring and executing other pipelines.
+Features include:
+
+- A web UI for building and executing data science workflows.
+- An extensive toolbox of graph analytics operations powered by NVIDIA RAPIDS (CUDA).
+- An integrated collaborative code editor makes it easy to add new operations.
+- An environment for visually designing neural network model architectures.
+- The infrastructure for easily creating other workflow design environments. See `lynxkite-pillow-example` for a simple example.
+
+This is the next evolution of the classical [LynxKite](https://github.com/lynxkite/lynxkite).
+The two tools offer similar functionality, but are not compatible.
+This version runs on GPU clusters instead of Hadoop clusters.
+It targets CUDA instead of Apache Spark. It is much more extensible.
 
 ## Structure
 
@@ -67,3 +75,9 @@ To work on the documentation:
 uv pip install mkdocs-material mkdocstrings[python]
 mkdocs serve
 ```
+
+## License
+
+LynxKite 2000:MM Enterprise is built on top of the open-source [LynxKite 2000:MM](https://github.com/lynxkite/lynxkite-2000).
+
+Inquire with [Lynx Analytics](https://www.lynxanalytics.com/) for the licensing of this repository.

docs/index.md

@@ -1,3 +1,5 @@
-# Getting started
+---
+title: Overview
+---
 
-Good luck getting started!
+--8<-- "README.md"

docs/license.md

@@ -0,0 +1,11 @@
+# License
+
+LynxKite 2000:MM is available under the GNU AGPLv3 license below.
+
+Additionally, [Lynx Analytics](https://www.lynxanalytics.com/) offers a commercial license of LynxKite 2000:MM
+that includes additional features and support. Get in touch if you are interested in life sciences tools
+and cluster deployment!
+
+```
+--8<-- "LICENSE"
+```

docs/reference/lynxkite-core/executors/one_by_one.md

@@ -0,0 +1 @@
+::: lynxkite.core.executors.one_by_one

docs/reference/lynxkite-core/executors/simple.md

@@ -0,0 +1 @@
+::: lynxkite.core.executors.simple

docs/reference/lynxkite-core/ops.md

@@ -0,0 +1 @@
+::: lynxkite.core.ops

docs/reference/lynxkite-core/workspace.md

@@ -0,0 +1 @@
+::: lynxkite.core.workspace

docs/reference/lynxkite-graph-analytics/core.md

@@ -0,0 +1 @@
+::: lynxkite_graph_analytics.core

docs/reference/lynxkite-graph-analytics/operations.md

@@ -0,0 +1,3 @@
+::: lynxkite_graph_analytics.lynxkite_ops
+::: lynxkite_graph_analytics.ml_ops
+::: lynxkite_graph_analytics.networkx_ops

docs/usage/plugins.md

@@ -0,0 +1,278 @@
+# Plugin development
+
+Plugins can provide additional operations for an existing LynxKite environment,
+and they can also provide new environments.
+
+## Creating a new plugin
+
+`.py` files inside the LynxKite data directory are automatically imported each time a
+workspace is executed. You can create a new plugin by creating a new `.py` file in the
+data directory. LynxKite even includes an integrated editor for this purpose.
+Click **New code file** in the directory where you want to create the file.
+
+Plugins in subdirectories of the data directory are imported when executing workspaces
+within those directories. This allows you to create plugins that are only available
+in specific workspaces.
+
+You can also create and distribute plugins as Python packages. In this case the
+module name must start with `lynxkite_` for it to be automatically imported on startup.
+
+### Plugin dependencies
+
+When creating a plugin as a "code file", you can create a `requirements.txt` file in the same
+directory. This file will be used to install the dependencies of the plugin.
+
+## Adding new operations
+
+Any piece of Python code can easily be wrapped into a LynxKite operation.
+Let's say we have some code that calculates the length of a string column in a Pandas DataFrame:
+
+```python
+df["length"] = df["my_column"].str.len()
+```
+
+We can turn it into a LynxKite operation using the
+[`@op`](../reference/lynxkite-core/ops.md#lynxkite.core.ops.op) decorator:
+
+```python
+import pandas as pd
+from lynxkite.core.ops import op
+
+@op("LynxKite Graph Analytics", "Get column length")
+def get_length(df: pd.DataFrame, *, column_name: str):
+    """
+    Gets the length of a string column.
+
+    Args:
+        column_name: The name of the column to get the length of.
+    """
+    df = df.copy()
+    df["length"] = df[column_name].str.len()
+    return df
+```
+
+Let's review the changes we made.
+
+### The `@op` decorator
+
+The [`@op`](../reference/lynxkite-core/ops.md#lynxkite.core.ops.op) decorator registers a
+function as a LynxKite operation. The first argument is the name of the environment,
+the second argument is the name of the operation.
+
+When defining multiple operations, you can use
+[`ops.op_registration`](../reference/lynxkite-core/ops.md#lynxkite.core.ops.op_registration)
+for convenience:
+```python
+op = ops.op_registration("LynxKite Graph Analytics")
+
+@op("An operation")
+def my_op():
+    ...
+```
+
+### The function signature
+
+`*` in the list of function arguments marks the start of keyword-only arguments.
+The arguments before `*` will become _inputs_ of the operation. The arguments after `*` will
+be its _parameters_.
+
+```python
+#              /--- inputs ---\     /- parameters -\
+def get_length(df: pd.DataFrame, *, column_name: str):
+```
+
+LynxKite uses the type annotations of the function arguments to provide input validation,
+conversion, and the right UI on the frontend.
+
+The types supported for **inputs** are determined by the environment. For graph analytics,
+the possibilities are:
+
+- `pandas.DataFrame`
+- `networkx.Graph`
+- [`lynxkite_graph_analytics.Bundle`](../reference/lynxkite-graph-analytics/core.md#lynxkite_graph_analytics.core.Bundle)
+
+The inputs of an operation are automatically converted to the right type, when possible.
+
+To make an input optional, use an optional type, like `pd.DataFrame | None`.
+
+The position of the input and output connectors can be controlled using the
+[`@ops.input_position`](../reference/lynxkite-core/ops.md#lynxkite.core.ops.input_position) and
+[`@ops.output_position`](../reference/lynxkite-core/ops.md#lynxkite.core.ops.output_position)
+decorators. By default, inputs are on the left and outputs on the right.
+
+All **parameters** are stored in LynxKite workspaces as strings. If a type annotation is provided,
+LynxKite will convert the string to the right type and provide the right UI.
+
+- `str`, `int`, `float` are presented as a text box and converted to the given type.
+- `bool` is presented as a checkbox.
+- [`lynxkite.core.ops.LongStr`](../reference/lynxkite-core/ops.md#lynxkite.core.ops.LongStr)
+  is presented as a text area.
+- Enums are presented as a dropdown list.
+- Pydantic models are presented as their JSON string representations. (Unless you add custom UI
+  for them.) They are converted to the model object when your function is called.
