Update fork to AlphaFold 3 v3.0.3

.github/workflows/ci.yaml

@@ -1,7 +1,6 @@
 name: Continuous Integration
 
 on:
-  # Trigger the workflow on push or pull request, only on the main branch.
   push:
     branches:
       - main
@@ -18,21 +17,28 @@ jobs:
       matrix:
         include:
           - name-prefix: "all tests"
-            python-version: '3.11'
+            python-version: '3.12'
             os: ubuntu-latest
+
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+    - uses: actions/checkout@v6
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v7
       with:
-        python-version: ${{ matrix.python-version }}
+        enable-cache: true
+        cache-dependency-glob: "uv.lock"
+
+    - name: Set up Python ${{ matrix.python-version }}
+      run: uv python install ${{ matrix.python-version }}
+
     - name: Install dependencies
-      run: |
-        sudo apt-get install -y hmmer
-        pip install --upgrade pip
-        pip install -r dev-requirements.txt
-        pip install --no-deps .
-        build_data
+      run: sudo apt-get install -y hmmer
+
+    - name: Install Python dependencies
+      run: uv sync --frozen --all-groups
+
+    - name: Build data
+      run: uv run build_data
+
     - name: Run CPU-only tests
-      run: |
-        python run_alphafold_data_test.py
+      run: uv run python run_alphafold_data_test.py

CMakeLists.txt

@@ -1,14 +1,28 @@
 # Copyright 2024 DeepMind Technologies Limited
 #
-# AlphaFold 3 source code is licensed under CC BY-NC-SA 4.0. To view a copy of
-# this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/
+# AlphaFold 3 source code is licensed under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with the
+# License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 #
 # To request access to the AlphaFold 3 model parameters, follow the process set
 # out at https://github.com/google-deepmind/alphafold3. You may only use these
 # if received directly from Google. Use is subject to terms of use available at
 # https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md
 
 cmake_minimum_required(VERSION 3.28)
+
+# This forces Git to use the 'files' backend for all FetchContent operations.
+# This fixes libcifpp and dssp incompatibility with newer git versions.
+set(ENV{GIT_CONFIG_PARAMETERS} "'init.defaultRefFormat=files'")
+
 project(
   "${SKBUILD_PROJECT_NAME}"
   LANGUAGES CXX

CONTRIBUTING.md

@@ -0,0 +1,36 @@
+# How to Contribute
+
+We welcome small patches related to bug fixes and documentation, but we do not
+plan to make any major changes to this repository.
+
+## AI Generated Code
+
+We welcome the use of AI tools for the generation of code, documentation and/or
+Pull Request (PR) description as long as:
+
+1.  It has been transparently labelled as such. Make sure to declare it in the
+    PR message.
+2.  You have manually reviewed the code before sending the PR.
+3.  The change has been manually tested. We might ask you to fold a certain
+    input to check correctness of the PR.
+
+Please do not submit AI generated PRs where test results have been hallucinated.
+
+## Contributor License Agreement
+
+Contributions to this project must be accompanied by a Contributor License
+Agreement. You (or your employer) retain the copyright to your contribution,
+this simply gives us permission to use and redistribute your contributions as
+part of the project. Head over to <https://cla.developers.google.com/> to see
+your current agreements on file or to sign a new one.
+
+You generally only need to submit a CLA once, so if you've already submitted one
+(even if it was for a different project), you probably don't need to do it
+again.
+
+## Code reviews
+
+All submissions, including submissions by project members, require review. We
+use GitHub pull requests for this purpose. Consult
+[GitHub Help](https://help.github.com/articles/about-pull-requests/) for more
+information on using pull requests.