Bump GitHub Actions and pre-commit Hooks

.github/dependabot.yml

@@ -17,8 +17,6 @@ updates:
     insecure-external-code-execution: "deny"
     pull-request-branch-name:
       separator: "/"
-    reviewers:
-      - "andthum"
     labels:
       - "dependencies"
       - "patch"
@@ -33,8 +31,6 @@ updates:
     insecure-external-code-execution: "deny"
     pull-request-branch-name:
       separator: "/"
-    reviewers:
-      - "andthum"
     labels:
       - "dependencies"
       - "skip-changelog"
@@ -49,8 +45,6 @@ updates:
     insecure-external-code-execution: "deny"
     pull-request-branch-name:
       separator: "/"
-    reviewers:
-      - "andthum"
     labels:
       - "dependencies"
       - "skip-changelog"
@@ -62,8 +56,6 @@ updates:
       interval: "weekly"
     pull-request-branch-name:
       separator: "/"
-    reviewers:
-      - "andthum"
     labels:
       - "dependencies"
       - "skip-changelog"

.github/workflows/cff-validator.yml

@@ -27,9 +27,9 @@ jobs:
     runs-on: "${{ matrix.os }}"
     steps:
       - name: "Checkout repository"
-        uses: "actions/checkout@v4"
+        uses: "actions/checkout@v6"
       - name: "Set up Python ${{ matrix.python-version }}"
-        uses: "actions/setup-python@v5"
+        uses: "actions/setup-python@v6"
         with:
           python-version: "${{ matrix.python-version }}"
       - name: "Export ${HOME}/.local/bin to ${PATH}"
@@ -44,7 +44,7 @@ jobs:
           python -m pip install --user --upgrade pip
           echo "dir=$(pip cache dir)" >> ${GITHUB_OUTPUT}
       - name: "Create/Restore cache"
-        uses: "actions/cache@v4"
+        uses: "actions/cache@v5"
         with:
           path: "${{ steps.pip-cache.outputs.dir }}/**"
           key: |

.github/workflows/codeql-analysis.yml

@@ -27,9 +27,9 @@ jobs:
       security-events: "write"
     steps:
       - name: "Checkout repository"
-        uses: "actions/checkout@v4"
+        uses: "actions/checkout@v6"
       - name: "Set up Python ${{ matrix.python-version }}"
-        uses: "actions/setup-python@v5"
+        uses: "actions/setup-python@v6"
         with:
           python-version: "${{ matrix.python-version }}"
       - name: "Export ${HOME}/.local/bin to ${PATH}"
@@ -44,7 +44,7 @@ jobs:
           python -m pip install --user --upgrade pip
           echo "dir=$(pip cache dir)" >> ${GITHUB_OUTPUT}
       - name: "Create/Restore cache"
-        uses: "actions/cache@v4"
+        uses: "actions/cache@v5"
         with:
           path: "${{ steps.pip-cache.outputs.dir }}/**"
           key: |
@@ -72,12 +72,12 @@ jobs:
           # executable that includes the dependencies.
           echo "CODEQL_PYTHON=$(which python)" >> ${GITHUB_ENV}
       - name: "Initialize CodeQL"
-        uses: "github/codeql-action/init@v3"
+        uses: "github/codeql-action/init@v4"
         with:
           languages: "python"
           # Override the default behavior so that the action doesn't
           # attempt to auto-install Python dependencies.  See
           # https://docs.github.com/en/code-security/secure-coding/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#analyzing-python-dependencies
           setup-python-dependencies: false
       - name: "Perform CodeQL Analysis"
-        uses: "github/codeql-action/analyze@v3"
+        uses: "github/codeql-action/analyze@v4"

.github/workflows/tests-skip.yml

@@ -53,27 +53,23 @@ jobs:
     strategy:
       matrix:
         # Tests must be run on all target platforms and Python versions.
-        # Python <3.8 is not supported in the MacOS 14 runner.
         os:
           - "ubuntu-latest"
-          - "macos-13"
           - "windows-latest"
         python-version:
           - "3.6"
           - "3.7"
           - "3.8"
           - "3.9"
-        # Python 3.6 is not supported anymore in the Ubuntu 22.04 runner
-        # https://github.com/actions/setup-python/issues/544#issuecomment-1332535877
-        # Python 3.7 is not supported anymore in the Ubuntu 24.04 runner
         exclude:
+          # Python 3.6 is not supported anymore in the Ubuntu 22.04 runner
+          # https://github.com/actions/setup-python/issues/544#issuecomment-1332535877
+          # Python 3.7 is not supported anymore in the Ubuntu 24.04 runner
           - os: "ubuntu-latest"
             python-version: "3.6"
           - os: "ubuntu-latest"
             python-version: "3.7"
         include:
-          - os: "ubuntu-20.04"
-            python-version: "3.6"
           - os: "ubuntu-22.04"
             python-version: "3.7"
       # Do not cancel in-progress jobs if any matrix job fails

