Update README, About page, and add Codecov to CI

Replace template placeholder README with real content: badges
(tests, codecov, docs, pypi, license), features, installation,
quick start examples, data licensing note, and NAR 2026 citation.
CI workflow now generates coverage XML and uploads to Codecov.
Drops Python 3.9 from the test matrix (requires-python >= 3.10).

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: deeenes

.github/workflows/ci-testing-unit.yml

@@ -7,7 +7,7 @@ jobs:
         runs-on: ubuntu-latest
         strategy:
             matrix:
-                python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
+                python-version: ['3.10', '3.11', '3.12', '3.13']
         steps:
         -   uses: actions/checkout@v4
         -   uses: ./.github/actions/setup
@@ -16,9 +16,10 @@ jobs:
         -   name: Run tests with coverage
             run: |
                 source .venv/bin/activate
-                pytest --cov=omnipath_client tests/
-        -   name: Upload coverage report
-            uses: actions/upload-artifact@v4
+                pytest --cov=omnipath_client --cov-report=xml tests/
+        -   name: Upload coverage to Codecov
+            if: matrix.python-version == '3.12'
+            uses: codecov/codecov-action@v5
             with:
-                name: coverage-report-${{ matrix.python-version }}
-                path: .coverage*
+                files: coverage.xml
+                fail_ci_if_error: false

README.md

@@ -1,60 +1,89 @@
-![project-banner](./docs/assets/project-banner-readme.png)
-
 # omnipath-client
 
-- [ ] TODO: Add badges to your project.
-
-[![Tests](https://img.shields.io/github/actions/workflow/status/saezlab/omnipath-client/test.yml?branch=master)](https://github.com/saezlab/omnipath-client/actions/workflows/test.yml)
+[![Tests](https://img.shields.io/github/actions/workflow/status/saezlab/omnipath-client/ci-testing-unit.yml?branch=master&label=tests)](https://github.com/saezlab/omnipath-client/actions/workflows/ci-testing-unit.yml)
+[![Codecov](https://img.shields.io/codecov/c/github/saezlab/omnipath-client)](https://codecov.io/gh/saezlab/omnipath-client)
 [![Docs](https://img.shields.io/badge/docs-MkDocs-blue)](https://saezlab.github.io/omnipath-client/)
-![Pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)
-![PyPI](https://img.shields.io/pypi/v/omnipath-client)
-![Python](https://img.shields.io/pypi/pyversions/omnipath-client)
-![License](https://img.shields.io/github/license/saezlab/omnipath-client)
-![Issues](https://img.shields.io/github/issues/saezlab/omnipath-client)
-![Last Commit](https://img.shields.io/github/last-commit/saezlab/omnipath-client)
-
-## Description
-
-The new implementation for the OmniPath Python client
+[![PyPI](https://img.shields.io/pypi/v/omnipath-client)](https://pypi.org/project/omnipath-client/)
+[![Python](https://img.shields.io/pypi/pyversions/omnipath-client)](https://pypi.org/project/omnipath-client/)
+[![License](https://img.shields.io/github/license/saezlab/omnipath-client)](https://github.com/saezlab/omnipath-client/blob/master/LICENSE)
+
+Python client for the [OmniPath](https://omnipathdb.org/) molecular biology
+prior-knowledge web API.
+
+## Features
+
+- Export **entities**, **interactions**, and **associations** (complexes,
+  pathways, reactions) as DataFrames
+- **Ontology** term lookup, search, and hierarchy trees
+- Multi-backend output: [polars](https://pola.rs/) (default),
+  [pandas](https://pandas.pydata.org/), or
+  [pyarrow](https://arrow.apache.org/docs/python/)
+- Optional graph conversion to [annnet](https://github.com/saezlab/annnet)
+  objects
+- Query validation against the API schema
+- Caching via [download-manager](https://github.com/saezlab/download-manager)
 
 ## Installation
 
-- [ ] TODO: Add installation instructions for your project, if applicable.
-
 ```bash
-# Example
-pip install <name-of-my-project>
+pip install omnipath-client
 ```
 
-## Usage
+With polars (recommended default backend):
+
+```bash
+pip install omnipath-client polars
+```
 