+
+### Slow operations
+
+If the function takes a significant amount of time to run, we must either:
+
+- Write an asynchronous function.
+- Pass `slow=True` to the `@op` decorator. LynxKite will run the function in a separate thread.
+
+`slow=True` also causes the results of the operation to be cached on disk. As long as
+its inputs don't change, the operation will not be run again. This is useful for both
+synchronous and synchronous operations.
+
+### Documentation
+
+The docstring of the function is used as the operation's description. You can use
+Google-style or Numpy-style docstrings.
+(See [Griffe's documentation](https://mkdocstrings.github.io/griffe/reference/docstrings/).)
+
+The docstring should be omitted for simple operations like the one above.
+
+### Outputting results
+
+The return value of the function is the output of the operation. It will be passed to the
+next operation in the pipeline.
+
+An operation can have multiple outputs. In this case, the return value must be a dictionary,
+and the list of outputs must be declared in the `@op` decorator.
+
+```python
+@op("LynxKite Graph Analytics", "Train/test split", outputs=["train", "test"])
+def test_split(df: pd.DataFrame, *, test_ratio=0.1):
+    test = df.sample(frac=test_ratio).reset_index()
+    train = df.drop(test.index).reset_index()
+    return {"train": train, "test": test}
+```
+
+### Displaying results
+
+The outputs of the operation can be used by other operations. But we can also generate results
+that are meant to be viewed by the user. The different options for this are controlled by the `view`
+argument of the `@op` decorator.
+
+The `view` argument can be one of the following:
+
+- `matplotlib`: Just plot something with Matplotlib and it will be displayed in the UI.
+
+    ```python
+    @op("LynxKite Graph Analytics", "Plot column histogram", view="matplotlib")
+    def plot(df: pd.DataFrame, *, column_name: str):
+        df[column_name].value_counts().sort_index().plot.bar()
+    ```
+
+- `visualization`: Draws a chart using [ECharts](https://echarts.apache.org/examples/en/index.html).
+  You need to return a dictionary with the chart configuration, which ECharts calls `option`.
+
+    ```python
+    @op("View loss", view="visualization")
+    def view_loss(bundle: core.Bundle):
+        loss = bundle.dfs["training"].training_loss.tolist()
+        v = {
+            "title": {"text": "Training loss"},
+            "xAxis": {"type": "category"},
+            "yAxis": {"type": "value"},
+            "series": [{"data": loss, "type": "line"}],
+        }
+        return v
+    ```
+
+- `image`: Return an image as a
+  [data URL](https://developer.mozilla.org/en-US/docs/Web/URI/Reference/Schemes/data)
+  and it will be displayed.
+- `molecule`: Return a molecule as a PDB or SDF string, or an `rdkit.Chem.Mol` object.
+  It will be displayed using [3Dmol.js](https://3Dmol.org/).
+- `table_view`: Return
+  [`Bundle.to_dict()`](../reference/lynxkite-graph-analytics/core.md#lynxkite_graph_analytics.core.Bundle.to_dict).
+
+## Adding new environments
+
+A new environment means a completely new set of operations, and (optionally) a new
+executor. There's nothing to be done for setting up a new environment. Just start
+registering operations into it.
+
+### No executor
+
+By default, the new environment will have no executor. This can be useful!
+
+LynxKite workspaces are stored as straightforward JSON files and updated on every modification.
+You can use LynxKite for configuring workflows and have a separate system
+read the JSON files.
+
+Since the code of the operations is not executed in this case, you can create functions that do nothing.
+Alternatively, you can use the
+[`register_passive_op`](../reference/lynxkite-core/ops.md#lynxkite.core.ops.register_passive_op)
+and
+[`passive_op_registration`](../reference/lynxkite-core/ops.md#lynxkite.core.ops.passive_op_registration)
+functions to easily whip up a set of operations:
+
+```python
+from lynxkite.core.ops import passive_op_registration, Parameter as P
+
+op = passive_op_registration("My Environment")
+op('Scrape documents', params=[P('url', '')])
+op('Conversation logs')
+op('Extract graph')
+op('Compute embeddings', params=[P.options('method', ['LLM', 'graph', 'random']), P('dimensions', 1234)])
+op('Vector DB', params=[P.options('backend', ['ANN', 'HNSW'])])
+op('Chat UI', outputs=[])
+op('Chat backend')
+```
+
+### Built-in executors
+
+LynxKite comes with two built-in executors. You can register these for your environment
+and you're good to go.
+
+```python
+from lynxkite.core.executors import simple
+simple.register("My Environment")
+```
+
+The [`simple` executor](../reference/lynxkite-core/executors/simple.md)
+runs each operation once, passing the output of the preceding operation
+as the input to the next one. No tricks. You can use any types as inputs and outputs.
+
+```python
+from lynxkite.core.executors import one_by_one
+one_by_one.register("My Environment")
+```
+
+The [`one_by_one` executor](../reference/lynxkite-core/executors/one_by_one.md)
+expects that the code for operations is the code for transforming
+a single element. If an operation returns an iterable, it will be split up
+into its elements, and the next operation is called for each element.
+
+Sometimes you need the full contents of an input. The `one_by_one` executor
+lets you choose between the two modes by the orientation of the input connector.
+If the input connector is horizontal (left or right), it takes single elements.
+If the input connector is vertical (top or bottom), it takes an iterable of all the incoming data.
+
+A unique advantage of this setup is that horizontal inputs can have loops across
+horizontal inputs. Just make sure that loops eventually discard all elements, so you don't
+end up with an infinite loop.
+
+### Custom executors
+
+A custom executor can be registered using
+[`@ops.register_executor`](../reference/lynxkite-core/ops.md#lynxkite.core.ops.register_executor).
+
+```python
+@ops.register_executor(ENV)
+async def execute(ws: workspace.Workspace):
+    catalog = ops.CATALOGS[ws.env]
+    ...
+```
+
+The executor must be an asynchronous function that takes a
+[`workspace.Workspace`](../reference/lynxkite-core/workspace.md#lynxkite.core.workspace.Workspace)
+as an argument. The return value is ignored and it's up to you how you process the workspace.
+
+To update the frontend as the executor processes the workspace, call
+[`WorkspaceNode.publish_started`](../reference/lynxkite-core/workspace.md#lynxkite.core.workspace.WorkspaceNode.publish_started)
+when starting to execute a node, and
+[`WorkspaceNode.publish_result`](../reference/lynxkite-core/workspace.md#lynxkite.core.workspace.WorkspaceNode.publish_result)
+to publish the results. Use
+[`WorkspaceNode.publish_error`](../reference/lynxkite-core/workspace.md#lynxkite.core.workspace.WorkspaceNode.publish_error)
+if the node failed.

