update and fix docs format

.gitignore

@@ -7,6 +7,8 @@ CanDI/setup/data/coessentiality
 tests.py
 build
 
+docs/output
+
 **/__pycache__/
 **/.ipynb_checkpoints/
 **.pyc

CanDI/__version__.py

@@ -1 +1 @@
-version = "0.2.3"
+version = "0.2.4"

README.md

@@ -0,0 +1,92 @@
+# CanDI - A global cancer data integrator
+
+[![PyPI](https://img.shields.io/pypi/v/PyCanDI)](https://pypi.org/project/PyCanDI/)
+[![Downloads](https://static.pepy.tech/badge/pycandi)](https://pepy.tech/project/pycandi)
+[![Documentation Status](https://readthedocs.org/projects/candi/badge/?version=latest)](https://candi.readthedocs.io/en/latest/?badge=latest)
+[![DOI](https://zenodo.org/badge/DOI/10.1186/s13073-021-00987-8.svg)](https://doi.org/10.1186/s13073-021-00987-8)
+[![Dataverse](https://img.shields.io/badge/Dataverse-10.7910/DVN/JIAT0H-red)](https://doi.org/10.7910/DVN/JIAT0H)
+
+## Installation
+
+CanDI is now available on [PyPI](https://pypi.org/project/PyCanDI/) and
+can be installed with pip. Then, a command from CanDI will automatically
+download stable datasets from
+[Dataverse](https://doi.org/10.7910/DVN/JIAT0H).
+
+``` bash
+# Package Installation
+pip install PyCanDI
+
+# Prepare Datasets
+candi-install
+```
+
+Downloaded and formatted datasets would organize this way:
+
+``` 
+.
+├── config.ini # modified after Installation 
+├── depmap
+│   ├── CCLE_expression.csv
+│   ├── CCLE_fusions.csv
+│   ├── CCLE_gene_cn.csv
+│   ├── CCLE_mutations.csv
+│   ├── CCLE_RNAseq_reads.csv
+│   ├── CRISPR_gene_dependency.csv
+│   ├── CRISPR_gene_effect.csv
+│   └── sample_info.csv
+├── genes
+│   └── gene_info.csv
+└── locations
+    └── merged_locations.csv
+```
+
+**Note**:
+
+:   *Currently, DepMap API is not available for public use. Therefore,
+    we are providing the preprocessed datasets for the users based on
+    DepMap 21Q4 release. DepMap API will be available in the future to
+    download the latest datasets.*
+
+## Usage
+
+### Import CanDI into python
+
+``` python
+from CanDI import candi
+```
+
+### CanDI Objects
+
+-   `data` : Container for all candi datasets. All access to datasets go
+    through data object.
+-   `Gene` : Provides cross dataset indexing from the gene perspective.
+-   `CellLine` : Provides cross dataset indexing from the cell line
+    perspective.
+-   `Cancer` : Provides cross dataset indexing by a group of cell lines
+    that are all the same tissue.
+-   `Organelle`: Provides cross dataset indexing for a group of genes
+    whose proteins localize to the same organelle.
+-   `CellLineCluster` : Provides cross dataset indexing for a group of
+    user defined cell lines.
+-   `GeneCluster` : Provides cross dataset indexing for a group of user
+    defined genes.
+
+### Demos
+
+| Name | Description |
+|------|-------------|
+| Getting Started | [Link to notebook](notebooks/get-started.ipynb) |
+| *BRCA* Heatmap | [Link to notebook](notebooks/brca_heatmap.ipynb) |
+| *KRAS* and *EGFR* Scatter plot | [Link to notebook](notebooks/kras_egfr_scatter.ipynb) |
+| CanDI and DESeq2 | [Link to notebook](notebooks/deseq_setup.ipynb) |
+
+## Citation
+
+If you use CanDI in your research, please cite the following paper:
+
+``` bibtex
+Yogodzinski C, Arab A, Pritchard JR, Goodarzi H, Gilbert LA. 
+A global cancer data integrator reveals principles of synthetic lethality, sex disparity and immunotherapy. 
+Genome Med. 2021;13(1):167. Published 2021 Oct 18. doi:10.1186/s13073-021-00987-8
+```

docs/environment.yaml

@@ -4,9 +4,8 @@ channels:
   - conda-forge
 dependencies:
   - python>=3.11,<4.0
-  - myst-parser=0.18.1
-  - sphinx=5.3.0
-  - sphinx_rtd_theme=1.1.1
+  - myst-parser
+  - sphinx>=7.0.0
   - jinja2<=3.1
   - pandas
   - numpy
@@ -16,7 +15,8 @@ dependencies:
   - tqdm
   - pip
   - pip:
-    - nbsphinx
+    - myst-nb
+    - sphinx_rtd_theme
     - pydeseq2
     - adpbulk
     - pycandi

docs/requirements.txt

@@ -1,8 +1,8 @@
-nbsphinx
-readthedocs-sphinx-search==0.3.2
+readthedocs-sphinx-search
 myst-parser=0.18.1
-sphinx=5.3.0
-sphinx_rtd_theme=1.1.1
+myst-nb
+sphinx>=7.0.0
+sphinx_rtd_theme
 jinja2<=3.1
 pandas
 configparser

docs/source/README.md

@@ -0,0 +1 @@
+../../README.md