Improve markdown docs formatting for consistency and readability

docs/docs/installation/azure.md

@@ -1,6 +1,8 @@
 ## Azure DevOps Pipeline
+
 You can use a pre-built Action Docker image to run PR-Agent as an Azure devops pipeline.
 add the following file to your repository under `azure-pipelines.yml`:
+
 ```yaml
 # Opt out of CI triggers
 trigger: none
@@ -49,6 +51,7 @@ stages:
         openai__key: $(OPENAI_KEY)
       displayName: 'Run Qodo Merge'
 ```
+
 This script will run Qodo Merge on every new merge request, with the `improve`, `review`, and `describe` commands.
 Note that you need to export the `azure_devops__pat` and `OPENAI_KEY` variables in the Azure DevOps pipeline settings (Pipelines -> Library -> + Variable group):
 
@@ -61,7 +64,8 @@ Make sure to give pipeline permissions to the `pr_agent` variable group.
 ## Azure DevOps from CLI
 
 To use Azure DevOps provider use the following settings in configuration.toml:
-```
+
+```toml
 [config]
 git_provider="azure"
 ```
@@ -74,7 +78,8 @@ If PAT was chosen, you can assign the value in .secrets.toml.
 If DefaultAzureCredential was chosen, you can assigned the additional env vars like AZURE_CLIENT_SECRET directly,
 or use managed identity/az cli (for local development) without any additional configuration.
 in any case, 'org' value must be assigned in .secrets.toml:
-```
+
+```toml
 [azure_devops]
 org = "https://dev.azure.com/YOUR_ORGANIZATION/"
 # pat = "YOUR_PAT_TOKEN" needed only if using PAT for authentication
@@ -85,11 +90,12 @@ org = "https://dev.azure.com/YOUR_ORGANIZATION/"
 To trigger from an Azure webhook, you need to manually [add a webhook](https://learn.microsoft.com/en-us/azure/devops/service-hooks/services/webhooks?view=azure-devops).
 Use the "Pull request created" type to trigger a review, or "Pull request commented on" to trigger any supported comment with /<command> <args> comment on the relevant PR. Note that for the "Pull request commented on" trigger, only API v2.0 is supported.
 
-
 For webhook security, create a sporadic username/password pair and configure the webhook username and password on both the server and Azure DevOps webhook. These will be sent as basic Auth data by the webhook with each request:
-```
+
+```toml
 [azure_devops_server]
 webhook_username = "<basic auth user>"
 webhook_password = "<basic auth password>"
 ```
+
 > :warning: **Ensure that the webhook endpoint is only accessible over HTTPS** to mitigate the risk of credential interception when using basic authentication.

docs/docs/installation/bitbucket.md

@@ -57,7 +57,7 @@ python cli.py --pr_url https://git.onpreminstanceofbitbucket.com/projects/PROJEC
 
 To run PR-Agent as webhook, build the docker image:
 
-```
+```bash
 docker build . -t codiumai/pr-agent:bitbucket_server_webhook --target bitbucket_server_webhook -f docker/Dockerfile
 docker push codiumai/pr-agent:bitbucket_server_webhook  # Push to your Docker repository
 ```

docs/docs/installation/github.md

@@ -40,6 +40,7 @@ The GITHUB_TOKEN secret is automatically created by GitHub.
 When you open your next PR, you should see a comment from `github-actions` bot with a review of your PR, and instructions on how to use the rest of the tools.
 
 4) You may configure Qodo Merge by adding environment variables under the env section corresponding to any configurable property in the [configuration](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml) file. Some examples:
+
 ```yaml
       env:
         # ... previous environment values
@@ -47,9 +48,11 @@ When you open your next PR, you should see a comment from `github-actions` bot w
         PR_REVIEWER.REQUIRE_TESTS_REVIEW: "false" # Disable tests review
         PR_CODE_SUGGESTIONS.NUM_CODE_SUGGESTIONS: 6 # Increase number of code suggestions
 ```
+
 See detailed usage instructions in the [USAGE GUIDE](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#github-action)
 
 ### Using a specific release
+
 !!! tip ""
     if you want to pin your action to a specific release (v0.23 for example) for stability reasons, use:
     ```yaml
@@ -72,6 +75,7 @@ See detailed usage instructions in the [USAGE GUIDE](https://qodo-merge-docs.qod
     ```
 
 ### Action for GitHub enterprise server
+
 !!! tip ""
     To use the action with a GitHub enterprise server, add an environment variable `GITHUB.BASE_URL` with the API URL of your GitHub server.
 
@@ -82,10 +86,10 @@ See detailed usage instructions in the [USAGE GUIDE](https://qodo-merge-docs.qod
             GITHUB.BASE_URL: "https://github.mycompany.com/api/v3"
     ```
 
-
 ---
 
 ## Run as a GitHub App
+
 Allowing you to automate the review process on your private or public repositories.
 
 1) Create a GitHub App from the [Github Developer Portal](https://docs.github.com/en/developers/apps/creating-a-github-app).
@@ -102,7 +106,7 @@ Allowing you to automate the review process on your private or public repositori
 
 2) Generate a random secret for your app, and save it for later. For example, you can use:
 
-```
+```bash
 WEBHOOK_SECRET=$(python -c "import secrets; print(secrets.token_hex(10))")
 ```
 
