From cf5d657fbbce5734e1e7a2ffb03c7c05320d9226 Mon Sep 17 00:00:00 2001
From: Joseph Szymborski <jszym@users.noreply.github.com>
Date: Fri, 9 Feb 2024 18:41:32 +0000
Subject: [PATCH 1/4] Update README.md

---
 README.md | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/README.md b/README.md
index f92641c..8003af6 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 <https://www.gnu.org/licenses/>.

From b5588dc4bf09f028aeae65c16ecb5e1dbdfc6089 Mon Sep 17 00:00:00 2001
From: Joseph Szymborski <jszym@users.noreply.github.com>
Date: Fri, 9 Feb 2024 18:41:43 +0000
Subject: [PATCH 2/4] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 8003af6..bb2ff3c 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@ This is the codebase for PPI.bio, the software that powers [PPI.bio](https://ppi
 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
+You can read the documentation at https://emad-combine-lab.github.io/ppi.bio
 
 ## License
 

From d1c1a0a6dc203617dfaa3cb3a91b2509530f524d Mon Sep 17 00:00:00 2001
From: Joseph Szymborski <jszym@users.noreply.github.com>
Date: Fri, 9 Feb 2024 18:54:57 +0000
Subject: [PATCH 3/4] Update documentation.yml

---
 .github/workflows/documentation.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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

From ec3e60847059bfa1bb1ffef84341c61736edec7c Mon Sep 17 00:00:00 2001
From: Joseph Szymborski <jszym@users.noreply.github.com>
Date: Fri, 9 Feb 2024 18:57:16 +0000
Subject: [PATCH 4/4] Update getting_started.rst

Changed weights in docs to the new default.
---
 docs/getting_started.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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.