Merge pull request #55 from saezlab/dev

Merge `dev` to `main`

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.0
+current_version = 0.4.0
 commit = True
 tag = True
 files = pyproject.toml networkcommons/_metadata.py

.github/workflows/test.yaml

@@ -63,7 +63,7 @@ jobs:
             run: |
               poetry install --no-interaction --no-root
         -   name: Install library
-            run: poetry install --no-interaction
+            run: poetry install --no-interaction -E corneto-backends
         -   name: Tests and coverage
             if: ${{ github.event_name == 'push' }}
             run: |

.gitignore

@@ -30,3 +30,10 @@ licensetools11.0.1_linux64/
 /data/
 /_build/
 api
+.nextflow
+.nextflow*
+report*
+trace*
+work/
+test.ipynb
+flop.png

README.md

@@ -1,11 +1,17 @@
-# NetworkCommons - Integrated framework for network inference and evaluation using prior knowledge and omics data
+# NetworkCommons - Bridging the gap between data, methods and knowledge in the network inference field
 
-Networkcommons is a package which allows users to download data and prior knowledge to perform static network inference using different methodologies. The package also provides different visualization and evaluation strategies.
+NetworkCommons is a community-driven platform designed to simplify access to tools and resources for inferring context-specific protein interaction networks by integrating context-agnostic prior knowledge with omics data. These networks have a wide range of applications, from omics data interpretation to identifying drug targets and key driver mutations.
 
 [![codecov][badge-cov]][link-cov]
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
 
+[![NetworkCommons API](./docs/src/_static/nc_graphabs.svg)](https://networkcommons.readthedocs.io)
+
+Addressing the complexity and fragmentation of data, methods, and tools across multiple repositories, NetworkCommons offers an API that provides access to raw and preprocessed omics data, directed and/or signed template graphs, and various network inference methods. By streamlining accessibility, we aim to support systematic benchmarking, enhance critical assessment, and foster collaborative advancements in network biology.
+
+We welcome any contribution to this project! For more information, please check [our documentation](https://networkcommons.readthedocs.io). 
+
 ## Contributors
 
 Martin Garrido-Rodriguez, Olga Ivanova, Victor Paton, Denes Turei

docs/src/_static/css/custom.css

@@ -8,4 +8,8 @@
 
   .wy-nav-content {
       max-width: 1200px;
-  }
+  }
+
+  section {
+    text-align: justify;
+}