.github/workflows/tests.yml

@@ -37,9 +37,9 @@ jobs:
     runs-on: "${{ matrix.os }}"
     steps:
       - name: "Checkout repository"
-        uses: "actions/checkout@v4"
+        uses: "actions/checkout@v6"
       - name: "Set up Python ${{ matrix.python-version }}"
-        uses: "actions/setup-python@v5"
+        uses: "actions/setup-python@v6"
         with:
           python-version: "${{ matrix.python-version }}"
       - name: "Export ${HOME}/.local/bin to ${PATH}"
@@ -54,7 +54,7 @@ jobs:
           python -m pip install --user --upgrade pip
           echo "dir=$(pip cache dir)" >> ${GITHUB_OUTPUT}
       - name: "Create/Restore cache"
-        uses: "actions/cache@v4"
+        uses: "actions/cache@v5"
         with:
           path: "${{ steps.pip-cache.outputs.dir }}/**"
           key: |
@@ -148,37 +148,33 @@ jobs:
     strategy:
       matrix:
         # Tests must be run on all target platforms and Python versions.
-        # Python <3.8 is not supported in the MacOS 14 runner.
         os:
           - "ubuntu-latest"
-          - "macos-13"
           - "windows-latest"
         python-version:
           - "3.6"
           - "3.7"
           - "3.8"
           - "3.9"
-        # Python 3.6 is not supported anymore in the Ubuntu 22.04 runner
-        # https://github.com/actions/setup-python/issues/544#issuecomment-1332535877
-        # Python 3.7 is not supported anymore in the Ubuntu 24.04 runner
         exclude:
+          # Python 3.6 is not supported anymore in the Ubuntu 22.04 runner
+          # https://github.com/actions/setup-python/issues/544#issuecomment-1332535877
+          # Python 3.7 is not supported anymore in the Ubuntu 24.04 runner
           - os: "ubuntu-latest"
             python-version: "3.6"
           - os: "ubuntu-latest"
             python-version: "3.7"
         include:
-          - os: "ubuntu-20.04"
-            python-version: "3.6"
           - os: "ubuntu-22.04"
             python-version: "3.7"
       # Do not cancel in-progress jobs if any matrix job fails
       fail-fast: false
     runs-on: "${{ matrix.os }}"
     steps:
       - name: "Checkout repository"
-        uses: "actions/checkout@v4"
+        uses: "actions/checkout@v6"
       - name: "Set up Python ${{ matrix.python-version }}"
-        uses: "actions/setup-python@v5"
+        uses: "actions/setup-python@v6"
         with:
           python-version: "${{ matrix.python-version }}"
       - name: "Export ${HOME}/.local/bin to ${PATH}"
@@ -193,7 +189,7 @@ jobs:
           python -m pip install --user --upgrade pip
           echo "dir=$(pip cache dir)" >> ${GITHUB_OUTPUT}
       - name: "Create/Restore cache"
-        uses: "actions/cache@v4"
+        uses: "actions/cache@v5"
         with:
           path: |
             ${{ steps.pip-cache.outputs.dir }}/**
@@ -215,7 +211,7 @@ jobs:
           python -m pip install --user --upgrade setuptools wheel
           python -m pip install --user --upgrade python-dev-tools
           python -m pip install --user "Cython <3.0"
-          python -m pip install --user "numpy >=1.19.2"
+          python -m pip install --user "numpy >=1.19.2,<2.0"
       - name: "Test installation of MDTools"
         run: |
           python -m pip install --user .

.pre-commit-config.yaml

@@ -38,6 +38,8 @@ ci:
 
 repos:
   - repo: "https://github.com/pre-commit/pre-commit-hooks"
+    # Stay at pre-commit-hooks version 5, because pre-commit-hooks drops
+    # support for Python 3.8 in version 6.  Latest 5 version is v5.0.0.
     rev: "v5.0.0"
     hooks:
       ### Git ###
@@ -116,7 +118,10 @@ repos:
       - id: "check-pre-commit-ci-config"
 
   - repo: "https://github.com/python-jsonschema/check-jsonschema"
-    rev: "0.31.2"
+    # Stay at version 0.30.0 together with jsonschema <=4.18, because
+    # higher versions require regress>=2024.11.1, but only
+    # regress <=2024.8.1 seems to support Python 3.8
+    rev: "0.30.0"
     hooks:
       # Validate Dependabot Config (v2) against the schema provided by
       # SchemaStore.
@@ -186,6 +191,9 @@ repos:
           - "--color"
 
   - repo: "https://github.com/PyCQA/flake8"
+    # Stay at flake8 version 7.1.2, because higher versions require
+    # pycodestyle >=2.13.0, but only pycodestyle <=2.12.1 seems to
+    # support Python 3.8
     rev: "7.1.2"
     hooks:
       # Lint Python code with Flake8.
@@ -208,7 +216,9 @@ repos:
           - "pep8-naming >=0.1, <1.0"
 
