Commit 8f62c852 authored by Bharath Ramsundar's avatar Bharath Ramsundar Committed by GitHub
Browse files

Prune old requirements and add pylint command.

parent 6f4b6332
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+15 −28
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@@ -30,9 +30,6 @@ Stanford and originally created by [Bharath Ramsundar](http://rbharath.github.io
* [sklearn](https://github.com/scikit-learn/scikit-learn.git)
* [numpy](https://store.continuum.io/cshop/anaconda/)
* [keras](http://keras.io)
* [six](https://pypi.python.org/pypi/six)
* [dill](https://pypi.python.org/pypi/dill)
* [ipyparallel](https://ipyparallel.readthedocs.io/en/latest/)
* [mdtraj](http://mdtraj.org/)
* [tensorflow](https://www.tensorflow.org/)

@@ -80,31 +77,17 @@ Installation from source is the only currently supported format. ```deepchem```
   ```
   See [keras docs](https://keras.io/backend/) for more details and alternate methods of setting backend.

8. `six`
   ```bash
   conda install six
   ```
9. `dill`
    ```bash
    conda install dill
    ```

10. `ipyparallel`
    ```bash
    conda install ipyparallel
    ```

11. `mdtraj`
8. `mdtraj`
   ```bash
   conda install -c omnia mdtraj
   ```
   
12. `scikit-learn`
9. `scikit-learn`
   ```bash
   conda install scikit-learn 
   ```

13. `tensorflow`: Installing `tensorflow` on older versions of Linux (which
10. `tensorflow`: Installing `tensorflow` on older versions of Linux (which
    have glibc < 2.17) can be very challenging. For these older Linux versions,
    contact your local sysadmin to work out a custom installation. If your
    version of Linux is recent, then the following command will work:
@@ -112,12 +95,12 @@ Installation from source is the only currently supported format. ```deepchem```
    conda install -c https://conda.anaconda.org/jjhelmus tensorflow
    ```

14. `h5py`:
11. `h5py`:
    ```
    conda install h5py
    ```

15. `deepchem`: Clone the `deepchem` github repo:
12. `deepchem`: Clone the `deepchem` github repo:
    ```bash
    git clone https://github.com/deepchem/deepchem.git
    ```
@@ -126,7 +109,7 @@ Installation from source is the only currently supported format. ```deepchem```
    python setup.py install
    ```

16. To run test suite, install `nosetests`:
13. To run test suite, install `nosetests`:
    ```bash
    pip install nose --user
    ```
@@ -137,7 +120,7 @@ Installation from source is the only currently supported format. ```deepchem```
    You might need to uninstall a system install of `nosetests` if
    there is a conflict.

17. If installation has been successful, all tests in test suite should pass:
14. If installation has been successful, all tests in test suite should pass:
    ```bash
    nosetests -v deepchem --nologcapture 
    ```
@@ -339,7 +322,11 @@ We actively encourage community contributions to DeepChem. The first place to st
Once you've got a sense of how the package works, we encourage the use of Github issues to discuss more complex changes,  raise requests for new features or propose changes to the global architecture of DeepChem. Once consensus is reached on the issue, please submit a PR with proposed modifications. All contributed code to DeepChem will be reviewed by a member of the DeepChem team, so please make sure your code style and documentation style match our guidelines!

### Code Style Guidelines
DeepChem broadly follows the [Google Python Style Guide](https://google.github.io/styleguide/pyguide.html). In terms of practical changes, the biggest effect is that all code uses 2-space indents instead of 4-space indents. We encourage new contributors to make use of [pylint](https://www.pylint.org/). Aim for a score of at least 8/10 on contributed files.
DeepChem broadly follows the [Google Python Style Guide](https://google.github.io/styleguide/pyguide.html). In terms of practical changes, the biggest effect is that all code uses 2-space indents instead of 4-space indents. We encourage new contributors to make use of [pylint](https://www.pylint.org/) with the following command
```
pylint --disable=invalid-name --indent-string "  " --extension-pkg-whitelist=numpy [file.py]
```
Aim for a score of at least 8/10 on contributed files.

### Documentation Style Guidelines
DeepChem uses [NumPy style documentation](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt). Please follow these conventions when documenting code, since we use [Sphinx+Napoleon](http://www.sphinx-doc.org/en/stable/ext/napoleon.html) to automatically generate docs on [deepchem.io](deepchem.io).