diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index bffceac..fb02225 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -20,7 +20,7 @@ jobs: pip install furo - name: Sphinx build run: | - cd docs && sphinx-build . _build + cd docs && make html - name: Deploy to GitHub Pages uses: peaceiris/actions-gh-pages@v3 if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} @@ -28,4 +28,4 @@ jobs: publish_branch: gh-pages github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: docs/_build/html - force_orphan: true \ No newline at end of file + force_orphan: true diff --git a/README.md b/README.md index f92641c..bb2ff3c 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,27 @@ # PPI.bio This is the codebase for PPI.bio, the software that powers [PPI.bio](https://ppi.bio). + +A server for protein-protein inference using the RAPPPID and INTREPPPID algorithms. + +## Documentation +You can read the documentation at https://emad-combine-lab.github.io/ppi.bio + +## License + +>PPI.bio - A server for protein-protein inference using the RAPPPID and INTREPPPID algorithms. +> +>Copyright (C) 2023 Joseph Szymborski +> +>This program is free software: you can redistribute it and/or modify +>it under the terms of the GNU Affero General Public License as published by +>the Free Software Foundation, either version 3 of the License, or +>(at your option) any later version. +> +>This program is distributed in the hope that it will be useful, +>but WITHOUT ANY WARRANTY; without even the implied warranty of +>MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +>GNU Affero General Public License for more details. +> +>You should have received a copy of the GNU Affero General Public License +>along with this program. If not, see . diff --git a/docs/getting_started.rst b/docs/getting_started.rst index a8fd09a..218e3e9 100644 --- a/docs/getting_started.rst +++ b/docs/getting_started.rst @@ -116,7 +116,7 @@ the database. To do this, run the following command: .. code-block:: bash - python manage.py proteome_embed 9606 nest-much + python manage.py proteome_embed 9606 distinct-stylishly This will pre-compute the embeddings for all the human sequences using the "nest-much" weights. The "nest-much" weights come installed out-of-the-box, and are trained on Human PPI data from the v11.5 of the @@ -133,4 +133,4 @@ You can run the test server locally with the following command: python manage.py runserver -This will output a URL that you can visit to go to your PPI.bio server. \ No newline at end of file +This will output a URL that you can visit to go to your PPI.bio server.