Update joss branch

.github/workflows/python-app.yml

@@ -0,0 +1,39 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: KinOpt application
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest

CONTRIBUTING.md

@@ -0,0 +1,62 @@
+# Community Guidelines for KinOpt
+
+Welcome to the KinOpt community! This project is open to contributors from all backgrounds, and we aim to foster a collaborative and respectful environment focused on chemical kinetics and kinetic modeling.
+
+This document provides clear guidance for third parties who wish to:
+
+---
+
+## 1. Contribute to the Software
+
+We welcome contributions that improve the functionality, performance, or usability of KinOpt. If you would like to contribute:
+
+- For most users with a chemical kinetics background, your primary interest will likely be in adding new kinetic models. These should be added to the file:  
+  `kinopt/src/kinetic_models.py`
+
+- When adding a model:
+  - Create a function named in the format:  
+    `rate_for_[name_of_the_model]`
+  - The first two arguments **must** be:
+    - `extent`: extent of reaction  
+    - `T`: temperature of the reaction
+  - Any additional arguments should correspond to **user input parameters**
+
+- Please ensure your code is:
+  - Well-documented  
+  - Properly tested (include tests if possible)  
+  - Consistent with the existing codebase and style
+
+- Submit contributions via a **Pull Request** on GitHub:  
+  [https://github.com/alan-tabore/KinOpt](https://github.com/alan-tabore/KinOpt)
+
+---
+
+## 2. Report Issues or Problems
+
+We encourage users to report bugs, unexpected behavior, or any other problems with the software.
+
+- Please check the [Issues page](https://github.com/alan-tabore/KinOpt/issues) to see if your concern has already been raised.
+- When reporting a new issue:
+  - Be clear and concise  
+  - Include your operating system, Python version, and KinOpt version  
+  - If possible, provide a minimal reproducible example
+
+---
+
+## 3. Seek Support
+
+If you need help using KinOpt or understanding how to contribute:
+
+- Feel free to open a **discussion or issue** on the GitHub page:  
+  [https://github.com/alan-tabore/KinOpt](https://github.com/alan-tabore/KinOpt)
+
+- When asking for help:
+  - Describe your problem clearly  
+  - Include relevant code or context  
+  - Be respectful of the maintainers’ time
+
+---
+
+## General Conduct
+
+While our community is primarily technical, we expect all interactions to remain professional and respectful. Disruptive or abusive behavior will not be tolerated.

README.md

@@ -41,13 +41,10 @@ Once you’ve downloaded the project, you can install the required python module
 
 Open a command prompt in the KinOpt folder and execute:
 ``` bash
-python -m pip install requirements.txt
-```
-or with conda:
-``` bash
-conda install requirements.txt
+python -m pip install -r requirements.txt
 ```
 
+
 ### Tutorials
 
 Tutorials are available on Youtube to show you how to install and use the software:

docs/source/launch_data_extraction.rst

@@ -8,5 +8,9 @@ Store them in the same folder and:
 
 1. Click on the "Add file(s)" button of the data extraction dock
 2. Navigate to the folder containing your data
-3. Selected all your files
-4. Make sure that the file list becomes green (indicating the extraction was successful)
+3. Select all your files
+4. Click the "open" button. (your files should now be loaded)
+5. Check the box "has header" if the first line of your file is a header. (if you have multiple lines to skip at the beginning of your file, indicate the number of lines to skip in the entry box "Number of lines to skip".
+6. Indicate the delimiter of your data in the "Delimiter" entry box. If no delimiter is indicated, the default delimiter (a comma ",") will be used. The delimiter used in the example data files is a comma ",". The tab delimiter can be specified as "\t" or "tab"
+7. Click the extract button.
+8. Make sure that the file list becomes green (indicating the extraction was successful)