migrate: update docs and examples for new standalone CLI

docs/docs/core/basics.md

@@ -101,4 +101,4 @@ As an indexing flow is long-lived, it needs to store intermediate data to keep t
 CocoIndex uses internal storage for this purpose.
 
 Currently, CocoIndex uses Postgres database as the internal storage.
-See [Initialization](initialization) for configuring its location, and `cocoindex setup` CLI command (see [CocoIndex CLI](cli)) creates tables for the internal storage.
+See [Settings](settings#databaseconnectionspec) for configuring its location, and `cocoindex setup` CLI command (see [CocoIndex CLI](cli)) creates tables for the internal storage.

docs/docs/core/cli.mdx

@@ -8,60 +8,59 @@ import TabItem from '@theme/TabItem';
 
 # CocoIndex CLI
 
-CocoIndex CLI embeds CLI functionality in your program.
-It provides a bunch of commands for easily managing and inspecting your flows and indexes.
+CocoIndex CLI is a standalone tool for easily managing and inspecting your flows and indexes.
 
-## Enable CocoIndex CLI
+## Invoke the CLI
 
-### Use Packaged Main
+Once CocoIndex is installed, you can invoke the CLI directly using the `cocoindex` command. Most commands require an `APP_TARGET` argument, which tells the CLI where your flow definitions are located.
 
-The easiest way is to use a packaged main function:
+### APP_TARGET Format
 
-<Tabs>
-<TabItem value="python" label="Python" default>
+The `APP_TARGET` can be:
+1.  A **path to a Python file** defining your flows (e.g., `main.py`, `path/to/my_flows.py`).
+2.  An **installed Python module name** that contains your flow definitions (e.g., `my_package.flows`).
+3.  For commands that operate on a *specific flow* (like `show`, `update`, `evaluate`), you can combine the application reference with a flow name:
+    * `path/to/my_flows.py:MyFlow`
+    * `my_package.flows:MyFlow`
 
-```python title="main.py"
-import cocoindex
+### Environment Variables
 
-@cocoindex.main_fn()
-def main():
-  ...
-```
+Environment variables are needed as CocoIndex library settings, as described in [CocoIndex Settings](settings#list-of-environment-variables).
 
-</TabItem>
-</Tabs>
+You can set environment variables in an environment file.
 
-With this, when the program is executed with `cocoindex` as its first argument, CocoIndex CLI will take over the control. For example:
+*   By default, the `cocoindex` CLI searches upward from the current directory for a `.env` file.
+*   You can use `--env-file <path>` to specify one explicitly:
 
-```sh
-$ python main.py cocoindex ls       # Run "ls" subcommand: list all flows
-```
+    ```sh
+    cocoindex --env-file path/to/custom.env <COMMAND> ...
+    ```
+
+Loaded variables do *NOT* override existing system ones.
+If no file is found, only existing system environment variables are used.
 
-You may also provide a `cocoindex_cmd` argument to the `main_fn` decorator to change the command from `cocoindex` to something else.
+### Global Options
 
-### Explicitly CLI Invoke
+CocoIndex CLI supports the following global options:
 
-An alternative way is to use `cocoindex.cli.cli` (with type [`click.Group`](https://click.palletsprojects.com/en/stable/api/#click.Group)).
-For example, you may invoke the CLI explicitly with additional arguments:
+* `--env-file <path>`: Load environment variables from a specified `.env` file. If not provided, `.env` in the current directory is loaded if it exists.
+* `--version`: Show the CocoIndex version and exit.
+* `--help`: Show the main help message and exit.
 
-<Tabs>
-<TabItem value="python" label="Python" default>
+:::caution Deprecated Usage
 
-```python
-cocoindex.cli.cli.main(args)
-```
+The old method of invoking the CLI using `python main.py cocoindex ...` via the `@cocoindex.main_fn()` decorator is now deprecated. Please remove `@cocoindex.main_fn()` from your scripts and use the standalone cocoindex command as described.
 
