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add pip installation instructions (PyPi)
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- explain package name is alchemistry-flamel
- installation
- uninstallation
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orbeckst committed Nov 7, 2022
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Expand Up @@ -13,13 +13,36 @@ of the now unsupported [alchemical-analysis](https://github.com/MobleyLab/alchem

## Installation

Clone flamel and install
The package containing `flamel` is called **alchemistry-flamel**. The
latest release can be installed with `pip` or alternatively, install
from source. Both methods are explained below.

### `pip`
*flamel* is available from the Python Package index (PyPi) under the
name **alchemistry-flamel** and can be installed with
```shell
pip install alchemistry-flamel
```
The installed package makes the `flamel` script available.


### From sources
Clone the *flamel* repository https://github.com/alchemistry/flamel
and install with `pip`
```shell
git clone [email protected]:alchemistry/flamel.git
cd flamel
pip install .
pip install flamel/
```

### Uninstalling
If you want to remove *flamel* after having it installed with `pip`,
run
```shell
pip uninstall alchemistry-flamel
```
to delete `flamel` and its associated files.


## Usage

The analysis can be invoked with the following command
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