[doc] clean up commands

README.md

@@ -116,7 +116,7 @@ If you're new to CocoIndex, we recommend checking out
 
 1. Install CocoIndex Python library
 
-```bash
+```sh
 pip install -U cocoindex
 ```
 

dev/README.md

@@ -10,7 +10,7 @@ Automatically generates CLI documentation from the CocoIndex Click commands.
 
 **Usage:**
 
-```bash
+```sh
 python dev/generate_cli_docs.py
 ```
 

docs/docs/ai/llm.mdx

@@ -122,7 +122,7 @@ cocoindex.functions.EmbedText(
 
 *   [Download](https://ollama.com/download) and install Ollama.
 *   Pull your favorite LLM models by the `ollama pull` command, e.g.
-    ```bash
+    ```sh
     ollama pull llama3.2
     ```
 You can find the [list of models](https://ollama.com/library) supported by Ollama.
@@ -146,7 +146,7 @@ cocoindex.LlmSpec(
 
 For text embedding with Ollama, you'll need to pull an embedding model first:
 
-```bash
+```sh
 ollama pull nomic-embed-text
 ```
 
@@ -330,7 +330,7 @@ To use the LiteLLM API, you need to set the environment variable `LITELLM_API_KE
 
 #### 1. Install LiteLLM Proxy
 
-```bash
+```sh
 pip install 'litellm[proxy]'
 ```
 
@@ -367,7 +367,7 @@ You need to set the environment variable `GROQ_API_KEY` to your Groq API key.
 
 #### 3. Run LiteLLM Proxy
 
-```bash
+```sh
 litellm --config config.yml
 ```
 
@@ -415,13 +415,13 @@ You can find the full list of models supported by OpenRouter [here](https://open
 
 Install vLLM:
 
-```bash
+```sh
 pip install vllm
 ```
 
 Run vLLM Server
 
-```bash
+```sh
 vllm serve deepseek-ai/deepseek-coder-1.3b-instruct
 ```
 

docs/docs/core/cli-commands.md

@@ -13,7 +13,7 @@ Modes of operation:
 
 **Usage:**
 
-```bash
+```sh
 cocoindex drop [OPTIONS] [APP_TARGET] [FLOW_NAME]...
 ```
 
@@ -45,7 +45,7 @@ flow.
 
 **Usage:**
 
-```bash
+```sh
 cocoindex evaluate [OPTIONS] APP_FLOW_SPECIFIER
 ```
 
@@ -72,7 +72,7 @@ the backend.
 
 **Usage:**
 
-```bash
+```sh
 cocoindex ls [OPTIONS] [APP_TARGET]
 ```
 
@@ -95,7 +95,7 @@ It will allow tools like CocoInsight to access the server.
 
 **Usage:**
 
-```bash
+```sh
 cocoindex server [OPTIONS] APP_TARGET
 ```
 
@@ -128,7 +128,7 @@ storage and target (to export to).
 
 **Usage:**
 
-```bash
+```sh
 cocoindex setup [OPTIONS] APP_TARGET
 ```
 
@@ -160,7 +160,7 @@ flow.
 
 **Usage:**
 
-```bash
+```sh
 cocoindex show [OPTIONS] APP_FLOW_SPECIFIER
 ```
 
@@ -184,7 +184,7 @@ or `module:FlowName`. If `:FlowName` is omitted, updates all flows.
 
 **Usage:**
 
-```bash
+```sh
 cocoindex update [OPTIONS] APP_FLOW_SPECIFIER
 ```
 

docs/docs/examples/examples/00_codebase_index.md

@@ -51,7 +51,7 @@ The flow is composed of the following steps:
 - Install Postgres, follow [installation guide](https://cocoindex.io/docs/getting_started/installation#-install-postgres).
 - Install CocoIndex
 
-  ```bash
+  ```sh
   pip install -U cocoindex
   ```
 
@@ -206,7 +206,7 @@ if __name__ == "__main__":
 
 - Install dependencies
 
-    ```bash
+    ```sh
     pip install -e .
     ```
 
@@ -234,8 +234,8 @@ The returned results - each entry contains score (Cosine Similarity), filename,
 To get a better understanding of the indexing flow, you can use CocoInsight to help the development step by step.
 To spin up, it is super easy.
 
-```
-cocoindex server main.py -ci
+```sh
+cocoindex server -ci main
 ```
 
 Follow the url from the terminal - `https://cocoindex.io/cocoinsight` to access the CocoInsight.

docs/docs/examples/examples/02_academic_papers_index.md

@@ -341,7 +341,6 @@ If you need assist with writing the query, please feel free to reach out to us a
 
 You can walk through the project step by step in [CocoInsight](https://www.youtube.com/watch?v=MMrpUfUcZPk) to see exactly how each field is constructed and what happens behind the scenes.
 
-
 ```sh
 cocoindex server -ci main
 ```

docs/docs/examples/examples/03_postgres_source.md

@@ -182,25 +182,25 @@ For example, the following image shows the lineage of the `embedding` field, you
 
 1. Set up dependencies:
 
-    ```bash
+    ```sh
     pip install -e .
     ```
 
 2. Create the source table with sample data:
 
-    ```bash
+    ```sh
     psql "postgres://cocoindex:cocoindex@localhost/cocoindex" -f ./prepare_source_data.sql
     ```
 
 3. Setup tables and update the index:
 
-    ```bash
+    ```sh
     cocoindex update main
     ```
 
 4. Run CocoInsight:
 
-    ```bash
+    ```sh
     cocoindex server -ci main
     ```
 
@@ -210,8 +210,8 @@ For example, the following image shows the lineage of the `embedding` field, you
 
