From 418b798631266c2e00d234172ee15d3415617d69 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sun, 12 Oct 2025 14:01:56 +0100 Subject: [PATCH 01/10] Bump build through to py3.14 --- pyproject.toml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 9916bf3..34053bb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,10 +27,10 @@ classifiers = [ 'Operating System :: MacOS :: MacOS X', 'Operating System :: Microsoft :: Windows', 'Programming Language :: Python', - 'Programming Language :: Python :: 3.9', - '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', 'Programming Language :: C', 'Topic :: Scientific/Engineering', 'Topic :: Scientific/Engineering :: Bio-Informatics', @@ -38,7 +38,7 @@ classifiers = [ 'Topic :: Software Development :: Libraries :: Python Modules', ] urls = {Homepage = "http://mdanalysis.org/pytng"} -requires-python = ">= 3.9" +requires-python = ">= 3.10" dependencies = [ "numpy>1.22.3", ] From 588d6faae2791d35c1aadd79170224e9e72519ff Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sun, 12 Oct 2025 14:02:52 +0100 Subject: [PATCH 02/10] Update build.yml --- .github/workflows/build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 88ca5c0..28ee15d 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -28,7 +28,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest, macos-13, windows-latest] - python-version: ['3.9', '3.10', '3.11', '3.12'] + python-version: ['3.11', '3.12', '3.13', '3.14'] steps: - uses: actions/checkout@v4 @@ -58,7 +58,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest, macos-13, windows-latest] - python: ["3.9", "3.10", "3.11", "3.12"] + python: ["3.11", "3.12", "3.13", "3.14"] steps: - uses: actions/checkout@v4 From f0f99ac5f37b08a3057ea680182936db2b5f4612 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sun, 12 Oct 2025 14:06:01 +0100 Subject: [PATCH 03/10] Update deploy.yaml --- .github/workflows/deploy.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml index a10db44..99e45ff 100644 --- a/.github/workflows/deploy.yaml +++ b/.github/workflows/deploy.yaml @@ -29,16 +29,17 @@ jobs: matrix: buildplat: - [ubuntu-22.04, manylinux_x86_64, x86_64] - - [macos-11, macosx_*, x86_64] - - [windows-2019, win_amd64, AMD64] - python: ["cp39", "cp310", "cp311", "cp312"] + - [macos-13, macosx_*, x86_64] + - [windows-2022, win_amd64, AMD64] + - [macos-14, macos_*, arm64] + python: ["cp311", "cp312", "cp313", "cp314"] steps: - uses: actions/checkout@v4 with: fetch-depth: 0 - name: Build wheels - uses: pypa/cibuildwheel@v2.19.1 + uses: pypa/cibuildwheel@v3.2.1 env: CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }} CIBW_ARCHS: ${{ matrix.buildplat[2] }} @@ -94,7 +95,7 @@ jobs: path: dist - name: upload_source_and_wheels - uses: pypa/gh-action-pypi-publish@v1.8.10 + uses: pypa/gh-action-pypi-publish@v1.13.0 with: skip_existing: true repository_url: https://test.pypi.org/legacy/ From 9b5a9b621b85ddd59fd803f5aa564d8bde83222e Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sun, 12 Oct 2025 14:06:17 +0100 Subject: [PATCH 04/10] Update docs.yml --- .github/workflows/docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 7c40ab6..0522e67 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -13,7 +13,7 @@ jobs: - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v4 with: - python-version: 3.9 + python-version: 3.11 - name: Install dependencies run: | From a11b969a2de0da80ad9382660e0de980ae241d0e Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sun, 12 Oct 2025 14:06:46 +0100 Subject: [PATCH 05/10] Update build.yml --- .github/workflows/build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 28ee15d..25979f2 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -27,7 +27,7 @@ jobs: max-parallel: 12 fail-fast: false matrix: - os: [ubuntu-latest, macos-13, windows-latest] + os: [ubuntu-latest, macos-13, macos-latest, windows-latest] python-version: ['3.11', '3.12', '3.13', '3.14'] steps: @@ -57,7 +57,7 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-latest, macos-13, windows-latest] + os: [ubuntu-latest, macos-13, macos-latest, windows-latest] python: ["3.11", "3.12", "3.13", "3.14"] steps: From e27f46d1af9b544b4d50df629e07c3b3dbd64fd7 Mon Sep 17 00:00:00 2001 From: hmacdope Date: Mon, 13 Oct 2025 19:54:22 +1100 Subject: [PATCH 06/10] dep change --- environment.yaml | 2 +- pyproject.toml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/environment.yaml b/environment.yaml index 51ea60a..aa9e7d9 100644 --- a/environment.yaml +++ b/environment.yaml @@ -11,6 +11,6 @@ dependencies: - pytest-cov - pip # docs - - mdanalysis-sphinx-theme >=1.0.1 + - mdanalysis-sphinx-theme - pip: - sphinx-sitemap diff --git a/pyproject.toml b/pyproject.toml index 34053bb..f56cd9c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [build-system] # Minimum requirements for the build system to execute requires = [ - "cython>=0.28,<3.0", + "cython", "setuptools>=61.2", "versioningit", "wheel", @@ -51,7 +51,7 @@ test = [ "pytest-cov", ] docs = [ - "mdanalysis-sphinx-theme>=1.0.1", + "mdanalysis-sphinx-theme", "sphinx-sitemap", ] From c331e82718432972e8ef30077fdb4bd692acb7f9 Mon Sep 17 00:00:00 2001 From: hmacdope Date: Mon, 13 Oct 2025 19:57:21 +1100 Subject: [PATCH 07/10] theme? --- environment.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yaml b/environment.yaml index aa9e7d9..abec0c2 100644 --- a/environment.yaml +++ b/environment.yaml @@ -11,6 +11,6 @@ dependencies: - pytest-cov - pip # docs - - mdanalysis-sphinx-theme + - mdanalysis-sphinx-theme >=1.3.0 - pip: - - sphinx-sitemap + - sphinx-sitemap From 62d98462cfdb2ec415d68cd04c7448bd746fa22b Mon Sep 17 00:00:00 2001 From: hmacdope Date: Mon, 13 Oct 2025 20:01:06 +1100 Subject: [PATCH 08/10] mamba --- .github/workflows/build.yml | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 25979f2..4c13ea5 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -27,19 +27,18 @@ jobs: max-parallel: 12 fail-fast: false matrix: - os: [ubuntu-latest, macos-13, macos-latest, windows-latest] + os: [ubuntu-latest, macos-latest, windows-latest] python-version: ['3.11', '3.12', '3.13', '3.14'] steps: - uses: actions/checkout@v4 - name: Setup Miniconda - uses: conda-incubator/setup-miniconda@v3 + uses: mamba-org/setup-micromamba@v1 with: - auto-update-conda: true - use-mamba: true - python-version: ${{ matrix.python-version }} environment-file: environment.yaml - activate-environment: pytng + environment-name: pytng + create-args: >- + python=${{ matrix.python-version }} - name: Install Pytng run: | python -m pip install . @@ -57,7 +56,7 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-latest, macos-13, macos-latest, windows-latest] + os: [ubuntu-latest, macos-latest, windows-latest] python: ["3.11", "3.12", "3.13", "3.14"] steps: From b717e1ba8996a9583d0ab8ed14554dc85e41f6e1 Mon Sep 17 00:00:00 2001 From: hmacdope Date: Mon, 13 Oct 2025 20:02:07 +1100 Subject: [PATCH 09/10] fix --- .github/workflows/build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 4c13ea5..68338b4 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -37,8 +37,8 @@ jobs: with: environment-file: environment.yaml environment-name: pytng - create-args: >- - python=${{ matrix.python-version }} + create-args: >- + python=${{ matrix.python-version }} - name: Install Pytng run: | python -m pip install . From b3776c0853c89d3fb7a4b06f07cf96fd5a7f594f Mon Sep 17 00:00:00 2001 From: hmacdope Date: Mon, 13 Oct 2025 20:22:52 +1100 Subject: [PATCH 10/10] switch to pip --- environment.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yaml b/environment.yaml index abec0c2..65e5631 100644 --- a/environment.yaml +++ b/environment.yaml @@ -11,6 +11,6 @@ dependencies: - pytest-cov - pip # docs - - mdanalysis-sphinx-theme >=1.3.0 - pip: - sphinx-sitemap + - mdanalysis-sphinx-theme