From 1d6741ffc385ab5f0b7fc3a31f817b753b0afd5b Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 25 Jun 2026 12:04:44 -0700 Subject: [PATCH 1/5] enable dependabot version updates for actions fix #30 --- .github/dependabot.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 .github/dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..dfd0e30 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,10 @@ +# Set update schedule for GitHub Actions + +version: 2 +updates: + + - package-ecosystem: "github-actions" + directory: "/" + schedule: + # Check for updates to GitHub Actions every week + interval: "weekly" From f1700b43ec3e13661fa6033e1c8fd92b45b23550 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 25 Jun 2026 12:08:29 -0700 Subject: [PATCH 2/5] manually updated all GH actions fix #28 --- .github/workflows/deploy.yaml | 4 ++-- .github/workflows/docs.yaml | 8 ++++---- .github/workflows/gh-ci.yaml | 14 +++++++------- 3 files changed, 13 insertions(+), 13 deletions(-) diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml index a546e80..1511067 100644 --- a/.github/workflows/deploy.yaml +++ b/.github/workflows/deploy.yaml @@ -22,7 +22,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v7 - name: testpypi_deploy uses: MDAnalysis/pypi-deployment@main @@ -45,7 +45,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v7 - name: pypi_deploy uses: MDAnalysis/pypi-deployment@main diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index ac33ba4..38e9f77 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -21,12 +21,12 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v7 with: fetch-depth: 0 - name: setup_miniconda - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v4 with: python-version: 3.11 environment-file: docs/requirements.yaml @@ -46,7 +46,7 @@ jobs: cd docs && sphinx-build -b html source build - name: deploy docs - uses: peaceiris/actions-gh-pages@v3 + uses: peaceiris/actions-gh-pages@v4 if: github.event_name != 'pull_request' with: github_token: ${{ secrets.GITHUB_TOKEN }} @@ -54,7 +54,7 @@ jobs: user_name: 'github-actions' user_email: 'github-action@users.noreply.github.com' - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v7 if: github.event_name == 'pull_request' with: name: pr_docs diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index d95b817..41beeaa 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -40,7 +40,7 @@ jobs: mdanalysis-version: "latest" steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v7 - name: Build information run: | @@ -50,7 +50,7 @@ jobs: # More info on options: https://github.com/conda-incubator/setup-miniconda - name: Install conda dependencies - uses: conda-incubator/setup-miniconda@v3 + uses: conda-incubator/setup-miniconda@v4 with: python-version: ${{ matrix.python-version }} environment-file: devtools/conda-envs/test_env.yaml @@ -93,7 +93,7 @@ jobs: - name: codecov if: github.repository == 'MDAnalysis/pathsimanalysis' && github.event_name != 'schedule' - uses: codecov/codecov-action@v4 + uses: codecov/codecov-action@v7 with: file: coverage.xml name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} @@ -106,10 +106,10 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v7 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v6 with: python-version: "3.11" @@ -131,10 +131,10 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v7 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v6 with: python-version: "3.11" From f9d684310f831a6c4e690bd680c9f2d194a46180 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 25 Jun 2026 12:18:05 -0700 Subject: [PATCH 3/5] update mamba installation - updated to use miniforge3 with conda-incubator/setup-miniconda - remove defaults channel use from CI --- .github/workflows/docs.yaml | 2 +- .github/workflows/gh-ci.yaml | 13 +++++++------ .readthedocs.yaml | 2 +- devtools/conda-envs/test_env.yaml | 1 - 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index 38e9f77..3251496 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -33,7 +33,7 @@ jobs: auto-update-conda: true channel-priority: flexible channels: conda-forge - miniforge-variant: Mambaforge + miniforge-version: latest use-mamba: true - name: Build and install package diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index 41beeaa..8ba8449 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -30,14 +30,14 @@ jobs: fail-fast: false matrix: os: [macOS-latest, ubuntu-latest, windows-latest] - python-version: ["3.10", "3.11", "3.12"] + python-version: ["3.11", "3.12", "3.13", "3.14"] mdanalysis-version: ["latest", "develop"] # Manually exclude any combinations of the test matrix that can't be run - exclude: + #exclude: # The latest release of MDAnalysis only supports up to Python 3.11 # so we exclude 3.12 from the test matrix (issue #20) - - python-version: "3.12" - mdanalysis-version: "latest" + #- python-version: "3.12" + # mdanalysis-version: "latest" steps: - uses: actions/checkout@v7 @@ -56,9 +56,10 @@ jobs: environment-file: devtools/conda-envs/test_env.yaml add-pip-as-python-dependency: true - miniforge-variant: Mambaforge + miniforge-version: latest use-mamba: true - channels: conda-forge, defaults + channels: conda-forge + conda-remove-defaults: "true" activate-environment: pathsimanalysis-test auto-update-conda: true diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 0037358..b2b2f8e 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -6,7 +6,7 @@ sphinx: build: os: ubuntu-lts-latest tools: - python: "mambaforge-4.10" + python: "miniforge3-latest" python: install: diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index 520fe92..613d2a9 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -1,7 +1,6 @@ name: pathsimanalysis-test channels: - conda-forge - - defaults dependencies: # Base depends - python From e5c84627a096232d48f30e67977e83838e0e0bf1 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 25 Jun 2026 12:32:14 -0700 Subject: [PATCH 4/5] increased supported Python version to 3.11 - updated CHANGELOG and pyproject.toml - CI tests were updated previously --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 89b5aa3..ea4f11f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,10 +22,10 @@ classifiers = [ "License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)", "Programming Language :: C", "Programming Language :: Python", - "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", "Topic :: Scientific/Engineering", "Topic :: Software Development :: Libraries :: Python Modules", ] From d624cfec5a384980f954563f14e91f8fe599744e Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 25 Jun 2026 12:54:03 -0700 Subject: [PATCH 5/5] switch MDAnalysis/install-mdanalysis installer to conda See if this helps with failure to run windows-latest / latest CI --- .github/workflows/gh-ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index 8ba8449..a1f70ec 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -71,7 +71,7 @@ jobs: with: version: ${{ matrix.mdanalysis-version }} install-tests: true - installer: mamba + installer: conda shell: bash -l {0} - name: Install package