@@ -113,28 +117,29 @@ WEBHOOK_SECRET=$(python -c "import secrets; print(secrets.token_hex(10))")
 
 4) Clone this repository:
 
-```
+```bash
 git clone https://github.com/Codium-ai/pr-agent.git
 ```
 
 5) Copy the secrets template file and fill in the following:
 
-```
+```bash
 cp pr_agent/settings/.secrets_template.toml pr_agent/settings/.secrets.toml
 # Edit .secrets.toml file
 ```
 
-   - Your OpenAI key.
-   - Copy your app's private key to the private_key field.
-   - Copy your app's ID to the app_id field.
-   - Copy your app's webhook secret to the webhook_secret field.
-   - Set deployment_type to 'app' in [configuration.toml](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml)
+- Your OpenAI key.
+- Copy your app's private key to the private_key field.
+- Copy your app's ID to the app_id field.
+- Copy your app's webhook secret to the webhook_secret field.
+- Set deployment_type to 'app' in [configuration.toml](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml)
 
     > The .secrets.toml file is not copied to the Docker image by default, and is only used for local development.
     > If you want to use the .secrets.toml file in your Docker image, you can add remove it from the .dockerignore file.
     > In most production environments, you would inject the secrets file as environment variables or as mounted volumes.
     > For example, in order to inject a secrets file as a volume in a Kubernetes environment you can update your pod spec to include the following,
     > assuming you have a secret named `pr-agent-settings` with a key named `.secrets.toml`:
+
     ```
            volumes:
             - name: settings-volume
@@ -152,7 +157,7 @@ cp pr_agent/settings/.secrets_template.toml pr_agent/settings/.secrets.toml
 
 6) Build a Docker image for the app and optionally push it to a Docker repository. We'll use Dockerhub as an example:
 
