Merge pull request #5 from CDDLeiden/dev/cleanup

Dev/cleanup

Author: bolak92

.gitattributes

@@ -20,4 +20,4 @@ images/** linguist-documentation
 *.py linguist-language=Python
 
 # Ensure Python sources in uqdd/ are detectable (the default, but kept explicit for clarity)
-uqdd/** linguist-detectable=true
+uqdd/** linguist-detectable=true

.github/ISSUE_TEMPLATE/bug_report.md

@@ -4,14 +4,14 @@ about: Create a report to help us improve
 title: ''
 labels: ''
 assignees: ''
-
 ---
 
 **Describe the bug**
 A clear and concise description of what the bug is.
 
 **To Reproduce**
 Steps to reproduce the behavior:
+
 1. Go to '...'
 2. Click on '....'
 3. Scroll down to '....'
@@ -24,15 +24,11 @@ A clear and concise description of what you expected to happen.
 If applicable, add screenshots to help explain your problem.
 
 **Desktop (please complete the following information):**
- - OS: [e.g. iOS]
- - Browser [e.g. chrome, safari]
- - Version [e.g. 22]
-
-**Smartphone (please complete the following information):**
- - Device: [e.g. iPhone6]
- - OS: [e.g. iOS8.1]
- - Browser [e.g. stock browser, safari]
- - Version [e.g. 22]
+
+- OS & its version: [e.g. Redhat, Ubuntu, Windows]
+- Python version [e.g. 3.11]
+- Environment [e.g. environment_linux.yml or else]
+
 
 **Additional context**
 Add any other context about the problem here.

CONTRIBUTING.md

@@ -1,46 +1,56 @@
 # Contributing to Our Project
 
-First off, thank you for considering contributing to our project! It's people like you that make our project such a great tool.
+First off, thank you for considering contributing to our project! It's people like you that make our project such a
+great tool.
 
-We welcome contributions in various forms, including bug reports, feature requests, documentation improvements, and code contributions.
+We welcome contributions in various forms, including bug reports, feature requests, documentation improvements, and code
+contributions.
 
 ## Reporting Bugs
 
-If you encounter a bug, please help us by submitting an issue to our GitHub repository. When you are creating a bug report, please include as many details as possible. Fill out the required template, the information it asks for helps us resolve issues faster.
+If you encounter a bug, please help us by submitting an issue to our GitHub repository. When you are creating a bug
+report, please include as many details as possible. Fill out the required template, the information it asks for helps us
+resolve issues faster.
 
 ## Suggesting Enhancements
 
-If you have an idea for a new feature or an improvement to an existing one, please submit an issue to our GitHub repository. Clearly describe the proposed enhancement and its potential benefits.
+If you have an idea for a new feature or an improvement to an existing one, please submit an issue to our GitHub
+repository. Clearly describe the proposed enhancement and its potential benefits.
 
 ## Code Contribution Guidelines
 
 We follow a standard Fork & Pull Request workflow.
 
-1.  **Fork the repository:** Start by forking the main repository to your GitHub account.
-2.  **Create a branch:** For any new feature or bug fix, create a new branch in your forked repository. Use a descriptive name for your branch (e.g., `fix-login-bug` or `add-new-feature`).
-3.  **Make your changes:** Make your code changes in your branch. Ensure your code adheres to any existing coding standards and include tests if applicable.
-4.  **Test your changes:** Run the test suite to ensure your changes don't break existing functionality.
-5.  **Commit your changes:** Write clear and concise commit messages.
-6.  **Submit a Pull Request (PR):** Push your changes to your forked repository and then open a Pull Request to the main repository. Provide a clear description of the changes in your PR.
+1. **Fork the repository:** Start by forking the main repository to your GitHub account.
+2. **Create a branch:** For any new feature or bug fix, create a new branch in your forked repository. Use a descriptive
+   name for your branch (e.g., `fix-login-bug` or `add-new-feature`).
+3. **Make your changes:** Make your code changes in your branch. Ensure your code adheres to any existing coding
+   standards and include tests if applicable.
+4. **Test your changes:** Run the test suite to ensure your changes don't break existing functionality.
+5. **Commit your changes:** Write clear and concise commit messages.
+6. **Submit a Pull Request (PR):** Push your changes to your forked repository and then open a Pull Request to the main
+   repository. Provide a clear description of the changes in your PR.
 
 ## Setting up the Development Environment
 
 To set up the development environment, you will need Conda.
 
-1.  Clone your forked repository to your local machine.
-2.  Navigate to the project's root directory.
-3.  Create and activate the Conda environment using the provided `environment_{OS}.yml` file, for example in Linux:
-    ```bash
-    conda env create -f environment.yml
-    conda activate uqdd-env
-    ```
+1. Clone your forked repository to your local machine.
+2. Navigate to the project's root directory.
+3. Create and activate the Conda environment using the provided `environments/environment_{OS}.yml` file, for example in Linux:
+   ```bash
+   conda env create -f environments/environment_linux.yml
+   conda activate uqdd-env
+   ```
 
 ## Pull Request Process
 
-1.  Ensure any install or build dependencies are removed before the end of the layer when doing a build.
-2.  Update the README.md with details of changes to the interface, this includes new environment variables, exposed ports, useful file locations and container parameters.
-3.  Increase the version numbers in any examples files and the README.md to the new version that this Pull Request would represent. The versioning scheme we use is SemVer.
-4.  Your PR will be reviewed by a maintainer. They may ask for changes or provide feedback.
-5.  Once your PR is approved and passes all checks, it will be merged into the main codebase.
+1. Ensure any install or build dependencies are removed before the end of the layer when doing a build.
+2. Update the README.md with details of changes to the interface, this includes new environment variables, exposed
+   ports, useful file locations and container parameters.
+3. Increase the version numbers in any examples files and the README.md to the new version that this Pull Request would
+   represent. The versioning scheme we use is SemVer.
+4. Your PR will be reviewed by a maintainer. They may ask for changes or provide feedback.
+5. Once your PR is approved and passes all checks, it will be merged into the main codebase.
 
 Thank you for your contribution!