From 32e64af43ab3401157f5ae4328c2ff9dfc772435 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 5 Jun 2026 08:04:41 +0000 Subject: [PATCH 1/4] Bump pytest from 6.2.2 to 9.0.3 Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.2.2 to 9.0.3. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/6.2.2...9.0.3) --- updated-dependencies: - dependency-name: pytest dependency-version: 9.0.3 dependency-type: direct:development ... Signed-off-by: dependabot[bot] --- dev-requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dev-requirements.txt b/dev-requirements.txt index 5ddf330..4e445d0 100644 --- a/dev-requirements.txt +++ b/dev-requirements.txt @@ -7,6 +7,6 @@ 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 From 03ecde25f0d3ae26b570bf75afafae83cbdecada Mon Sep 17 00:00:00 2001 From: Mihai Todor Date: Thu, 11 Jun 2026 16:17:11 +0100 Subject: [PATCH 2/4] Update actions/upload-artifact for CI Signed-off-by: Mihai Todor --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f0711d7..00078a8 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -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/ From 3924704aecf111aa4e7a161c5b7ebfb25367ca34 Mon Sep 17 00:00:00 2001 From: Mihai Todor Date: Thu, 11 Jun 2026 16:19:48 +0100 Subject: [PATCH 3/4] Update python for CI Signed-off-by: Mihai Todor --- .github/workflows/main.yml | 4 ++-- Dockerfile | 2 +- dev-requirements.txt | 4 ++-- setup.cfg | 6 ++---- 4 files changed, 7 insertions(+), 9 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 00078a8..3d925ab 100644 --- a/.github/workflows/main.yml +++ b/.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 diff --git a/Dockerfile b/Dockerfile index 2485c64..871fe36 100644 --- a/Dockerfile +++ b/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 diff --git a/dev-requirements.txt b/dev-requirements.txt index 4e445d0..4e6f44c 100644 --- a/dev-requirements.txt +++ b/dev-requirements.txt @@ -1,8 +1,8 @@ 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 diff --git a/setup.cfg b/setup.cfg index c916318..2ceff5c 100644 --- a/setup.cfg +++ b/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 From 7408c6c095270e9b477c38155a4aa634227e07a8 Mon Sep 17 00:00:00 2001 From: Mihai Todor Date: Thu, 11 Jun 2026 16:34:43 +0100 Subject: [PATCH 4/4] Fix broken tests Signed-off-by: Mihai Todor --- pdbe_complexes/utils/get_annotated_name.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/pdbe_complexes/utils/get_annotated_name.py b/pdbe_complexes/utils/get_annotated_name.py index 958c3cd..64d30f4 100644 --- a/pdbe_complexes/utils/get_annotated_name.py +++ b/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()