python_requires >=3.7, test 3.11

add pyupgrade to pre-commit

.github/workflows/build.yaml

@@ -13,15 +13,15 @@ jobs:
         - windows-latest
         - macOS-latest
         python-version:
-        - "3.6"
-        - "3.8"
+        - "3.7"
+        - "3.11"
         networkx-version:
         - "1.*"
         - "2.*"
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -30,6 +30,6 @@ jobs:
         python -m pip install --upgrade pip
         pip install ".[dev]"
     - name: Run pre-commit
-      uses: pre-commit/action@v2.0.0
+      uses: pre-commit/action@v3.0.0
     - name: Test with pytest
       run: pytest --color=yes

.pre-commit-config.yaml

@@ -7,6 +7,11 @@ repos:
       - id: mixed-line-ending
       - id: check-case-conflict
       - id: check-yaml
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.2.1
+    hooks:
+      - id: pyupgrade
+        args: [--py37-plus]
   - repo: https://github.com/timothycrosley/isort
     rev: 5.10.1
     hooks:

obonet/io.py

@@ -1,7 +1,6 @@
 import importlib
 import io
 import mimetypes
-import pathlib
 import re
 from urllib.request import urlopen
 
@@ -16,8 +15,6 @@ def open_read_file(path):
     # Convert pathlike objects to string paths
     if hasattr(path, "__fspath__"):
         path = path.__fspath__()
-    elif isinstance(path, pathlib.Path):
-        path = str(path)  # For Python 3.4 and 3.5
 
     if not isinstance(path, str):
         # Passthrough open file buffers without modification

obonet/read.py

@@ -102,7 +102,7 @@ def parse_tag_line(line):
     """
     match = re.match(tag_line_pattern, line)
     if match is None:
-        message = "Tag-value pair parsing failed for:\n{}".format(line)
+        message = f"Tag-value pair parsing failed for:\n{line}"
         raise ValueError(message)
     tag = match.group("tag")
     value = match.group("value")

setup.cfg

@@ -32,7 +32,7 @@ keywords =
 packages = obonet
 zip_safe = False
 include_package_data = True
-python_requires = >=3.5
+python_requires = >=3.7
 install_requires =
     networkx
 

tests/test_obo_reading.py

@@ -15,7 +15,7 @@ def test_read_taxrank_file():
     """
     pytest.importorskip("networkx", minversion="2.0")
     path = os.path.join(directory, "data", "taxrank.obo")
-    with open(path, "rt") as read_file:
+    with open(path) as read_file:
         taxrank = obonet.read_obo(read_file)
     assert len(taxrank) == 61
     assert taxrank.nodes["TAXRANK:0000001"]["name"] == "phylum"
@@ -65,7 +65,7 @@ def test_read_obo(ontology):
     """
     Test that reading ontology does not error.
     """
-    url = "http://purl.obolibrary.org/obo/{}.obo".format(ontology)
+    url = f"http://purl.obolibrary.org/obo/{ontology}.obo"
     graph = obonet.read_obo(url)
     assert graph