update ci

.github/workflows/ci.yml

@@ -4,66 +4,53 @@ on:
   push:
     branches: [ master ]
   pull_request:
-    branches: [ master ]
+    branches: [ master, dev ]
 
 jobs:
-  ubuntu_3_11:
-    runs-on: ubuntu-latest
+  ubuntu_matrix:
+    runs-on: ubuntu-22.04 # latest fails testing python 3.7 - https://github.com/actions/setup-python/issues/962
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         pip install -e .
         pip install -e ".[dev]"
     - name: Run tests
-      run: python -m unittest discover
-
-  ubuntu_3_7:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.7'
-    - name: Install dependencies
-      run: |
-        pip install -e .
-        pip install -e ".[dev]"
-    - name: Run tests
-      run: python -m unittest discover
+      run: python -m unittest discover tests/
 
   macos:
     runs-on: macos-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.9'
+        python-version: '3.11'
     - name: Install dependencies
       run: |
         pip install -e .
         pip install -e ".[dev]"
     - name: Run tests
-      run: python -m unittest discover
+      run: python -m unittest discover tests/
 
   windows:
     runs-on: windows-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.9'
+        python-version: '3.11'
     - name: Install dependencies
       run: |
         pip install -e .
         pip install -e ".[dev]"
     - name: Run tests
-      run: python -m unittest discover
-
+      run: python -m unittest discover tests/

pyproject.toml

@@ -16,6 +16,7 @@ classifiers = [
   "Development Status :: 5 - Production/Stable",
   "License :: OSI Approved :: MIT License",
   "Operating System :: OS Independent",
+  "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.10",

src/UniProtMapper/field_base_classes.py

@@ -4,7 +4,7 @@
 """
 
 import re
-from typing import Union
+from typing import List, Union
 
 from .utils import read_fields_table
 
@@ -38,7 +38,7 @@ class QueryBuilder:
         'NOT reviewed:true OR (organism_id:9606 AND length:[100 TO 200])'
     """
 
-    def __init__(self, query: Union[list[Union[str, "AnyField"]], "AnyField"]) -> None:
+    def __init__(self, query: Union[List[Union[str, "AnyField"]], "AnyField"]) -> None:
         """Initialize QueryBuilder with a query."""
         # Convert single field to list for consistency
         self.query = [query] if hasattr(query, "field_name") else query

src/UniProtMapper/idmapping_api.py

@@ -40,10 +40,10 @@ class ProtMapper(BaseUniProt):
 
     def __init__(
         self,
-        pooling_interval=3,
-        total_retries=5,
-        backoff_factor=0.25,
-        api_url="https://rest.uniprot.org",
+        pooling_interval: int = 3,
+        total_retries: int = 5,
+        backoff_factor: float = 0.25,
+        api_url: str = "https://rest.uniprot.org",
     ) -> None:
         """Initialize the class. This will set up the session and retry mechanism.
 

src/UniProtMapper/interface.py

@@ -24,10 +24,10 @@ class BaseUniProt(ABC):
 
     def __init__(
         self,
-        pooling_interval=3,
-        total_retries=5,
-        backoff_factor=0.25,
-        api_url="https://rest.uniprot.org",
+        pooling_interval: int = 3,
+        total_retries: int = 5,
+        backoff_factor: float = 0.25,
+        api_url: str = "https://rest.uniprot.org",
     ) -> None:
         """Initialize the class. This will set up the session and retry mechanism.
 
@@ -46,7 +46,7 @@ def __init__(
         self._re_next_link = re.compile(r'<(.+)>; rel="next"')
 
     @property
-    def fields_table(self):
+    def fields_table(self) -> None:
         return read_fields_table()
 
     def _setup_retries(self, total_retries, backoff_factor) -> None:
@@ -59,14 +59,14 @@ def _setup_retries(self, total_retries, backoff_factor) -> None:
     def _setup_session(self) -> None:
         self.session.mount("https://", HTTPAdapter(max_retries=self.retries))
 
-    def check_response(self, response):
+    def check_response(self, response) -> None:
         try:
             response.raise_for_status()
         except requests.HTTPError:
             print(response.json())
             raise
 
-    def get_next_link(self, headers):
+    def get_next_link(self, headers) -> str:
         if "Link" in headers:
             match = self._re_next_link.match(headers["Link"])
             if match:

src/UniProtMapper/uniprotkb_api.py

@@ -2,7 +2,7 @@
 field classes found in `UniProtMapper.uniprotkb_fields`."""
 
 from logging import info
-from typing import Generator, Optional, Union
+from typing import Generator, List, Optional, Tuple, Union
 
 import pandas as pd
 import requests
@@ -56,7 +56,7 @@ def __init__(
     def _build_search_url(
         self,
         query: str,
-        fields: list[str],
+        fields: List[str],
         format: str = "tsv",
         include_isoform: bool = False,
         compressed: bool = False,
@@ -111,7 +111,7 @@ def submit_query(
 
     def _get_batches(
         self, initial_response
-    ) -> Generator[tuple[requests.Response, int], None, None]:
+    ) -> Generator[Tuple[requests.Response, int], None, None]:
         """Generator that yields batches of results with pagination.
 
