Use Sapiens 1.1.0

Author: prihoda

.gitignore

@@ -7,4 +7,4 @@ work
 .kube-tmp-token
 tests/robot/results
 data
-
+build

biophi/__version__.py

@@ -1 +1 @@
-__version__ = '1.0.9'
+__version__ = '1.0.11'

biophi/common/cli/web.py

@@ -6,7 +6,7 @@
 
 @click.command()
 @click.option('--host', default='localhost', help='Server port')
-@click.option('--port', type=int, default=5000, help='Server port')
+@click.option('--port', type=int, default=5001, help='Server port')
 def web(host, port):
     """Run the BioPhi web interface in simplified mode (without a processing queue)"""
     logo()

biophi/humanization/methods/humanization.py

@@ -246,10 +246,12 @@ def sapiens_humanize_chain(parental_chain: Chain, params: SapiensHumanizationPar
     )
 
 
-def sapiens_predict_chain(chain, model_version='latest', return_all_hiddens=False):
+def sapiens_predict_chain(chain, model_version='latest', return_embeddings=False):
+    # model_version is unused but kept for backwards compatibility
+    assert model_version == "latest"
+
     return sapiens.predict_scores(
         seq=chain.seq,
         chain_type=chain.chain_type,
-        model_version=model_version,
-        return_all_hiddens=return_all_hiddens
+        return_embeddings=return_embeddings
     )

environment.yml

@@ -4,7 +4,7 @@ channels:
   - conda-forge
 dependencies:
   - python = 3.9
-  - pip<24.1 # due to error in omegaconf (dependency of fairseq)
+  - pip
   - abnumber == 0.3.2
   - anarci == 2020.04.23
   - hmmer >= 3.1
@@ -22,4 +22,4 @@ dependencies:
     - tqdm
     - xlsxwriter
     - humanize
-    - sapiens >= 1.0.5
+    - sapiens >= 1.1.0