docs/usage/quickstart.md

@@ -0,0 +1,25 @@
+# Quickstart
+
+Install the LynxKite application with `pip`:
+```bash
+pip install lynxkite
+```
+
+To be able to do anything useful, you also need to install one or more LynxKite environments.
+If you want to work with data science and graph analytics, install the `lynxkite-graph-analytics` package:
+```bash
+pip install lynxkite-graph-analytics
+```
+
+Create a folder for storing your LynxKite projects:
+```bash
+mkdir ~/lynxkite_projects
+```
+
+You're ready to run LynxKite!
+```bash
+cd ~/lynxkite_projects
+lynxkite
+```
+
+Open [http://localhost:8000/](http://localhost:8000/) in your browser.

lynxkite-app/pyproject.toml

@@ -12,6 +12,10 @@ dependencies = [
     "sse-starlette>=2.2.1",
     "griffe>=1.7.3",
 ]
+classifiers = ["Private :: Do Not Upload"]
+
+[project.urls]
+Homepage = "https://github.com/lynxkite/lynxkite-2000/"
 
 [project.optional-dependencies]
 dev = [

lynxkite-app/src/lynxkite_app/main.py

@@ -33,10 +33,17 @@ app.include_router(crdt.router)
 app.add_middleware(GZipMiddleware)
 
 
+def _get_ops(env: str):
+    catalog = ops.CATALOGS[env]
+    res = {op.name: op.model_dump() for op in catalog.values()}
+    res.setdefault("Comment", ops.COMMENT_OP.model_dump())
+    return res
+
+
 @app.get("/api/catalog")
 def get_catalog(workspace: str):
     ops.load_user_scripts(workspace)
-    return {k: {op.name: op.model_dump() for op in v.values()} for k, v in ops.CATALOGS.items()}
+    return {env: _get_ops(env) for env in ops.CATALOGS}
 
 
 class SaveRequest(workspace.BaseConfig):

lynxkite-app/web/package-lock.json

@@ -38,21 +38,17 @@
         "yjs": "^13.6.20"
       },
       "devDependencies": {
-        "@eslint/js": "^9.15.0",
         "@playwright/test": "^1.50.1",
+        "@tailwindcss/typography": "^0.5.16",
         "@types/node": "^22.13.1",
         "@types/react": "^18.3.14",
         "@types/react-dom": "^18.3.2",
         "@vitejs/plugin-react-swc": "^3.5.0",
         "autoprefixer": "^10.4.20",
-        "eslint": "^9.15.0",
-        "eslint-plugin-react-hooks": "^5.0.0",
-        "eslint-plugin-react-refresh": "^0.4.14",
         "globals": "^15.12.0",
         "postcss": "^8.4.49",
         "tailwindcss": "^3.4.16",
         "typescript": "~5.6.2",
-        "typescript-eslint": "^8.15.0",
         "vite": "^6.3.4"
       },
       "optionalDependencies": {
@@ -801,146 +797,6 @@
         "node": ">=18"
       }
     },
-    "node_modules/@eslint-community/eslint-utils": {
-      "version": "4.4.1",
-      "resolved": "https://registry.npmjs.org/@eslint-community/eslint-utils/-/eslint-utils-4.4.1.tgz",
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-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "eslint-visitor-keys": "^3.4.3"
-      },
-      "engines": {
-        "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
-      },
-      "funding": {
-        "url": "https://opencollective.com/eslint"
-      },
-      "peerDependencies": {
-        "eslint": "^6.0.0 || ^7.0.0 || >=8.0.0"
-      }
-    },
-    "node_modules/@eslint-community/eslint-utils/node_modules/eslint-visitor-keys": {
-      "version": "3.4.3",
-      "resolved": "https://registry.npmjs.org/eslint-visitor-keys/-/eslint-visitor-keys-3.4.3.tgz",
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-      "dev": true,
-      "license": "Apache-2.0",
-      "engines": {
-        "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
-      },
-      "funding": {
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-      }
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-    "node_modules/@eslint-community/regexpp": {
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-      "resolved": "https://registry.npmjs.org/@eslint-community/regexpp/-/regexpp-4.12.1.tgz",
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-      "license": "MIT",
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-      "dev": true,
-      "license": "Apache-2.0",
-      "dependencies": {
-        "@eslint/object-schema": "^2.1.5",
-        "debug": "^4.3.1",
-        "minimatch": "^3.1.2"
-      },
-      "engines": {
-        "node": "^18.18.0 || ^20.9.0 || >=21.1.0"
-      }
-    },
-    "node_modules/@eslint/core": {
-      "version": "0.9.1",
-      "resolved": "https://registry.npmjs.org/@eslint/core/-/core-0.9.1.tgz",
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-      "dev": true,
-      "license": "Apache-2.0",
-      "dependencies": {
-        "@types/json-schema": "^7.0.15"
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-      }
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@@ -4763,34 +3946,32 @@
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       }
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-      "funding": {
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       "license": "MIT"
     },
+    "node_modules/lodash.castarray": {
+      "version": "4.4.0",
+      "resolved": "https://registry.npmjs.org/lodash.castarray/-/lodash.castarray-4.4.0.tgz",
+      "integrity": "sha512-aVx8ztPv7/2ULbArGJ2Y42bG1mEQ5mGjpdvrbJcJFU3TbYybe+QlLS4pst9zV52ymy2in1KpFPiZnAOATxD4+Q==",
+      "dev": true,
+      "license": "MIT"
+    },
     "node_modules/lodash.debounce": {
       "version": "4.0.8",
       "resolved": "https://registry.npmjs.org/lodash.debounce/-/lodash.debounce-4.0.8.tgz",
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       "license": "MIT"
     },
+    "node_modules/lodash.isplainobject": {
+      "version": "4.0.6",
+      "resolved": "https://registry.npmjs.org/lodash.isplainobject/-/lodash.isplainobject-4.0.6.tgz",
+      "integrity": "sha512-oSXzaWypCMHkPC3NvBEaPHf0KsA5mvPrOPgQWDsbg8n7orZ290M0BmC/jgRZ4vcJ6DTAhjrsSYgdsW/F+MFOBA==",
+      "dev": true,
+      "license": "MIT"
+    },
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       "version": "4.6.2",
       "resolved": "https://registry.npmjs.org/lodash.merge/-/lodash.merge-4.6.2.tgz",
@@ -5494,19 +4675,6 @@