-    ```
+    ```bash
     docker build . -t codiumai/pr-agent:github_app --target github_app -f docker/Dockerfile
     docker push codiumai/pr-agent:github_app  # Push to your Docker repository
     ```
@@ -180,14 +185,19 @@ For example: `GITHUB.WEBHOOK_SECRET` --> `GITHUB__WEBHOOK_SECRET`
 
 1. Follow steps 1-5 from [here](#run-as-a-github-app).
 2. Build a docker image that can be used as a lambda function
+
     ```shell
     docker buildx build --platform=linux/amd64 . -t codiumai/pr-agent:serverless -f docker/Dockerfile.lambda
    ```
+
 3. Push image to ECR
+
     ```shell
-	docker tag codiumai/pr-agent:serverless <AWS_ACCOUNT>.dkr.ecr.<AWS_REGION>.amazonaws.com/codiumai/pr-agent:serverless
-	docker push <AWS_ACCOUNT>.dkr.ecr.<AWS_REGION>.amazonaws.com/codiumai/pr-agent:serverless
+
+ docker tag codiumai/pr-agent:serverless <AWS_ACCOUNT>.dkr.ecr.<AWS_REGION>.amazonaws.com/codiumai/pr-agent:serverless
+ docker push <AWS_ACCOUNT>.dkr.ecr.<AWS_REGION>.amazonaws.com/codiumai/pr-agent:serverless
     ```
+
 4. Create a lambda function that uses the uploaded image. Set the lambda timeout to be at least 3m.
 5. Configure the lambda function to have a Function URL.
 6. In the environment variables of the Lambda function, specify `AZURE_DEVOPS_CACHE_DIR` to a writable location such as /tmp. (see [link](https://github.com/Codium-ai/pr-agent/pull/450#issuecomment-1840242269))
@@ -201,28 +211,27 @@ For example: `GITHUB.WEBHOOK_SECRET` --> `GITHUB__WEBHOOK_SECRET`
 Not all features have been added to CodeCommit yet.  As of right now, CodeCommit has been implemented to run the Qodo Merge CLI on the command line, using AWS credentials stored in environment variables.  (More features will be added in the future.)  The following is a set of instructions to have Qodo Merge do a review of your CodeCommit pull request from the command line:
 
 1. Create an IAM user that you will use to read CodeCommit pull requests and post comments
-    * Note: That user should have CLI access only, not Console access
+    - Note: That user should have CLI access only, not Console access
 2. Add IAM permissions to that user, to allow access to CodeCommit (see IAM Role example below)
 3. Generate an Access Key for your IAM user
 4. Set the Access Key and Secret using environment variables (see Access Key example below)
 5. Set the `git_provider` value to `codecommit` in the `pr_agent/settings/configuration.toml` settings file
 6. Set the `PYTHONPATH` to include your `pr-agent` project directory
-    * Option A: Add `PYTHONPATH="/PATH/TO/PROJECTS/pr-agent` to your `.env` file
-    * Option B: Set `PYTHONPATH` and run the CLI in one command, for example:
-        * `PYTHONPATH="/PATH/TO/PROJECTS/pr-agent python pr_agent/cli.py [--ARGS]`
+    - Option A: Add `PYTHONPATH="/PATH/TO/PROJECTS/pr-agent` to your `.env` file
+    - Option B: Set `PYTHONPATH` and run the CLI in one command, for example:
+        - `PYTHONPATH="/PATH/TO/PROJECTS/pr-agent python pr_agent/cli.py [--ARGS]`
 
 ---
 
-
 #### AWS CodeCommit IAM Role Example
 
 Example IAM permissions to that user to allow access to CodeCommit:
 
-* Note: The following is a working example of IAM permissions that has read access to the repositories and write access to allow posting comments
-* Note: If you only want pr-agent to review your pull requests, you can tighten the IAM permissions further, however this IAM example will work, and allow the pr-agent to post comments to the PR
-* Note: You may want to replace the `"Resource": "*"` with your list of repos, to limit access to only those repos
+- Note: The following is a working example of IAM permissions that has read access to the repositories and write access to allow posting comments
+- Note: If you only want pr-agent to review your pull requests, you can tighten the IAM permissions further, however this IAM example will work, and allow the pr-agent to post comments to the PR
+- Note: You may want to replace the `"Resource": "*"` with your list of repos, to limit access to only those repos
 
-```
+```json
 {
     "Version": "2012-10-17",
     "Statement": [

docs/docs/installation/gitlab.md

@@ -1,7 +1,9 @@
 ## Run as a GitLab Pipeline
+
 You can use a pre-built Action Docker image to run PR-Agent as a GitLab pipeline. This is a simple way to get started with Qodo Merge without setting up your own server.
 
 (1) Add the following file to your repository under `.gitlab-ci.yml`:
+
 ```yaml
 stages:
   - pr_agent
@@ -26,10 +28,10 @@ pr_agent_job:
   rules:
     - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
 ```
+
 This script will run Qodo Merge on every new merge request. You can modify the `rules` section to run Qodo Merge on different events.
 You can also modify the `script` section to run different Qodo Merge commands, or with different parameters by exporting different environment variables.
 
-
 (2) Add the following masked variables to your GitLab repository (CI/CD -> Variables):
 
 - `GITLAB_PERSONAL_ACCESS_TOKEN`: Your GitLab personal access token.
@@ -40,7 +42,6 @@ Note that if your base branches are not protected, don't set the variables as `p
 
 > **Note**: The `$CI_SERVER_FQDN` variable is available starting from GitLab version 16.10. If you're using an earlier version, this variable will not be available. However, you can combine `$CI_SERVER_HOST` and `$CI_SERVER_PORT` to achieve the same result. Please ensure you're using a compatible version or adjust your configuration.
 
-
 ## Run a GitLab webhook server
 
 1. In GitLab create a new user and give it "Reporter" role ("Developer" if using Pro version of the agent) for the intended group or project.
@@ -49,41 +50,41 @@ Note that if your base branches are not protected, don't set the variables as `p
 
 3. Generate a random secret for your app, and save it for later (`shared_secret`). For example, you can use:
 
-```
+```bash
 SHARED_SECRET=$(python -c "import secrets; print(secrets.token_hex(10))")
 ```
 
