dayhoff-tools 1.1.6__tar.gz → 1.1.8__tar.gz

{dayhoff_tools-1.1.6 → dayhoff_tools-1.1.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.1.6
+Version: 1.1.8
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com
@@ -10,27 +10,23 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Provides-Extra: lite
-Requires-Dist: biopython (>=1.84)
-Requires-Dist: boto3 (>=1.36.8)
-Requires-Dist: docker (>=7.1.0)
-Requires-Dist: fair-esm (>=2.0.0)
+Provides-Extra: full
+Requires-Dist: biopython (>=1.84) ; extra == "full"
+Requires-Dist: boto3 (>=1.36.8) ; extra == "full"
+Requires-Dist: docker (>=7.1.0) ; extra == "full"
+Requires-Dist: fair-esm (>=2.0.0) ; extra == "full"
 Requires-Dist: firebase-admin (>=6.5.0)
-Requires-Dist: firebase-admin (>=6.5.0) ; extra == "lite"
-Requires-Dist: h5py (>=3.11.0)
-Requires-Dist: pandas (>=2.2.3)
+Requires-Dist: h5py (>=3.11.0) ; extra == "full"
+Requires-Dist: pandas (>=2.2.3) ; extra == "full"
 Requires-Dist: pyyaml (>=6.0)
-Requires-Dist: pyyaml (>=6.0) ; extra == "lite"
 Requires-Dist: questionary (>=2.0.1)
-Requires-Dist: rdkit-pypi (>=2022.9.5)
+Requires-Dist: rdkit-pypi (>=2022.9.5) ; extra == "full"
 Requires-Dist: requests (>=2.31.0)
-Requires-Dist: requests (>=2.31.0) ; extra == "lite"
-Requires-Dist: sentencepiece (>=0.2.0)
-Requires-Dist: sqlalchemy (>=2.0.40,<3.0.0)
+Requires-Dist: sentencepiece (>=0.2.0) ; extra == "full"
+Requires-Dist: sqlalchemy (>=2.0.40,<3.0.0) ; extra == "full"
 Requires-Dist: toml (>=0.10)
-Requires-Dist: transformers (==4.36.2)
+Requires-Dist: transformers (==4.36.2) ; extra == "full"
 Requires-Dist: typer (>=0.9.0)
-Requires-Dist: typer (>=0.9.0) ; extra == "lite"
 Description-Content-Type: text/markdown
 
 # dayhoff-tools

{dayhoff_tools-1.1.6 → dayhoff_tools-1.1.8}/dayhoff_tools/deployment/processors.py

@@ -160,7 +160,7 @@ class MMSeqsProfileProcessor(Processor):
         self.num_threads = str(num_threads)  # MMseqs2 expects string for threads
 
         default_mmseqs_args = {
-            "memory_limit_gb": "30",
+            "memory_limit_gb": "25",
             "evalue": "10",
             "sensitivity": "7.5",
             "max_seqs_search": "300",

{dayhoff_tools-1.1.6 → dayhoff_tools-1.1.8}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "dayhoff-tools"
-version = "1.1.6"
+version = "1.1.8"
 description = "Common tools for all the repos at Dayhoff Labs"
 authors = [
     {name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}
@@ -18,27 +18,23 @@ dependencies = [
     "requests>=2.31.0",
     "typer>=0.9.0",
     "toml>=0.10",
+    "questionary>=2.0.1",
+]
+requires-python = ">=3.10,<4.0"
+
+[project.optional-dependencies]
+full = [
     "biopython>=1.84",
     "boto3>=1.36.8",
     "docker>=7.1.0",
     "fair-esm>=2.0.0",
     "h5py>=3.11.0",
     "pandas>=2.2.3",
-    "questionary>=2.0.1",
     "rdkit-pypi>=2022.9.5",
     "sqlalchemy (>=2.0.40,<3.0.0)",
     "transformers==4.36.2",
     "sentencepiece>=0.2.0",
 ]
-requires-python = ">=3.10,<4.0"
-
-[project.optional-dependencies]
-lite = [
-    "firebase-admin>=6.5.0",
-    "pyyaml>=6.0",
-    "requests>=2.31.0",
-    "typer>=0.9.0",
-]
 
 [[tool.uv.index]]
 name = "torch-cuda"