diff --git a/.github/workflows/pylint.yaml b/.github/workflows/pylint.yaml
new file mode 100644
index 0000000..987a65b
--- /dev/null
+++ b/.github/workflows/pylint.yaml
@@ -0,0 +1,19 @@
+name: PyLint
+
+on: push
+
+jobs:
+ lint:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v4
+ - name: Install Python
+ uses: actions/setup-python@v5
+ with:
+ python-version: "3.11"
+ - name: Install dependencies
+ run: |
+ python -m pip install --upgrade pip
+ pip install pylint
+ - name: Run pylint
+ run: pylint src/aidsorb/
diff --git a/.github/workflows/unittest.yaml b/.github/workflows/unittest.yaml
new file mode 100644
index 0000000..7b4287c
--- /dev/null
+++ b/.github/workflows/unittest.yaml
@@ -0,0 +1,15 @@
+name: Unittest
+
+on: push
+
+jobs:
+ test:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v4
+ - name: Install Python
+ uses: actions/setup-python@v5
+ with:
+ python-version: "3.11"
+ - name: Run unit tests
+ run: python -m unittest
diff --git a/README.md b/README.md
index 3e875ef..0372cdc 100644
--- a/README.md
+++ b/README.md
@@ -1,39 +1,67 @@
-AIdsorb is a Python package for processing molecular point clouds.
+
+ 
+
-Currently, only the `PointNet` [^1] architecture is implemented and can be
-found under `src/aidsorb/models.py`. In this implementation, the input `T-Net`
-transformation from the original paper is not applied, *since is it is not
-guaranteed to be a rigid one*.
+
+
+
+
+
+
+
+
+
+**AIdsorb** is a Python package for **deep learning on molecular point clouds**.
+
+**AIdsorb** aims to provide a **fast, easy-to-use and reproduce** interface for:
+
+- 📥 **Creating molecular point clouds**
+
+- 🤖 **Training DL algorithms on molecular point clouds**
+
+
+
+ 
+
## ⚙️ Installation
-> Currently not available in PyPI.
+> [!IMPORTANT]
+> It is strongly recommended to **perform the installation inside a virtual environment**.
-**It is strongly recommended to perform the installation inside a virtual environment**.
+Assuming an activated virtual environment:
```bash
-git clone https://github.com/adosar/aidsorb && cd aidsorb
-(venvir) pip install -e .
+pip install aidsorb
```
-## 📖 Usage
-You can create molecular point clouds form a directory containing molecular
-files and save them in a `.npz` file.
+## 🚀 Usage
+> [!NOTE]
+> Refer to the 📚 Documentation for more information.
-```python
-from aidsorb.utils import pcd_from_dir
-pcd_from_dir('/path/to/dir', file='point_clouds.npz')
-```
+Here is a summary of what you can do from the command line:
-## 📇 TODO
-* Add atoms featurization
-* Add more architectures
+1. Visualize a molecular point cloud:
+ ```bash
+ aidsorb visualize path/to/structure
+ ```
+
+2. Create and prepare point clouds:
+ ```bash
+ aidsorb create path/to/inp path/to/out # Create point clouds
+ aidsorb prepare path/to/out # Split point clouds to train, val and test
+ ```
+ where `path/to/inp` is a directory containing molecular structures.
+
+3. Train and test a model:
+ ```bash
+ aidsorb-lit fit --config=path/to/config.yaml
+ aidsorb-lit test --config=path/to/config.yaml --ckpt_path=path/to/ckpt
+ ```
+ Currently, only [PointNet](https://arxiv.org/abs/1612.00593) is supported.
## 📰 Citing AIdsorb
-> Currently N/A.
+If you use AIdsorb in your research, please consider citing the following work:
+
+ Currently, not available.
## 📑 License
-MOXελ is released under the [GNU General Public License v3.0 only](https://spdx.org/licenses/GPL-3.0-only.html).
-
-[^1]: R. Q. Charles, H. Su, M. Kaichun and L. J. Guibas, "PointNet: Deep
-Learning on Point Sets for 3D Classification and Segmentation," 2017 IEEE
-Conference on Computer Vision and Pattern Recognition (CVPR), Honolulu, HI,USA,
-2017, pp. 77-85, doi: 10.1109/CVPR.2017.16.
+AIdosrb is released under the [GNU General Public License v3.0 only](https://spdx.org/licenses/GPL-3.0-only.html).
diff --git a/docs/source/auto_examples/resume_codeobj.pickle b/docs/source/auto_examples/resume_codeobj.pickle
index 9355e9e..55e6258 100644
Binary files a/docs/source/auto_examples/resume_codeobj.pickle and b/docs/source/auto_examples/resume_codeobj.pickle differ
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 752554a..2b55352 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -6,7 +6,6 @@
# -- Project information -----------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
-from urllib.parse import quote
import sys, os
import subprocess
from plotly.io._sg_scraper import plotly_sg_scraper
diff --git a/docs/source/images/pcd.gif b/docs/source/images/pcd.gif
new file mode 100644
index 0000000..4b72dad
Binary files /dev/null and b/docs/source/images/pcd.gif differ
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 33e4b2b..1b16d5c 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -12,7 +12,7 @@
About
=====
-**AIdsorb** is a :fa:`python; fa-fade` Python package for **Deep Learning on
+**AIdsorb** is a :fa:`python; fa-fade` Python package for **deep learning on
molecular point clouds**.
