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Update README with new installation instructions
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mattwthompson committed May 31, 2022
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Expand Up @@ -21,45 +21,41 @@ practical use in force field parameterization [2].

For a more extensive history and explanation, see our [preprint](http://doi.org/10.26434/chemrxiv.8304578.v1) [3].

## Prerequisites

We test with Python 3.6 and 3.7 and expect any version above 3.5 to behave well.
## Installation

This is a python tool kit with a few dependencies. We recommend installing
[miniconda](http://conda.pydata.org/miniconda.html). Then you can create an
environment with the following commands:
Chemper is available via `conda-forge`:

```bash
conda create -n [my env name] python=3.6 numpy networkx pytest
source activate [my env name]
```shell
conda install -c conda-forge chemper
```

This command will install all dependencies besides a toolkit for cheminformatics or storing of molecule
information. We seek to keep this tool independent of cheminformatics toolkit, but currently only support
[RDKit](http://www.rdkit.org/docs/index.html) and [OpenEye Toolkits](https://www.eyesopen.com/).
If you wish to add support please feel free to submit a pull request.
Make sure one of these tool kits is installed in your environment before installing chemper.

#### RDKit environment
information. Also install [RDKit](http://www.rdkit.org/docs/Install.html) and/or
[OpenEye toolkits](https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html) by
running:

Conda installation according to [RDKit documentation](http://www.rdkit.org/docs/Install.html):
```bash
conda install -c rdkit rdkit
conda install -c conda-forge rdkit
```

#### OpenEye environment
Conda installation according to [OpenEye documentation](https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html)
and/or

```bash
conda install -c openeye openeye-toolkits
```

## Installation

Hopefully chemper will be conda installable in the near future, but for now the best option
is to download or clone this repository and then install `chemper` from inside the `chemper` directory with:
```bash
pip install -e .
```
## Supported Python versions

We test with whatever Python versions are found in `.github/workflows/ci.yaml`. Chemper may function
on some older and/or newer versions as well.

## Supported chemiformatics toolkits

We seek to keep this tool independent of cheminformatics toolkit, but currently only support
[RDKit](http://www.rdkit.org/docs/index.html) and [OpenEye Toolkits](https://www.eyesopen.com/).
If you wish to add support please feel free to submit a pull request.
Make sure one of these toolkits is installed in your environment before installing chemper.

# Documentation

Expand Down Expand Up @@ -151,6 +147,8 @@ for automated chemical perception. However, the API is still in flux and nothing
This release matches the work published in our [preprint](http://doi.org/10.26434/chemrxiv.8304578.v1).
While the code is stable and there are tests showing how it should work the science it represents is still in the early stages and big changes to the algorithms and API should be expected in future releases.

### Version 1.0.1
This release includes non-behavior-breaking changes to support distribution on Python 3.10.

## Contributors

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