Use python 3.8.9

Spaces runs on Python 3.8.9

.python-version

@@ -0,0 +1 @@
+3.8.9

hexviz/attention.py

@@ -1,5 +1,6 @@
 from enum import Enum
 from io import StringIO
+from typing import List, Tuple
 from urllib import request
 
 import streamlit as st
@@ -32,7 +33,7 @@ def get_structure(pdb_code: str) -> Structure:
     structure = parser.get_structure(pdb_code, file)
     return structure
 
-def get_sequences(structure: Structure) -> list[str]:
+def get_sequences(structure: Structure) -> List[str]:
     """
     Get list of sequences with residues on a single letter format
 
@@ -47,7 +48,7 @@ def get_sequences(structure: Structure) -> list[str]:
         sequences.append(list(residues_single_letter))
     return sequences
 
-def get_protT5() -> tuple[T5Tokenizer, T5EncoderModel]:
+def get_protT5() -> Tuple[T5Tokenizer, T5EncoderModel]:
     device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
     tokenizer = T5Tokenizer.from_pretrained(
         "Rostlab/prot_t5_xl_half_uniref50-enc", do_lower_case=False
@@ -61,32 +62,32 @@ def get_protT5() -> tuple[T5Tokenizer, T5EncoderModel]:
 
     return tokenizer, model
 
-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_data
 def get_attention(
-    sequence: list[str], model_type: ModelType = ModelType.TAPE_BERT  
+    sequence: List[str], model_type: ModelType = ModelType.TAPE_BERT  
 ):
-    match model_type:
-        case ModelType.TAPE_BERT:
-            tokenizer, model = get_tape_bert()
-            token_idxs = tokenizer.encode(sequence).tolist()
-            inputs = torch.tensor(token_idxs).unsqueeze(0)
-            with torch.no_grad():
-                attns = model(inputs)[-1]
-                # Remove attention from <CLS> (first) and <SEP> (last) token
-            attns = [attn[:, :, 1:-1, 1:-1] for attn in attns]
-            attns = torch.stack([attn.squeeze(0) for attn in attns])
-        case ModelType.PROT_T5:
+    if model_type == ModelType.TAPE_BERT:
+        tokenizer, model = get_tape_bert()
+        token_idxs = tokenizer.encode(sequence).tolist()
+        inputs = torch.tensor(token_idxs).unsqueeze(0)
+        with torch.no_grad():
+            attns = model(inputs)[-1]
+            # Remove attention from <CLS> (first) and <SEP> (last) token
+        attns = [attn[:, :, 1:-1, 1:-1] for attn in attns]
+        attns = torch.stack([attn.squeeze(0) for attn in attns])
+    elif model_type == ModelType.PROT_T5:
             attns = None
             # Space separate sequences
             sequences = [" ".join(sequence) for sequence in sequences]
             tokenizer, model = get_protT5()
-        case _:
-            raise ValueError(f"Model {model_type} not supported")
+    else:
+        raise ValueError(f"Model {model_type} not supported")
+
     return attns
 
 def unidirectional_sum_filtered(attention, layer, head, threshold):

poetry.lock

@@ -122,6 +122,17 @@ 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"
@@ -451,6 +462,21 @@ 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"
@@ -632,8 +658,10 @@ 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\""}
@@ -653,6 +681,7 @@ 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"
@@ -930,6 +959,7 @@ 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 = "*"
@@ -1152,6 +1182,7 @@ 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\""},
 ]
@@ -1212,6 +1243,14 @@ 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"
@@ -1425,6 +1464,7 @@ 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]]
@@ -1518,6 +1558,7 @@ 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)"]
@@ -1973,6 +2014,7 @@ 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\""}
 
@@ -2091,8 +2133,8 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-co
 
 [metadata]
 lock-version = "1.1"
-python-versions = "^3.10"
-content-hash = "ad6054ae4a119d961e9941f135489d1b89310303aefc27d3132fbd1ed1c35a0f"
+python-versions = "^3.8.9"
+content-hash = "c4902982dd427349993b8019f7130f81583d025190b4bd2a2452166c7d146249"
 
 [metadata.files]
 altair = []
@@ -2132,6 +2174,7 @@ 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 = []
@@ -2170,6 +2213,7 @@ gitpython = []
 huggingface-hub = []
 idna = []
 importlib-metadata = []
+importlib-resources = []
 iniconfig = []
 ipykernel = []
 ipyspeck = []
@@ -2240,6 +2284,7 @@ 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 <aksel.lenes@gmail.com>"]
 
 [tool.poetry.dependencies]
-python = "^3.10"
+python = "^3.8.9"
 streamlit = "^1.20.0"
 stmol = "^0.0.9"
 biopython = "^1.81"