fixed linting

docs/README.md

@@ -15,4 +15,4 @@ We welcome contributions to our documentation! Please see the [Contributing](con
 
 ## License
 
-This project is licensed under the [LICENSE](../LICENSE) file in the root directory of this source tree.
+This project is licensed under the [LICENSE](../LICENSE) file in the root directory of this source tree.

docs/changelog.md

@@ -8,4 +8,4 @@ The changelog documents all notable changes to the project. This file is updated
 
 ## [Version] - [Release Date]
 
-- List changes for each version.
+- List changes for each version.

docs/contributing.md

@@ -3,9 +3,10 @@
 We love contributions from the community! This document explains how you can contribute to the project.
 
 ## How to Contribute
-#### Generate and install the python installable API
 
-After making any changes to the logic, it is worth regenerating the API with the OpenAPI Generator. 
+### Generate and install the python installable API
+
+After making any changes to the logic, it is worth regenerating the API with the OpenAPI Generator.
 
 Generating the installable APIs (Python + Typescript) involves running the server, getting the `/openapi.json`, and running `openapi-generator`.
 
@@ -16,21 +17,24 @@ The `regenerate_api.py` script does this for us in a few ways:
 3. Spins up the server itself.
 
 You can simply run:
+
 ```bash
 # this will start the api.server, so make sure you have the dependencies installed,
 python regenerate_api.py \
     && pip install .
 ```
 
 or if you prefer the Docker approach (eg: for CI), this command will build the docker container and supply it to `regenerate_api.py`:
+
 ```bash
 # SM_DOCKER is a known env variable to regenerate_api.py
 export SM_DOCKER="cpg/metamist-server:dev"
 docker build --build-arg SM_ENVIRONMENT=local -t $SM_DOCKER -f deploy/api/Dockerfile .
 python regenerate_api.py
 ```
 
-#### Developing the UI
+### Developing the UI
+
 ```bash
 # Ensure you have started metamist server locally on your computer already, then in another tab open the UI.
 # This will automatically proxy request to the server.
@@ -39,6 +43,7 @@ npm install
 npm run compile
 npm start
 ```
+
 This will start a web server using Vite, running on `localhost:5173`.
 
 ### OpenAPI and Swagger
@@ -70,4 +75,4 @@ The deploy github action builds the container, and is deployed.
 
 Additionally you can access metamist through the identity-aware proxy (IAP),
 which handles the authentication through OAuth, allowing you to access the
-front-end.
+front-end.

docs/installation.md

@@ -3,12 +3,10 @@
 This document provides detailed instructions on how to install the project. Follow these steps to set up the project on your local system.
 
 ## Prerequisites
-#### Mac
-[Homebrew](https://brew.sh) is the simplest way to install system dependencies needed for this project.
 
+[Homebrew](https://brew.sh) is the simplest way to install system dependencies needed for this project.
 
-#### Windows
-[Chocolatey](https://community.chocolatey.org/) is a good equivalent to Homebrew for package management in Windows. 
+[Chocolatey](https://community.chocolatey.org/) is a good equivalent to Homebrew for package management in Windows.
 
 ## System Requirements
 
@@ -21,7 +19,8 @@ This document provides detailed instructions on how to install the project. Foll
 - **pyenv**
 - **wget** *(optional)*
 
-#### Mac
+### Mac
+
 ```bash
 brew install nvm
 brew install java
@@ -30,11 +29,12 @@ brew install pyenv
 brew install wget
 
 # skip if you wish to install via docker
-brew install [email protected] 
+brew install [email protected]
 
 ```
 
-#### Windows
+### Windows
+
 ```bash
 # Assuming you have Chocolatey
 choco install nvm
@@ -45,7 +45,6 @@ choco install wget
 
 # skip if you wish to install via docker
 choco install mariadb --version=10.8.3
-
 ```
 
 ```bash
@@ -55,19 +54,20 @@ nvm install --lts
 # Once you have npm set up, install the OpenAPI generator:
 npm install @openapitools/openapi-generator-cli -g
 openapi-generator-cli version-manager set 5.3.0
-
 ```
 
 ## Installation Steps
 
-#### Creating the environment
+### Creating the environment
+
 - Python dependencies for the `metamist` API package are listed in `setup.py`.
 - Additional dev requirements are listed in `requirements-dev.txt`.
 - Packages for the sever-side code are listed in `requirements.txt`.
 
-We _STRONGLY_ encourage the use of `pyenv` for managing Python versions. Debugging and the server will run on a minimum python version of 3.10.
+We *STRONGLY* encourage the use of `pyenv` for managing Python versions. Debugging and the server will run on a minimum python version of 3.10.
 