         Args:
@@ -138,7 +138,7 @@ def _get_batches(
     def get(
         self,
         query: Union[QueryBuilder, str],
-        fields: Optional[list[str]] = None,
+        fields: Optional[List[str]] = None,
         include_isoform: bool = False,
         compressed: bool = False,
         size: int = 500,

src/UniProtMapper/utils.py

@@ -7,13 +7,23 @@
 from typing import Optional
 
 import pandas as pd
-import pkg_resources
 import requests
 
 
+def get_resource_file(filename: str) -> str:
+    try:
+        import pkg_resources
+
+        return pkg_resources.resource_filename("UniProtMapper", filename)
+    except ImportError:
+        from importlib import resources
+
+        return str(resources.files("UniProtMapper") / filename)
+
+
 def get_resources_root() -> Path:
     """Returns the path to the resources folder."""
-    return Path(pkg_resources.resource_filename("UniProtMapper", "resources"))
+    return Path(get_resource_file("resources"))
 
 
 def fetch_cross_referenced_db_details(
@@ -60,19 +70,15 @@ def read_fields_table():
     - `has_full_version`: whether the annotated field contains the full version of the
     dataset or not (in case of cross-references).
     - `type`: the type of data. Either "cross_reference" or "uniprot_field"."""
-    csv_path = pkg_resources.resource_filename(
-        "UniProtMapper", "resources/uniprot_return_fields.csv"
-    )
+    csv_path = get_resource_file("resources/uniprot_return_fields.csv")
     return pd.read_csv(csv_path)
 
 
 def supported_mapping_dbs():
     """Return a list of the supported datasets as UniProt cross references. This list
     is used to validate the arguments `to_db` and `from_db` in the `FieldRetriever.get()` method.
     """
-    _mapping_dbs_path = pkg_resources.resource_filename(
-        "UniProtMapper", "resources/uniprot_mapping_dbs.json"
-    )
+    _mapping_dbs_path = get_resource_file("resources/uniprot_mapping_dbs.json")
     with open(_mapping_dbs_path, "r") as f:
         dbs_dict = json.load(f)
     return sorted([dbs_dict[k][i] for k in dbs_dict for i in range(len(dbs_dict[k]))])

tests/test_idmapping_api.py

@@ -2,21 +2,21 @@
 
 import pandas as pd
 
-from UniProtMapper.idmapping_api import ProtMapper
+from UniProtMapper import ProtMapper
 
 # Test data
 test_ids = ["P30542", "Q16678", "Q02880"]
 
 # Initialize the UniProtRetriever object
-uni_retriever = ProtMapper()
+mapper = ProtMapper()
 
 
 class TestProtMapper(unittest.TestCase):
     def setUp(self):
         self.fields_table = ProtMapper().fields_table
 
     def test_supported_dbs(self):
-        supported_dbs = uni_retriever._supported_dbs
+        supported_dbs = mapper._supported_dbs
         self.assertIsInstance(supported_dbs, list)
         self.assertIn("UniProtKB_AC-ID", supported_dbs)
 
@@ -25,7 +25,7 @@ def test_fields_table(self):
         self.assertIn("accession", self.fields_table["returned_field"].values)
 
     def test_retrieve_fields_default(self):
-        result_df, failed = uni_retriever(test_ids)
+        result_df, failed = mapper.get(test_ids)
         self.assertIsInstance(result_df, pd.DataFrame)
         self.assertEqual(len(result_df), len(test_ids))
         self.assertEqual(len(failed), 0)
@@ -45,7 +45,7 @@ def test_retrieve_fields_custom(self):
         result_columns = self.fields_table[
             self.fields_table["returned_field"].isin(custom_fields)
         ]["label"]
-        result_df, failed = uni_retriever(test_ids, fields=custom_fields)
+        result_df, failed = mapper.get(test_ids, fields=custom_fields)
         self.assertIsInstance(result_df, pd.DataFrame)
         self.assertEqual(len(result_df), len(test_ids))
         self.assertEqual(len(failed), 0)
@@ -54,15 +54,15 @@ def test_retrieve_fields_custom(self):
 
     def test_retrieve_fields_invalid_field(self):
         with self.assertRaises(ValueError):
-            uni_retriever(test_ids, fields=["invalid_field"])
+            mapper.get(test_ids, fields=["invalid_field"])
 
     def test_retrieve_fields_invalid_from_db(self):
         with self.assertRaises(ValueError):
-            uni_retriever(test_ids, from_db="InvalidDB")
+            mapper.get(test_ids, from_db="InvalidDB")
 
     def test_retrieve_fields_invalid_to_db(self):
         with self.assertRaises(ValueError):
-            uni_retriever(test_ids, to_db="InvalidDB")
+            mapper.get(test_ids, to_db="InvalidDB")
 
 
 if __name__ == "__main__":