diff --git a/.gitignore b/.gitignore
index 0c1bc8bd966744f01c0dd002b562d9e62034b0e7..8c9c1fcf9f253046c2067756e320566e85c3f8f0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,7 +13,7 @@ __pycache__
~$*
# Build
-.tox/
+venv/*
# ACMC phenotype build files
diff --git a/docs/index.md b/docs/index.md
index 65807987d161d6cd0538758b1973bdac57dbcb76..a2416745ecd872c0ea6594ac3b582d20a06f356c 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -172,10 +172,142 @@ The `phen` command is used phenotype-related operations.
- `-d`, `--phen-dir`: (Optional) Directory of current phenotype configuration (the default is ./build/phen).
- `-old`, `--phen-dir-old`: (Required) Directory of old phenotype version)
-
-# GitLab Workflow for Managing Releases
-## Branching Strategy
+# Development Guide
+
+## Prerequisites
+To install the ACMC package for development, ensure you have Python 3.9 or later installed.
+
+### Clone the Repository
+```sh
+git clone https://git.soton.ac.uk/meldb/concepts-processing.git
+cd concepts-processing
+```
+
+### Set Up a Virtual Environment
+It is recommended to use a virtual environment to manage dependencies.
+
+```sh
+python -m venv venv
+source venv/bin/activate # On Windows use `venv\Scripts\activate`
+```
+
+### Install Dependencies
+Using `hatch`, you can install the necessary dependencies easily.
+
+```sh
+pip install --upgrade pip
+pip install hatch
+```
+This will create a virtual environment with all required dependencies.
+
+## Development Environment
+
+We have two separate environments to ensure that development dependencies (such as testing tools, linters, or other utilities) don't interfere the production environment.
+
+- default environment: includes the core dependencies to run acmc (e.g., requests, etc.).
+- dev environment: includes additional tools for testing, code formatting, linting, and other development workflows (e.g., pytest, black, mypy, etc.).
+
+### Activate the Development Environment
+To enter the (dev) development environment, use:
+
+```sh
+hatch shell dev
+```
+
+### Activate Production Environment
+To enter the (acmc) production environment, use:
+
+```sh
+hatch shell
+```
+
+### Deactivate Environment
+To exist an environment from hatch, use:
+
+```sh
+exit
+```
+
+### Code Formatting
+The project uses `black` for code formatting. Ensure your code is properly formatted before committing
+
+To check if any of the code needs to be formatted, run black with the `--check` option
+
+```sh
+hatch run black --check acmc
+```
+
+To format the coode and modify the files, use
+
+```sh
+hatch run black acmc
+```
+
+### Type Checking
+The project uses `mypy` for type checking:
+
+```sh
+hatch run mypy -p acmc
+```
+
+### Running Tests
+To run tests using `pytest`, use:
+
+```sh
+hatch run pytest
+```
+
+## Building the Package
+To build the package, use:
+
+```sh
+hatch build
+```
+
+## Running the CLI
+The package provides a command-line interface (CLI) entry point.
+
+```sh
+acmc --help
+```
+
+## Contributing
+
+### GitLab Basic Workflow Overview
+
+1. Create an new issue in the [Issue Tracker](https://git.soton.ac.uk/meldb/concepts-processing/-/issues)
+
+2. Create a new branch for your feature
+
+You can do this from the issue page in GitLab by selecting "Create Branch", then checkout using:
+
+ ```sh
+ git checkout -b feature-branch origin/feature-branch
+ ```
+
+This works if someone has already created the branch and you want to work on it.
+
+You can also create a new branch in your local repo if it does not exist and it will be created when you push
+
+ ```sh
+ git checkout -b feature-branch
+ ```
+
+4. Make changes and commit them:
+ ```sh
+ git add .
+ git commit -m "Description of changes"
+ ```
+5. Push your branch:
+ ```sh
+ git push origin feature-branch
+ ```
+6. Open a merge request in GitLab.
+
+If you make changes, ensure all tests pass and code formatting is correct before submitting a merge request.
+
+## GitLab Workflow for Managing Releases
### 1. Main Branch (`main`)
- Represents the stable production-ready code.
@@ -221,14 +353,18 @@ The `phen` command is used phenotype-related operations.
- Deploy to production after approval.
- Requires authorization from a repository maintainer or admin before merging.
-## Commit Message Guidelines
+### Commit Message Guidelines
- Use clear and descriptive commit messages.
- Format: `<type>(<scope>): <description>`
-- Example: `docs (documentation): git workflow documentation (#issue)`
-- Types: `feat` (feature), `fix` (bug fix), `docs` (documentation), `refactor` (code refactoring), `test` (tests), `chore` (maintenance).
+- Example: `docs: git workflow documentation (#issue)`
+- Types: `feat`, `fix`, `docs`, `refactor`, `test`, `chore`.
## Additional Guidelines
- Always pull the latest changes before starting a new feature: `git pull origin dev`
- Write unit tests for new features.
- Keep feature branches short-lived and regularly updated with `dev`.
+## Additional Resources
+- [Repository](https://git.soton.ac.uk/meldb/concepts-processing)
+- [Documentation](https://git.soton.ac.uk/meldb/concepts-processing/docs)
+- [Issue Tracker](https://git.soton.ac.uk/meldb/concepts-processing/-/issues)
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index aeb94388c9a0e46b0627dc71a99e322d692f6d0b..096598aa1580b8140d49c63cad237207f839d420 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -47,23 +47,26 @@ Repository = "https://git.soton.ac.uk/meldb/concepts-processing"
Documentation = "https://git.soton.ac.uk/meldb/concepts-processing/docs"
Issues = "https://git.soton.ac.uk/meldb/concepts-processing/-/issues"
-[tool.hatch.build]
-include = ["acmc/**"] # Ensure only the acmc package is included
-
-[tool.hatch.build.targets.sdist]
-include = [
- "acmc/**",
-]
-
[tool.hatch.build.targets.wheel]
packages = ["acmc"]
[tool.hatch.envs.default]
dependencies = [
"hatch",
- "pytest"
+ "pytest",
]
-[tool.hatch.envs.default.scripts]
-dev = "python -m acmc"
-test = "pytest tests"
\ No newline at end of file
+[tool.hatch.envs.dev]
+dependencies = [
+ "pytest",
+ "black",
+ "mypy"
+]
+
+[tool.hatch.build]
+include = ["acmc/**"] # Ensure only the acmc package is included
+
+[tool.hatch.build.targets.sdist]
+include = [
+ "acmc/**",
+]
\ No newline at end of file