Fix environment.yml for conda-forge and review README.md

README.md

@@ -5,45 +5,51 @@ The implementation is based on Ben-Eliezer et al. 2015 (https://doi.org/10.1002/
 
 ## Install
 
-Recommended and tested is to clone git repository.
-From the repository root, run with a name of your choice:
+Recommended and tested is to clone the git repository.
+From the repository root, create a conda environment with an `env_name` of your choice by running:
 
-`conda env create -f environment.yml -n <env_name>`
+```shell
+conda env create -f environment.yml -n env_name
 
-`conda activate <env_name>`
+conda activate env_name
+```
+
+If you don't have a conda installation, 
+we recommend using [Miniforge](https://conda-forge.org/miniforge/).
+You should also consider calling `mamba` instead of `conda` for a faster resolution of dependencies.
 
 ## Usage
 
 The Package contains simulation of dictionary databases as well as the fitting of data to such databases.
+
 #### Simulation
-To simulate with configuration found in the "example/simulate" folder run:
 
-`python simulate.py`
+To simulate with the configuration found in the `example/simulate` folder run:
 
+```shell
+python simulate.py
+```
 
 To see all options run
 
-`python simulate.py --help`
-
+```shell
+python simulate.py --help
+```
 
 The simulation needs information about Gradients and RF events.
-The basic inputs can be seen in the "example/simulate/emc_params.json" file.
-Default configuration will create a database and some plots within the "example/simulate/" folder.
-
+The basic inputs can be seen in the `example/simulate/emc_params.json` file.
+The default configuration will create a database and plots within the `example/simulate/` folder.
 
 #### Fit
-To fit with a configuration found in the "example/fit" folder run:
 
-`python fit.py`
+To fit with the configuration found in the `example/fit` folder run:
 
+`python fit.py`
 
 To see all options run
 
 `python fit.py --help`
 
-
 The fit can take additional input files and needs specification of data and database.
-The basic inputs can be seen in the "example/fit/fit_config.json" file.
-Default configuration will use the data within the "examples/fit" folder and b1 regularization.
-
-
+The basic inputs can be seen in the `example/fit/fit_config.json` file.
+The default configuration will use the data within the `examples/fit` folder and b1 regularization.

environment.yml

@@ -1,7 +1,6 @@
 name: emc_env
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - python=3.10
   - pandas=2.0.3
@@ -13,4 +12,5 @@ dependencies:
   - plotly=5.16.1
   - simple-parsing
   - tqdm
-  - nibabel
+  - nibabel
+  - wandb