update README, add jupyter as dependency

README.md

@@ -1,23 +1,47 @@
 
 ## Installation
+```bash
+# clone the repository
+git clone https://github.com/mackelab/labproject.git
 
-First, clone the repository with `git clone https://github.com/mackelab/labproject.git` and then install the package `labproject` with its dependencies with `pip install -e 
-.` or when you also want to edit the tutorials `pip install -e ".[docs]"`. 
-You may want to do this in an environment but you can also use your standard Python installation. 
+# (optional but recommended) create conda environment
+conda create -n labproject python=3.9
+conda activate labproject
 
-## Coding
+# install labproject package with dependencies
+pip install -e .
+# if you want to edit the tutorials, install the docs dependencies
+pip install -e ".[docs]"
+```
+
+`pip install -e .` installs the labproject package in editable mode, i.e. changes to the code are immediately reflected in the package.
+
+The environment now contains, `numpy`, `scipy`, `matplotlib`, `torch`, and `jupyter`.
+
+## Development
 
 Develop code in your desired way, e.g. in local notebooks (you don't commit, the public notebooks for the website can be found in `docs/notebooks/`). 
+
 Once you want other people to see your figure/experiment, add them to `plotting.py` and `experiments.py` and call the corresponding functions in `run.py`. 
+
 After committing and pushing your changes, GitHub will execute `run.py` and update the figures in Overleaf. 
 
 You can obviously also run it yourself with `python labproject/run.py`.
 
+
+
 ## Documentation
 
 We use mkdocs to create the public version of our tutorials (notebooks) and the API documentation. mkdocs are written in Markdown and are found in `docs/`. 
 After installing the necessary dependencies with `pip install -e ".[docs]"`, you can view your local version with `mkdocs serve` in `labproject/` and then open http://127.0.0.1:8000/. 
 This especially helpful when editing the documentation. 
 
 ### Notebooks
-The jupyter notebooks are found in `docs/notebooks/`
+The jupyter notebooks are found in `docs/notebooks/`.
+
+For your convenience, at the beginning of the jupyter notebook, run    
+```python
+%load_ext autoreload
+%autoreload 2
+```
+for automatic reloading of modules, in case you make any running changes to the labproject code.

pyproject.toml

@@ -7,6 +7,7 @@ name = "labproject"
 version = "0.1"
 
 dependencies = [
+    "jupyter",
     "numpy",
     "scipy",
     "matplotlib",