update to main

README.md

@@ -1,5 +1,9 @@
-CREsted: Cis Regulatory Element Sequence Training, Explanation, and Design
-==========================================================================
+<div align="center">
+   <img src="https://raw.githubusercontent.com/aertslab/CREsted/main/docs/_static/img/crested_banner.png",
+   height=300>
+</div>
+
+# CREsted: Cis Regulatory Element Sequence Training, Explanation, and Design
 
 ![PyPI - Downloads](https://img.shields.io/pypi/dm/crested)
 [![Tests][badge-tests]][link-tests]
@@ -9,33 +13,50 @@ CREsted: Cis Regulatory Element Sequence Training, Explanation, and Design
 [link-tests]: https://github.com/aertslab/CREsted/actions/workflows/test.yaml
 [badge-docs]: https://img.shields.io/readthedocs/CREsted
 
-**IN PROGRESS, NOT RELEASED YET**
+## Introduction
+
+**CREsted** (Cis-Regulatory Element Sequence Training, Explanation, and Design) is an easy-to-use deep learning package for training enhancer models on single-cell ATAC sequencing (scATAC-seq) data. CREsted provides comprehensive analyses and tutorials to study enhancer codes and the ability to design synthetic enhancer sequences at a cell type-specific, nucleotide-level resolution. Integrated into the **scverse** framework, CREsted is compatible with outcomes from established scATAC-seq processing tools. It employs novel scATAC-seq preprocessing techniques, such as peak height normalization across cell types, offers flexibility and variety in deep learning modeling architectures and tasks, and contains thorough analysis of the cell type-specific enhancer codes captured during modeling that can also be used for the design of synthetic sequences.
 
 ## Getting started
 
 Please refer to the [documentation][link-docs]. In particular, the
 
--   [API documentation][link-api].
+-   [Tutorials][link-tutorials]
+-   [API documentation][link-api]
 
 ## Installation
 
-You need to have Python 3.9 or newer installed on your system. If you don't have
-Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
+You need to have Python 3.9 or newer installed on your system and a deep learning backend to be able to use CREsted.
 
-There are several alternative options to install CREsted:
+CREsted is build on top of keras 3.0 and can therefore be used with your deep learning backend of choice (Tensorflow or Pytorch).
 
-<!--
-1) Install the latest release of `CREsted` from `PyPI <https://pypi.org/project/CREsted/>`_:
+1. Install either [Tensorflow](https://www.tensorflow.org/install) or [Pytorch](https://pytorch.org/get-started/locally/) for GPU.
+   Refer to the installation instructions on those pages to ensure you have the correct version of CUDA and cuDNN installed.
+   If you don't have a preference and don't know which backend to choose, refer to [choosing your backend](#choosing-your-backend).
+   If you have all the latest drivers installed, this installation boils down to doing:
 
 ```bash
-pip install CREsted
+pip install tensorflow[and-cuda]
+# or
+pip install torch
 ```
--->
 
-1. Install the latest development version:
+2. Install the latest release of `crested` from [PyPI](https://pypi.org/project/CREsted/)
 
 ```bash
-pip install git+https://github.com/aertslab/CREsted/.git@main
+pip install crested
+```
+
+3. If you plan on using the tf-modisco (lite) functionality inside CREsted, you will need to run the following additional install:
+
+```bash
+pip install crested[tfmodisco]
+```
+
+This requires a cmake installation on your system. If you don't have it, you can install it with:
+
+```bash
+pip install cmake
 ```
 
 ## Release notes
@@ -44,14 +65,22 @@ See the [changelog][changelog].
 
 ## Contact
 
-For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
-If you found a bug, please use the [issue tracker][issue-tracker].
+For questions and help requests, please use the [issue tracker][issue-tracker].
 