-- [ ] TODO: Add usage instructions for your project.
+## Quick start
 
 ```python
-import foobar
+import omnipath_client as op
 
-# returns 'words'
-foobar.pluralize("word")
+# All interactions as a polars DataFrame
+df = op.interactions()
 
-# returns 'geese'
-foobar.pluralize("goose")
+# Directed interactions only
+df = op.interactions(direction='directed')
 
-# returns 'phenomenon'
-foobar.singularize("phenomena")
+# Human entities
+df = op.entities(taxonomy_ids=['9606'])
+
+# Interactions as an annnet graph
+g = op.interactions(as_graph=True)
+
+# Ontology term lookup
+result = op.ontology_terms(['GO:0006915', 'MI:0326'])
+
+# Choose a different backend
+df = op.entities(backend='pandas')
 ```
 
-## Contributing
+For more examples, see the [quickstart guide](https://saezlab.github.io/omnipath-client/quickstart/).
 
-Pull requests are welcome. For major changes, please open an issue first
-to discuss what you would like to change.
+## Documentation
 
-Please make sure to update tests as appropriate.
+Full documentation: [saezlab.github.io/omnipath-client](https://saezlab.github.io/omnipath-client/)
 
-- [ ] TODO: add contribution guidelines. All of them can be modified in the mkdocs documentation (./docs/community)
+## Data licensing
 
-## License
+The data served by OmniPath is combined from many original resources, each
+with their own license terms. The OmniPath client software is BSD-3-Clause,
+but the **data** is subject to the licenses of the original sources. Some
+resources restrict commercial use. Tools and documentation for managing
+license-based access control will be provided in a future release.
 
-[MIT](https://choosealicense.com/licenses/mit/)
+## Citation
+
+If you use OmniPath in your research, please cite:
+
+> Türei D, Schaul J, Palacio-Escat N, *et al.* (2026)
+> OmniPath: integrated knowledgebase for multi-omics analysis.
+> *Nucleic Acids Research* 54(D1):D652-D660.
+> [doi:10.1093/nar/gkaf1126](https://doi.org/10.1093/nar/gkaf1126)
+
+## License
 
-- [ ] TODO: Modify this based on the license you choose.
-- [ ] TODO: Modify the LICENSE file based on the license you choose.
+The client software is licensed under
+[BSD-3-Clause](https://github.com/saezlab/omnipath-client/blob/master/LICENSE).
+See [Data licensing](#data-licensing) above for information about the data.

docs/about.md

@@ -10,18 +10,25 @@ omnipath-client is developed by the
 - **API**: [dev.omnipathdb.org](https://dev.omnipathdb.org/)
 - **Issues**: [github.com/saezlab/omnipath-client/issues](https://github.com/saezlab/omnipath-client/issues)
 
+## Data licensing
+
+The data served by OmniPath is combined from many original resources, each
+with their own license terms. The OmniPath client software is BSD-3-Clause,
+but the **data** is subject to the licenses of the original sources. Some
+resources restrict commercial use. Tools and documentation for managing
+license-based access control will be provided in a future release.
+
 ## License
 
-BSD-3-Clause. See the
+The client software is licensed under BSD-3-Clause. See the
 [LICENSE](https://github.com/saezlab/omnipath-client/blob/master/LICENSE)
 file for details.
 
 ## Citation
 
-If you use OmniPath data in your research, please cite:
+If you use OmniPath in your research, please cite:
 
-> Turei D, Valdeolivas A, Gul L, Palacio-Escat N, Klein M, Ivanova O,
-> Olbei M, Gabor A, Theis F, Korcsmaros T, Saez-Rodriguez J. (2021)
-> Integrated intra- and intercellular signaling knowledge for multicellular
-> omics analysis. *Molecular Systems Biology* 17:e9923.
-> [doi:10.15252/msb.20209923](https://doi.org/10.15252/msb.20209923)
+> Türei D, Schaul J, Palacio-Escat N, *et al.* (2026)
+> OmniPath: integrated knowledgebase for multi-omics analysis.
+> *Nucleic Acids Research* 54(D1):D652-D660.
+> [doi:10.1093/nar/gkaf1126](https://doi.org/10.1093/nar/gkaf1126)