 Use of a virtual environment to contain all requirements is highly recommended:
+
 ```bash
 virtualenv venv
 source venv/bin/activate
@@ -79,6 +79,7 @@ pip install --editable .
 ```
 
 You will also need to set the following environment variables. Adjust the paths if you installed the dependencies using an alternate means:
+
 ```bash
 # homebrew should export this on an M1 Mac
 # the intel default is /usr/local
@@ -112,7 +113,7 @@ export SM_DEV_DB_USER=sm_api # makes it easier to copy liquibase update command
 
 You can also add these to your shell config file e.g `.zshrc` or `.bashrc` for persistence to new sessions.
 
-#### Database Setup - Native Installation
+### Database Setup - Native Installation
 
 Set the following environment variables:
 
@@ -124,7 +125,7 @@ export SM_DEV_DB_PORT=3306 # default mariadb port
 export SM_DEV_DB_NAME=sm_dev;
 ```
 
-Next, create the database `sm_dev` in MariaDB. 
+Next, create the database `sm_dev` in MariaDB.
 
 > In newer versions of MariaDB, the root user is protected.
 
@@ -159,21 +160,24 @@ liquibase \
 popd
 ```
 
-#### Database Setup - Docker Installation
+### Database Setup - Docker Installation
 
 Ensure you have Docker installed or follow [this guide](https://docs.docker.com/engine/install/) to setup.
 
 Pull the image:
+
 ```bash
 docker pull mariadb:10.8.3
 ```
 
 Run the container on port 3306:
+
 ```bash
 docker run --name mariadb-p3306 -e MYSQL_ALLOW_EMPTY_PASSWORD=1 -p 3306:3306 -d docker.io/library/mariadb:10.8.3
 ```
 
 If you have a local MySQL instance already running on port 3306, you can map the docker container to run on 3307:
+
 ```bash
 docker run --name mariadb-p3307 -e MYSQL_ALLOW_EMPTY_PASSWORD=1 -p 3307:3306 -d docker.io/library/mariadb:10.8.3
 ```
@@ -185,6 +189,7 @@ docker exec -it mariadb-p3306 bash
 ```
 
 Set up the database with the `sm_api` user and appropriate permissions:
+
 ```bash
 mysql -u root --execute "
   CREATE DATABASE sm_dev;
@@ -215,6 +220,7 @@ popd
 ```
 
 Ensure the database port environment variable matches the mapping above:
+
 ```bash
 export SM_DEV_DB_PORT=3306 # or 3307
 ```
@@ -223,7 +229,7 @@ export SM_DEV_DB_PORT=3306 # or 3307
 
 You'll want to set the following environment variables (permanently) in your local development environment.
 
-The `SM_ENVIRONMENT`, `SM_LOCALONLY_DEFAULTUSER` and `SM_ALLOWALLACCESS` environment variables allow access to a local metamist server without providing a bearer token. 
+The `SM_ENVIRONMENT`, `SM_LOCALONLY_DEFAULTUSER` and `SM_ALLOWALLACCESS` environment variables allow access to a local metamist server without providing a bearer token.
 
 This will allow you to test the front-end components that access data. This happens automatically on the production instance through the Google identity-aware-proxy.
 
@@ -238,18 +244,22 @@ export SM_LOCALONLY_DEFAULTUSER=$(whoami)
 ```
 
 With those variables set, it is a good time to populate some test data if this is your first time running this server:
+
 ```bash
 python3 test/data/generate_data.py
 ```
+
 You can now run the server:
+
 ```bash
 # start the server
 python3 -m api.server
 # OR
 # uvicorn --port 8000 --host 0.0.0.0 api.server:app
 ```
 
-#### Running and Debugging in VS Code
+### Running and Debugging in VS Code
+
 The following `launch.json` is a good base to debug the web server in VS Code:
 
 ```json
@@ -279,13 +289,5 @@ You can now place breakpoints anywhere and debug the API with "Run API" under th
 
 
 ## Contributing
-See the [Contributing](contributing.md) page for instructions on how to make changes and regenerate the API.
-
-
-
-
-
-
-
-
 
+See the [Contributing](contributing.md) page for instructions on how to make changes and regenerate the API.

docs/introduction.md

@@ -1,7 +1,7 @@
 # Introduction
 
 
-**Metamist** is a database designed for storing de-identified -omics metadata. 
+**Metamist** is a database designed for storing **de-identified** -omics metadata.
 
 ## Purpose
 
@@ -14,7 +14,7 @@ The project provides an interface to interact with the -omics database via the P
   - `dataset-sample-metadata-main-read`: For read-only access.
   - `dataset-sample-metadata-main-write`: For write access.
 - **Efficiency Note**: Members of Google Groups are cached in a blob to optimize performance, as group-membership identity lookups can be slow.
- 
+
 ## High-Level Architecture
 
 It comprises three key components:
@@ -45,5 +45,6 @@ The codebase contains the following modules worth noting:
 - `api/routes`: HTTP + OpenAPI
 
 And metamist maintains two clients:
+
 - `web`  -> React app that consumes a generated Typescript API + GraphQL
-- `metamist` -> autogenerated Python API
+- `metamist` -> autogenerated Python API