 ## Citation
 
 > t.b.a
 
+## Choosing your backend
+
+CREsted is build on top of keras 3.0 and can therefore be used with your deep learning backend of choice (Tensorflow or Pytorch). If you don't have a preference, you can take the following into account:
+
+1. From our (and Keras' official) benchmarking, **Tensorflow** is generally faster than pytorch for training (up to 2x) since Tensorflow operates in graph mode whereas Pytorch uses eager mode. If you plan on training many models, Tensorflow might be the better choice.
+2. **Pytorch** is easier to debug and get going. Tensorflow will easily throw a bunch of warnings or fail to detect CUDA if you don't have the exact right versions of CUDA and cuDNN installed. Pytorch seems more lenient in this regard. If you only plan on running predictions or training a few models, Pytorch might be the easier choice.
+3. Current Keras 3.0 is still in active development and some features (mainly multi GPU training and weights and biases logging) are currently only supported with the Tensorflow backend. If you plan on using these features, you should choose Tensorflow. We will implement these features in a backend agnostic way as soon as Keras 3.0 has done so (it is on their roadmap).
+
 [issue-tracker]: https://github.com/aertslab/CREsted/issues
 [changelog]: https://CREsted.readthedocs.io/latest/changelog.html
 [link-docs]: https://CREsted.readthedocs.io
-[link-api]: https://CREsted.readthedocs.io/latest/api.html
+[link-tutorials]: https://CREsted.readthedocs.io/latest/tutorials/index.html
+[link-api]: https://CREsted.readthedocs.io/latest/api.html

docs/api/datasets.md

@@ -0,0 +1,14 @@
+# Datasets
+
+Downloading of use case datasets which ar explored in the example analyses.
+
+```{eval-rst}
+.. currentmodule:: crested
+```
+
+```{eval-rst}
+.. autosummary::
+    :toctree: _autosummary
+
+    get_dataset
+```

docs/api/index.md

@@ -7,6 +7,7 @@ import crested
 ```{toctree}
 :maxdepth: 2
 
+datasets
 io
 preprocessing
 tools/index.md

docs/index.md

@@ -6,7 +6,8 @@
 :hidden: true
 :maxdepth: 1
 
-tutorials/index.md
+installation
+tutorials/index
 api/index
 changelog
 contributing

docs/installation.md

@@ -0,0 +1,42 @@
+# Installation
+
+You need to have Python 3.9 or newer installed on your system and a deep learning backend to be able to use CREsted.
+
+CREsted is build on top of keras 3.0 and can therefore be used with your deep learning backend of choice (Tensorflow or Pytorch).
+
+1. Install either [Tensorflow](https://www.tensorflow.org/install) or [Pytorch](https://pytorch.org/get-started/locally/) for GPU.
+   Refer to the installation instructions on those pages to ensure you have the correct version of CUDA and cuDNN installed.
+   If you don't have a preference and don't know which backend to choose, refer to [choosing your backend](#choosing-your-backend).
+   If you have all the latest drivers installed, this installation boils down to doing:
+
+```bash
+pip install tensorflow[and-cuda]
+# or
+pip install torch
+```
+
+2. Install the latest release of `crested` from [PyPI](https://pypi.org/project/CREsted/)
+
+```bash
+pip install crested
+```
+
+3. If you plan on using the tf-modisco (lite) functionality inside CREsted, you will need to run the following additional install:
+
+```bash
+pip install crested[tfmodisco]
+```
+
+This requires a cmake installation on your system. If you don't have it, you can install it with:
+
+```bash
+pip install cmake
+```
+
+## Choosing your backend
+
+CREsted is build on top of keras 3.0 and can therefore be used with your deep learning backend of choice (Tensorflow or Pytorch). If you don't have a preference, you can take the following into account:
+
+1. From our (and Keras' official) benchmarking, **Tensorflow** is generally faster than pytorch for training (up to 2x) since Tensorflow operates in graph mode whereas Pytorch uses eager mode. If you plan on training many models, Tensorflow might be the better choice.
+2. **Pytorch** is easier to debug and get going. Tensorflow will easily throw a bunch of warnings or fail to detect CUDA if you don't have the exact right versions of CUDA and cuDNN installed. Pytorch seems more lenient in this regard. If you only plan on running predictions or training a few models, Pytorch might be the easier choice.
+3. Current Keras 3.0 is still in active development and some features (mainly multi GPU training and weights and biases logging) are currently only supported with the Tensorflow backend. If you plan on using these features, you should choose Tensorflow. We will implement these features in a backend agnostic way as soon as Keras 3.0 has done so (it is on their roadmap).

docs/tutorials/index.md

@@ -5,4 +5,5 @@
 
 introduction
 mouse_biccn
-```
+multi_gpu
+```