.. grid:: 4
diff --git a/docs/source/tutorial.rst b/docs/source/tutorial.rst
index e50c98d..535cab2 100644
--- a/docs/source/tutorial.rst
+++ b/docs/source/tutorial.rst
@@ -58,6 +58,14 @@ Introduction
4:]`` any **additional features**. If ``C == 0``, then the only features are the
atomic numbers.
+
+.. tip::
+ You can visualize a molecular point cloud with:
+
+ .. code-block:: console
+
+ $ aidsorb visualize path/to/structure
+
Deep learning on molecular point clouds
---------------------------------------
@@ -66,7 +74,7 @@ AIdsorb, the following components are needed:
* A directory containing files of **molecular structures**.
* A ``.csv`` file containing the **labels of the molecular structures**.
-* A ``.yaml`` **configuration file** for orchestrating the ML part.
+* A ``.yaml`` **configuration file** for orchestrating the DL part.
.. note::
You are solely responsible for these 3 components.
diff --git a/pyproject.toml b/pyproject.toml
index 63a79f8..7ee7bab 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,6 +7,11 @@ where = ["src"]
[tool.setuptools_scm]
+[tool.pylint.main]
+jobs = 0
+disable = ["C"]
+fail-under = 8
+
[project]
name = "aidsorb"
dynamic = ["version"]
diff --git a/src/aidsorb/__init__.py b/src/aidsorb/__init__.py
index fe31a5d..535c1ac 100644
--- a/src/aidsorb/__init__.py
+++ b/src/aidsorb/__init__.py
@@ -15,7 +15,7 @@
# along with this program. If not, see .
r"""
-**AIdsorb** is a :fa:`python; fa-fade` Python package for **Deep Learning on
+**AIdsorb** is a :fa:`python; fa-fade` Python package for **deep learning on
molecular point clouds**.
diff --git a/src/aidsorb/models.py b/src/aidsorb/models.py
index 9f6b806..dc3c4fc 100644
--- a/src/aidsorb/models.py
+++ b/src/aidsorb/models.py
@@ -37,9 +37,6 @@
.. todo::
Add more architectures for point cloud processing.
-.. danger::
- Check all docstrings.
-
References
----------
@@ -429,7 +426,8 @@ def forward(self, x):
class PointNet(nn.Module):
r"""
- A deep learning architecture for processing point clouds.
+ Vanilla version from the [PointNet]_ paper where :class:`TNet`'s have been
+ removed.
``PointNet`` takes as input a point cloud and produces one or more outputs.
*The type of the task is determined by* ``head``.
diff --git a/tests/test_data.py b/tests/test_data.py
index b864fce..aadf2b6 100644
--- a/tests/test_data.py
+++ b/tests/test_data.py
@@ -31,7 +31,6 @@
import pandas as pd
from torch.utils.data import DataLoader
from aidsorb import data
-from aidsorb._internal import _check_shape
from aidsorb.utils import pcd_from_dir
from aidsorb.transforms import Centering
from aidsorb.data import (
diff --git a/tests/test_datamodules.py b/tests/test_datamodules.py
index 20a33f9..28edf2a 100644
--- a/tests/test_datamodules.py
+++ b/tests/test_datamodules.py
@@ -24,7 +24,7 @@
import os
import unittest
import tempfile
-from itertools import combinations, product
+from itertools import combinations
from torch.utils.data import RandomSampler, SequentialSampler
from aidsorb.utils import pcd_from_dir
from aidsorb.data import prepare_data, Collator
diff --git a/tests/test_litmodels.py b/tests/test_litmodels.py
index 9ac17da..5477d05 100644
--- a/tests/test_litmodels.py
+++ b/tests/test_litmodels.py
@@ -22,7 +22,6 @@
"""
import doctest
-import unittest
from aidsorb import litmodels
diff --git a/tests/test_models.py b/tests/test_models.py
index a24cf1d..a182eb3 100644
--- a/tests/test_models.py
+++ b/tests/test_models.py
@@ -22,7 +22,6 @@
"""
import doctest
-import unittest
from aidsorb import models
diff --git a/tests/test_transforms.py b/tests/test_transforms.py
index 54104cb..abc590a 100644
--- a/tests/test_transforms.py
+++ b/tests/test_transforms.py
@@ -22,7 +22,6 @@
"""
import doctest
-import unittest
from aidsorb import transforms