 4. Clone this repository:
 
-```
+```bash
 git clone https://github.com/qodo-ai/pr-agent.git
 ```
 
 5. Prepare variables and secrets. Skip this step if you plan on setting these as environment variables when running the agent:
-  1. In the configuration file/variables:
+1. In the configuration file/variables:
     - Set `config.git_provider` to "gitlab"
 
-  2. In the secrets file/variables:
+2. In the secrets file/variables:
     - Set your AI model key in the respective section
     - In the [gitlab] section, set `personal_access_token` (with token from step 2) and `shared_secret` (with secret from step 3)
 
 6. Build a Docker image for the app and optionally push it to a Docker repository. We'll use Dockerhub as an example:
-```
+
+```bash
 docker build . -t gitlab_pr_agent --target gitlab_webhook -f docker/Dockerfile
 docker push codiumai/pr-agent:gitlab_webhook  # Push to your Docker repository
 ```
 
 7. Set the environmental variables, the method depends on your docker runtime. Skip this step if you included your secrets/configuration directly in the Docker image.
 
-```
-"CONFIG.GIT_PROVIDER": "gitlab"
-"GITLAB.PERSONAL_ACCESS_TOKEN": "<personal_access_token>"
-"GITLAB.SHARED_SECRET": "<shared_secret>"
-"GITLAB.URL": "https://gitlab.com"
-"OPENAI.KEY": "<your_openai_api_key>"
+```bash
+CONFIG__GIT_PROVIDER=gitlab
+GITLAB__PERSONAL_ACCESS_TOKEN=<personal_access_token>
+GITLAB__SHARED_SECRET=<shared_secret>
+GITLAB__URL=https://gitlab.com
+OPENAI__KEY=<your_openai_api_key>
 ```
 
-8. Create a webhook in your GitLab project. Set the URL to ```http[s]://<PR_AGENT_HOSTNAME>/webhook```, the secret token to the generated secret from step 3, and enable the triggers `push`, `comments` and `merge request events`.
+8. Create a webhook in your GitLab project. Set the URL to `http[s]://<PR_AGENT_HOSTNAME>/webhook`, the secret token to the generated secret from step 3, and enable the triggers `push`, `comments` and `merge request events`.
 
 9. Test your installation by opening a merge request or commenting on a merge request using one of PR Agent's commands.
-

docs/docs/installation/index.md

@@ -11,6 +11,7 @@ There are several ways to use self-hosted PR-Agent:
 - [Azure DevOps integration](./azure.md)
 
 ## Qodo Merge 💎
+
 Qodo Merge, an app hosted by QodoAI for GitHub\GitLab\BitBucket, is also available.
 <br>
 With Qodo Merge, installation is as simple as adding the Qodo Merge app to your relevant repositories.

docs/docs/installation/locally.md

@@ -3,7 +3,6 @@ To run PR-Agent locally, you first need to acquire two keys:
 1. An OpenAI key from [here](https://platform.openai.com/api-keys){:target="_blank"}, with access to GPT-4 and o3-mini (or a key for other [language models](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/), if you prefer).
 2. A personal access token from your Git platform (GitHub, GitLab, BitBucket) with repo scope. GitHub token, for example, can be issued from [here](https://github.com/settings/tokens){:target="_blank"}
 
-
 ## Using Docker image
 
 A list of the relevant tools can be found in the [tools guide](../tools/).
@@ -11,27 +10,33 @@ A list of the relevant tools can be found in the [tools guide](../tools/).
 To invoke a tool (for example `review`), you can run PR-Agent directly from the Docker image. Here's how:
 
 - For GitHub:
-    ```
+
+    ```bash
     docker run --rm -it -e OPENAI.KEY=<your key> -e GITHUB.USER_TOKEN=<your token> codiumai/pr-agent:latest --pr_url <pr_url> review
     ```
+
     If you are using GitHub enterprise server, you need to specify the custom url as variable.
     For example, if your GitHub server is at `https://github.mycompany.com`, add the following to the command:
-    ```
+
+    ```bash
     -e GITHUB.BASE_URL=https://github.mycompany.com/api/v3
     ```
 
 - For GitLab:
-    ```
+
+    ```bash
     docker run --rm -it -e OPENAI.KEY=<your key> -e CONFIG.GIT_PROVIDER=gitlab -e GITLAB.PERSONAL_ACCESS_TOKEN=<your token> codiumai/pr-agent:latest --pr_url <pr_url> review
     ```
 
     If you have a dedicated GitLab instance, you need to specify the custom url as variable:
-    ```
+
+    ```bash
     -e GITLAB.URL=<your gitlab instance url>
     ```
 
 - For BitBucket:
-    ```
+
+    ```bash
     docker run --rm -it -e CONFIG.GIT_PROVIDER=bitbucket -e OPENAI.KEY=$OPENAI_API_KEY -e BITBUCKET.BEARER_TOKEN=$BITBUCKET_BEARER_TOKEN codiumai/pr-agent:latest --pr_url=<pr_url> review
     ```
 
@@ -46,7 +51,7 @@ The `<TABLE>` refers to a table/section in a configuration file and `<KEY>=<VALU
 For example, suppose you want to run `pr_agent` that connects to a self-hosted GitLab instance similar to an example above.
 You can define the environment variables in a plain text file named `.env` with the following content:
 
-```
+```bash
 CONFIG__GIT_PROVIDER="gitlab"
 GITLAB__URL="<your url>"
 GITLAB__PERSONAL_ACCESS_TOKEN="<your token>"
@@ -76,7 +81,7 @@ Same goes for other providers, make sure to check the [documentation](https://qo
 
 Install the package:
 
-```
+```bash
 pip install pr-agent
 ```
 
