Merge branch 'main' of github.com:jszym/ppi.bio

.github/workflows/documentation.yml

@@ -20,12 +20,12 @@ 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' }}
         with:
           publish_branch: gh-pages
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: docs/_build/html
-          force_orphan: true
+          force_orphan: true

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 <https://www.gnu.org/licenses/>.

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.
+This will output a URL that you can visit to go to your PPI.bio server.