Use Python 3.10.5

.python-version

@@ -1 +1 @@
-3.8.9
+3.10.5

README.md

@@ -5,6 +5,7 @@ colorFrom: green
 colorTo: purple
 sdk: streamlit
 sdk_version: 1.17.0
+python_version: 3.10.5
 app_file: ./hexviz/🧬Attention_Visualization.py
 pinned: true
 tags: ["protein language models", "attention analysis", "protein structure", "biology"]

hexviz/attention.py

@@ -1,5 +1,4 @@
 from io import StringIO
-from typing import List, Optional
 from urllib import request
 
 import requests
@@ -40,7 +39,7 @@ def get_pdb_from_seq(sequence: str) -> str:
     pdb_str = res.text
     return pdb_str
 
-def get_chains(structure: Structure) -> List[str]:
+def get_chains(structure: Structure) -> list[str]:
     """
     Get list of chains in a structure
     """
@@ -127,7 +126,7 @@ def unidirectional_avg_filtered(attention, layer, head, threshold):
     return unidirectional_avg_for_head
  
 @st.cache
-def get_attention_pairs(pdb_str: str, layer: int, head: int, chain_ids: Optional[str] = None ,threshold: int = 0.2, model_type: ModelType = ModelType.TAPE_BERT, top_n: int = 2):
+def get_attention_pairs(pdb_str: str, layer: int, head: int, chain_ids: str | None ,threshold: int = 0.2, model_type: ModelType = ModelType.TAPE_BERT, top_n: int = 2):
     structure = PDBParser().get_structure("pdb", StringIO(pdb_str))
     if chain_ids:
         chains = [ch for ch in structure.get_chains() if ch.id in chain_ids]

hexviz/models.py

@@ -1,5 +1,4 @@
 from enum import Enum
-from typing import Tuple
 
 import streamlit as st
 import torch
@@ -22,20 +21,20 @@ class Model:
 
 
 @st.cache
-def get_tape_bert() -> Tuple[TAPETokenizer, ProteinBertModel]:
+def get_tape_bert() -> tuple[TAPETokenizer, ProteinBertModel]:
     tokenizer = TAPETokenizer()
     model = ProteinBertModel.from_pretrained('bert-base', output_attentions=True)
     return tokenizer, model
 
 @st.cache
-def get_zymctrl() -> Tuple[AutoTokenizer, GPT2LMHeadModel]:
+def get_zymctrl() -> tuple[AutoTokenizer, GPT2LMHeadModel]:
     device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
     tokenizer = AutoTokenizer.from_pretrained('nferruz/ZymCTRL')
     model = GPT2LMHeadModel.from_pretrained('nferruz/ZymCTRL').to(device)
     return tokenizer, model
 
 @st.cache
-def get_prot_bert() -> Tuple[BertTokenizer, BertForMaskedLM]:
+def get_prot_bert() -> tuple[BertTokenizer, BertForMaskedLM]:
     tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False )
     model = BertForMaskedLM.from_pretrained("Rostlab/prot_bert")
     return tokenizer, model

poetry.lock

@@ -122,17 +122,6 @@ category = "main"
 optional = false
 python-versions = "*"
 
-[[package]]
-name = "backports.zoneinfo"
-version = "0.2.1"
-description = "Backport of the standard library zoneinfo module"
-category = "main"
-optional = false
-python-versions = ">=3.6"
-
-[package.extras]
-tzdata = ["tzdata"]
-
 [[package]]
 name = "beautifulsoup4"
 version = "4.11.2"
@@ -510,21 +499,6 @@ docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo"
 perf = ["ipython"]
 testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8", "importlib-resources (>=1.3)"]
 
-[[package]]
-name = "importlib-resources"
-version = "5.12.0"
-description = "Read resources from Python packages"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-
-[package.dependencies]
-zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
-
-[package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8"]
-
 [[package]]
 name = "iniconfig"
 version = "2.0.0"
@@ -706,10 +680,8 @@ python-versions = ">=3.7"
 attrs = ">=17.4.0"
 fqdn = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
 idna = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
-importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
 isoduration = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
 jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format-nongpl\""}
-pkgutil-resolve-name = {version = ">=1.3.10", markers = "python_version < \"3.9\""}
 pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
 rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
 rfc3986-validator = {version = ">0.1.0", optional = true, markers = "extra == \"format-nongpl\""}
@@ -729,7 +701,6 @@ optional = false
 python-versions = ">=3.8"
 