@@ -109,18 +114,17 @@ if __name__ == '__main__':
     main()
 ```
 
-
 ## Run from source
 
 1. Clone this repository:
 
-```
+```bash
 git clone https://github.com/Codium-ai/pr-agent.git
 ```
 
 2. Navigate to the `/pr-agent` folder and install the requirements in your favorite virtual environment:
 
-```
+```bash
 pip install -e .
 ```
 
@@ -128,7 +132,7 @@ pip install -e .
 
 3. Copy the secrets template file and fill in your OpenAI key and your GitHub user token:
 
-```
+```bash
 cp pr_agent/settings/.secrets_template.toml pr_agent/settings/.secrets.toml
 chmod 600 pr_agent/settings/.secrets.toml
 # Edit .secrets.toml file
@@ -136,7 +140,7 @@ chmod 600 pr_agent/settings/.secrets.toml
 
 4. Run the cli.py script:
 
-```
+```bash
 python3 -m pr_agent.cli --pr_url <pr_url> review
 python3 -m pr_agent.cli --pr_url <pr_url> ask <your question>
 python3 -m pr_agent.cli --pr_url <pr_url> describe
@@ -148,6 +152,7 @@ python3 -m pr_agent.cli --issue_url <issue_url> similar_issue
 ```
 
 [Optional] Add the pr_agent folder to your PYTHONPATH
-```
+
+```bash
 export PYTHONPATH=$PYTHONPATH:<PATH to pr_agent folder>
 ```

docs/docs/installation/pr_agent.md

@@ -46,4 +46,4 @@ Configure PR-Agent with Azure DevOps as:
 - Azure DevOps pipeline job
 - Local Azure DevOps webhook
 
-[View Azure DevOps Integration Guide →](https://qodo-merge-docs.qodo.ai/installation/azure/)
+[View Azure DevOps Integration Guide →](https://qodo-merge-docs.qodo.ai/installation/azure/)

docs/docs/installation/qodo_merge.md

@@ -23,7 +23,7 @@ For open-source projects, Qodo Merge is available for free usage. To install Qod
 
 ## Install Qodo Merge for Bitbucket
 
-###  Bitbucket Cloud
+### Bitbucket Cloud
 
 Qodo Merge for Bitbucket Cloud is available for installation through the following [link](https://bitbucket.org/site/addons/authorize?addon_key=d6df813252c37258)
 
@@ -33,8 +33,7 @@ Qodo Merge for Bitbucket Cloud is available for installation through the followi
 
 To use Qodo Merge application on your private Bitbucket Server, you will need to contact us for starting an [Enterprise](https://www.qodo.ai/pricing/) trial.
 
-
-## Install Qodo Merge for GitLab 
+## Install Qodo Merge for GitLab
 
 ### GitLab Cloud