Added development notes, updated README.

README.md

@@ -0,0 +1,29 @@
+# NQRduckumentation
+
+Welcome to the NQRduckumentation - the central place for all documentation regarding the NQRduck software.
+
+This is obviously only the README file. The actual documentation is built using Sphinx.
+
+## Installation
+
+If for some reason you want to build the documentation yourself, you can do so by following these steps:
+
+1. Clone the repository:
+
+2. Install the required dependencies:
+
+    ```bash
+    pip install -r requirements.txt
+    ```
+
+3. Build the documentation:
+
+    ```bash
+    make html
+    ```
+
+4. Open the documentation found at `build/html/index.html` with your browser.
+
+## License
+
+The code itself is licensed under the MIT license.

source/api_reference/quackseq.rst

@@ -1,6 +1,9 @@
 QuackSeq
 ========
 
+QuackSeq is a pulse programming framework for magnetic resonance spectroscopy experiments. 
+Sequences can bei either run on an Software Defined Radio (SDR) based spectrometer or simulated.
+
 .. autosummary::
     :toctree: _autosummary
     :recursive:

source/index.md

@@ -38,6 +38,9 @@ The core of the program is the nqrduck. It provides a central interface for comm
 
 The focus for spectrometers currently lies on LimeSDR based spectrometers (LimeSDR USB, LimeSDR Mini 2.0).
 
