Numpy 2

.github/workflows/docs.yml

@@ -11,11 +11,11 @@ jobs:
   build-and-publish:
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
       - name: set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
       - name: install dependencies

.github/workflows/tests.yml

@@ -16,28 +16,28 @@ jobs:
         include:
           - os: windows-2019
             python-version: "3.8"
-          - os: macos-11
+          - os: macos-14
             python-version: "3.8"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
       - name: set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: setup MSVC command prompt
         uses: ilammy/msvc-dev-cmd@v1
       - name: install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install tox
+          pip install "tox <=4.14.0"
       - name: run tests
         run: tox
       - name: run extra checks
         run: |
           ./scripts/check-used-functions.py
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           file: .tox/coverage.xml
           fail_ci_if_error: true

.github/workflows/wheels.yml

@@ -12,10 +12,10 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-11]
+        os: [ubuntu-20.04, windows-2019, macos-14]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
 
@@ -55,11 +55,11 @@ jobs:
     name: build sdist
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
 

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8.12)
+cmake_minimum_required(VERSION 3.16)
 
 # Prevent CMake from looking for a C and a C++ compilers, as we might not
 # need them. They will be found by cmake if we are using the internal chemfiles

src/chemfiles/residue.py

@@ -55,7 +55,7 @@ def __iter__(self):
             yield self[i]
 
     def __repr__(self):
-        return "[" + ", ".join([i.__repr__() for i in self]) + "]"
+        return "[" + ", ".join([str(int(i)) for i in self]) + "]"
 
     def append(self, atom):
         """Add the atom index ``atom`` in the :py:class:`Residue`."""

tests/residue.py

@@ -1,7 +1,6 @@
 import copy
 import unittest
 
-import numpy as np
 from _utils import remove_warnings
 
 from chemfiles import ChemfilesError, Residue