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-      "license": "ISC",
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-      },
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       "version": "1.2.8",
       "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.8.tgz",
@@ -5587,13 +4755,6 @@
       "license": "MIT",
       "optional": true
     },
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-      "version": "1.4.0",
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-      "dev": true,
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@@ -5671,56 +4832,6 @@
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       }
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-      "integrity": "sha512-6IpQ7mKUxRcZNLIObR0hz7lxsapSSIYNZJwXPGeF0mTVqGKFIXj1DQcMoT22S3ROcLyY/rz0PWaWZ9ayWmad9g==",
-      "dev": true,
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-      "dependencies": {
-        "deep-is": "^0.1.3",
-        "fast-levenshtein": "^2.0.6",
-        "levn": "^0.4.1",
-        "prelude-ls": "^1.2.1",
-        "type-check": "^0.4.0",
-        "word-wrap": "^1.2.5"
-      },
-      "engines": {
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-      "resolved": "https://registry.npmjs.org/p-limit/-/p-limit-3.1.0.tgz",
-      "integrity": "sha512-TYOanM3wGwNGsZN2cVTYPArw454xnXj5qmWF1bEoAc4+cU/ol7GVh7odevjp1FNHduHc3KZMcFduxU5Xc6uJRQ==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "yocto-queue": "^0.1.0"
-      },
-      "engines": {
-        "node": ">=10"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/sindresorhus"
-      }
-    },
-    "node_modules/p-locate": {
-      "version": "5.0.0",
-      "resolved": "https://registry.npmjs.org/p-locate/-/p-locate-5.0.0.tgz",
-      "integrity": "sha512-LaNjtRWUBY++zB5nE/NwcaoMylSPk+S+ZHNB1TzdbMJMny6dynpAGt7X/tl/QYq3TIeE6nxHppbo2LGymrG5Pw==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "p-limit": "^3.0.2"
-      },
-      "engines": {
-        "node": ">=10"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/sindresorhus"
-      }
-    },
     "node_modules/package-json-from-dist": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/package-json-from-dist/-/package-json-from-dist-1.0.1.tgz",
@@ -5796,16 +4907,6 @@
         "url": "https://github.com/sponsors/sindresorhus"
       }
     },
-    "node_modules/path-exists": {
-      "version": "4.0.0",
-      "resolved": "https://registry.npmjs.org/path-exists/-/path-exists-4.0.0.tgz",
-      "integrity": "sha512-ak9Qy5Q7jYb2Wwcey5Fpvg2KoAc/ZIhLSLOSBmRmygPsGwkVVt0fZa0qrtMz+m6tJTAHfZQ8FnmB4MG4LWy7/w==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=8"
-      }
-    },
     "node_modules/path-key": {
       "version": "3.1.1",
       "resolved": "https://registry.npmjs.org/path-key/-/path-key-3.1.1.tgz",
@@ -6104,16 +5205,6 @@
       "dev": true,
       "license": "MIT"
     },
-    "node_modules/prelude-ls": {
-      "version": "1.2.1",
-      "resolved": "https://registry.npmjs.org/prelude-ls/-/prelude-ls-1.2.1.tgz",
-      "integrity": "sha512-vkcDPrRZo1QZLbn5RLGPpg/WmIQ65qoWWhcGKf/b5eplkkarX0m9z8ppCat4mlOqUsWpyNuYgO3VRyrYHSzX5g==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">= 0.8.0"
-      }
-    },
     "node_modules/prettier": {
       "version": "3.4.2",
       "resolved": "https://registry.npmjs.org/prettier/-/prettier-3.4.2.tgz",
@@ -6152,16 +5243,6 @@
       "license": "MIT",
       "optional": true
     },
-    "node_modules/punycode": {
-      "version": "2.3.1",
-      "resolved": "https://registry.npmjs.org/punycode/-/punycode-2.3.1.tgz",
-      "integrity": "sha512-vYt7UD1U9Wg6138shLtLOvdAu+8DsC/ilFtEVHcH+wydcSpNE20AfSOduf6MkRFahL5FY7X1oU7nKVZFtfq8Fg==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=6"
-      }
-    },
     "node_modules/queue-microtask": {
       "version": "1.2.3",
       "resolved": "https://registry.npmjs.org/queue-microtask/-/queue-microtask-1.2.3.tgz",
@@ -6508,19 +5589,6 @@
         "loose-envify": "^1.1.0"
       }
     },
-    "node_modules/semver": {
-      "version": "7.6.3",
-      "resolved": "https://registry.npmjs.org/semver/-/semver-7.6.3.tgz",
-      "integrity": "sha512-oVekP1cKtI+CTDvHWYFUcMtsK/00wmAEfyqKfNdARm8u1wNVhSgaX7A8d4UuIlUI5e84iEwOhs7ZPYRmzU9U6A==",
-      "dev": true,
-      "license": "ISC",
-      "bin": {
-        "semver": "bin/semver.js"
-      },
-      "engines": {
-        "node": ">=10"
-      }
-    },
     "node_modules/set-cookie-parser": {
       "version": "2.7.1",
       "resolved": "https://registry.npmjs.org/set-cookie-parser/-/set-cookie-parser-2.7.1.tgz",
@@ -6726,19 +5794,6 @@
         "node": ">=8"
       }
     },
-    "node_modules/strip-json-comments": {
-      "version": "3.1.1",
-      "resolved": "https://registry.npmjs.org/strip-json-comments/-/strip-json-comments-3.1.1.tgz",
-      "integrity": "sha512-6fPc+R4ihwqP6N/aIv2f1gMH8lOVtWQHoqC4yK6oSDVVocumAsfCqjkXnqiYMhmMwS/mEHLp7Vehlt3ql6lEig==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=8"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/sindresorhus"
-      }
-    },
     "node_modules/style-to-object": {
       "version": "1.0.8",
       "resolved": "https://registry.npmjs.org/style-to-object/-/style-to-object-1.0.8.tgz",
@@ -6771,19 +5826,6 @@
         "node": ">=16 || 14 >=14.17"
       }
     },
-    "node_modules/supports-color": {
-      "version": "7.2.0",
-      "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-7.2.0.tgz",
-      "integrity": "sha512-qpCAvRl9stuOHveKsn7HncJRvv501qIacKzQlO/+Lwxc9+0q2wLyv4Dfvt80/DPn2pqOBsJdDiogXGR9+OvwRw==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "has-flag": "^4.0.0"
-      },
-      "engines": {
-        "node": ">=8"
-      }
-    },
     "node_modules/supports-preserve-symlinks-flag": {
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/supports-preserve-symlinks-flag/-/supports-preserve-symlinks-flag-1.0.0.tgz",
@@ -6958,19 +6000,6 @@
         "url": "https://github.com/sponsors/wooorm"
       }
     },
-    "node_modules/ts-api-utils": {
-      "version": "1.4.3",