-</TabItem>
-</Tabs>
+:::
 
 ## Subcommands
 
 The following subcommands are available:
 
 | Subcommand | Description |
 | ---------- | ----------- |
-| `ls` | List all flows present in the current process. Or list all persisted flows under the current app namespace if `--all` is specified. |
-| `show` | Show the spec for a specific flow. |
+| `ls` | List all flows present in the given file/module. Or list all persisted flows under the current app namespace if no file/module specified. |
+| `show` | Show the spec and schema for a specific flow. |
 | `setup` | Check and apply backend setup changes for flows, including the internal and target storage (to export). |
 | `drop` | Drop the backend setup for specified flows. |
 | `update` | Update the index defined by the flow. |
@@ -71,6 +70,6 @@ The following subcommands are available:
 Use `--help` to see the full list of subcommands, and `subcommand --help` to see the usage of a specific one.
 
 ```sh
-python main.py cocoindex --help       # Show all subcommands
-python main.py cocoindex show --help  # Show usage of "show" subcommand
+cocoindex --help       # Show all subcommands
+cocoindex show --help  # Show usage of "show" subcommand
 ```

docs/docs/core/flow_def.mdx

@@ -313,7 +313,7 @@ Following metrics are supported:
 
 ### Getting App Namespace
 
-You can use the [`app_namespace` setting](initialization#app-namespace) or `COCOINDEX_APP_NAMESPACE` environment variable to specify the app namespace,
+You can use the [`app_namespace` setting](settings#app-namespace) or `COCOINDEX_APP_NAMESPACE` environment variable to specify the app namespace,
 to organize flows across different environments (e.g., dev, staging, production), team members, etc.
 
 In the code, You can call `flow.get_app_namespace()` to get the app namespace, and use it to name certain backends. It takes the following arguments:

docs/docs/core/flow_methods.mdx

@@ -1,13 +1,13 @@
 ---
-title: Flow Running
+title: Run a Flow
 toc_max_heading_level: 4
 description: Run a CocoIndex Flow, including build / update data in the target storage and evaluate the flow without changing the target storage.
 ---
 
 import Tabs from '@theme/Tabs';
 import TabItem from '@theme/TabItem';
 
-# Running a CocoIndex Flow
+# Run a CocoIndex Flow
 
 After a flow is defined as discussed in [Flow Definition](/docs/core/flow_def), you can start to transform data with it.
 
@@ -30,17 +30,7 @@ def demo_flow(flow_builder: cocoindex.FlowBuilder, data_scope: cocoindex.DataSco
 ```
 
 It creates a `demo_flow` object in `cocoindex.Flow` type.
-To enable CLI, you also need to make sure you have a main function decorated with `@cocoindex.main_fn()`:
 
-
-```python title="main.py"
-@cocoindex.main_fn()
-def main():
-    ...
-
-if __name__ == "__main__":
-    main()
-```
 </TabItem>
 </Tabs>
 
@@ -78,7 +68,7 @@ The `cocoindex update` subcommand creates/updates data in the target storage.
 Once it's done, the target data is fresh up to the moment when the function is called.
 
 ```sh
-python main.py cocoindex update
+cocoindex update main.py
 ```
 
 #### Library API
@@ -115,7 +105,7 @@ Change capture mechanisms enable CocoIndex to continuously capture changes from
 To perform live update, run the `cocoindex update` subcommand with `-L` option:
 
 ```sh
-python main.py cocoindex update -L
+cocoindex update main.py -L
 ```
 
 If there's at least one data source with change capture mechanism enabled, it will keep running until the aborted (e.g. by `Ctrl-C`).
@@ -232,7 +222,7 @@ It takes the following options:
 Example:
 
 ```sh
-python main.py cocoindex evaluate --output-dir ./eval_output
+cocoindex evaluate main.py --output-dir ./eval_output
 ```
 
 ### Library API