+Additionally, the nqrduck framework has it's own modules for vendor independent control execution of pulse sequences. The pulse programming framework is called QuackSeq and a detailed documentation can be found [here](api_reference/quackseq.html).
+Different QuackSeq sequences can either be executed on the LimeSDR or on a simulated spectrometer.
+
 ```{toctree}
 :maxdepth: 1
 :caption: Contents:

source/installation.md

@@ -31,3 +31,14 @@
 6. You now need to restart the program.
 
 7. You can switch between different modules with the toolbar. You can customize the appearance of the program in `Settings -> Preferences`. Settings are saved and restored on the next start.
+Some settings need a restart to take effect - so it's recommended to restart the program after changing settings.
+
+## Uninstall
+
+To uninstall the NQRduck, you can simply delete the virtual environment. If you additionally want the nqrduck package to remove any other files, you can run:
+
+```bash
+nqrduck --uninstall
+```
+
+This removes the desktop file and the icon from the system.

source/software_structure/development.md

@@ -1,9 +1,168 @@
 # Development
 
-This section describes the process of developing the NQRduck software. 
+This section describes the process of developing the NQRduck software.
+
+## Development of NQRduck modules
+
+Here, an exemplary workflow for the development of new NQRduck modules is given.
+
+If one wants to develop a new module, a template is provided [here](https://github.com/nqrduck/nqrduck-module). This template can be used as a starting point for a new module.
+
+For example, if one wants to develop a new module called *myduck*, one would first clone the repository.
+
+The template repository has the following file structure:
+
+```bash
+nqrduck-module/
+|-- .gitignore
+|-- LICENCE
+|-- README.md
+|-- pyproject.toml
+|-- src/
+|   |-- nqrduck_module/
+|   |   |-- __init__.py
+|   |   |-- controller.py
+|   |   |-- model.py
+|   |   |-- module.py
+|   |   |-- resources/
+|   |   |    |-- module.ini
+|   |   |    |-- module_widget.ui
+|   |   |-- view.py
+|   |   |-- widget.py
+```
+
+*File structure of the NQRDuck module Git repository.*
+
+If one would now like to create a module with the example name *myduck*, the folder and file names would be modified in the following way:
+
+```bash
+nqrduck-myduck/
+|-- .gitignore
+|-- LICENCE
+|-- README.md
+|-- pyproject.toml
+|-- src/
+|   |-- nqrduck_myduck/
+|   |   |-- __init__.py
+|   |   |-- controller.py
+|   |   |-- model.py
+|   |   |-- myduck.py
+|   |   |-- resources/
+|   |   |    |-- module.ini
+|   |   |    |-- myduck_widget.ui
+|   |   |-- view.py
+|   |   |-- widget.py
+
+```
+
+*File structure of the newly created *myduck* module.*
+
+The class names inside the model, view, and controller classes should also be modified to have a more representative name (e.g., `MyDuckController`, `MyDuckView`, `MyDuckModel`). The object created in the `myduck` file should also be renamed:
+
+```python
+from nqrduck.module.module import Module
+from .model import MyDuckModel
+from .view import MyDuckView
+from .controller import MyDuckController
+
+MyDuck = Module(MyDuckModel, MyDuckView, MyDuckController)
+```
+
+Then the `.ini` file inside the resources folder should be modified to represent the *myduck* module.
+
+```toml
+[META]
+name = nqrduck-myduck
+category = MyOwnModules
+toolbar_name = MyDuck
+tooltip = Template for a new module
+```
+
+*Example for the modified .ini file. The category, toolbar name, and tooltip can be freely chosen.*
+
+Additionally, the `pyproject.toml` has to be modified to represent the new module structure:
+
+```toml
+[project]
+name = "nqrduck-myduck"
+version = "0.0.1"
+authors = [
+  { name="YOUR NAME", email="your@e.mail" },
+]
+
+description = "Your description"
+
+...
+
+dependencies = [
+    "nqrduck",
+    "pyqt6",
+    ...
+]
+
+[project.entry-points."nqrduck"]
+"nqrduck-myduck" = "nqrduck_myduck.myduck:MyDuck"
+```
+
+Now functionality can be implemented. For example, the `myduck_widget.ui` could be modified using Qt Designer. The `widget.py` file can then be updated using `pyuic6`.
+
+```bash
+# Navigate to the repository directory
+cd nqrduck-myduck
+
+# Generate your widget.py
+pyuic6 src/nqrduck_myduck/resources/myduck_widget.ui > src/nqrduck_myduck/widget.py
+```
+
+The module should be installed to test its functionality. Ideally, the module is installed with the `-e` argument of `pip` to install it in editable mode. This means changes in the source code of the project will be applied without reinstalling the module.
+
+```bash
+# Navigate to the repository directory
+cd nqrduck-myduck
+
+# Install the package and all dependencies
+pip install -e .
+```
+
+## Example pyproject.toml
+
+```toml
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "nqrduck-module"
+version = "0.0.1"
+authors = [
+  { name="Author Name", email="author@e.mail" },
+]
+
+description = "A template for nqrduck modules."
+readme = "README.md"
+license = { file="LICENSE" }
+requires-python = ">=3.8"
+
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+
+dependencies = [
+    "matplotlib",
+    "pyqt6",
+    "nqrduck",
+]
+
+[project.entry-points."nqrduck"]
+"nqrduck-module" = "nqrduck_module.module:module"
+```
 
 ## Style
 
+Here the style guide for the NQRduck software is described.
+
 ### Linting
 
 Linting is done using [ruff](https://astral.sh/ruff) with the following configuration specified in the `pyproject.toml` file:
@@ -44,7 +203,6 @@ Documentation is implemented with [Sphinx](https://www.sphinx-doc.org/en/master/
 
 For docstrings in the code, the [Google style](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html) is used.
 
-
 ## Branching
 
 The main branch is used for releases. Development is done on a development branch. Feature branches are created from the development branch and merged back into it. The development branch is merged into the main branch for releases. Releases are tagged with a version number starting with `v` (e.g. `v0.1.0`) and should follow [semantic versioning](https://semver.org/) (right now they don't).
@@ -58,4 +216,4 @@ Right now the tests are not very extensive, but they are a good starting point f
 
 - The software is deployed via [PyPI](https://pypi.org/). Different modules are distributed as separate packages. The Action is run on a tag push to the main branch starting with `v` (e.g. `v0.1.0`).
 
-- For Cython modules, `aarch64` and `x86_64` wheels are built using GitHub Actions. The wheels are deployed alongside the source distribution to PyPI.
+- For Cython modules, `aarch64` and `x86_64` wheels are built using GitHub Actions. The wheels are deployed alongside the source distribution to PyPI.