 For continuous updating when the source changes, add `-L`:
 
-```bash
-cocoindex server -ci -L main
+```sh
+cocoindex update -L main
 ```
 
 Check [live updates](https://cocoindex.io/docs/tutorials/live_updates) for more details.

docs/docs/examples/examples/custom_targets.md

@@ -189,7 +189,7 @@ output_html.export(
 
 ## Run the example
 
-```bash
+```sh
 pip install -e .
 cocoindex update main
 ```
@@ -198,9 +198,9 @@ You can add, modify, or remove files in the `data/` directory — CocoIndex will
 
 For **real-time updates**, run in live mode:
 
-```bash
-cocoindex update -L main.py
-```
+    ```sh
+    cocoindex update -L main
+    ```
 
 This keeps your knowledge graph continuously synchronized with your document source — perfect for fast-changing environments like internal wikis or technical documentation.
 

docs/docs/examples/examples/image_search_clip.md

@@ -265,7 +265,7 @@ You can check the frontend code [here](https://github.com/cocoindex-io/cocoindex
 
 ## Time to have fun!
 - Create a collection in Qdrant
-    ```bash
+    ```sh
     curl -X PUT 'http://localhost:6333/collections/image_search' \
     -H 'Content-Type: application/json' \
     -d '{
@@ -279,18 +279,18 @@ You can check the frontend code [here](https://github.com/cocoindex-io/cocoindex
     ```
 
 - Setup indexing flow
-    ```bash
-    cocoindex setup main.py
+    ```sh
+    cocoindex setup main
     ```
     It is setup with a live updater, so you can add new files to the folder and it will be indexed within a minute.
 
 - Run backend
-    ```bash
+    ```sh
     uvicorn main:app --reload --host 0.0.0.0 --port 8000
     ```
 
 - Run frontend
-    ```bash
+    ```sh
     cd frontend
     npm install
     npm run dev
@@ -306,7 +306,7 @@ Wait a minute for the new image to be processed and indexed.
 
 ![Search](/img/examples/image_search_clip/search3.png)
 
-If you want to monitor the indexing progress, you can view it in CocoInsight `cocoindex server -ci main `.
+If you want to monitor the indexing progress, you can view it in CocoInsight `cocoindex server -ci main`.
 
 ![Index Status In CocoInsight](/img/examples/image_search_clip/index-status.png)
 

docs/docs/examples/examples/manual_extraction.md

@@ -225,14 +225,15 @@ modules_index.export(
 
 ## Query and test your index
 Run the following command to setup and update the index.
+
 ```sh
-cocoindex update -L main.py
+cocoindex update -L main
 ```
 You'll see the index updates state in the terminal
 
 After the index is built, you have a table with the name `modules_info`. You can query it at any time, e.g., start a Postgres shell:
 
-```bash
+```sh
 psql postgres://cocoindex:cocoindex@localhost/cocoindex
 ```
 

docs/docs/examples/examples/multi_format_index.md

@@ -192,7 +192,6 @@ search_results = client.query_points(
 
 You can walk through the project step by step in [CocoInsight](https://www.youtube.com/watch?v=MMrpUfUcZPk) to see exactly how each field is constructed and what happens behind the scenes.
 
-
 ```sh
 cocoindex server -ci main
 ```

docs/docs/examples/examples/patient_form_extraction.md

@@ -225,7 +225,7 @@ patients_index.export(
 
 ### Install dependencies
 
-    ```bash
+    ```sh
     pip install -e .
     ```
 
@@ -240,7 +240,7 @@ patients_index.export(
 
 After the index is built, you have a table with the name `patients_info`. You can query it at any time, e.g., start a Postgres shell:
 
-```bash
+```sh
 psql postgres://cocoindex:cocoindex@localhost/cocoindex
 ```
 
@@ -258,7 +258,7 @@ For mission-critical use cases, it is important to evaluate the quality of the e
 
 1. Dump the extracted data to YAML files.
 
-    ```bash
+    ```sh
     python3 main.py cocoindex evaluate
     ```
 
@@ -269,7 +269,7 @@ For mission-critical use cases, it is important to evaluate the quality of the e
 
     You can run the following command to see the diff:
 
-    ```bash
+    ```sh
     diff -r data/eval_PatientIntakeExtraction_golden data/eval_PatientIntakeExtraction_output
     ```
 
@@ -290,7 +290,7 @@ We could troubleshoot in two steps:
 
 I also use CocoInsight to help me troubleshoot.
 
-```bash
+```sh
 cocoindex server -ci main
 ```
 

docs/docs/examples/examples/patient_form_extraction_baml.md

@@ -287,23 +287,23 @@ Exports the index to Postgres as the `patients` table, with automatic updates an
 
 **Generate BAML client code** (required step, in case you didn’t do it earlier. )
 
-```bash
+```sh
 baml generate
 ```
 
 This generates the `baml_client/` directory with Python code to call your BAML functions.
 
 Update the index:
 
-```bash
+```sh
 cocoindex update main
 ```
 
 **CocoInsight**
 
-I used CocoInsight (Free beta now) to troubleshoot the index generation and understand the data lineage of the pipeline. It just connects to your local CocoIndex server, with zero pipeline data retention. 
+I used CocoInsight (Free beta now) to troubleshoot the index generation and understand the data lineage of the pipeline. It just connects to your local CocoIndex server, with zero pipeline data retention.
 
-```bash
+```sh
 cocoindex server -ci main
 ```