-      "resolved": "https://registry.npmjs.org/ts-api-utils/-/ts-api-utils-1.4.3.tgz",
-      "integrity": "sha512-i3eMG77UTMD0hZhgRS562pv83RC6ukSAC2GMNWc+9dieh/+jDM5u5YG+NHX6VNDRHQcHwmsTHctP9LhbC3WxVw==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=16"
-      },
-      "peerDependencies": {
-        "typescript": ">=4.2.0"
-      }
-    },
     "node_modules/ts-interface-checker": {
       "version": "0.1.13",
       "resolved": "https://registry.npmjs.org/ts-interface-checker/-/ts-interface-checker-0.1.13.tgz",
@@ -6990,19 +6019,6 @@
       "integrity": "sha512-FHncC10WpBd2eOmGwpmQsWLDoK4cqsA/UT/GqNoaKOQnT8uzhtCbg3EoUDMvqpOSAI0S26mr0rkjzbOO6S3v1g==",
       "license": "ISC"
     },
-    "node_modules/type-check": {
-      "version": "0.4.0",
-      "resolved": "https://registry.npmjs.org/type-check/-/type-check-0.4.0.tgz",
-      "integrity": "sha512-XleUoc9uwGXqjWwXaUTZAmzMcFZ5858QA2vvx1Ur5xIcixXIP+8LnFDgRplU30us6teqdlskFfu+ae4K79Ooew==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "prelude-ls": "^1.2.1"
-      },
-      "engines": {
-        "node": ">= 0.8.0"
-      }
-    },
     "node_modules/typescript": {
       "version": "5.6.3",
       "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.6.3.tgz",
@@ -7017,33 +6033,6 @@
         "node": ">=14.17"
       }
     },
-    "node_modules/typescript-eslint": {
-      "version": "8.17.0",
-      "resolved": "https://registry.npmjs.org/typescript-eslint/-/typescript-eslint-8.17.0.tgz",
-      "integrity": "sha512-409VXvFd/f1br1DCbuKNFqQpXICoTB+V51afcwG1pn1a3Cp92MqAUges3YjwEdQ0cMUoCIodjVDAYzyD8h3SYA==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "@typescript-eslint/eslint-plugin": "8.17.0",
-        "@typescript-eslint/parser": "8.17.0",
-        "@typescript-eslint/utils": "8.17.0"
-      },
-      "engines": {
-        "node": "^18.18.0 || ^20.9.0 || >=21.1.0"
-      },
-      "funding": {
-        "type": "opencollective",
-        "url": "https://opencollective.com/typescript-eslint"
-      },
-      "peerDependencies": {
-        "eslint": "^8.57.0 || ^9.0.0"
-      },
-      "peerDependenciesMeta": {
-        "typescript": {
-          "optional": true
-        }
-      }
-    },
     "node_modules/ufo": {
       "version": "1.5.4",
       "resolved": "https://registry.npmjs.org/ufo/-/ufo-1.5.4.tgz",
@@ -7248,16 +6237,6 @@
       "integrity": "sha512-4hLB8Py4zZce5s4yd9XzopqwVv/yGNhV1Bl8NTmCq1763HeK2+EwVTv+leGeL13Dnh2wfbqowVPXCIO0z4taYw==",
       "license": "(MIT AND Zlib)"
     },
-    "node_modules/uri-js": {
-      "version": "4.4.1",
-      "resolved": "https://registry.npmjs.org/uri-js/-/uri-js-4.4.1.tgz",
-      "integrity": "sha512-7rKUyy33Q1yc98pQ1DAmLtwX109F7TIfWlW1Ydo8Wl1ii1SeHieeh0HHfPeL2fMXK6z0s8ecKs9frCuLJvndBg==",
-      "dev": true,
-      "license": "BSD-2-Clause",
-      "dependencies": {
-        "punycode": "^2.1.0"
-      }
-    },
     "node_modules/use-sync-external-store": {
       "version": "1.2.2",
       "resolved": "https://registry.npmjs.org/use-sync-external-store/-/use-sync-external-store-1.2.2.tgz",
@@ -7427,16 +6406,6 @@
         "node": ">= 8"
       }
     },
-    "node_modules/word-wrap": {
-      "version": "1.2.5",
-      "resolved": "https://registry.npmjs.org/word-wrap/-/word-wrap-1.2.5.tgz",
-      "integrity": "sha512-BN22B5eaMMI9UMtjrGd5g5eCYPpCPDUy0FJXbYsaT5zYxjFOckS53SQDE3pWkVoWpHXVb3BrYcEN4Twa55B5cA==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=0.10.0"
-      }
-    },
     "node_modules/wrap-ansi": {
       "version": "8.1.0",
       "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-8.1.0.tgz",
@@ -7673,19 +6642,6 @@
         "url": "https://github.com/sponsors/dmonad"
       }
     },
-    "node_modules/yocto-queue": {
-      "version": "0.1.0",
-      "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
-      "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=10"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/sindresorhus"
-      }
-    },
     "node_modules/zrender": {
       "version": "5.6.0",
       "resolved": "https://registry.npmjs.org/zrender/-/zrender-5.6.0.tgz",

lynxkite-app/web/package.json

@@ -41,6 +41,7 @@
   },
   "devDependencies": {
     "@playwright/test": "^1.50.1",
+    "@tailwindcss/typography": "^0.5.16",
     "@types/node": "^22.13.1",
     "@types/react": "^18.3.14",
     "@types/react-dom": "^18.3.2",

lynxkite-app/web/src/Tooltip.tsx

@@ -10,7 +10,7 @@ export default function Tooltip(props: any) {
       <a data-tooltip-id={id} tabIndex={0}>
         {props.children}
       </a>
-      <ReactTooltip id={id} className="tooltip" place="top-end">
+      <ReactTooltip id={id} className="tooltip prose" place="top-end">
         {props.doc.map?.(
           (section: any, i: number) =>
             section.kind === "text" && <Markdown key={i}>{section.value}</Markdown>,

lynxkite-app/web/src/index.css

@@ -100,15 +100,6 @@ body {
     font-size: 16px;
     font-weight: initial;
     max-width: 300px;
-
-    p {
-      margin-top: 1em;
-      line-height: normal;
-    }
-
-    p:first-child {
-      margin-top: 0;
-    }
   }
 
   .expanded .lynxkite-node {
@@ -293,6 +284,26 @@ body {
     }
   }
 
+  .react-flow__node-comment {
+    width: auto !important;
+    height: auto !important;
+    max-width: 400px;
+
+    .comment-view {
+      border-radius: 4px;
+      padding: 5px 10px;
+    }
+
+    .comment-editor {
+      width: 400px;
+      box-shadow: 0px 5px 20px 0px rgba(0, 0, 0, 0.3);
+      border-radius: 4px;
+      padding: 5px 10px;
+      border: 1px solid #ccc;
+      overflow-y: hidden;
+    }
+  }
+
   .env-select {
     background: transparent;
     color: #39bcf3;
@@ -515,6 +526,7 @@ body {
   z-index: -10 !important;
 }
 
+.selected .comment-view,
 .selected .lynxkite-node {
   outline: var(--xy-selection-border, var(--xy-selection-border-default));
   outline-offset: 7.5px;

lynxkite-app/web/src/workspace/Workspace.tsx

@@ -37,6 +37,7 @@ import LynxKiteEdge from "./LynxKiteEdge.tsx";