   - repo: "https://github.com/PyCQA/bandit"
-    rev: "1.8.3"
+    # Stay at bandit version 1.7.10, because bandit drops support for
+    # Python 3.8 in version 1.8.0.  Latest 1.7 version is 1.7.10.
+    rev: "1.7.10"
     hooks:
       # Check code security with bandit.
       - id: "bandit"
@@ -230,6 +240,8 @@ repos:
   ######################################################################
 
   - repo: "https://github.com/maxwinterstein/shfmt-py"
+    # Stay at shfmt-py version v3.7.0.1, because shfmt-py drops support
+    # for Python 3.8 in version v3.11.0.2.
     rev: "v3.7.0.1"
     hooks:
       # Format shell scripts with shfmt.
@@ -251,6 +263,8 @@ repos:
           - "-l"
 
   - repo: "https://github.com/shellcheck-py/shellcheck-py"
+    # Stay at shellcheck-py version v0.10.0.1, because shellcheck-py
+    # drops support for Python 3.8 in version v0.11.0.1.
     rev: "v0.10.0.1"
     hooks:
       # Lint shell scripts with shellcheck.

docs/requirements-docs.txt

@@ -6,5 +6,5 @@
 # on sphinx >=1.6, <6.0
 # => The sphix requirement must not be >=6.0
 
-sphinx >=5.0, <9.0
+sphinx >=5.0, <10.0
 sphinx-rtd-theme >=1.0, <3.0

docs/source/conf.py

@@ -241,7 +241,7 @@
 .. |explanation_of_these_terms| replace::
     :raw-html:`<a href="https://userguide.mdanalysis.org/stable/groups_of_atoms.html">explanation of these terms</a>`
 .. |MDA_always_guesses_atom_masses| replace::
-    :raw-html:`<a href="https://userguide.mdanalysis.org/formats/guessing.html">MDAnalysis always guesses atom masses</a>`
+    :raw-html:`<a href="https://userguide.mdanalysis.org/stable/guessing.html">MDAnalysis always guesses atom masses</a>`
 
 .. |shfmt| replace::
     :raw-html:`<a href="https://github.com/mvdan/sh#shfmt">shfmt</a>`
@@ -479,6 +479,7 @@
 linkcheck_ignore = [
     # 403 Client Error: Forbidden for url.
     r"https://www\.cabdirect\.org/cabdirect/abstract/19272700028",
+    r"https://docutils\.sourceforge\.io/docs/ref/rst/restructuredtext\.html#bullet-lists",  # noqa: E501
     r"https://doi\.org/10\.1002/9781118033005",
     r"https://doi\.org/10\.1021/acs\.jctc\.2c00327",
     r"https://doi\.org/10\.1063/1\.1320826",
@@ -491,6 +492,12 @@
     r"https://doi\.org/10\.1103/PhysRevB\.74\.184430",
     r"https://doi\.org/10\.1103/PhysRevLett\.98\.227802",
     r"https://doi\.org/10\.3233/DS-190026",
+    r"https://doi\.org/10\.5281/zenodo\.1172987",
+    r"https://doi\.org/10\.5281/zenodo\.1212495",
+    r"https://doi\.org/10\.5281/zenodo\.3233853",
+    r"https://doi\.org/10\.5281/zenodo\.7615177",
+    r"https://zenodo\.org/badge/DOI/10\.5281/zenodo\.7615177\.svg",
+    r"https://zenodo\.org/record/1172988",
     # 418 Client Error: Unknown for url.
     r"https://doi\.org/10\.1109/TSMC\.1979\.4310076",
 ]

setup.py

@@ -160,7 +160,6 @@ def get_content(fname="README.rst"):
             "Intended Audience :: Science/Research",
             "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",  # noqa: E501
             "Natural Language :: English",
-            "Operating System :: MacOS",
             "Operating System :: Microsoft :: Windows",
             "Operating System :: POSIX :: Linux",
             "Programming Language :: Python :: 3",

src/mdtools/check.py

@@ -1548,7 +1548,7 @@ def masses(ag, flash_test=True):
     of mass.
 
     .. _MDAnalysis always guesses atom masses:
-        https://userguide.mdanalysis.org/formats/guessing.html
+        https://userguide.mdanalysis.org/stable/guessing.html
 
     Parameters
     ----------
@@ -1615,7 +1615,7 @@ def masses_new(ag, verbose=False):
     center of mass.
 
     .. _MDAnalysis always guesses atom masses:
-        https://userguide.mdanalysis.org/formats/guessing.html
+        https://userguide.mdanalysis.org/stable/guessing.html
 
     Parameters
     ----------

src/mdtools/structure.py

@@ -951,7 +951,7 @@ def com(ag, pbc=False, compound="group", make_whole=False, debug=False):
         :class:`~MDAnalysis.core.groups.Atom` coordinates.
 
     .. _MDAnalysis always guesses atom masses:
-        https://userguide.mdanalysis.org/formats/guessing.html
+        https://userguide.mdanalysis.org/stable/guessing.html
     """
     if compound == "atoms":
         if pbc: