Bump pytest from 6.2.2 to 9.0.3

.github/workflows/main.yml

@@ -11,12 +11,12 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.7]
+        python-version: ["3.10"]
 
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -41,7 +41,7 @@ jobs:
         python setup.py sdist bdist_wheel
     - name: Upload artifact for publish job
       if: github.ref == 'refs/heads/main'
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: ${{ env.PACKAGE_NAME }}-app
         path: dist/

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.9
+FROM python:3.10
 WORKDIR /app
 COPY requirements.txt /app/requirements.txt
 RUN pip install -r requirements.txt

dev-requirements.txt

@@ -1,12 +1,12 @@
 attrs==20.3.0
 coverage==5.5
 iniconfig==1.1.1
-packaging==20.9
-pluggy==0.13.1
+packaging==22.0
+pluggy==1.5.0
 py==1.10.0
 pyparsing==2.4.7
 pytest-cov==2.11.1
 pytest-mock==3.5.1
-pytest==6.2.2
+pytest==9.0.3
 toml==0.10.2
 pre-commit==2.11.1

pdbe_complexes/utils/get_annotated_name.py

@@ -1,5 +1,6 @@
 import csv
 import logging
+
 import requests
 
 
@@ -41,6 +42,8 @@ def _read_molecule_names(self, molecule_name_file):
             lines = (line.decode("utf-8") for line in r.iter_lines())
             next(lines)
             for row in csv.reader(lines):
+                if not row:
+                    continue
                 complex_id = row[0].strip()
                 name = row[1].strip()
                 self.molecule_names[complex_id] = name
@@ -59,6 +62,8 @@ def _read_components(self, component_file):
             lines = (line.decode("utf-8") for line in r.iter_lines())
             next(lines)
             for row in csv.reader(lines):
+                if not row:
+                    continue
                 complex_id = row[0].strip()
                 accession = row[1].strip()
                 stoichiometry = row[2].strip()

setup.cfg

@@ -11,16 +11,14 @@ classifiers =
   Development Status :: 4 - Beta
   Intended Audience :: Life Science/Structural Biology
   Intended Audience :: Developers
-  Programming Language :: Python :: 3.7
-  Programming Language :: Python :: 3.8
-  Programming Language :: Python :: 3.9
+  Programming Language :: Python :: 3.10
 long_description = file: README.md
 long_description_content_type = text/markdown
 license_files =
   LICENSE.txt
 
 [options]
-python_requires = >= 3.7
+python_requires = >= 3.10
 packages = find_namespace:
 zip_safe: False
 include_package_data = True