 import { LynxKiteState } from "./LynxKiteState";
 import NodeSearch, { type OpsOp, type Catalog, type Catalogs } from "./NodeSearch.tsx";
 import NodeWithGraphCreationView from "./nodes/GraphCreationNode.tsx";
+import NodeWithComment from "./nodes/NodeWithComment.tsx";
 import NodeWithImage from "./nodes/NodeWithImage.tsx";
 import NodeWithMolecule from "./nodes/NodeWithMolecule.tsx";
 import NodeWithParams from "./nodes/NodeWithParams";
@@ -77,8 +78,8 @@ function LynxKiteFlow() {
         if (!state.workspace.nodes) return;
         if (!state.workspace.edges) return;
         for (const n of state.workspace.nodes) {
-          if (n.dragHandle !== ".bg-primary") {
-            n.dragHandle = ".bg-primary";
+          if (n.dragHandle !== ".drag-handle") {
+            n.dragHandle = ".drag-handle";
           }
         }
         const nodes = reactFlow.getNodes();
@@ -183,6 +184,7 @@ function LynxKiteFlow() {
       table_view: NodeWithTableView,
       graph_creation_view: NodeWithGraphCreationView,
       molecule: NodeWithMolecule,
+      comment: NodeWithComment,
     }),
     [],
   );

lynxkite-app/web/src/workspace/nodes/LynxKiteNode.tsx

@@ -90,7 +90,7 @@ function LynxKiteNodeComponent(props: LynxKiteNodeProps) {
     >
       <div className="lynxkite-node" style={props.nodeStyle}>
         <div
-          className={`title bg-primary ${data.status}`}
+          className={`title bg-primary drag-handle ${data.status}`}
           style={titleStyle}
           onClick={titleClicked}
         >

lynxkite-app/web/src/workspace/nodes/NodeWithComment.tsx

@@ -0,0 +1,58 @@
+import { useReactFlow } from "@xyflow/react";
+import { useState } from "react";
+import Markdown from "react-markdown";
+import type { UpdateOptions } from "./NodeParameter";
+
+export default function NodeWithComment(props: any) {
+  const reactFlow = useReactFlow();
+  const [editing, setEditing] = useState(false);
+  function setComment(newValue: string, opts?: UpdateOptions) {
+    reactFlow.updateNodeData(props.id, (prevData: any) => ({
+      ...prevData,
+      params: { text: newValue },
+      __execution_delay: opts?.delay || 0,
+    }));
+  }
+  function onClick(e: React.MouseEvent<HTMLDivElement, MouseEvent>) {
+    // Start editing on double-click.
+    if (e.detail === 2) {
+      setEditing(true);
+    }
+  }
+  function finishEditing(el: HTMLTextAreaElement) {
+    setComment(el.value);
+    setEditing(false);
+  }
+  function onKeyDown(e: React.KeyboardEvent<HTMLTextAreaElement>) {
+    if (e.key === "Escape") {
+      finishEditing(e.currentTarget);
+    }
+  }
+  function onInput(el: HTMLTextAreaElement | null) {
+    if (!el) return;
+    el.focus();
+    // Resize the textarea to the content.
+    el.style.height = "auto";
+    el.style.height = `${el.scrollHeight}px`;
+  }
+  if (editing) {
+    return (
+      <textarea
+        className="comment-editor"
+        onBlur={(e) => finishEditing(e.currentTarget)}
+        onKeyDown={onKeyDown}
+        onInput={(e) => onInput(e.currentTarget)}
+        ref={(el) => onInput(el)}
+        defaultValue={props.data.params.text}
+        onClick={(e) => e.stopPropagation()}
+        placeholder="Enter workspace comment"
+      />
+    );
+  }
+  const text = props.data.params.text || "_double-click to edit_";
+  return (
+    <div className="comment-view drag-handle prose" onClick={onClick}>
+      <Markdown>{text}</Markdown>
+    </div>
+  );
+}

lynxkite-app/web/tailwind.config.js

@@ -5,7 +5,7 @@ export default {
   theme: {
     extend: {},
   },
-  plugins: [require("daisyui")],
+  plugins: [require("daisyui"), require("@tailwindcss/typography")],
   daisyui: {
     logs: false,
     themes: [

lynxkite-app/web/tests/basic.spec.ts

@@ -21,7 +21,7 @@ test("Box creation & deletion per env", async () => {
   const envs = await workspace.getEnvs();
   for (const env of envs) {
     await workspace.setEnv(env);
-    const catalog = await workspace.getCatalog();
+    const catalog = (await workspace.getCatalog()).filter((box) => box !== "Comment");
     expect(catalog).not.toHaveLength(0);
     const op = catalog[0];
     await workspace.addBox(op);

lynxkite-app/web/tests/errors.spec.ts

@@ -33,9 +33,9 @@ test("unknown operation", async () => {
   await workspace.addBox("NX › Scale-Free Graph");
   const graphBox = workspace.getBox("NX › Scale-Free Graph 1");
   await graphBox.getByLabel("n", { exact: true }).fill("10");
-  await workspace.setEnv("LynxScribe");
+  await workspace.setEnv("Pillow");
   const csvBox = workspace.getBox("NX › Scale-Free Graph 1");
-  await expect(csvBox.locator(".error")).toHaveText('Operation "NX › Scale-Free Graph" not found.');
+  await expect(csvBox.locator(".error")).toHaveText("Unknown operation.");
   await workspace.setEnv("LynxKite Graph Analytics");
   await expect(csvBox.locator(".error")).not.toBeVisible();
 });

lynxkite-app/web/tests/examples.spec.ts

@@ -3,12 +3,9 @@ import { expect, test } from "@playwright/test";
 import { Workspace } from "./lynxkite";
 
 const WORKSPACES = [
-  // "AIMO",
   "Airlines demo",
   "Bio Cypher demo",
-  // "Graph RAG",
   "Image processing",
-  // "LynxScribe demo",
   "NetworkX demo",
   "Model use",
 ];

lynxkite-core/pyproject.toml

@@ -6,6 +6,10 @@ readme = "README.md"
 requires-python = ">=3.11"
 dependencies = [
 ]
+classifiers = ["Private :: Do Not Upload"]
+
+[project.urls]
+Homepage = "https://github.com/lynxkite/lynxkite-2000/"
 
 [project.optional-dependencies]
 dev = [

lynxkite-core/src/lynxkite/core/executors/one_by_one.py

@@ -1,4 +1,6 @@
-"""A LynxKite executor that assumes most operations operate on their input one by one."""
+"""
+A LynxKite executor that assumes most operations operate on their input one by one.
+"""
 
 from .. import ops
 from .. import workspace
@@ -11,24 +13,24 @@ import typing
 
 
 class Context(ops.BaseConfig):
-    """Passed to operation functions as "_ctx" if they have such a parameter."""
+    """Passed to operation functions as "_ctx" if they have such a parameter.
+
+    Attributes:
+        node: The workspace node that this context is associated with.
+        last_result: The last result produced by the operation.
+          This can be used to incrementally build a result, when the operation
+          is executed for multiple items.
+    """
 
     node: workspace.WorkspaceNode
     last_result: typing.Any = None
 
 
-class Output(ops.BaseConfig):
-    """Return this to send values to specific outputs of a node."""
-
-    output_handle: str
-    value: dict
-
-
-def df_to_list(df):
+def _df_to_list(df):
     return df.to_dict(orient="records")
 
 
-def has_ctx(op):
+def _has_ctx(op):
     sig = inspect.signature(op.func)
     return "_ctx" in sig.parameters
 
@@ -37,16 +39,22 @@ CACHES = {}
 
 
 def register(env: str, cache: bool = True):
-    """Registers the one-by-one executor."""
+    """Registers the one-by-one executor.
+
+    Usage:
+
+        from lynxkite.core.executors import one_by_one
+        one_by_one.register("My Environment")
+    """
     if cache:
         CACHES[env] = {}
         cache = CACHES[env]
     else:
         cache = None
-    ops.EXECUTORS[env] = lambda ws: execute(ws, ops.CATALOGS[env], cache=cache)
+    ops.EXECUTORS[env] = lambda ws: _execute(ws, ops.CATALOGS[env], cache=cache)
 
 
-def get_stages(ws, catalog: ops.Catalog):
+def _get_stages(ws, catalog: ops.Catalog):
     """Inputs on top/bottom are batch inputs. We decompose the graph into a DAG of components along these edges."""
     nodes = {n.id: n for n in ws.nodes}
     batch_inputs = {}
@@ -81,20 +89,20 @@ def _default_serializer(obj):
     return {"__nonserializable__": id(obj)}
 
 
-def make_cache_key(obj):
+def _make_cache_key(obj):
     return orjson.dumps(obj, default=_default_serializer)
 
 
 EXECUTOR_OUTPUT_CACHE = {}
 
 
-async def await_if_needed(obj):
+async def _await_if_needed(obj):
     if inspect.isawaitable(obj):
         return await obj
     return obj
 
 
-async def execute(ws: workspace.Workspace, catalog: ops.Catalog, cache=None):
+async def _execute(ws: workspace.Workspace, catalog: ops.Catalog, cache=None):
     nodes = {n.id: n for n in ws.nodes}
     contexts = {n.id: Context(node=n) for n in ws.nodes}
     edges = {n.id: [] for n in ws.nodes}
@@ -113,7 +121,7 @@ async def execute(ws: workspace.Workspace, catalog: ops.Catalog, cache=None):
             tasks[node.id] = [NO_INPUT]
     batch_inputs = {}
     # Run the rest until we run out of tasks.
-    stages = get_stages(ws, catalog)
+    stages = _get_stages(ws, catalog)
     for stage in stages:
         next_stage = {}
         while tasks:
@@ -124,7 +132,7 @@ async def execute(ws: workspace.Workspace, catalog: ops.Catalog, cache=None):
             node = nodes[n]
             op = catalog[node.data.title]
             params = {**node.data.params}
-            if has_ctx(op):
+            if _has_ctx(op):
                 params["_ctx"] = contexts[node.id]
             results = []
             node.publish_started()
@@ -148,15 +156,15 @@ async def execute(ws: workspace.Workspace, catalog: ops.Catalog, cache=None):
                         node.publish_error(f"Missing input: {', '.join(missing)}")
                         break
                     if cache is not None:
-                        key = make_cache_key((inputs, params))
+                        key = _make_cache_key((inputs, params))
                         if key not in cache:
                             result: ops.Result = op(*inputs, **params)
-                            result.output = await await_if_needed(result.output)
+                            result.output = await _await_if_needed(result.output)
                             cache[key] = result
                         result = cache[key]
                     else:
                         result = op(*inputs, **params)
-                    output = await await_if_needed(result.output)
+                    output = await _await_if_needed(result.output)
                 except Exception as e:
                     traceback.print_exc()
                     node.publish_error(e)
@@ -164,13 +172,13 @@ async def execute(ws: workspace.Workspace, catalog: ops.Catalog, cache=None):
                 contexts[node.id].last_result = output
                 # Returned lists and DataFrames are considered multiple tasks.
                 if isinstance(output, pd.DataFrame):
-                    output = df_to_list(output)
+                    output = _df_to_list(output)
                 elif not isinstance(output, list):
                     output = [output]
                 results.extend(output)
             else:  # Finished all tasks without errors.
                 if result.display:
-                    result.display = await await_if_needed(result.display)
+                    result.display = await _await_if_needed(result.display)
                 for edge in edges[node.id]:
                     t = nodes[edge.target]
                     op = catalog[t.data.title]

lynxkite-core/src/lynxkite/core/executors/simple.py

@@ -9,7 +9,13 @@ import graphlib
 
 
 def register(env: str):
-    """Registers the one-by-one executor."""
+    """Registers the simple executor.
+
+    Usage:
+
+        from lynxkite.core.executors import simple
+        simple.register("My Environment")
+    """
     ops.EXECUTORS[env] = lambda ws: execute(ws, ops.CATALOGS[env])
 
 

lynxkite-core/src/lynxkite/core/ops.py

@@ -41,6 +41,7 @@ def type_to_json(t):
 
 Type = Annotated[typing.Any, pydantic.PlainSerializer(type_to_json, return_type=dict)]
 LongStr = Annotated[str, {"format": "textarea"}]
+"""LongStr is a string type for parameters that will be displayed as a multiline text area in the UI."""
 PathStr = Annotated[str, {"format": "path"}]
 CollapsedStr = Annotated[str, {"format": "collapsed"}]
 NodeAttribute = Annotated[str, {"format": "node attribute"}]
@@ -268,7 +269,7 @@ def op(
                 _params.append(Parameter.basic(n, param.default, param.annotation))
         if params:
             _params.extend(params)
-        if outputs:
+        if outputs is not None:
             _outputs = [Output(name=name, type=None) for name in outputs]
         else:
             _outputs = [Output(name="output", type=None)] if view == "basic" else []
@@ -314,24 +315,41 @@ def matplotlib_to_image(func):
     return wrapper
 
 
-def input_position(**kwargs):
-    """Decorator for specifying unusual positions for the inputs."""
+def input_position(**positions):
+    """
+    Decorator for specifying unusual positions for the inputs.
+
+    Example usage:
+
+        @input_position(a="bottom", b="bottom")
+        @op("test", "maybe add")
+        def maybe_add(a: list[int], b: list[int] | None = None):
+            return [a + b for a, b in zip(a, b)] if b else a
+    """
 
     def decorator(func):
         op = func.__op__
-        for k, v in kwargs.items():
+        for k, v in positions.items():
             op.get_input(k).position = Position(v)
         return func
 
     return decorator
 
 
-def output_position(**kwargs):
-    """Decorator for specifying unusual positions for the outputs."""