 [package.dependencies]
-importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
 jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
 python-dateutil = ">=2.8.2"
 pyzmq = ">=23.0"
@@ -923,7 +894,6 @@ python-versions = ">=3.8"
 contourpy = ">=1.0.1"
 cycler = ">=0.10"
 fonttools = ">=4.22.0"
-importlib-resources = {version = ">=3.2.0", markers = "python_version < \"3.10\""}
 kiwisolver = ">=1.0.1"
 numpy = ">=1.20"
 packaging = ">=20.0"
@@ -1036,7 +1006,6 @@ python-versions = ">=3.7"
 beautifulsoup4 = "*"
 bleach = "*"
 defusedxml = "*"
-importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
 jinja2 = ">=3.0"
 jupyter-core = ">=4.7"
 jupyterlab-pygments = "*"
@@ -1259,7 +1228,6 @@ python-versions = ">=3.8"
 
 [package.dependencies]
 numpy = [
-    {version = ">=1.20.3", markers = "python_version < \"3.10\""},
     {version = ">=1.21.0", markers = "python_version >= \"3.10\""},
     {version = ">=1.23.2", markers = "python_version >= \"3.11\""},
 ]
@@ -1320,14 +1288,6 @@ python-versions = ">=3.7"
 docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"]
 tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
 
-[[package]]
-name = "pkgutil-resolve-name"
-version = "1.3.10"
-description = "Resolve a name to an object."
-category = "main"
-optional = false
-python-versions = ">=3.6"
-
 [[package]]
 name = "platformdirs"
 version = "3.1.1"
@@ -1552,7 +1512,6 @@ optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 
 [package.dependencies]
-"backports.zoneinfo" = {version = "*", markers = "python_version >= \"3.6\" and python_version < \"3.9\""}
 tzdata = {version = "*", markers = "python_version >= \"3.6\""}
 
 [[package]]
@@ -1646,7 +1605,6 @@ python-versions = ">=3.7.0"
 [package.dependencies]
 markdown-it-py = ">=2.2.0,<3.0.0"
 pygments = ">=2.13.0,<3.0.0"
-typing-extensions = {version = ">=4.0.0,<5.0", markers = "python_version < \"3.9\""}
 
 [package.extras]
 jupyter = ["ipywidgets (>=7.5.1,<9)"]
@@ -2119,7 +2077,6 @@ optional = false
 python-versions = ">=3.6"
 
 [package.dependencies]
-"backports.zoneinfo" = {version = "*", markers = "python_version < \"3.9\""}
 pytz-deprecation-shim = "*"
 tzdata = {version = "*", markers = "platform_system == \"Windows\""}
 
@@ -2238,8 +2195,8 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-co
 
 [metadata]
 lock-version = "1.1"
-python-versions = ">=3.8.9,<3.9.7 || >3.9.7,<4.0.0"
-content-hash = "4583c3e7b0104de5e04c6438baa75cacda39164b118e28c71828ab1aa7a5eb13"
+python-versions = "^3.10"
+content-hash = "79f191c2f3cc09035f7d0f543aa08c44c0a39de462336ca23eeea26ac29218de"
 
 [metadata.files]
 altair = []
@@ -2279,7 +2236,6 @@ backcall = [
     {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"},
     {file = "backcall-0.2.0.tar.gz", hash = "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e"},
 ]
-"backports.zoneinfo" = []
 beautifulsoup4 = []
 biopython = []
 bleach = []
@@ -2321,7 +2277,6 @@ gitpython = []
 huggingface-hub = []
 idna = []
 importlib-metadata = []
-importlib-resources = []
 iniconfig = []
 ipykernel = []
 ipyspeck = []
@@ -2394,7 +2349,6 @@ pickleshare = [
     {file = "pickleshare-0.7.5.tar.gz", hash = "sha256:87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca"},
 ]
 pillow = []
-pkgutil-resolve-name = []
 platformdirs = []
 pluggy = [
     {file = "pluggy-1.0.0-py2.py3-none-any.whl", hash = "sha256:74134bbf457f031a36d68416e1509f34bd5ccc019f0bcc952c7b909d06b37bd3"},

pyproject.toml

@@ -5,7 +5,7 @@ description = "Visualize and analyze attention patterns for protein language mod
 authors = ["Aksel Lenes <[email protected]>"]
 
 [tool.poetry.dependencies]
-python = ">=3.8.9,<3.9.7 || >3.9.7,<4.0.0"
+python = "^3.10"
 streamlit = "1.17"
 stmol = "^0.0.9"
 biopython = "^1.81"