Merge pull request #366 from KosinskiLab/rearange-backend-initialisation

Rearange backend initialisation
KosinskiLab · Jun 14, 2024 · a5d3f74 · a5d3f74
2 parents 0e3af95 + 03fc096
commit a5d3f74
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Showing 3 changed files with 29 additions and 17 deletions.
diff --git a/.github/workflows/github_actions.yml b/.github/workflows/github_actions.yml
@@ -46,12 +46,12 @@ jobs:
           pip install -e alphafold --no-deps
           export PYTHONPATH=$PWD/AlphaLink2:$PYTHONPATH
           # install dependencies for AlphaLink backend
-          pip install torch==1.13.0+cu117 --extra-index-url https://download.pytorch.org/whl/cu117
-          pip install setuptools==69.5.1 # Downgrade setuptools to avoid crashes when installing unicore
-          git clone https://github.com/dptech-corp/Uni-Core.git
-          cd Uni-Core
-          python setup.py install --disable-cuda-ext
-          cd ../
+          # pip install torch==1.13.0+cu117 --extra-index-url https://download.pytorch.org/whl/cu117
+          # pip install setuptools==69.5.1 # Downgrade setuptools to avoid crashes when installing unicore
+          # git clone https://github.com/dptech-corp/Uni-Core.git
+          # cd Uni-Core
+          # python setup.py install --disable-cuda-ext
+          # cd .
           python test/test_python_imports.py
       - if: matrix.install-type == 'developer'
         run: |
@@ -124,4 +124,4 @@ jobs:
           context: .
           file: ./docker/analysis.dockerfile
           push: true
-          tags: ${{ secrets.DOCKER_USERNAME }}/fold_analysis:${{ github.event.release.tag_name }}
+          tags: ${{ secrets.DOCKER_USERNAME }}/fold_analysis:${{ github.event.release.tag_name }}
diff --git a/alphapulldown/folding_backend/__init__.py b/alphapulldown/folding_backend/__init__.py
@@ -3,14 +3,13 @@
     Copyright (c) 2023 European Molecular Biology Laboratory
 
     Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+            Dingquan Yu <dingquan.yu@embl-hamburg.de>
 """
 
 from typing import Dict, List
-
+from absl import logging
 from .alphafold_backend import AlphaFoldBackend
-from .alphalink_backend import AlphaLinkBackend
-from .unifold_backend import UnifoldBackend
-
+logging.set_verbosity(logging.INFO)
 
 class FoldingBackendManager:
     """
@@ -31,14 +30,28 @@ class FoldingBackendManager:
 
     def __init__(self):
         self._BACKEND_REGISTRY = {
-            "alphafold": AlphaFoldBackend,
-            "unifold": UnifoldBackend,
-            "alphalink": AlphaLinkBackend
+            "alphafold": AlphaFoldBackend
         }
+        self.import_backends()
         self._backend_name = "alphafold"
         self._backend = self._BACKEND_REGISTRY[self._backend_name]()
         self._backend_args = {}
 
+    def import_backends(self) -> None:
+        """Import all available backends"""
+        try:
+            from .alphalink_backend import AlphaLinkBackend
+            self._BACKEND_REGISTRY.update({"alphalink": AlphaLinkBackend})
+        except Exception as e:
+            logging.warning("Failed to import AlphaLinkBackend. Perhaps you haven't installed all the required dependencies.")
+
+        try:
+            from .unifold_backend import UnifoldBackend
+            self._BACKEND_REGISTRY.update({"unifold": UnifoldBackend})
+
+        except Exception as e:
+            logging.warning("Failed to import UnifoldBackend. Perhaps you haven't installed all the required dependencies.")
+
     def __repr__(self):
         return f"<BackendManager: using {self._backend_name}>"
 

diff --git a/test/test_python_imports.py b/test/test_python_imports.py
@@ -1,5 +1,4 @@
 from alphapulldown.utils import *
-from alphapulldown.folding_backend import *
 import io
 import warnings
 import subprocess
@@ -13,8 +12,8 @@
 from typing import Dict, List
 from os.path import exists, join
 
-from alphapulldown.folding_backend import backend
-from alphapulldown.objects import MultimericObject
+from alphapulldown.folding_backend import FoldingBackendManager
+from alphapulldown.objects import MultimericObject, MonomericObject
 from alphapulldown.utils.modelling_setup import create_interactors
 from absl import logging
 logging.set_verbosity(logging.INFO)