+def output_position(**positions):
+    """Decorator for specifying unusual positions for the outputs.
+
+    Example usage:
+
+        @output_position(output="top")
+        @op("test", "maybe add")
+        def maybe_add(a: list[int], b: list[int] | None = None):
+            return [a + b for a, b in zip(a, b)] if b else a
+    """
 
     def decorator(func):
         op = func.__op__
-        for k, v in kwargs.items():
+        for k, v in positions.items():
             op.get_output(k).position = Position(v)
         return func
 
@@ -359,6 +377,16 @@ def register_passive_op(env: str, name: str, inputs=[], outputs=["output"], para
     return op
 
 
+COMMENT_OP = Op(
+    func=no_op,
+    name="Comment",
+    params=[Parameter.basic("text", "", LongStr)],
+    inputs=[],
+    outputs=[],
+    type="comment",
+)
+
+
 def register_executor(env: str):
     """Decorator for registering an executor.
 

lynxkite-graph-analytics/pyproject.toml

@@ -14,6 +14,7 @@ dependencies = [
     "osmnx>=2.0.2",
     "pandas>=2.2.3",
     "polars>=1.25.2",
+    "pyarrow>=19.0.1",
     "torch>=2.7.0",
     "torch-geometric>=2.6.1",
     "umap-learn>=0.5.7",

lynxkite-graph-analytics/src/lynxkite_graph_analytics/core.py

@@ -17,16 +17,28 @@ ENV = "LynxKite Graph Analytics"
 
 @dataclasses.dataclass
 class RelationDefinition:
-    """Defines a set of edges."""
+    """
+    Defines a set of edges.
+
+    Attributes:
+        df: The name of the DataFrame that contains the edges.
+        source_column: The column in the edge DataFrame that contains the source node ID.
+        target_column: The column in the edge DataFrame that contains the target node ID.
+        source_table: The name of the DataFrame that contains the source nodes.
+        target_table: The name of the DataFrame that contains the target nodes.
+        source_key: The column in the source table that contains the node ID.
+        target_key: The column in the target table that contains the node ID.
+        name: Descriptive name for the relation.
+    """
 
-    df: str  # The DataFrame that contains the edges.
-    source_column: str  # The column in the edge DataFrame that contains the source node ID.
-    target_column: str  # The column in the edge DataFrame that contains the target node ID.
-    source_table: str  # The DataFrame that contains the source nodes.
-    target_table: str  # The DataFrame that contains the target nodes.
-    source_key: str  # The column in the source table that contains the node ID.
-    target_key: str  # The column in the target table that contains the node ID.
-    name: str | None = None  # Descriptive name for the relation.
+    df: str
+    source_column: str
+    target_column: str
+    source_table: str
+    target_table: str
+    source_key: str
+    target_key: str
+    name: str | None = None
 
 
 @dataclasses.dataclass
@@ -34,7 +46,16 @@ class Bundle:
     """A collection of DataFrames and other data.
 
     Can efficiently represent a knowledge graph (homogeneous or heterogeneous) or tabular data.
-    It can also carry other data, such as a trained model.
+
+    By convention, if it contains a single DataFrame, it is called `df`.
+    If it contains a homogeneous graph, it is represented as two DataFrames called `nodes` and
+    `edges`.
+
+    Attributes:
+        dfs: Named DataFrames.
+        relations: Metadata that describes the roles of each DataFrame.
+            Can be empty, if the bundle is just one or more DataFrames.
+        other: Other data, such as a trained model.
     """
 
     dfs: dict[str, pd.DataFrame] = dataclasses.field(default_factory=dict)
@@ -91,7 +112,10 @@ class Bundle:
         return graph
 
     def copy(self):
-        """Returns a medium depth copy of the bundle. The Bundle is completely new, but the DataFrames and RelationDefinitions are shared."""
+        """
+        Returns a shallow copy of the bundle. The Bundle and its containers are new, but
+        the DataFrames and RelationDefinitions are shared. (The contents of `other` are also shared.)
+        """
         return Bundle(
             dfs=dict(self.dfs),
             relations=list(self.relations),

lynxkite-pillow-example/pyproject.toml

@@ -11,6 +11,10 @@ dependencies = [
     "requests>=2.32.3",
     "aiohttp>=3.11.11",
 ]
+classifiers = ["Private :: Do Not Upload"]
+
+[project.urls]
+Homepage = "https://github.com/lynxkite/lynxkite-2000/"
 
 [tool.uv.sources]
 lynxkite-core = { path = "../lynxkite-core" }

mkdocs.yml

@@ -1,6 +1,25 @@
-site_name: "LynxKite"
-repo_url: https://github.com/lynxkite/lynxkite
-repo_name: lynxkite/lynxkite
+site_name: "LynxKite 2000:MM"
+repo_url: https://github.com/lynxkite/lynxkite-2000
+repo_name: lynxkite/lynxkite-2000
+watch: [mkdocs.yml, README.md, lynxkite-core, lynxkite-graph-analytics, lynxkite-app]
+
+nav:
+- Home:
+  - Overview: index.md
+  - License: license.md
+- Usage:
+  - usage/quickstart.md
+  - usage/plugins.md
+- API reference:
+  - LynxKite Core:
+    - reference/lynxkite-core/ops.md
+    - reference/lynxkite-core/workspace.md
+    - Executors:
+      - reference/lynxkite-core/executors/simple.md
+      - reference/lynxkite-core/executors/one_by_one.md
+  - LynxKite Graph Analytics:
+    - reference/lynxkite-graph-analytics/core.md
+    - reference/lynxkite-graph-analytics/operations.md
 
 theme:
   name: "material"
@@ -13,13 +32,35 @@ theme:
     - navigation.path
     - navigation.instant
     - navigation.instant.prefetch
+    - navigation.footer
+    - content.code.annotate
+    - content.code.copy
 
 extra_css:
   - stylesheets/extra.css
 
 plugins:
 - search
+- autorefs
 - mkdocstrings:
     handlers:
       python:
-        paths: ["./lynxkite-app/src", "./lynxkite-core/src", "./lynxkite-graph-analytics/src", "./lynxkite-lynxscribe/src"]
+        paths: ["./lynxkite-app/src", "./lynxkite-core/src", "./lynxkite-graph-analytics/src"]
+        options:
+          show_source: false
+          show_symbol_type_heading: true
+          show_symbol_type_toc: true
+          docstring_section_style: spacy
+          separate_signature: true
+          show_signature_annotations: true
+          signature_crossrefs: true
+markdown_extensions:
+- pymdownx.highlight:
+    anchor_linenums: true
+    line_spans: __span
+    pygments_lang_class: true
+- pymdownx.inlinehilite
+- pymdownx.snippets
+- pymdownx.superfences
+- toc:
+    permalink: "¤"